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Physics
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Experimental Condensed Matter Physics
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MCQ
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Ionization and temperature measurements in warm dense copper using x-ray absorption spectroscopy.
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https://arxiv.org/abs/2509.13272
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September 16, 2025
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Researchers investigated the ionization and temperature of warm dense copper (Cu) using X-ray absorption spectroscopy (XAS) at the OMEGA Laser Facility to characterize plasmas at several times solid density. The experimental configuration consists of a planar target and a separate backlighter positioned 3 mm away. A series of 60 laser beams, delivering 3.4–5.4 kJ per side of 351 nm light, and the achieved laser intensity is 161 - 770 TW/cm2 over the three pulse length configurations, was symmetrically focused onto a planar buried-layer target composed of 125 μm CH ablators enclosing a 10 μm-thick Cu foil (8.96 g/cm3 solid density) with a 500 µm diameter, surrounded by an Au washer. The laser spot (≈approximately 880 μm diameter) was smoothed with distributed phase plates and spectral dispersion to generate uniform counter-propagating shocks. A 6 μm Ge backlighter foil, coated on graphite and irradiated with six additional beams (≈1.2 kJ, 500 ps pulse), is produced at a spot diameter of 140 μm. The transmitted x-rays were recorded using the EFX flat-crystal spectrometer (Si 111) over the 6.3–11.4 keV range on an image plate with Mn, Fe, and W filters serving as fiducial markers. Shock timing and planarity, as well as shock break-in and break-out of the Cu layer, were verified through a line-imaging VISAR system and a streaked optical pyrometer (SOP) on one-sided targets, ensuring symmetric compression and precise backlighter synchronization. 3 VISAR measurement is done with 1 ns, 2 ns, or 3 ns square pulses using 14 beams per side, respectively. Each measurement has two VISAR channels with different sensitivities; one leg was set with 33.66 µm/ns/fringe, and the second with 13.538 µm/ns/fringe.
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- Shock breakout times (in ns) and planarity were measured with the VISAR system.
- Shock velocity time history as a function of position across the target measured with the VISAR system.
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An investigation into shock breakout times and shock velocity time histories as a function of position across the target of warm dense copper (Cu) plasma is conducted using a VISAR system. The experimental configuration consists of a planar target and a separate backlighter positioned 3 mm away. A series of 60 laser beams was symmetrically focused onto a planar buried-layer target surrounded by an Au washer. The laser spot was smoothed with distributed phase plates and spectral dispersion to generate uniform counter-propagating shocks, compressing the Cu layer. A Ge backlighter foil, coated on graphite and irradiated with six additional beams, is produced. The transmitted X-rays were also recorded using the EFX flat-crystal spectrometer. Which behavior is most likely observed?
a) Shocks were non-planar over the target region, and warm dense copper shows Ionization Potential Depression (IPD).
b) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features blue shift of both the K-edge and the bound-bound resonance 1s→3p absorption relative to the cold edge.
c) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features red shift of both the K-edge and the bound-bound resonance 1s→3p absorption relative to the cold edge.
d) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features blue shift of the K-edge relative to the cold edge, but no shift for the bound-bound resonance 1s→3p absorption.
|
b) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features blue shift of both the K-edge and the bound-bound resonance 1s→3p absorption relative to the cold edge.
|
- Generating warm dense matter in the laboratory often involves significant temporal and spatial gradients that complicate the analysis of experimental observables. Incorporating gradients in the analysis of experimental data, while possible, increases the uncertainties in the inferred plasma conditions.
- At these high-density conditions, the measured Cu K-edge exhibits sensitivity to the electron temperature, allowing for a direct inference of the temperature from the slope of the Cu K-edge.
- Temperature sensitivity of the K-edge can still be the dominant edge effect, in general, as the temperature nears the Fermi energy, the K-edge shape of the non-degenerate material becomes unsuitable as a temperature inference.
|
[{"label":"RBK Item","value":"Generating WDM in the laboratory often involves significant temporal and spatial gradients that complicate the analysis of experimental observables. Incorporating gradients in the analysis of experimental data, while possible, increases the uncertainties in the inferred plasma conditions. "},{"label":"Title","value":"Quantifying electron temperature distributions from time-integrated x-ray emission spectra"},{"label":"URL","value":"https://pubs.aip.org/aip/rsi/article-abstract/93/9/093517/2849062/Quantifying-electron-temperature-distributions?redirectedFrom=fulltext"},{"label":"Date","value":"Sep 26, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 7 in the paper"},{"label":"RBK Item","value":"Temperature sensitivity of the K-edge can still be the dominant edge effect, in general, as the temperature nears the Fermi energy, the K-edge shape of the non-degenerate material becomes unsuitable as a temperature inference."},{"label":"Title","value":"X-ray absorption 𝐾 edge as a diagnostic of the electronic temperature in warm dense aluminum"},{"label":"URL","value":"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.92.085117"},{"label":"Date","value":"Aug 10, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 10 in the paper"}]
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Biology
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Neurobiology, Animal Behavior and Cognition.
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Free-Format Question
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Dopamine induces fear extinction by activating the reward-responding amygdala neurons
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https://pmc.ncbi.nlm.nih.gov/articles/PMC12067255/
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April 28, 2025.
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Researchers tested whether ventral tegmental area (VTA) dopamine signaling in the basolateral amygdala (BLA) drives fear extinction by acting on reward-responding posterior BLA (pBLA) neurons versus fear-coding anterior BLA (aBLA) neurons, using adult mice (DAT-IRES-Cre; EYFP controls; subtype mapping with Rspo2-Cre for aBLA and Ppp1r1b/Cartpt-Cre for pBLA). DAT-Cre mice received bilateral VTA injections of Cre-dependent ChR2-EYFP (activation) or eNpHR3.0-EYFP (inhibition); controls received EYFP; optic fibers were implanted over pBLA or aBLA to manipulate VTA→BLA terminals. Training: Day 1 contextual fear conditioning (baseline ~3 min, then 3 footshocks, 0.60 mA, 2 s); Day 2 45-min extinction (no shocks); Day 3 10-min retrieval. Intervention (extinction only): starting 5 min into extinction, deliver 8 cycles of 3-min light separated by 2-min no-light (activation: blue 450–470 nm, 8–12 mW, 20 Hz pulses; inhibition: green 520–550 nm, 8–12 mW, continuous) with fibers targeted to pBLA or aBLA. Behavior videos were recorded with VideoFreeze software and freezing level was scored manually by experimenters who were blinded to conditions or automatically with DeepLabCut behavior analysis toolbox and custom Python code (68). Freezing was quantified in 5-min bins across extinction and again during retrieval.
|
- Extinction learning: Percent freezing per 5-min bin across the 45-min Day 2 session (9 bins). Scored manually by experimenters who were blinded to conditions or automatically with DeepLabCut behavior analysis toolbox and custom Python code (68).
- Extinction memory: Percent freezing during the Day 3 retrieval test (10 min). Scored manually by experimenters who were blinded to conditions or automatically with DeepLabCut behavior analysis toolbox and custom Python code (68).
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Mice underwent contextual fear conditioning (Day 1: context + three 0.60 mA, 2 s shocks), 45-min extinction (Day 2, no shocks), and 10-min retrieval (Day 3). During extinction, VTA dopamine terminals in pBLA (Ppp1r1b⁺) or aBLA (Rspo2⁺) were optogenetically manipulated beginning 5 min into the session using 8 cycles of 3 min light separated by 2 min: activation (blue 450–470 nm, 8–12 mW, 20 Hz) or inhibition (green 520–550 nm, 8–12 mW, constant). Freezing was binned in 5-min windows across extinction and measured again at retrieval. How do these projection-specific manipulations (activation and inhibition of VTA dopamine terminals in the pBLA and in aBLA) affect fear extinction and retrieval compared with EYFP controls?
|
Activation of VTA dopamine terminals in the pBLA promotes faster extinction and improved retrieval, indicating an enhancement of extinction learning. In contrast, inhibition of pBLA dopamine input impairs both extinction and retrieval. Activation of VTA terminals in the aBLA leads to increased freezing later in extinction and poorer retrieval performance, suggesting interference with extinction memory formation, while inhibition of aBLA terminals produces no reliable behavioral change.
|
- Fear extinction is a form of new learning that allows for the adaptive control of fear behaviors and is commonly studied using Pavlovian conditioning tasks.
- aBLA Rspo+ neurons encode negative valence and drive aversive behaviors whereas pBLA Ppp1r1b+ neurons encode positive valence and drive appetitive behaviors.
- VTA dopamine as a teaching signal: DA activity to shock omission can initiate extinction learning and is required for extinction.
- Terminal activation (ChR2, blue, pulsed) vs inhibition (eNpHR3.0, green, constant) at BLA terminals tests sufficiency/necessity of VTA→BLA pathways.
- Freezing is the behavioral measure; decreases across 5-minute bins and at retrieval indicate successful extinction.
|
[{"label":"RBK Item","value":"Fear extinction is a form of new learning that allows for the adaptive control of fear behaviors and is commonly studied using Pavlovian conditioning tasks."},{"label":"Title","value":"Conditioned reflexes: An investigation of the physiological activity of the cerebral cortex"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC4116985/"},{"label":"Date","value":"Jul, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"aBLA Rspo+ neurons encode negative valence and drive aversive behaviors whereas pBLA Ppp1r1b+ neurons encode positive valence and drive appetitive behaviors."},{"label":"Title","value":"Antagonistic negative and positive neurons of the basolateral amygdala"},{"label":"URL","value":"https://www.nature.com/articles/nn.4414"},{"label":"Date","value":"Oct 17, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"VTA dopamine as a teaching signal: DA activity to shock omission can initiate extinction learning and is required for extinction."},{"label":"Title","value":"A dopaminergic switch for fear to safety transitions"},{"label":"URL","value":"https://www.nature.com/articles/s41467-018-04784-7"},{"label":"Date","value":"Jun 27, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
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Physiology
|
Free-Format Question
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Effect of combined Respiratory Muscle Training on Sleep and
Cardiovascular Biometrics in a non-clinical cohort
|
https://www.biorxiv.org/content/10.1101/2025.06.27.661934v1
|
July 1, 2025
|
This prospective study investigated the effects of combined inspiratory and expiratory RMT (cRMT) on sleep parameters and cardiovascular biometrics, specifically heart rate variability (HRV), in a non-clinical adult cohort. Utilizing a wearable device for remote data collection, this randomized controlled trial included 67 participants divided into good and poor sleeper groups based on historical sleep data. Participants were selected from existing users of the Biostrap EVO (Biostrap LLC) wearable device. Participants were selected into two sub-samples based on their historical sleep characteristics.
Participants who met the following criteria based on historical Biostrap data were considered good sleepers (n = 44): less than five awakenings per night, an average sleep score >70 out of 100, and an average sleep SpO2 of >96 24. The sleep score was determined from factors including total sleep duration,
minutes of deep sleep (estimated), number of involuntary awakenings, relative HR compared to an individual's rolling 30 day average, and absolute number of low SpO2 readings with bins of 90-95, 80 to 89, and below 80 representing specific penalties. This gives a gross sleep score that is then corrected
based on sleep efficiency, calculated as the total time asleep relative to the time in bed with a 5% buffer (no penalty). The remaining participants who did not meet these criteria were considered poor sleepers (n= 23). Within each subsample, participants were randomized into control and intervention groups. All participants signed a written informed consent form prior to participating in the study.
All participants completed a one-week baseline phase, during which participants were required to wear their wrist-worn Biostrap wearable device each night while sleeping. Following the baseline phase, all participants completed a five-week experimental phase including combined inspiratory and expiratory combined RMT (cRMT). Participants randomized to the intervention group (n = 29) were required to use the Breather Fit (PN Medical, FL, USA), an cRMT device. The device provides adjustable resistance during inhale and exhale for strengthening the inspiratory and expiratory muscle groups. The training protocol included three sets of 10 breaths, twice per day on six days of the week. The target intensity of cRMT was 70% of maximum effort and those in the intervention group were supplied with an instructional
video on cRMT and device care. Participants of the control group (n = 38) received no respiratory exercise. All participants were required to continue wearing the Biostrap EVO device throughout the experimental phase. Lastly, all participants completed a one-week washout phase, during which they
continued wearing the Biostrap device but ceased using the RMT device.
|
-Measurement of sleep parameters and cardiovascular biometrics of the participants.
- Heart rate variability (HRV) in participants in the intervention and control groups.
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During a five-week intervention period, participants in the intervention group underwent cRMT using a Breather Fit device, while control group participants did not receive the intervention. What would you expect to happen in terms of heart rate variability and sleep parameters between the participants in intervention and control groups?
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Study findings demonstrated a significant increase in overnight HRV metrics during the intervention period compared to the baseline, indicating improved autonomic cardiac function. However, no significant changes were observed in any parameters of sleep quality.
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-Insufficient sleep has various short- and long-term consequences, including an elevated risk of cardiovascular and metabolic diseases.
-Previous research has demonstrated that resistive respiratory muscle training (RMT) can enhance both sleep quality and cardiovascular health in individuals diagnosed with obstructive sleep apnea, underscoring its efficacy as a non-pharmacological
therapeutic strategy for this patient group.
-Sleep-breathing disorders such as obstructive sleep apnea (OSA) increase the incidence of major adverse events in patients with
cardiovascular disease.
-Given the intricate relationship between sleep-breathing disorders and cardiovascular health, heart rate variability (HRV) emerges as a critical non-invasive biomarker for assessing the autonomic nervous
system’s response to these conditions.
-HRV is the variation or irregularity in duration of beat-to-beat or interbeat intervals.
|
[{"label":"RBK Item","value":"-Insufficient sleep has various short- and long-term consequences, including an elevated risk of cardiovascular and metabolic diseases. "},{"label":"Title","value":"Short- and long-term health consequences of sleep disruption"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/28579842/"},{"label":"Date","value":"May 19, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-Previous research has demonstrated that resistive respiratory muscle training (RMT) can enhance both sleep quality and cardiovascular health in individuals diagnosed with obstructive sleep apnea, underscoring its efficacy as a non-pharmacological therapeutic strategy for this patient group. "},{"label":"Title","value":"Effects of inspiratory muscle training in patients with obstructive sleep apnoea syndrome: a systematic review and meta-analysis"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/36419804/"},{"label":"Date","value":"Dec 1, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-Sleep-breathing disorders such as obstructive sleep apnea (OSA) increase the incidence of major adverse events in patients with cardiovascular disease."},{"label":"Title","value":"A systematic review on the association of sleep-disordered breathing with cardiovascular pathology in adults"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/36253378/\n"},{"label":"Date","value":"Oct 17, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-Given the intricate relationship between sleep-breathing disorders and cardiovascular health, heart rate variability (HRV) emerges as a critical non-invasive biomarker for assessing the autonomic nervous system’s response to these conditions. "},{"label":"Title","value":"An Overview of Heart Rate Variability Metrics and Norms"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/29034226/ "},{"label":"Date","value":"Sep 28, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-HRV is the variation or irregularity in duration of beat-to-beat or interbeat intervals."},{"label":"Title","value":"A healthy heart is not a metronome: an integrative review of the heart's anatomy and heart rate variability"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25324790/"},{"label":"Date","value":"Sep 30, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Organic Chemistry
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Free-Format Question
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Total Synthesis of Eudesmanolides Alantolactone, Isoalantodiene, Alloalantolactone, and 5α,6α-Epoxyalantolactone
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https://chemrxiv.org/engage/chemrxiv/article-details/68a9905d23be8e43d6a01501
|
August 29, 2025
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To a flamed dried round-bottomed flask was added thiourea Jacobsen's organocatalyst (40.0 mg, 0.104 mmol, 5 mol%), 1-(4-Bromofuran-2-yl)-5-methylhex-5-en-1-one
(0.535 g, 2.08 mmol, 1 equiv) and CH₂Cl₂ (4.2 mL, 0.5 M). The reaction flask was cooled to –78 °C in an acetone/dry ice bath, and TMSCN (0.57 mL, 4.56 mmol, 2.22 equiv) was added dropwise. The reaction was stirred for 15 min at the same temperature and 2,2,2-trifluoroethanol (0.16 mL, 2.12 mmol, 1 equiv) was then added to the reaction flask. The mixture was stirred for 4 days at –78 °C using a cryocooler. After warming to rt the reaction was concentrated in vacuo, and the yellow oil obtained in this manner was purified by silica gel flash column chromatography (eluting with 5% Et₂O/hexanes) to yield the title compound (22, 0.50 g, 67%) as a clear, colorless oil.
The enantiomers of the product could not be resolved by chiral GC or SFC analyses. Consequently, the researchers advanced the material to stereoselective IMDAF and desilylation, where these products were resolvable by chiral SFC analysis.
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- Yield of the enantiomeric mixture using NMR.
- Enantiomeric excess determined by chiral SFC analysis
|
1-(4-bromofuran-2-yl)-5-methylhex-5-en-1-one was reacted with TMSCN (excess) and Jacobsen's thiourea catalyst (5 mol%) in CH₂Cl₂ at -78 °C for 4 d. What is the name of the product obtained?
|
2-(4-bromofuran-2-yl)-6-methyl-2-((trimethylsilyl)oxy)hept-6-enenitrile
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- Ketones can be enantioselectively cyanosilylated in the presence of Jacobsen's thiourea catalyst and TMSCN
-Alantolactone and isoalantolactone, members of the eudesmanolide class of
sesquiterpenoid lactones, have been extensively investigated for their pharmacological function
|
[{"label":"RBK Item","value":"Ketones can be enantioselectively cyanosilylated in the presence of Jacobsen's thiourea catalyst and TMSCN."},{"label":"Title","value":"Thiourea-Catalyzed Enantioselective Cyanosilylation of Ketones"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/ja052511x"},{"label":"Date","value":"June 4, 2005"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled "},{"label":"RBK Item","value":"Alantolactone and isoalantolactone, members of the eudesmanolide class of\nsesquiterpenoid lactones, have been extensively investigated for their pharmacological function"},{"label":"Title","value":"Alantolactone: A Natural Plant Extract as a Potential Therapeutic Agent for Cancer"},{"label":"URL","value":"https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2021.781033/full"},{"label":"Date","value":"November 25, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Alantolactone and isoalantolactone, members of the eudesmanolide class of\nsesquiterpenoid lactones, have been extensively investigated for their pharmacological function"},{"label":"Title","value":"Isoalantolactone: a review on its pharmacological effects"},{"label":"URL","value":"https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1453205/full"},{"label":"Date","value":"September 22, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Physics
|
Spintronics
|
MCQ
|
Enhanced Spin Pumping and Magnetization dynamics in Ni_80Fe_20/MoS_2 stack via interface modification
|
https://arxiv.org/abs/2505.09248
|
May 14, 2025
|
An experiment is conducted to investigate the magnetization dynamics at the interface of a spintronic heterostructure. A thin film of Permalloy ($Ni_{80}Fe_{20}$, or Py) with a thickness of 5 nm is deposited via DC magnetron sputtering onto a silicon substrate ($Si/SiO_{2}$) that is covered by a monolayer of molybdenum disulfide ($ML-MoS_{2}$). For comparison, a reference sample of 5 nm Py is also deposited directly onto a bare $Si/SiO_{2}$ substrate. The quality and thickness of the deposited layers are confirmed via X-ray reflectivity (XRR) using a Rigaku X-ray diffractometer. The dynamic magnetic properties of the samples are then characterized at room temperature using broadband ferromagnetic resonance (FMR) spectroscopy, where the derivative of the microwave absorption is measured as a function of an in-plane applied DC magnetic field. These measurements were conducted at room temperature using a lock-in-based broadband FMR setup (NanOsc). The spectra were recorded at a microwave frequency of 11 GHz.
|
- Ferromagnetic resonance (FMR) spectra showing the derivative of microwave absorption (dI/dH) as a function of the in-plane DC magnetic field ($H_{DC}$) for the reference Py (5 nm) and ML-MoS_{2}/Py (5 nm) sample.
|
An experiment compares the ferromagnetic resonance (FMR) spectrum of a 5 nm Permalloy (Py) film deposited on a bare silicon substrate with an identical Py film deposited on a silicon substrate covered by a monolayer of $MoS_{2}$. Based on the principles of magnetization dynamics, what is the most likely shape of the FMR spectrum for the Py film deposited on the monolayer $MoS_{2}$?
A) The spectrum exhibits two distinct resonance peaks, as the discontinuous, island-like MoS_{2} underlayer creates two different magnetic environments.
B) The spectrum shows a single resonance peak that is significantly broadened compared to the reference sample, due to increased Gilbert damping from spin pumping into the $MoS_{2}$ layer.
C) The spectrum shows a single resonance peak that is shifted to a lower magnetic field compared to the reference sample, caused by a change in the interfacial anisotropy.
D) The spectrum shows a single resonance peak that is significantly sharper and narrower than the reference sample, as the two-dimensional nature of the $MoS_{2}$ interface reduces magnetic inhomogeneities.
|
A) The spectrum exhibits two distinct resonance peaks, as the discontinuous, island-like MoS_{2} underlayer creates two different magnetic environments.
|
- Pure spin currents can be generated via spin pumping on material interfaces.
- Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena.
- Gilbert damping can be enhanced at material interfaces.
- The intrinsic FMR linewidth for conduction electrons arises from spin-orbit coupling.
|
[{"label":"RBK Item","value":"Pure spin currents can be generated via spin pumping on material interfaces.\n"},{"label":"Title","value":"Spin pumping and magnetization dynamics in metallic multilayers"},{"label":"URL","value":"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.66.224403"},{"label":"Date","value":"December 5, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 7)."},{"label":"RBK Item","value":"Pure spin currents can be generated via spin pumping on material interfaces."},{"label":"Title","value":"Nonlocal magnetization dynamics in ferromagnetic heterostructures"},{"label":"URL","value":"https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.77.1375"},{"label":"Date","value":"December 1, 2005"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 6)."},{"label":"RBK Item","value":"Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena."},{"label":"Title","value":"Atomically Thin MoS₂: A New Direct-Gap Semiconductor"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevLett.105.136805"},{"label":"Date","value":"September 24, 2010 "},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 12)."},{"label":"RBK Item","value":"Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena."},{"label":"Title","value":"Giant spin-orbit-induced spin splitting in two-dimensional transition-metal dichalcogenide semiconductors"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevB.84.153402"},{"label":"Date","value":"October 14, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 13)."},{"label":"RBK Item","value":"Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena."},{"label":"Title","value":"Control of valley polarization in monolayer MoS2 by optical helicity"},{"label":"URL","value":" https://doi.org/10.1038/nnano.2012.96"},{"label":"Date","value":"June 17, 2012 "},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 14)."},{"label":"RBK Item","value":"Gilbert damping can be enhanced at material interfaces."},{"label":"Title","value":"Study of fully epitaxial Fe/Pt bilayers for spin pumping by ferromagnetic resonance spectroscopy"},{"label":"URL","value":"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.134405"},{"label":"Date","value":"April 5, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 41)."},{"label":"RBK Item","value":"The intrinsic FMR linewidth for conduction electrons arises from spin-orbit coupling."},{"label":"Title","value":"Origin of Intrinsic Gilbert Damping"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevLett.102.137601"},{"label":"Date","value":"March 31, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 38)."}]
|
Chemistry
|
Archaeological chemistry
|
MCQ
|
Adjacent radiocarbon dating of Iron Age site foundation
|
https://chemrxiv.org/engage/chemrxiv/article-details/682ec5413ba0887c3332b980
|
May 28, 2025
|
Researchers have developed a chemical procedure for radiocarbon dating metal archaeological samples. A total of six samples from the iconic Iron Age site Creney-le-Paradis were analysed, all consisting of fibres extracted from mineralised textiles still in contact with a bronze substrate. The conversion of the samples to CO2 took place in sealed quartz tubes under vacuum (l = 16 cm, 0.8 cm diameter; Möller, Switzerland) and heated to 643 K for 30 min in a muffle furnace (SOLO Industrieöfen GmbH, Biel, Switzerland). After the combustion process, CO2 is purified in a dedicated vacuum line for cryo-trapping. Water is trapped in a Peltier module cooled to 248 K, while carbon dioxide is trapped in a calibrated volume cold finger fitted with a pressure sensor and cooled to 78 K with liquid nitrogen. The latter is finally transferred, frozen, and flame-sealed in a borosilicate tube cooled with a liquid nitrogen trap. 14C measurement of the purified CO2 fraction, corresponding to the mineral carbon in the carbonates, is carried out via a gas interface system (GIS) coupled to the accelerator mass spectrometer (AMS). The black solid residue left in the broken glass ampoule is treated with 1-M HCl, ensuring the removal of other carbonate contamination. The dried solid residue is packed in an aluminum boat and its 14C content is measured by direct combustion in an elemental analyzer (EA) coupled to the AMS. All radiocarbon measurements were performed on the compact Mini Carbon Dating System (MICADAS) at the Laboratory of Ion Beam Physics, ETH Zurich, Switzerland.
|
• Stable isotope ratios expressed as δ13C in ‰ units.
• Radiocarbon ages expressed in BP years units.
• Calendar ages expressed in BC years units.
|
Researchers have developed a chemical procedure for radiocarbon dating metallic archaeological samples. A total of six samples from the iconic Iron Age site Creney-le-Paradis were analysed, all consisting of fibres extracted from mineralised textiles still in contact with the bronze substrate. Two CO2 fractions were obtained by both thermal decomposition of copper carbonates and combustion of the remaining solid organic residue, if any. Then, the CO2 fractions were assessed by AMS, and their respective 13C/12C ratios were measured by IRMS. Radiocarbon ages were calibrated using Oxcal v.4.4 software with the Intcal20 atmospheric curve. Mark all the correct options.
A. The mean radiocarbon age is 2619 ± 11 yr BP, and the calendar age is 808-790 BC.
B. The calendar age is 2619 ± 11 yr BC, and the mean radiocarbon age is 808-790 BP.
C. δ13C values range from −27 to -22‰.
D. δ13C values range from −22 to −17‰.
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A. The mean radiocarbon age is 2619 ± 11 yr BP, and the calendar age is 808-790 BC.
D. δ13C values range from −22 to −17‰.
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• The advent of accelerator mass spectrometers (AMS) allows the number of 14C atoms to be measured relative to the number of 12C atoms.
• 13C/12C isotope ratio can be expressed as a δ13C value, which indicates the possible origin of the dated carbon fraction.
|
[{"label":"RBK Item","value":"The advent of accelerator mass spectrometers (AMS) allows the number of 14C atoms to be measured relative to the number of 12C atoms."},{"label":"Title","value":"Carbon-14: Direct Detection at Natural Concentrations"},{"label":"URL","value":"https://www.science.org/doi/10.1126/science.198.4316.507"},{"label":"Date","value":"November 4, 1977"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"13C/12C isotope ratio can be expressed as a δ13C value, which indicates the possible origin of the dated carbon fraction. "},{"label":"Title","value":"STABLE ISOTOPES IN ECOSYSTEM STUDIES"},{"label":"URL","value":"https://www.annualreviews.org/content/journals/10.1146/annurev.es.18.110187.001453"},{"label":"Date","value":"November 1, 1987"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Physics
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Applied physics, thermodynamics, mechanical engineering, energy and transport.
|
MCQ
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Reducing Temperature Swing and Rectifying Radiative Heat Transfer for Passive Dynamic Space Thermal Control with Variable-Emittance Coatings
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https://arxiv.org/abs/2509.13794
|
Sep 17, 2025
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Tunable VO2-based Fabry-Pérot (VO2FP) variable-emittance coating made of 55-nm VO2, 500-nm silicon, and 200-nm aluminum thin films was fabricated on a double-side polished silicon wafer via thin film sputtering. Black Actar and highly reflective tungsten mirrors are used to calibrate the parasitic head load and heat flux sensor sensitivity. With the cold finger at 80 K to mimic external radiative scenarios in space. A tungsten mirror was fabricated by sputtering 200-nm-thick tungsten at a rate of 0.15 nm/s onto a polished silicon wafer. Double-sided, polished silicon wafers, 280 µm thick, with various doping levels, were commercially purchased with different resistivities. A freshly deposited aluminum mirror was used as the reference. A commercial black Actar sample was attached to a polished silicon wafer with thermal paste. The spectral reflectance of these static-emittance samples was measured at a temperature of 25°C. The radiative thermal tests were conducted under high vacuum (<10^ (-3) Pa) inside a cryostat (Janis VPF-800) equipped with a cold finger and a custom-made sample mount. A test sample, along with a heat flux sensor (FluxTeq, PHFS-01) of ±5% accuracy and a polyimide thin-film heater (OMEGA Engineering, KHLVA-101/10-P), was first attached to a 5-mm-thick acrylic carrier plate of 1-inch square size. After the acrylic carrier plate was pinned onto the brackets with approximately 2 mm spacing between the sample and the cold finger, the cryostat was then brought down to high vacuum, followed by the filling of liquid nitrogen (LN2) to cool the cold finger to 80 K, which simulates the cold space thermal environment. A Fourier transform infrared spectrometer (Thermo Fisher Scientific, iS50) along with a variable-angle reflection accessory (Harrick Scientific, Seagull) was used to measure the spectral specular reflectance at 10° incidence angle in the wavelength range from 2 µm to 22 µm at a resolution of 4 cm-1 with each spectrum averaged over 32 scans. Spectral measurements were taken twice, once during the heating cycle and once during the cooling cycle, over the range of 27 °C to 91 °C. After each temperature reached the set point for 5 minutes, with a fluctuation of less than 1 °C, measurements were taken.
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- Spectral infrared reflectance (in %) measured against wavelength from 2 μm to 22 μm on a tunable VO₂FP variable-emittance coating in the heating cycle from 27 °C to 91 °C.
- Spectral infrared reflectance (in %) measured against wavelength from 2 μm to 22 μm on a tunable VO₂FP variable-emittance coating in the cooling cycle from 27 °C to 91 °C.
|
A tunable VO2-based Fabry-Pérot (VO2FP) variable-emittance coating, composed of VO2 and aluminum thin films, was fabricated on a double-sided polished silicon wafer via thin-film sputtering. A Fourier transform infrared spectrometer, along with a variable-angle reflection accessory (Harrick Scientific, Seagull), was used to measure the spectral specular reflectance at 10° incidence angle in the wavelength range from 2 μm to 22 μm. Predict which statements accurately describe the behavior of spectral infrared reflectance and emittance for the tunable VO₂FP emitter across heating and cooling cycles?
a) A high reflection dip around 19 - 21 μm wavelength and reflectance increases as the temperature decreases.
b) A high reflection dip around 19 - 21 μm wavelength and reflectance decreases as the temperature decreases.
c) A law reflecting a dip around 6 - 9 μm wavelength and reflectance decreases as the temperature decreases.
d) A law reflecting a dip around 6 - 9 μm wavelength and reflectance increases as the temperature decreases.
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d) A law reflecting a dip around 6 - 9 μm wavelength and reflectance increases as the temperature decreases.
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-Slight angular dependence of the total emittance for the VO2FP emitter at the metallic phase due to the nature of wave interference when FP resonance is excited; therefore, the total hemispherical emittance of the VO2FP emitter in the metallic phase is reduced by 10% from the total normal emittance, while it remains the same in the insulating phase without excitation of FP resonance.
- The undoped and medium-doped silicon samples have almost the same total hemispherical emittance with the tunable VO2FP emitter in its insulating and metallic phase, respectively.
|
[{"label":"RBK Item","value":"Slight angular dependence of the total emittance for the VO2FP emitter at the metallic phase due to the nature of wave interference when FP resonance is excited; therefore, the total hemispherical emittance of the VO2FP emitter in the metallic phase is reduced by 10% from the total normal emittance, while it remains the same in the insulating phase without excitation of FP resonance. "},{"label":"Title","value":"Vanadium dioxide based Fabry-Perot emitter for dynamic radiative cooling applications"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S002240731630574X?casa_token=Txf3yLnmKmQAAAAA:55GKPd5JdT7D7ILEzEajIolvZqK_C8PY5yy89APKv-c-DVpbM_TW7gQLTo6fwz_pKZ5uoj09z1kt"},{"label":"Date","value":"Aug, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Open-access, this is cited as reference 13 in the paper"}]
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Biology
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Biology/ Microbiology
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Free-Format Question
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Early Pregnancy Marks Significant Shifts in the Oral Microbiome
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https://www.biorxiv.org/content/10.1101/2025.09.29.679276v2
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November 5, 2025
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To analyze the development of the oral microbiome during pregnancy, the researchers recruited an Israeli cohort of pregnant women sampled during T1, T2, and T3. A total of 346 Israeli women were recruited, and 467 oral microbiome samples were processed: 235 from T1 (11-14 gestational weeks), 144 from T2 (24-28 gestational weeks), and 88 from T3 (32-38 gestational weeks). At recruitment, the height and current weight of the study participants were recorded, and participants were interviewed by a dietitian for stress level, working hours, sleeping hours, smoking, education, and a 24-hour recall for food intake, categorizing food remarks in 4: Normal, Vegan or Vegetarian, High Carb, and Gluten Free. Participants then provided a saliva sample, collected in 1.5 ml tubes and stored at 125 -80°C until processing. Similar procedures were repeated in the study population in T2 (24-28 gestational weeks) and T3 (32-38 gestational weeks) of pregnancy. DNA was extracted from all collected samples using the PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s instructions and following a 2˜min bead beating step (BioSpec, Bartlesville, OK, USA). The variable V4 region of the 16S rRNA gene was PCR-amplified using the 515F and 806R barcoded primers following the Earth Microbiome Project protocol. Each PCR reaction contained 25 µl with ∼40 ng/µl of DNA, 2 µl 515F (forward, 10 µM) primer, 2 µl 806R (reverse, 10 µM) primer, and 25 µl PrimeSTAR Max PCR Readymix (Takara, Mountain View, CA, USA). PCR conditions were as follows: 30 cycles of denaturation at 98°C for 10 s, annealing at 55°C for 5 s, and extension at 72° C for 20 s, followed by a final elongation at 72° C for 1 min. Amplicons were purified using AMPure magnetic beads(Beckman Coulter, Indianapolis, IN, USA) and quantified using the Picogreen dsDNA quantitation kit (ThermoFisher, Waltham, MA, USA). Equimolar amounts of DNA from individual samples were pooled and sequenced using the Illumina MiSeq platform at the Azrieli Faculty of Medicine’s Genome Center. Microbiome associations were obtained from analyzing DNA samples.
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-Microbiome associations obtained from processing of DNA samples collected from saliva of women at 3 stages of pregnancy (T1, T2, T3).
-Categories of food intake per women: normal, vegetarian or vegan, high carb, and gluten-free, registered from interviews with a dietary.
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Researchers analyzed the development of the oral microbiome during pregnancy by collecting saliva samples from 346 Israeli women at different pregnancy stages (T1, T2, and T3). Saliva samples were processed to extract DNA and obtain microbiome associations. Besides the sample collection, the 346 women were interviewed regarding their food intake habits, categorizing them in 4 different types of diet: normal, vegetarian or vegan, high carb, and gluten-free. Which of those types of diet would show the strongest and most consistent associations with oral microbiome composition?
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Gluten-free diet showed the strongest and most consistent associations with oral microbiome composition across all trimesters
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-The oral microbiome undergoes distinct compositional changes throughout pregnancy, influenced by hormonal, immunologic, and metabolic shifts.
- Pregnancy associated changes can increase susceptibility to oral disease and have been associated with adverse pregnancy outcomes.
-Conversely, diets rich in fiber, plant polyphenols, and micronutrients, such as vitamin D and calcium, are associated with greater oral microbial diversity, resilience, and anti-inflammatory properties.
|
[{"label":"RBK Item","value":"The oral microbiome undergoes distinct compositional changes throughout pregnancy, influenced by hormonal, immunologic, and metabolic shifts."},{"label":"Title","value":"Metabarcoding analysis of oral microbiome during pregnancy"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/39742335/"},{"label":"Date","value":"December 17, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Pregnancy associated changes can increase susceptibility to oral disease and have been associated with adverse pregnancy outcomes."},{"label":"Title","value":"Microbiome and Pregnancy Dysbiosis: A Narrative Review on Offspring Health"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/40292452/"},{"label":"Date","value":"March 15, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Conversely, diets rich in fiber, plant polyphenols, and micronutrients, such as vitamin D and calcium, are associated with greater oral microbial diversity, resilience, and anti-inflammatory properties."},{"label":"Title","value":"Acquiring and maintaining a normal oral microbiome: current perspective"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25019064/"},{"label":"Date","value":"June 26, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant Biology
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Free-Format Question
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Role of AtCPK5 and AtCPK6 in the regulation of the plant immune response triggered by rhamnolipids in Arabidopsis
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https://www.biorxiv.org/content/10.1101/2025.10.22.683368v1
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October 23, 2025
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Researchers examined the RL (Rhamnolipid)-induced resistance to Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000). To do this, the strain was grown at 28 °C under stirring in King’s B (KB) liquid medium supplemented with antibiotic: 50 μg/mL rifampicin. Arabidopsis plants (WT, cpk5, cpk6, and cpk5/6 double mutant) were grown individually for 4 weeks in soil. For each experiment, six pots per condition were used (biological replicates, n = 6). Two days before infection, plants were sprayed with RLs (0.6mg/mL) or water as a control and were placed in a high-humidity atmosphere. The plants were then infiltrated with bacterial suspension at a concentration of 10^7 CFU/mL (in 10 mM MgCl2) using a needleless syringe. Bacterial quantification in planta (colony-forming units;CFU) was performed 3 days post-infection (dpi). To this end, all plant leaves from the same pot were harvested, weighed, and crushed in a mortar with 10 mL of 10 mM MgCl2, and serial dilutions were performed. For each dilution, 10 μL were dropped on KB plate supplemented with appropriate antibiotics. CFU were counted after 2 days of incubation at 28 °C. The number of bacteria per milligram of plant fresh mass was obtained with the following formula: CFU.mg^-1 = ((N × Vd/Vi × 10^𝑛−1 × 100)/M) where N= CFU number, Vi= volume depot on plate, Vd= total volume, n=dilution number, and M=plant fresh mass).
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- Bacterial load (CFU/mg fresh weight;P. syringae) in Arabidopsis plants (WT, cpk5, cpk6, and cpk5/6 double mutant) pretreated with vs. without rhamnolipids.
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Researchers investigated how RL (rhamnolipid) treatment affects resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) in Arabidopsis wild-type and mutant plants (cpk5, cpk6, and cpk5/6). Two days before infection, plants were sprayed with RLs (0.6mg/mL) or water as a control and were placed in a high-humidity atmosphere. The plants were then infiltrated with bacterial suspension at a concentration of 10^7 CFU/mL (in 10 mM MgCl2) using a needleless syringe. Bacterial quantification in planta (colony-forming units;CFU) was performed 3 days post-infection (dpi). Plant leaves from the same pot were harvested, weighed, and crushed in a mortar with 10 mL of 10 mM MgCl2, and serial dilutions were performed. For each dilution, 10 μL were dropped on KB plate supplemented with appropriate antibiotics. CFU were counted after 2 days of incubation at 28 °C. The number of bacteria per milligram of plant fresh mass was obtained with the following formula: CFU.mg^-1 = ((N × Vd/Vi × 10^𝑛−1 × 100)/M) where N= CFU number, Vi= volume depot on plate, Vd= total volume, n=dilution number, and M=plant fresh mass).
Predict the relative disease sensitivity (bacterial susceptibility) of all Arabidopsis plant genotypes after RL pretreatment and infection with P. syringae pv. tomato DC3000.
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After pretreatment with RL, plant backgrounds will display similarly low disease senstivity.
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-Rhamnolipids (RLs) are natural, highly biodegradable molecules produced by some bacteria that can induce disease resistance to phytopathogens in various plant species, therefore activating the immune response.
- CPKs are involved in plant development and plant response to biotic and abiotic stress.
|
[{"label":"RBK Item","value":"Rhamnolipids (RLs) are natural, highly biodegradable molecules produced by some bacteria that can induce disease resistance to phytopathogens in various plant species, therefore activating the immune response."},{"label":"Title","value":"Biosurfactants in Plant Protection Against Diseases: Rhamnolipids and Lipopeptides Case Study"},{"label":"URL","value":"https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2020.01014/full"},{"label":"Date","value":"September 7, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"CPKs are involved in plant development and plant response to biotic and abiotic stress."},{"label":"Title","value":"The role of CDPKs in plant development, nutrient and stress signaling"},{"label":"URL","value":"https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.996203/full"},{"label":"Date","value":"September 29, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Behavioral ecology / Primatology
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MCQ
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Social Tolerance and Innovation in Capuchins: socially more tolerant brown capuchins are better problem-solvers than less tolerant white-faced capuchins
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https://www.biorxiv.org/content/10.1101/2025.09.05.674457v1.full
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September 7, 2025
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Researchers tested three groups of white-faced capuchins (Cebus capucinus)(n = 23 individuals in total) and three groups of brown capuchins (Sapajus apella) (n = 20 individuals in total) to explore and compare the relationship between social tolerance and problem-solving propensities. To measure social tolerance, they prepared an area of 1 m2 per five animals in the group, in which they distributed apple pieces and measured the proportion of individuals within the co-feeding area at each scan sample. To measure problem-solving propensities, they designed three versions of novel extractive foraging devices requiring one to three steps to acquire the food reward. For the first puzzle, animals had to rotate a door to either the left or right to access a hidden reward (1/24 of an apple) by reaching into a box. For the second puzzle, animals had to pull on a chain reaching out of a box, which moved a blockade out of the way so that they could push in a door and reach into the box. For the third puzzle, animals had to pull a metal rod blocking a slider that had to be pulled upwards and held in position to reach into the box and then pull on a chain to access the hidden reward. Researchers analyzed the approaching, exploring, and solving behaviour separately.
|
- Proportion of individuals within the co-feeding area at each scan sample (social tolerance)
- Proportion of individuals within the puzzle area at each scan sample (social tolerance)
- Number of approaches to a food puzzle area.
- Approaching a food puzzle area duration.
- Approaches to a food puzzle area latency
- Number of exploration events (touch, sniff, interact) during the approaches to a food puzzle area
- Number of times the capuchins successfully solved the puzzles
- Exploration of food puzzle events latency.
- Time to solve a puzzle
|
Researchers tested three groups of white-faced capuchins (Cebus capucinus) and three groups of brown capuchins (Sapajus apella) to explore and compare the relationship between social tolerance and problem-solving propensities. To measure social tolerance, they prepared an area of 1 m2 per five animals in the group, in which they distributed apple pieces and measured the proportion of individuals within the co-feeding area at each scan sample. To measure problem-solving propensities, they designed three versions of novel extractive foraging devices requiring one to three steps to acquire the food reward. Which of the following outcomes is most likely?
A. Both species should show the same levels of social tolerance and problem-solving propensities.
B. White-faced capuchins should show the highest level of social tolerance and problem-solving propensities.
C. White-faced capuchins should show the lowest level of social tolerance and problem-solving propensities.
D. White-faced capuchins should show the highest level of social tolerance and the lowest level of problem-solving propensities.
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C. White-faced capuchins should show the lowest level of social tolerance and problem-solving propensities.
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- Social tolerance has increasingly been linked to the facilitation of social learning across a variety of species, including chimpanzees, orangutans, macaques, capuchin monkeys, lemurs, and birds.
- White-faced capuchins (Cebus capucinus) and brown capuchins (Sapajus apella) exhibit a diverse array of traditions
- White-faced capuchins (Cebus capucinus) are less known for using tools (but see Barrett et al., 2018), but they regularly engage in object use (Boinski, 1988).
- Robust capuchins (Sapajus spp.) have fewer documented social traditions but exhibit a wide range of foraging traditions, including tool-use, and show notable social tolerance in these contexts, tolerating close proximity of conspecifics
|
[{"label":"RBK Item","value":"Social tolerance has increasingly been linked to the facilitation of social learning across a variety of species, including chimpanzees, orangutans, macaques, capuchin monkeys, lemurs, and birds. "},{"label":"Title","value":"Social tolerance and role model diversity increase tool use learning opportunities across chimpanzee ontogeny"},{"label":"URL","value":"https://www.nature.com/articles/s42003-025-07885-4"},{"label":"Date","value":"March 28, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"White-faced capuchins (Cebus capucinus) and brown capuchins (Sapajus apella) exhibit a diverse array of traditions."},{"label":"Title","value":"The Complete Capuchin: The Biology of the Genus Cebus"},{"label":"URL","value":"https://www.cambridge.org/br/universitypress/subjects/life-sciences/biological-anthropology-and-primatology/complete-capuchin-biology-genus-icebusi?format=PB&isbn=9780521667685#contents"},{"label":"Date","value":"June 21, 2004"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Reference book (the URL provided is for reference only)"},{"label":"RBK Item","value":"White-faced capuchins (Cebus capucinus) are less known for using tools (but see Barrett et al., 2018), but they regularly engage in object use"},{"label":"Title","value":"Habitual stone-tool-aided extractive foraging in white-faced capuchins, Cebus capucinus"},{"label":"URL","value":"https://royalsocietypublishing.org/doi/10.1098/rsos.181002"},{"label":"Date","value":"July 25, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Robust capuchins (Sapajus spp.) have fewer documented social traditions but exhibit a wide range of foraging traditions, including tool-use, and show notable social tolerance in these contexts, tolerating close proximity of conspecifics"},{"label":"Title","value":"Wild capuchin monkeys use stones and sticks to access underground food"},{"label":"URL","value":"https://www.nature.com/articles/s41598-024-61243-8"},{"label":"Date","value":"May 06, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Neuroscience
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Free-Format Question
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Developmental and Stress-Induced Effects on 5-HT3R-Expressing Interneurons within Auditory Cortex
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https://www.biorxiv.org/content/10.1101/2025.09.08.675013v1
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Sep 09, 2025
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Researchers characterized the cell type-specific expression profiles of 5-HT3R within two major subpopulations of 5-HT3R cells, NDNF⁺ and VIP⁺, in A1, to analyze their developmental trajectories under normal conditions and the influence of early life stress (ELS). Brain sections containing A1 were obtained from mixed-sex groups of Mongolian gerbils (Meriones unguiculatus) to study the development of cell populations. Two control groups, CTR10 and CTR15, were sacrificed at postnatal days 10 and 15, respectively, to characterize the timeline of normal development in A1 during the auditory cortex (ACx) critical period. A third control group, CTR30, was sacrificed at postnatal day 30 to assess the closure of the critical period. Two additional groups, “Restraint” ELS (ELSR) and “Open field” (ELSO), were subjected to a separate form of stress induction during the ACx critical period, and sacrificed at postnatal day 30. For each sample, coronal sections containing A1 were collected on a cryostat microtome, and adhered to SuperFrost Plus slides. RNA fluorescent in situ hybridization (FISH) was performed using RNAscope probes, which were hybridized at 40°C for 2 hours, followed by of signal amplification, and fluorescent labeling using channel-specific horseradish peroxidases and TSA vivid fluorophores All slides were counterstained with DAPI for 30s prior to coverslipping. NDNF⁺ and VIP⁺ cells were quantified through the neocortical layers 1-4 (L1, L2/3, and L4), which were visually identified based on packing densities illuminated by DAPI. Tiled images of A1 containing L1-L4 were taken at 40x in four channels to generate A1 “maps” which were used to identify all cells that expressed NDNF⁺ and VIP⁺ mRNA within the region of interest. The RNAscope assay was used to quantify the levels of Htr3a mRNA expression through the count of discrete fluorescent puncta of each NDNF⁺ and VIP⁺ cell within A1 image at 150x in three channels.
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- Comparison of NDNF⁺ and VIP⁺ cell densities across layers under normal development and the influence of ELS.
- Quantification of fluorescent puncta in NDNF⁺ and VIP⁺ cells under normal development and the influence of ELS.
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Two subpopulations of cells, NDNF⁺ and VIP⁺, contribute to 5-HT3R expression, which may play a role in regulating critical period plasticity in ACx. Quantification of cells and mRNA expression for each cell subpopulation was performed by manual counting of images obtained through RNA fluorescent in situ hybridization (FISH) to evaluate the effect of ELS. Results were compared between the A1 sections of L1-L4 from: a) control groups, sacrificed at postnatal days 10, 15, and 30; b) the ELSR group, sacrificed at postnatal day 30; c) the ELSO group, sacrificed at postnatal day 30. In NDNF⁺ Layer 1, what is the comparison of cell density between ELSR and CTR30?
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NDNF⁺ cell density is significantly higher in ELSR compared to CTR30
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- Early life stress (ELS) contributes to neuropsychiatric disease in both humans and animal models.
- The auditory cortex (ACx) is a brain region where exposure to ELS during a critical period impairs both neural and behavioral responses to a variety of auditory stimuli that rely on temporal processing.
- Serotonin (5-HT) is a neurotransmitter linked to stress, developmental plasticity, and the auditory system.
- 5-HT3 receptors (5-HT3R) are serotonin receptors that may have a role in regulating critical period plasticity in ACx. 5-HT3R gene expression can be affected by ELS.
- Vasoactive intestinal peptide (VIP) are cells that are densely populated in superficial cortical layers that express 5-HT3R.
- Neuron derived neurotrophic factor (NDNF) are cells that are mostly confined to L1, and that express 5-HT3R
|
[{"label":"RBK Item","value":"Early life stress (ELS) contributes to neuropsychiatric disease in both humans and animal models"},{"label":"Title","value":"Childhood adversities and adult psychopathology in the WHO World Mental Health Surveys"},{"label":"URL","value":"https://doi.org/10.1192/bjp.bp.110.080499"},{"label":"Date","value":"Nov, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"The auditory cortex (ACx) is a brain region where exposure to ELS during a critical period impairs both neural and behavioral responses to a variety of auditory stimuli that rely on temporal processing."},{"label":"Title","value":"Early-Life Stress Impairs Perception and Neural Encoding of Rapid Signals in the Auditory Pathway\n"},{"label":"URL","value":"https://doi.org/10.1523/JNEUROSCI.1787-22.2023."},{"label":"Date","value":"May 3, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Serotonin (5-HT) is a neurotransmitter linked to stress, developmental plasticity, and the auditory system."},{"label":"Title","value":"Context-dependent modulation of auditory processing by serotonin"},{"label":"URL","value":"https://doi.org/10.1016/j.heares.2010.12.015"},{"label":"Date","value":"Sep, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Vasoactive intestinal peptide (VIP) are cells that are densely populated in superficial cortical layers that express 5-HT3R."},{"label":"Title","value":"Primary auditory thalamus relays directly to cortical layer 1 interneurons"},{"label":"URL","value":"https://doi.org/10.1101/2024.07.16.603741"},{"label":"Date","value":"Jul 18, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Neuron derived neurotrophic factor (NDNF) are cells that are mostly confined to L1, and that express 5-HT3R"},{"label":"Title","value":"Primary auditory thalamus relays directly to cortical layer 1 interneurons"},{"label":"URL","value":"https://doi.org/10.1101/2024.07.16.603741"},{"label":"Date","value":"Jul 18, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Chemistry
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Analytical Chemistry
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Numerical Values
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Towards enhanced selection of antibiotics in a hospital laboratory – development of a rapid electrochemical-based antimicrobial sensitivity test for Urinary Tract Infections.
|
https://chemrxiv.org/engage/chemrxiv/article-details/68839d31728bf9025e354df8
|
July 29, 2025
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Clinical midstream urine samples received for culture and antibiotic susceptibility testing (AST) were collected across three external hospital laboratories: Glasgow Royal Infirmary (GRI, UK), the North-East Innovation Lab at the Newcastle upon Tyne Hospitals NHS Foundation Trust (NuTH, UK), and Breach Candy Hospital Trust (BCHT, India). A total of 89 clinically derived urine samples were screened, with site-specific inclusion criteria used to preferentially select UTI-positive specimens (e.g., leukocyte or nitrite positivity on urinalysis at GRI, predefined microscopy-based screening at NuTH, and pus cell count plus leucocyte esterase positivity at BCHT). For RapidPlate™ testing, 20 μL of each selected urine sample was directly inoculated into wells of a disposable electrochemical cartridge containing agar gels with nutrients, redox mediator, and a panel of six UTI-relevant antibiotics—amoxicillin, cefalexin, ciprofloxacin, fosfomycin, nitrofurantoin, and trimethoprim—each present at a single concentration corresponding to the EUCAST breakpoint and arranged in triplicate wells alongside positive and negative control wells. Cartridges were inserted into RapidPlate™ reader units, which performed electrochemical impedance spectroscopy–based monitoring of bacterial growth in the presence and absence of each antibiotic. In parallel, standard clinical AST was carried out on the same urine samples at each site using the routine reference methods: VITEK 2 automated broth microdilution (N445 card) at GRI and Kirby–Bauer disk diffusion (KBDD) at NuTH and BCHT, with species-specific breakpoints applied according to local clinical guidelines. For each clinical sample and antibiotic combination across all three clinical sites, the categorical AST result reported by the RapidPlate™ system (susceptible, resistant or, where applicable, intermediate/susceptible–increased exposure) was later compared with the corresponding categorical AST result from the site-specific reference method.
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- For each included clinical urine sample at each hospital site (Glasgow Royal Infirmary, Newcastle upon Tyne Hospitals, Breach Candy Hospital Trust) and for each antibiotic on the RapidPlate™ panel (amoxicillin, cefalexin, ciprofloxacin, fosfomycin, nitrofurantoin, trimethoprim), researchers recorded the categorical antibiotic susceptibility result reported by the RapidPlate™ system (e.g. susceptible, resistant or, where applicable, intermediate/susceptible–increased exposure) based on electrochemical impedance measurements collected during the cartridge run time.
- For the same clinical urine samples and antibiotics, at each site, researchers recorded the categorical antibiotic susceptibility result reported by the local routine reference method (VITEK 2 automated broth microdilution at Glasgow Royal Infirmary; Kirby–Bauer disk diffusion at Newcastle upon Tyne Hospitals and Breach Candy Hospital Trust), using site-specific species–antibiotic clinical breakpoints.
- For all sample–antibiotic pairs that had valid categorical results from both RapidPlate™ and the corresponding reference method, researchers counted the number of pairs in which RapidPlate™ and the reference method reported the same susceptibility category, as well as the total number of such pairs across all three clinical sites.
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Researchers used a RapidPlate electrochemical impedance–based antibiotic susceptibility test on clinical midstream urine samples at three hospital laboratories and compared its antibiotic susceptibility predictions to conventional reference methods (VITEK 2 broth microdilution and Kirby–Bauer disk diffusion). Considering all three clinical sites together, what was the overall categorical agreement (in percent) between RapidPlate™ and the reference methods?
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94% [89% - 99%]
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-Current standard methods for antibiotic susceptibility testing (AST) include automated systems such as VITEK 2 (bioMérieux, France), in addition to traditional techniques like Kirby-Bauer disk diffusion and broth microdilution
- Electrochemical impedance spectroscopy (EIS) is amongst the most sensitive electrochemical techniques for evaluating interfacial and bulk solution changes in a system. EIS can monitor differences in the electrical properties of the system over time by applying an alternating current at a range of frequencies.
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[{"label":"RBK Item","value":"Current standard methods for antibiotic susceptibility testing (AST) include automated systems such as VITEK 2 (bioMérieux, France), in addition to traditional techniques like Kirby-Bauer disk diffusion and broth microdilution"},{"label":"Title","value":"Current and Emerging Methods of Antibiotic Susceptibility Testing\n"},{"label":"URL","value":"https://www.mdpi.com/2075-4418/9/2/49"},{"label":"Date","value":"May 3, 2019"},{"label":"RBK Item","value":"- Electrochemical impedance spectroscopy (EIS) is amongst the most sensitive electrochemical techniques for evaluating interfacial and bulk solution changes in a system. EIS can monitor differences in the electrical properties of the system over time by applying an alternating current at a range of frequencies."},{"label":"Title","value":"10 - Impedance biosensors"},{"label":"URL","value":"https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780323884310000041"},{"label":"Date","value":"May 8, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
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Chemistry
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Catalysis
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Free-Format Question
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An investigation of the physical and chemical changes of Pd nanoparticles on carbon supports in response to the release of hydrogen from aqueous formate solutions
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https://chemrxiv.org/engage/chemrxiv/article-details/68d16d29f2aff16770fa93bd
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September 25, 2025
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Researchers prepared and analyzed Pd nanoparticles supported on carbon materials to examine their structural and chemical evolution during hydrogen release from aqueous sodium formate. Three supports were used: carbon black (Vulcan XC-72), nitrogen-doped carbon (NC), and graphitic carbon nitride (g-C₃N₄). Nitrogen-doped carbon was obtained by heating a melamine–carbon black mixture at 700 °C under nitrogen, while g-C₃N₄ was synthesized by heating urea at 500 °C in air. Pd catalysts were produced by reducing H₂PdCl₄ with NaBH₄ in trisodium citrate solution at 25 °C, yielding a 1 wt% Pd loading. The product was filtered, washed, and dried at 85 °C for 24 h, and selected samples were calcined at 250 °C for 3 h in air. Structural and compositional analyses included inductively coupled plasma–optical emission spectrometry (PerkinElmer 7300 DV) to determine Pd content, X-ray diffraction (Rigaku SmartLab SE, Cu Kα, 2θ = 2–100°) to assess crystallinity, and nitrogen physisorption (Micromeritics ASAP 2020) using BET and BJH models to measure surface area and pore volume. Pd dispersion was quantified by CO chemisorption (Micromeritics ASAP 2020C, 30 °C, pre-reduced at 100 °C for 0.5 h), and nanoparticle morphology was examined by aberration-corrected scanning transmission electron microscopy (Thermo Fisher Themis Z, 300 kV). Catalytic performance was tested in a 50 mL batch reactor containing 250 mg of catalyst and 10 mL of 1 M sodium formate at 65 °C under N₂ with stirring at 500 rpm for 2 h, where gas evolution was monitored by pressure change and analyzed using a micro-gas chromatograph. In-situ X-ray absorption spectroscopy was performed at the Stanford Synchrotron Radiation Lightsource beamline 4-1 to monitor Pd oxidation states during reaction using Pd K-edge XANES and EXAFS scans (24126–25238 eV, 0.5 × 4 mm beam). Catalyst reuse tests were carried out by recovering the solid after reaction, washing with deionized water, drying at 80 °C, and re-calcining at 180 or 250 °C for 3 h when required. All synthesis, characterization, and catalytic experiments were conducted under controlled temperature and atmospheric conditions to ensure reproducibility.
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- Pd oxidation state and local atomic structure characterized by in-situ X-ray Absorption Spectroscopy (XAS, SSRL beamline 4-1) with Pd K-edge XANES and EXAFS scans (24126–25238 eV, beam size 0.5 × 4 mm) under reaction conditions.
- Palladium loading (wt%) measured using Inductively Coupled Plasma–Optical Emission Spectroscopy (ICP-OES, PerkinElmer 7300 DV) to quantify Pd content on carbon supports.
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Palladium nanoparticles supported on carbon materials were assessed as catalysts for hydrogen release from aqueous sodium formate. Three supports- carbon black (Vulcan XC-72), nitrogen-doped carbon (NC), and graphitic carbon nitride (g-C₃N₄)- were employed, with NC synthesized by heating a melamine-carbon black mixture at 700 °C under N₂ and g-C₃N₄ prepared by urea pyrolysis at 500 °C in air. Pd catalysts (1 wt%) were obtained by reducing H₂PdCl₄ with NaBH₄ in trisodium citrate at 25 °C, followed by drying and optional calcination at 250 °C. Structural and chemical characterization included ICP–OES for Pd content, XRD for crystallinity, N₂ physisorption for surface area, CO chemisorption for Pd dispersion, and STEM for nanoparticle morphology. Catalytic performance was evaluated in a batch reactor (65 °C, 1 M sodium formate) by monitoring gas evolution and composition via micro-GC. In-situ XANES/EXAFS at the Pd K-edge tracked oxidation-state changes during reaction, and reuse tests examined catalyst stability following washing and re-calcination. What will in-situ XANES analysis reveal about the role of palladium oxide (PdO) as an active catalyst for formate dehydrogenation?
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In-situ XANES experiments unambiguously demonstrate that PdO is rapidly reduced to metallic Pd and then forms Pd hydride upon exposure to a formate solution, showing that PdO does not play a direct role in the mechanism of H2 formation.
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- Palladium nanoparticles on carbon supports (Pd/C) are effective for catalyzing hydrogen release from aqueous formate solutions but typically suffer from a gradual decrease of activity.
- Nitrogen doping of carbon supports is observed to enhance the rates of hydrogen release from aqueous formate solutions
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[{"label":"RBK Item","value":"Shin and cowrokers argued that desorption of hydrogen from the Pd metal is rate\nlimiting and the presence of nitrogen on a graphene sheet decreases the binding energy of hydrogen\nresulting in a lower barrier for the reaction. These results suggest that the benefits of N-containing\nsupports are twofold: retaining active Pd sites through an increased stability of Pd nanoparticles."},{"label":"Title","value":"Novel nanoporous N-doped\ncarbon-supported ultrasmall Pd nanoparticles: Efficient catalysts for hydrogen storage and\nrelease"},{"label":"URL","value":".\nhttps://doi.org/10.1016/j.apcatb.2016.10.080."},{"label":"Date","value":"29 October 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Koh and Jeon found that the electron-rich pyridinic and pyrrolic\nnitrogen groups could donate electrons to Pd, resulting in electron-enriched Pd through strong\ninteractions between Pd and nitrogen. Our XPS results show that although Pd/NC has only 2 at.%\nN, the large majority of this is pyridinic and pyrrolic. The N in the Pd/g-C₃N₄ catalyst\nis mostly pyridinic, and therefore the enhanced activity observed for both N-containing catalysts\nis likely derive from an electronic effect similar to that proposed by Koh and Jeon."},{"label":"Title","value":". Electronically modified Pd\ncatalysts supported on N-doped carbon for the dehydrogenation of formic acid."},{"label":"URL","value":"https://doi.org/10.1016/j.ijhydene.2016.04.102."},{"label":"Date","value":"August 20, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Biomaterials / Bone tissue engineering
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MCQ
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Tenascin-c functionalised self-assembling peptide hydrogels for critical-sized bone defect reconstruction
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https://www.sciencedirect.com/science/article/pii/S0142961225004727
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July 11, 2025
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Researchers aimed to explore the influence of functionalizing a self-assembling peptide hydrogel with Tenascin-c for bone defect reconstructions. The encoding nucleotide sequence of the tenascin-c monomer was collected from the NCBI public database (GeneID: 3371) and trimmed down to the 3rd to 5th units of the TNCIII domains, from G2725 to C3534 (transcript variant 1; NM_002160.4); the sequence was cross-referenced against the Uniprot database (P24821). The F3 (3rd TNCIII domain), F5 (5th TNCIII domain), and F35 (3rd, 4th, and 5th TNCIII domains) fragments had the peptide sequence 5′-GGGGFEFKFEFK-3′ added at the C-terminal to make them competent for self-functionalisation; a tetraglycine spacer was installed between the tenascin and peptide block units for flexibility. The inserts were capped with restriction sites at the 5’ (BamHI) and 3’ (XhoI) ends and submitted to the Genscript Gene Synthesis service for cloning into a pGEX-6P-1 vector harbouring a GST tag. Rosetta 2 pLysS/BL21-DE3 E. Coli were transformed with the different plasmids to produce the different Tenascin-c fragments, which were purified with a 1 mL sepharose column, dialysed for 45 min against PBS at pH 11.5 using a Slide-A-Lyser column (Thermo Fischer Scientific), and concentrated to 9 - 10 mg/mL by liquid evaporation. The Polymers & Peptides research group from the University of Manchester and Cell Guidance Systems Ltd provided the Delta1 peptide hydrogel. It was received as a ready-to-use peptide solution concentrated at 20 mg/mL. 0.5 μL of 5 M NaOH per 100 μL hydrogel was added to decrease fibre stability and facilitate the subsequent fragment incorporation. Hydrogel functionalisation consisted of adding the concentrated fragment stock to the Delta1 peptide solution, followed by rigorous vortexing. The fragment concentration in the hydrogels was kept consistent with the molarity of the F35 hydrogel group, functionalised at 1 mg/mL; accordingly, the F3 and F5 hydrogel groups were prepared at 0.66 mg/mL. The dilution factor was kept consistent across all hydrogel groups by supplementation of PBS at pH 11.5, where appropriate. Bone marrow-derived human mesenchymal stem cells (MSC) were harvested from a donor femoral head and supplied at passage 0 (P0) by PromoCell. The MSCs were expanded and sustained in basal media (DMEM) with 4.5 g/L glucose (Gibco), 11 mg/mL sodium pyruvate (Gibco), 1 % MEM non-essential amino acids (Gibco), 10 % fetal bovine serum (FBS) (Cytiva), 1 % penicillin/streptomycin (76 Units/mL and 76 μg/mL respectively) (Gibco), 2.3 mM L-glutamine (Sigma), and 0.25 μg/ mL Amphotericin B (Gibco)). Basal media was replenished every 72 h, and cells were passaged at 80 % confluency. Bone marrow-derived human mesenchymal stem cells (MSC), were consistently seeded at 1.000.000 cells/mL in the previously prepared hydrogel groups and rigorously vortexed; 50 μl of the cell/hydrogel mixture was formed in a non-tissue culture treated 48 well plate. The loaded gels were promptly submerged with 500 μL of basal media and left to incubate for 1 h in cell culture conditions, after which the media was replenished; the media was again replenished after 24 h and from there every 72 h. For the osteogenic differentiation of MSCs in vitro, hydrogel groups were prepared and supplemented with recombinant human BMP-2 to a 5 μg/mL concentration. The hydrogels were seeded, loaded in 50 μl volumes, and maintained over three weeks as previously described. Conditions were replicated thrice for the time points day 7, 14, and 21. The hydrogels were digested in pronase (5 mg/mL) (Merck) for 10 min at 37 °C, the RNA was subsequently extracted using the TriZol method. Recovered RNA was reverse-translated to a cDNA library using the QuantiTect Reverse Transcription Kit (Qiagen), as per the manufacturer's instructions. Samples were then used in the qPCR assay to quantify the expression of RPL13A (housekeeping gene), bone alkaline phosphatase (ALP), osteopontin (OPN), osterix (OSX), and osteocalcin (OCN) using the ΔΔCt method. Mineralisation was evaluated by Alizarin Red staining to visualise and compare calcium deposition across the hydrogel groups.
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- RT-qPCR: MSCs in Delta 1, F3, F5, and F35 hydrogel groups supplemented with recombinant human BMP-2 to 5 μg/mL, for genes RPL13A (housekeeping gene), ALP, OPN, OSX, and OCN using the ΔΔCt method (Day 7, Day 14, Day 21).
- Mineralisation (calcium deposit patterns) by Alizarin Red staining on day 21: Delta1 + BMP-2 vs functionalised hydrogels + BMP-2.
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Researchers aimed to investigate the impact of functionalizing a self-assembling peptide hydrogel with Tenascin-C for bone defect reconstructions. Three different fragments of the Tenascin-c protein ( i.e. F3: 3rd TNCIII domain; F5: 5th TNCIII domain; F35: 3rd, 4th, and 5th TNCIII domains) were generated in E. coli with the peptide sequence 5′-GGGGFEFKFEFK-3′ added at the C-terminal to make them competent for self-functionalisation and a tetraglycine spacer in-between the tenascin and peptide block units for flexibility. These were mixed with the Delta1 peptide hydrogel (Polymers & Peptides research group, University of Manchester), keeping the concentration in the hydrogels consistent with the molarity of the F35 hydrogel group (1 mg/mL); accordingly, the F3 and F5 hydrogel groups were prepared at 0.66 mg/mL. Bone marrow-derived human mesenchymal stem cells (MSC) were seeded at 1.000.000 cells/mL in the previously prepared hydrogel groups, and 50 μl of the cell/hydrogel mixture was formed in a non-tissue culture-treated 48-well plate. For the osteogenic differentiation of MSCs in vitro, the hydrogel groups were supplemented with recombinant human BMP-2 at a concentration of 5 μg/mL and cultured for 7, 14, and 21 days. At each time point, RT-qPCR was performed to assess the expression of osteogenic genes. To evaluate functional osteogenic outcomes, Alizarin Red staining was also performed to detect calcium deposition within the hydrogels. Which of the following outcomes is most likely?
A) Gene expression in F35 was comparable between Delta1 + BMP-2 and functionalised hydrogels + BMP-2, while mineralisation was comparable across all groups
B) Gene expression of osteogenic markers showed modest upregulation in functionalised hydrogels compared to Delta1 + BMP-2, with F35 trending highest, and mineralisation was comparable across all groups.
C) Functionalised hydrogels and Delta1 + BMP-2 showed similar gene expression overall, but F3 and F5 exhibited slightly higher early marker expression, while mineralisation was minimal in Delta1 and more robust in the functionalised groups
D) Gene expression was largely similar between Delta1 + BMP-2 and functionalised hydrogels + BMP-2, but mineralisation was stronger in the functionalised groups
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D) Gene expression was largely similar between Delta1 + BMP-2 and functionalised hydrogels + BMP-2, but mineralisation was stronger in the functionalised groups
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- The tenascin-c monomer contains ‘fibronectin type III-like’ domain type (TNCIII), containing the 3rd and 5th TNCIII domains an RGD integrin-binding motif and an heparin-binding domain.
- Self-assembling peptide hydrogels arise in an aqueous environment from the spontaneous assembly of customised peptide building blocks to form a supramolecular fibre network.
- Self-assembling peptide hydrogels can be functionalised through ‘self-functionalisation’: a bioactive molecule of interest conjugated with the peptide building block to allow its incorporation in the fibre architecture.
|
[{"label":"RBK Item","value":"- The tenascin-c monomer contains ‘fibronectin type III-like’ domain type (TNCIII), containing the 3rd and 5th TNCIII domains an RGD integrin-binding motif and an heparin-binding domain."},{"label":"Title","value":"The tenascin family of ECM glycoproteins: Structure, function, and regulation during embryonic development and tissue remodeling"},{"label":"URL","value":"https://doi.org/10.1002/(SICI)1097-0177(200006)218:2<235::AID-DVDY2>3.0.CO;2-G"},{"label":"Date","value":"May 24, 2000"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Self-assembling peptide hydrogels arise in an aqueous environment from the spontaneous assembly of customised peptide building blocks to form a supramolecular fibre network"},{"label":"Title","value":" Hierarchical self-assembly of chiral rod-like molecules as a model for peptide β-sheet tapes, ribbons, fibrils, and fibers;"},{"label":"URL","value":"https://doi.org/10.1073/pnas.191250198"},{"label":"Date","value":"October 09, 2001\n"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Self-assembling peptide hydrogels can be functionalised through ‘self-functionalisation’: a bioactive molecule of interest conjugated with the peptide building block to allow its incorporation in the fibre architecture"},{"label":"Title","value":"Nanofibrillar Peptide Hydrogels for the Immobilization of Biocatalysts for Chemical Transformations"},{"label":"URL","value":"https://doi.org/10.1002/marc.201400027"},{"label":"Date","value":"March 07, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Microbiology
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MCQ
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ICP1 bacteriophage treatment antagonizes colonization of the zebrafish larval intestine by Vibrio cholerae
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https://www.biorxiv.org/content/10.1101/2025.09.01.673471v1
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Sep 01, 2025
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Researchers evaluated the influence of the aquatic environment on phage infection by performing in vitro bacteria-bacteriophage predation experiments. At a concentration of 10⁹ cells per mL,Vibrio cholerae was added to two different medias: Lysogeny broth (LB), used as a control, and artificial fresh water (AFW), used as the experimental condition. The bacteria concentration was diluted 1:1000. Bacteriophage ICP 1 was added to the bacterial culture at a Multiplicity of Infection (MOI) value of 2. A separate experiment was performed in Rhine water following the protocol described in Silva-Valenzuela, et al. (2018), where overnight grown V. cholerae were diluted 1:1000 and grown for 8 hours at 37° C in LB. A 20 μL inoculum of V. cholerae was added into 2.5 mL of Rhine water. After overnight growth in Rhine water, Bacteriophage ICP 1 was added to the culture at a MOI of 2. At 0, 1, 2, 4, 7 and 24 hours serial dilutions, Colony Forming Units (CFU), and Plaque Forming Units (PFU) counts were performed for each media.
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- CFU of V. cholerae in LB at 0, 1, 2, 4, 7, and 24 hours.
- PFU of ICP1 in LB at 0, 1, 2, 4, 7, and 24 hours.
- CFU of V. cholerae in AFW at 0, 1, 2, 4, 7, and 24 hours.
- PFU of ICP1 in AFW at 0, 1, 2, 4, 7, and 24 hours.
- CFU of V. cholerae in Rhine water at 0, 1, 2, 4, 7, and 24 hours.
- PFU of ICP1 in Rhine water at 0, 1, 2, 4, 7, and 24 hours.
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The interaction between Vibrio cholerae and the bacteriophage ICP1 was evaluated in-vitro through predation experiments in two different aquatic environments: artificial fresh water (AFW), and Rhine water; and a control environment: Lysogeny broth (LB). Counts of CFU, and PFU were performed for each experiment at 0, 1, 2, 4, 7, and 24 hours. Which of the following outcomes is most likely?
a) Only Rhine water will show an increase in bacteriophage propagation activity.
b) Only AFW will show an increase in bacteriophage propagation activity.
c) None of the aquatic environments will show an increase in bacteriophage propagation activity.
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a) Only Rhine water will show an increase in bacteriophage propagation activity.
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- Vibrio cholerae is the causative agent of the diarrheal disease cholera.
- Vibrio cholerae has shown antimicrobial resistant strains, which necessitates the need for alternative
approaches to treat cholera.
- Bacteriophages are viruses that specifically infect bacteria, and offer a promising therapeutic strategy against bacteria due to their host specificity and self-limiting life cycles.
- ICP1 is a bacteriophage that has been previously oral administered to V. cholerae in a phage cocktail, and has shown to reduce disease severity of V. cholerae, marked by decreased diarrhea, and lower bacterial loads in feces.
- Zebrafish larvae (Danio rerio) naturally ingest V. cholerae from their surrounding aquatic environment.
- The protocol Silva-Valenzuela, et al. (2018) describes a method in the section Predation Assay in Aquatic Microcosms to culture V. cholerae in autoclaved filter sterilized fresh water or 0.7% Instant Ocean.
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[{"label":"RBK Item","value":"Bacteriophages are viruses that specifically infect bacteria, and offer a promising therapeutic strategy against bacteria due to their host specificity and self-limiting life cycles."},{"label":"Title","value":"Insights into Bacteriophage Application in Controlling Vibrio Species"},{"label":"URL","value":"https://doi.org/10.3389/fmicb.2016.01114"},{"label":"Date","value":"Jul 18, 2016 "},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"ICP1 is a bacteriophage that has been previously oral administered to V. cholerae in a phage cocktail, and has shown to reduce disease severity of V. cholerae, marked by decreased diarrhea, and lower bacterial loads in feces."},{"label":"Title","value":"A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models"},{"label":"URL","value":"https://doi.org/10.1038/ncomms14187"},{"label":"Date","value":"Feb 01, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Zebrafish larvae (Danio rerio) naturally ingest V. cholerae from their surrounding aquatic environment."},{"label":"Title","value":"Zebrafish as a Natural Host Model for Vibrio cholerae Colonization and Transmission"},{"label":"URL","value":"https://doi.org/10.1128/AEM.03580-13"},{"label":"Date","value":"Feb 14, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"The protocol Silva-Valenzuela, et al. (2018) describes a method in the section Predation Assay in Aquatic Microcosms to culture V. cholerae in autoclaved filter sterilized fresh water or 0.7% Instant Ocean. "},{"label":"Title","value":"Niche adaptation limits bacteriophage predation of Vibrio cholerae in a nutrient-poor aquatic environment"},{"label":"URL","value":"https://doi.org/10.1073/pnas.1810138116"},{"label":"Date","value":"Jan 11, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Neuroscience
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MCQ
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Modeling neurodegenerative diseases in Drosophila is conditioned by stress resistance and gut microbiome composition of the reference line
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https://www.biorxiv.org/content/10.1101/2025.09.03.673979v1
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Sep 8, 2025
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Researchers tested whether acute oxidative stress induced by ingestion of paraquat in two apparently identical but independent Drosophila lines of the w1118 strain, wlineA and wlineB, would show a comparable response. The w1118 lines were cultured under conventionally reared (CR) and germ-free (GF) conditions. Under CR conditions, flies were maintained at 25°C on standard cornmeal-yeast (CMY) agar medium supplemented with an antifungal agent, under a 12:12 light-dark cycle. Under GF conditions, female adults emerging from eggs deposited on autoclaved standard culture medium (supplemented with an antibiotic cocktail) were maintained on antibiotic-supplemented standard medium. Axenicity was confirmed by incubating whole-body lysates. To measure Drosophila oxidative stress resistance, 7-day-old non-virgin female flies reared under CR and GF conditions were starved, anesthetized, and transferred to Petri dishes containing two layers of Whatman filter paper soaked with 400 µl of 20 mM paraquat in 2% (w/v) sucrose, and incubated under saturated humidity. Fly survival was scored at multiple time points over a 4-day period.
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- Survival percentage after acute oxidative stress.
- Survival time after acute oxidative stress.
- Median survival time after acute oxidative stress.
- Resistance to oxidative stress curves.
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Acute oxidative stress induced by ingestion of paraquat was evaluated in two apparently identical but independent Drosophila lines of the w1118 strain, wlineA and wlineB, that were cultured conventionally reared (CR) and germ-free (GF) conditions. Fly survival was scored at several time points over a 4-days period following paraquat induction. Which of the following outcomes best describes the paraquat resistance on the w1118 lines under the different growth conditions?
a) wlineA showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR. wlineB showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR.
b) wlineA paraquat resistance increased when cultured under GF condition compared to CR. wlineB showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR.
c) wlineA showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR. wlineB paraquat resistance increased when cultured under GF condition compared to CR.
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b) wlineA paraquat resistance increased when cultured under GF condition compared to CR. wlineB showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR.
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- Drosophila is a genus of fly that is currently one of the major model organisms to study human diseases and progress in their treatments.
- Paraquat is a pro-oxidant herbicide commonly used to model drug-induced Parkinson Disease in Drosophila.
- w1118 is a mutant Drosophila strain which carries a null mutation in a gene (white) encoding an ABC-type guanine transporter involved in eye pigmentation.
|
[{"label":"RBK Item","value":"Drosophila is a genus of fly that is currently one of the major model organisms to study human diseases and progress in their treatments"},{"label":"Title","value":"Human Disease Models in Drosophila melanogaster and the Role of the Fly in Therapeutic Drug Discovery"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3082451/"},{"label":"Date","value":"Jun, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Paraquat is a pro-oxidant herbicide commonly used to model drug-induced Parkinson Disease in Drosophila"},{"label":"Title","value":"Interaction of Genetic and Environmental Factors in a Drosophila Parkinsonism Model\n"},{"label":"URL","value":"https://www.jneurosci.org/content/jneuro/27/10/2457.full.pdf"},{"label":"Date","value":"Mar 7, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"w1118 is a mutant Drosophila strain which carries a null mutation in a gene (white) encoding an ABC-type guanine transporter involved in eye pigmentation"},{"label":"Title","value":"Transformation of white locus DNA in Drosophila: Dosage compensation, zeste interaction, and position effects"},{"label":"URL","value":"https://doi.org/10.1016/0092-8674(84)90240-X"},{"label":"Date","value":"Feb, 1984"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
|
Biology
|
Biochemistry / Molecular Biology
|
Free-Format Question
|
Vitamin B12 supports skeletal muscle oxidative phosphorylation capacity in male mice
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https://www.biorxiv.org/content/10.1101/2025.05.19.654973v2
|
May 19, 2025
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Researchers measured the oxygen consumption rate (OCR) from mitochondrial homogenates of tibialis anterior (TA), and red muscle (cumulation of the soleus, and red portions from the quadriceps, and gastrocnemius) samples harvested from Male Mtr⁺ᐟ⁺, and Mtr⁺ᐟ⁻ mice to evaluate the effects of Mtr expression, and B12 content in the mitochondrial electron transport chain complexes (Complex I, Complex II and Complex IV). These mice had been previously weaned onto one of two defined diets for 7 weeks: a control AIN93G-based diet (C) containing 25 μg/kg vitamin B12, and a vitamin B12-deficient AIN93G-based diet (-B12) containing 0 μg/kg vitamin B12. Both diets included 1% succinyl sufathiazole antibiotics. Mice were sacrificed by cervical dislocation following CO2 euthanasia, and mitochondria were isolated from both skeletal muscle tissues. Quadricep, TA, gastrocnemius, and soleus wet wights were normalized to tibia length (mm), and stored at -80° C. In each sample, the OCR of each oxidative phosphorylation complex was determined. Mitochondria from frozen muscle were isolated in ice-cold MAS buffer using a Potter–Elvehjem (Teflon-glass) homogenizer with 25 strokes followed by centrifugation. Pierce BCA Protein Assay was performed to evaluate the protein concentration. Mitochondrial homogenates were loaded into the assay plates in the following conditions: a) TA in the Seahorse XFe24 microplate (150 µg of homogenate in 100 µl of MAS), and b) Red muscle in the Seahorse XFe96 (30 µg of homogenate in 70 µl of MAS), and then centrifuged (2,000 x g, 5 min., 4°C). The OCR was evaluated using Wave software (Agilent), and was defined by the highest respiratory capacity value following the injection of the corresponding complex-stimulating substrate: Complex I (1 mM NADH); Complex II (5 mM succinate + 2 µM rotenone); and Complex IV (0.5 mM N,N,N′,N′-Tetramethyl-pphenylenediamine dihydrochloride (TMPD) + 1 mM ascorbic acid).
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- Protein concentration in mitochondria isolated from skeletal muscle groups (tibialis anterior (TA) and red muscle) of male mice (Mtr⁺ᐟ⁺, and Mtr⁺ᐟ⁻) following different diets (control diet and vitamin B12-deficient diet).
- Oxygen consumption rate (OCR) (pmol O2/min/µg protein) across oxidative phosphorylation complexes (Complex I, II, and IV) in mitochondria isolated from skeletal muscle groups (tibialis anterior (TA) and red muscle) of male mice (Mtr⁺ᐟ⁺, and Mtr⁺ᐟ⁻) following different diets (control diet and vitamin B12-deficient diet).
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Levels of Mtr expression and dietary vitamin B12 content can influence the oxygen consumption rate (OCR) across oxidative phosphorylation complexes in mitochondria from skeletal muscle. These conditions were evaluated by measuring OCR in tibialis anterior (TA) and red muscle samples from male Mtr⁺/⁺ and Mtr⁺/⁻ mice exposed to two diets: a control diet (C; 25 μg/kg vitamin B12) and a vitamin B12-deficient diet (−B12; 0 μg/kg vitamin B12). Both diets included 1% succinyl sulfathiazole antibiotics. After 7 weeks, skeletal muscle tissues were collected and normalized to tibia length following mouse sacrifice. Mitochondria were isolated from the tissue in an ice-cold MAS buffer using a Potter–Elvehjem homogenizer and centrifugation. Protein concentration was determined using the Pierce BCA Protein Assay. Mitochondrial homogenates were loaded into assay plates (TA in Seahorse XFe24 and red muscle in Seahorse XFe96) before centrifugation. OCR was measured in the mitochondria using Wave software for each complex (Complex I, Complex II, and Complex IV). When evaluating Complex II from mitochondria isolated from TA, which conditions (mouse group and diet) would show the highest OCR?
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Mtr⁺/⁺ mice in a vitamin B-12 deficient diet
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- Vitamin B12 is an essential cofactor of the methionine synthase enzyme.
- Impaired FOCM, either by dietary or genetic means, leads to decreased dTMP synthesis and uracil misincorporation in mitochondrial DNA (mtDNA) as well as nDNA.
- mtDNA encodes proteins that are components of the electron transport chain complexes, which drive cellular energy production via oxidative phosphorylation in the mitochondria.
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[{"label":"RBK Item","value":"Vitamin B12 is an essential cofactor of the methionine synthase enzyme which is part of the folate-mediated one-carbon metabolism."},{"label":"Title","value":"Vitamin B12 deficiency"},{"label":"URL","value":"https://bevital.no/pdf_files/literature/green_2017%20_nrdp_3_17040.pdf"},{"label":"Date","value":"Jun 29, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Impaired FOCM, either by dietary or genetic means, leads to decreased dTMP synthesis and uracil misincorporation in mitochondrial DNA (mtDNA) as well as nDNA."},{"label":"Title","value":"Nuclear Folate Metabolism"},{"label":"URL","value":"https://doi.org/10.1146/annurev-nutr-071714-034441"},{"label":"Date","value":"Aug, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"mtDNA encodes proteins that are components of the electron transport chain complexes, which drive cellular energy production via oxidative phosphorylation in the mitochondria."},{"label":"Title","value":"The little big genome: the organization of mitochondrial DNA"},{"label":"URL","value":"https://doi.org/10.2741/4511"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Jan 01, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Molecular oncology
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MCQ
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Loss of the Y chromosome in bladder cancer drives metabolic reprogramming
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https://www.biorxiv.org/content/10.1101/2025.08.26.672471v1
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Aug 31, 2025
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Researchers evaluated whether the absence of the DDR2 gene in Loss of Y chromosome (LOY) tumour cells affected glucose fluctuations in the culture medium or within the clarified cell lysate, as well as its effects on L-lactate abundance. Two cell lines were used and cultured under DMEM medium: CON_YnegN as the control and DDR2KO_YnegN as the experimental cells. Culture medium was harvested, and cell lysates were prepared. Glucose and L-lactate levels were analyzed using a RayBiotech colorimetric assay kit and measured according to the manufacturer’s protocol. Approximately 1 × 10⁵ cells were seeded in each well of a 6-well plate for 72 hours before collecting culture media or cell lysates for analysis.
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- Optical density of Glucose in culture media and cell lysate.
- Optical density of Lactate in culture media.
- Relative glucose comparison between the culture media and the cell lysate for CON_YnegN and DDR2KO_YnegN.
- Relative lactate comparison in the culture media between CON_YnegN and DDR2KO_YnegN.
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A mutation in the DDR2 gene in LOY tumour cells may affect glucose levels and L-lactate abundance. The mutant cell line DDR2KO_YnegN and a control line were cultured in DMEM medium. The culture medium was then harvested, and cell lysates were prepared to measure glucose and L-lactate levels. For glucose, which of the following outcomes explains the DDR2KO_YnegN cells' metabolism in the culture medium and the cell lysates?
a) In both the culture medium and the cell lysates, glucose levels remained stable.
b) In the culture medium, glucose levels indicate increased consumption, while in the cell lysates, they suggest a decrease in intracellular glucose levels.
c) In the culture medium, glucose levels indicate reduced consumption, while in the cell lysates, they suggest an increase in intracellular glucose levels.
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c) In the culture medium, glucose levels indicate reduced consumption, while in the cell lysates, they suggest an increase in intracellular glucose levels.
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- Loss of the Y chromosome (LOY) contributes to both phenotypes in bladder cancer (BC), where metabolic reprogramming may provide a potential explanation.
- Metabolic reprogramming allows tumor cells to adapt their energy production and biosynthetic pathways, such as by shifting to aerobic glycolysis and lactate production even in the presence of oxygen.
- DDR2 is a collagen receptor that influences BC aggressiveness and tumor response to immune checkpoint inhibitors, and is known to influence cancer cell metabolism, particularly glycolysis.
- YnegN is a cell line in which cells naturally lack Y chromosome genes, also known as LOY.
- DDR2KO_YnegN are YnegN cells in which the DDR2 gene is knocked out using CRISPR-Cas9.
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[{"label":"RBK Item","value":"Loss of the Y chromosome (LOY) contributes to both phenotypes in bladder cancer (BC), where metabolic reprogramming may provide a potential explanation"},{"label":"Title","value":"Immunosurveillance encounters cancer metabolism"},{"label":"URL","value":"https://doi.org/10.1038/s44319-023-00038-w"},{"label":"Date","value":"Jan 12, 2024"},{"label":"Justification (“Paywalled”, “OA”, “No OA exists”, \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Metabolic reprogramming allows tumor cells to adapt their energy production and biosynthetic pathways, such as by shifting to aerobic glycolysis and lactate production even in the presence of oxygen."},{"label":"Title","value":"Understanding the Warburg effect: the metabolic requirements of cell proliferation"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2849637/"},{"label":"Date","value":"May 22, 2009"},{"label":"Justification (“Paywalled”, “OA”, “No OA exists”, \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"DDR2 is a collagen receptor that influences BC aggressiveness and tumor response to immune checkpoint inhibitors, and is known to influence cancer cell metabolism, particularly glycolysis."},{"label":"Title","value":"DDR2 coordinates EMT and metabolic reprogramming as a shared effector of FOXQ1 and SNAI1"},{"label":"URL","value":"https://doi.org/10.1158/2767-9764.crc-22-0013"},{"label":"Date","value":"Nov 09, 2022"},{"label":"Justification (“Paywalled”, “OA”, “No OA exists”, \"Other (justify)\")","value":"OA"}]
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Biology
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Plant Biology
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MCQ
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The Arabidopsis UMAMIT30 transporter contributes to amino acid root exudation
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https://www.biorxiv.org/content/10.1101/2025.08.23.671809v1
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Aug 27, 2025
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Researchers evaluated whether the loss of UMAMIT30 function, an amino acid transporter, affects Arabidopsis thaliana growth. Seeds from wild-type Arabidopsis thaliana Col-0 plants and UMAMIT30 mutants (umamit30-1 and umamit30-2) were surface sterilized three times in 10% bleach for two minutes each, followed by three washes with sterile water. The seeds were then resuspended in 0.1% phytoagar and stratified in the dark at 4°C for two days. Seeds were plated onto 1x MS agar plates (4.4 g/L Murashige and Skoog Basal Medium with vitamins, 0.5% sucrose, 0.5 g/L MES, and 0.7% PhytoAgar, pH 5.7). Plates were sealed and incubated vertically in a reach-in growth chamber at 25 ± 2°C, 75% RH, under a 16 h light/8 h dark cycle, and 100 µmoles/m²/s light intensity for two weeks. Fresh and dry biomass of whole plants, shoots, and roots was measured. For dry weight analysis, samples were freeze-dried overnight using a lyophilizer.
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- Biomass dry weight of the whole plant, shoots, and roots.
- Biomass fresh weight of the whole plant, shoots, and roots.
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Mutations in UMAMIT30, an amino acid transporter from Arabidopsis thaliana, may alter amino acids homeostasis and impact growth phenotypes. To evaluate the effect on growth, two seed mutants, umamit30-1 and umamit30-2, were grown in MS agar plates for two weeks after which fresh and dry biomass of the whole plant, shoots, and roots were measured. Which of the following outcomes is most likely?
a) Neither of the umamit30 mutants alters amino acid homeostasis and impacts growth phenotypes.
b) Only umamit30-1 mutants alter amino acid homeostasis and impact growth phenotypes.
c) Only umamit30-2 mutants alter amino acid homeostasis and impact growth phenotypes.
d) Both umamit30 mutants alter amino acids homeostasis and impact growth phenotypes.
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a) Neither of the UMAMIT30 mutants alters amino acid homeostasis and impacts growth phenotypes.
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- Arabidopsis thaliana is a plant species in which plant–environment interactions are influenced by root exudation.
- Plant root exudates typically consist of primary metabolites such as sugars, amino acids, and organic acids, as well as secondary metabolites.
- The amino acid composition of root exudates modulates bacterial metabolism, affecting the beneficial interaction between Arabidopsis roots and plant growth-promoting bacteria.
- UMAMIT transporters (Usually Multiple Amino acids Move In and out Transporters) are facilitator proteins that exhibit amino acid export activity in root-to-soil secretion.
- UMAMIT30 is a member of the UMAMIT transporter family.
- umamit30-1 is an Arabidopsis thaliana mutant in which UMAMIT30 expression is knocked out.
- umamit30-2 is an Arabidopsis thaliana mutant in which UMAMIT30 expression is knocked out.
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[{"label":"RBK Item","value":"Arabidopsis thaliana is a plant species in which plant–environment interactions are influenced by root exudation"},{"label":"Title","value":"Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?"},{"label":"URL","value":"https://escholarship.org/content/qt69z6h6mx/qt69z6h6mx.pdf "},{"label":"Date","value":"Jan, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Plant root exudates typically consist of primary metabolites such as sugars, amino acids, and organic acids, as well as secondary metabolites."},{"label":"Title","value":"Substrate flow in the rhizosphere"},{"label":"URL","value":"https://doi.org/10.1007/BF00011685\n"},{"label":"Date","value":"Dec, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"The amino acid composition of root exudates modulates bacterial metabolism, affecting the beneficial interaction between Arabidopsis roots and plant growth-promoting bacteria."},{"label":"Title","value":"The Arabidopsis LHT1 Amino Acid Transporter Contributes to Pseudomonas simiae-Mediated Plant Growth Promotion by Modulating Bacterial Metabolism in the Rhizosphere"},{"label":"URL","value":"https://doi.org/10.3390/plants12020371"},{"label":"Date","value":"Jan 12, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"UMAMIT transporters (Usually Multiple Amino acids Move In and out Transporters) are facilitator proteins that exhibit amino acid export activity in root-to-soil secretion."},{"label":"Title","value":"Amino Acid Export in Developing Arabidopsis Seeds Depends on UmamiT Facilitators"},{"label":"URL","value":"https://doi.org/10.1016/j.cub.2015.10.038"},{"label":"Date","value":"Dec 07, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Molecular oncology / Immunotherapy
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Free-Format Question
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Demonstration of SLU7 as a new pan-cancer target
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https://www.biorxiv.org/content/10.1101/2025.08.25.672085v1
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Aug 29, 2025
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To evaluate SLU7 as a potential cancer therapy target, two Pm299L-derived cell lines were generated: Pm299L-iCas9-sgSLU7 and Pm299L-iCas9-sgNTC. First, Pm299L cells were transduced with lentiviral vectors encoding a DOX-inducible Cas9, and a single clone with strong inducible expression (Pm299L-iCas9) was selected. This clone was then transduced with sgRNAs targeting SLU7 exon 3 or a non-targeting control (sgNTC). Cells were selected using neomycin and puromycin, and expanded. SLU7 knockdown in the cell lines after DOX treatment was confirmed by Western blot, using antibodies against SLU7, Cas9, and other relevant markers (PARP1, ACTIN, γ-H2AX).
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- Band intensity of each protein evaluated
- Comparison of protein expression levels of SLU7, Cas9, PARP1, ACTIN, and γ-H2AX, in the cell lines (Pm299L-iCas9-sgSLU7 and Pm299L-iCas9-sgNTC)
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The target protein SLU7, the effector protein Cas9, the marker proteins PARP1 and γ-H2AX, and the control proteins ACTIN and GAPDH were evaluated by Western blot to assess the potential of SLU7 as a cancer therapy target. These proteins were extracted from two generated cell lines: Pm299L-iCas9-sgSLU7, a transducted cell line in which SLU7 gene is knocked down after DOX administration, and Pm299L-iCas9-sgNTC, a non-targeting control. After DOX administration in Pm299L-iCas9-sgSLU7 cells, which protein bands would be expected to show increased intensity on the Western blot compared to the control?
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Cas9, PARP1, and γ-H2AX
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- SLU7 is an essential splicing factor required for the survival of cancer cells.
- SLU7 knockdown induces apoptosis across different cancer types, preceded by a cascade of molecular events including oxidative stress, R-loop accumulation, transcription-dependent genomic instability, DNA damage, replicative catastrophe, inhibition of DNA methylation, and disruption of NMD.
- sgRNA are single-guide RNAs.
- Pm299L is a mouse hepatocellular carcinoma (HCC) cell line.
- Doxycycline (DOX) induces high expression of Cas9 in an inducible manner in this system, while the cells constitutively express either a sgRNA directed against the SLU7 gene (sgSLU7) or a non-targeting control sgRNA (sgNTC).
- Pm299L-iCas9-sgSLU7 is a mouse Pm299L cell line that was first transduced with lentiviral particles encoding a (DOX)-inducible Cas9, along with a sgRNA targeting exon 3 of the SLU7 gene.
- Pm299L-iCas9-sgNTC is a mouse Pm299L cell line first transduced with lentiviral particles encoding a doxycycline (DOX)-inducible Cas9 and a non-targeting (NTC) sgRNA.
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[{"label":"RBK Item","value":"SLU7 is an essential splicing factor for the survival of cancer cells."},{"label":"Title","value":"Splicing regulator SLU7 preserves survival of hepatocellular carcinoma cells and other solid tumors via oncogenic miR-17-92 cluster expression"},{"label":"URL","value":"https://doi.org/10.1038/onc.2015.517"},{"label":"Date","value":"Jan 25, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"SLU7 knockdown induces apoptosis across different cancer types, preceded by a cascade of molecular events: oxidative stress, R-loop accumulation, transcription-dependent genomic instability, DNA damage, replicative catastrophe, inhibition of DNA methylation, and disruption of NMD."},{"label":"Title","value":"Splicing Factor SLU7 Prevents Oxidative Stress-Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage"},{"label":"URL","value":"https://doi.org/10.1002/hep.32029"},{"label":"Date","value":"Nov, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Zoology / Cryobiology
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MCQ
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Cryopreservation of Platynereis dumerilii larvae
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https://www.biorxiv.org/content/10.1101/2025.07.31.667934v2
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Aug 2, 2025
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Researchers tested different individuals and combinations of cryoprotectant agents (CPAs), such as dimethyl sulfoxide (Me₂SO), ethylene glycol (EG), propylene glycol (PG), glycerol (Gly), and sucrose (SUC), to develop a cryopreservation protocol that ensures long-term viability and supports proper post-thaw growth and development of Platynereis dumerilii. Platynereis dumerilii were kept in a 50/50 mix of natural seawater and artificial sea water, adjusted to a salinity of 35 ppt, a pH between 7.9 and 8.2, a general culture temperature at 18-20 °C for optimum growth rate, and a 16:8 light/dark cycle. To assess the cryoprotectant toxicity, eight-days old larvae were exposed to CPA solutions in two phases. In the first phase, larvaes exposure to each permeating CPA had a duration of 3 minutes. The individual CPA analyzed were the following: Me₂SO, 1.4M; EG, 1.4M; PG, 1.4M. In the second phase, the exposure was of 30 minutes to a combination of CPAs that were tested by reducing Me₂O content and supplementing it with glycerol and/or sucrose. The combination of CPAs analyzed were the following: Me₂SO, 0.8M; Me₂SO 0.8M + 0.1% SUC (w/v); Me₂SO 0.8M + Gly 0.68M; Me₂SO 0.8M + Gly 0.68M + 0.1% SUC (w/v). After the exposure, the larvae were filtered, and transferred to clean sea water for observation.
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- Exposure time in minutes after exposure to individual and combined CPAs.
- Survival post-thaw percentage after exposure to individual and combined CPAs.
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The cryoprotectant toxicity of individual and combined cryoprotectant agents (CPAs) were evaluated in eight day old Platynereis dumerilii to develop a cryopreservation protocol. Larvae were observed after being exposed to CPAs in two phases. The first phase consisted of a 3 minute exposure to individual CPAs: Me₂SO, 1.4M; EG, 1.4M; PG, 1.4M. The second phase involved a 30 minute exposure to combined CPAs: Me₂SO, 0.8M; Me₂SO 0.8M + 0.1% SUC (w/v); Me₂SO 0.8M + Gly 0.68M; Me₂SO 0.8M + Gly 0.68M + 0.1% SUC (w/v). Which of the CPAs would you expect to result in the highest post-thaw survival percentage after the 3-minute exposure?
a) All individual CPAs tested will result in the same post-thaw survival percentage.
b) Only Me₂SO 1.4M will result in the highest post-thaw survival percentage.
c) Only EG 1.4M will result in the highest post-thaw survival percentage.
d) Only PG 1.4M will result in the highest post-thaw survival percentage.
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a) All individual CPAs tested will result in the same post-thaw survival percentage.
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- Platynereis dumerilii is a marine annelid that has emerged as a significant model organism in chronobiological, neurobiological, developmental and evolutionary biology research.
- Cryopreservation offers a means to store and preserve biological materials for future use enabling long-term storage, facilitating sample transportation, and ensuring the availability of biological specimens.
- Cryoprotectant agents (CPAs) are substances used to preserve the biological samples in cryobiology with different modes of action, some penetrating the tissue while others protecting the surface.
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[{"label":"RBK Item","value":"Platynereis dumerilii is a marine annelid that has emerged as a significant model organism in chronobiological, neurobiological, developmental and evolutionary biology research."},{"label":"Title","value":"Seasonal variation in UVA light drives hormonal and behavioral changes in a marine annelid via a ciliary opsin"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7611595/"},{"label":"Date","value":"Jan 11, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Cryopreservation offers a means to store and preserve biological materials for future use enabling long-term storage, facilitating sample transportation, and ensuring the availability of biological specimens."},{"label":"Title","value":"Cryopreservation of Marine Invertebrates: From Sperm to Complex Larval Stages"},{"label":"URL","value":"https://doi.org/10.1007/978-1-0716-0783-1_18"},{"label":"Date","value":"Aug 15, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
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Biology
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Animal Behavior and Cognition
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MCQ
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Nighttime Caffeine Intake Increases Motor Impulsivity
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https://www.biorxiv.org/content/10.1101/2025.06.09.658656v1
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Jun 13, 2025
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Researchers examined whether nighttime caffeine consumption affected inhibitory control in female and male Drosophila melanogaster of the Canton-S (CS) wild-type strain. Flies were raised on a standard cornmeal/sucrose/yeast/agar medium at 25° C with 50 % relative humidity under a 12:12h light-dark cycle. For the experiment, flies were collected under carbon dioxide within two days after eclosion and housed in same-sex groups. For nighttime caffeine exposure, groups of female or male flies were transferred to vials containing caffeine-laced food 30 min before lights-off and remained on this food throughout the dark cycle. Caffeine concentrations used were 1, 5, 7.5, and 10 mg/ml. At the end of the dark cycle, the Go/No-Go assay was performed by placing individual flies into a clear rectangular plexiglass chamber connected to a filtered air source. After a 1-minute acclimation period, a continuous airflow of 10 L/min was applied for 10 minutes. Fly behavior was video recorded to monitor and analyze movements before and during airflow exposure. Movements exceeding 60 mm/sec were classified as loss of inhibition events (LIEs), which were scored per fly per min.
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- Number of movements exceeding 60 mm/sec following nighttime consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml).
- Number of loss of inhibition events (LIEs) following nighttime consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml).
- Comparison of the number of LIEs following consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml) between female and male flies.
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Nighttime consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml) in male and female Drosophila melanogaster of the Canton-S (CS) wild-type strain was evaluated to determine its effect on inhibitory control by loss of inhibition events (LIEs). Movements exceeding 60 mm/sec were counted as LIEs after nighttime caffeine exposure. These values were obtained through a Go/No-Go assay that was performed at the end of the dark cycle in flies by monitoring and analyzing movements before and during a continuous 10 L/min airflow exposure. Which of the following outcomes is most likely?
a) After nighttime caffeine consumption, male flies exhibited more LIEs than female flies at all concentrations tested.
b) After nighttime caffeine consumption, female flies exhibited more LIEs than male flies at all concentrations tested.
c) After nighttime caffeine consumption, there was no significant difference in LIEs between male and female flies at all concentrations tested.
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b) After nighttime caffeine consumption, female flies exhibited more LIEs than male flies at all concentrations tested.
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- Caffeine is a psychoactive substance that increases alertness, reduces fatigue, and improves performance, especially under conditions of sleep deprivation.
- Drosophila melanogaster is a fly species used as a model system to investigate how nighttime caffeine intake affects inhibitory control.
- Inhibitory control is a fundamental executive function responsible for suppressing inappropriate actions, such as impulsive flying in flies.
- Loss of inhibition event (LIEs) is a measure of impulsivity that in flies is quantified by rapid movements at speeds exceeding 60 mm/sec.
- Go/No-Go test measures the ability to suppress movement in response to adverse conditions such as strong airflow or predator sounds.
|
[{"label":"RBK Item","value":"Caffeine is a psychoactive substance that increases alertness, reduces fatigue, and improves performance, especially under conditions of sleep deprivation."},{"label":"Title","value":"Trends in intake and sources of caffeine in the diets of US adults: 2001–2010"},{"label":"URL","value":"https://doi.org/10.3945/ajcn.113.080077"},{"label":"Date","value":"May, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Loss of inhibition event (LIEs) is a measure of impulsivity that in flies is quantified by rapid movements at speeds exceeding 60 mm/sec."},{"label":"Title","value":"Social context and dopamine signaling converge in the mushroom body to drive impulsivity"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11870619/"},{"label":"Date","value":"Feb 22, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Go/No-Go test measures the ability to suppress movement in response to adverse conditions such as strong airflow or predator sounds."},{"label":"Title","value":"Social context and dopamine signaling converge in the mushroom body to drive impulsivity"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11870619/"},{"label":"Date","value":"Feb 22, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Microbiology
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MCQ
|
Streptococcus pneumoniae accessory capsular genes modulate fitness, pathogenicity and immune evasion
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https://www.biorxiv.org/content/10.1101/2025.09.11.675585v1.full
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September 15, 2025
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Researchers deleted all six acl (accessory capsular locus) genes from the Streptococcus pneumoniae serotype 3 GPSC9-ST5435 strain BVY11Z and reintroduced the genes into the capsular locus of serotype 3 GPSC10-ST700 strain BVY23H, using an allelic replacement strategy. To evaluate the role of the serotype 3 acl in modulating susceptibility to opsonophagocytic killing (OPK), they subjected WT ST700 and its acl reintroduction mutant (ST700 acl+ -cat), as well as WT5435 and its acl deletion mutant (ST5435 acl::cat), to an OPK assay. To determine if the bacterial tyrosine kinase (BYK) capsule regulation system plays a role in OPK susceptibility, they additionally tested the ST5435 cpsB deletion mutant (ST5435 cpsB::spec) and ST5435 cpsD deletion mutant (ST5435 cpsD::cat) in the OPK assay.
Genetic manipulation of S. pneumoniae was carried out using a competence-stimulating peptide (CSP)-mediated transformation assay. Strains were grown in 12 mL of THY pH 6.8 supplemented with 1 mM CaCl2 and 0.2% BSA at 37°C with 5% CO2 to an OD600 of 0.01-0.03. Cultures were then harvested and resuspended in 1 mL of pre-warmed THY pH 8.0, supplemented with 1 mM CaCl2 and 0.2% BSA. 400 ng/ml CSP was added to the bacterial suspension (CSP-1 for ST5435, CSP-2 for ST700; Cambridge Biosciences). Suspensions were incubated at room temperature (RT) for 5 minutes, mixed with 300-500 ng transforming DNA, and further incubated at 37°C with 5% CO2 for 2 hours. The entire suspension was then plated on blood agar plates supplemented with relevant antibiotics. To construct the transforming DNA for making the unencapsulated (cps::cat) mutants, the areas flanking the capsular locus were amplified using primer pairs 001/002 and 003/004 from WT ST700 genomic DNA and primer pairs 001/002 and 005/006 from WT ST5435 genomic DNA. The chloramphenicol resistance cassette (cat) was amplified from pEMcat using primer pairs 007/008. PCR products corresponding to the upstream and downstream regions and cat were joined using overlap extension PCR (OE-PCR) with primer pairs 001/004 or 001/006, respectively. The purified OE-PCR product was used in transformation assays. Transforming DNA for making the acl-mutant (acl::cat) was constructed as described above using primer pairs 001/002 and 009/010 to amplify the up/downstream region of acl from ST5435 and primer pair 001/010 to generate the OE-PCR product. Transforming DNA for making the cpsD mutant (cpsD::cat) was constructed similarly using primer pairs 011/012 and 013/014 for the initial PCR and primer pair 011/014 for the OE-PCR product. Transforming DNA for making the cpsB mutant (cpsB::spec) utilized primer pairs 015/016 and 017/018 to amplify the flanking region, and primer pair 015/018 for the OE-PCR. Instead of cat, a spectinomycin resistance cassette (spec) was amplified from pR412 using primer pair 019/020 and used in OE-PCR. To reintroduce acl into ST700 (acl+), the entire acl region was amplified in 3kb fragments from WT ST5435 genomic DNA using primer pairs 021/022 and 023/024. The downstream region, which encompasses part of the coding region for Ugd, was amplified from WT ST700 genomic DNA using primer pairs 025/010. The three PCR pieces and the cat cassette were assembled using NEB Gibson Assembly master mix to obtain the transforming DNA.
OPK analysis was performed using a WHO-approved standardized assay. The strains were compared to assess the reduction in killing against a reference serotype 3 strain (an optochin-resistant variant of the ST180 strain Wu2) using pooled serum samples from adults vaccinated with PCV13. THY and 4% filtered fetal bovine serum were used for the assay. Strains were incubated with serial dilutions of pooled human serum prior to treatment with HL-60 cells, baby rabbit complement, and plating onto agar plates. The opsonic index was calculated as the reciprocal of the serum dilution, reducing the bacterial colony forming units (CFU) to 50% of the no serum control.
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- Opsonic index (OI) for each tested strain
- Bacterial colony forming units (CFU).
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Researchers tested whether the absence of acl genes contributes to increased opsonophagocytic resistance in Streptococcus pneumoniae. To test this hypothesis, they deleted all six acl (accessory capsular locus) genes from the Streptococcus pneumoniae serotype 3 GPSC9-ST5435 strain BVY11Z (hereafter WT ST5435) and reintroduced the genes into the capsular locus of serotype 3 GPSC10-ST700 strain BVY23H (hereafter WT ST700). Then, they subjected these strains to a WHO standard OPK assay using pooled serum from PCV-immunised adults. Additionally, they tested the ST5435 cpsB deletion mutant (ST5435 cpsB::spec) and ST5435 cpsD deletion mutant (ST5435 cpsD::cat) in the OPK assay. Which of the following outcomes are most likely?
A. Reintroducing the acl region into GPSC10-ST700 would reduce its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would reduce its resistance to opsonophagocytic killing.
B. Reintroducing the acl region into GPSC10-ST700 would increase its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would increase its resistance to opsonophagocytic killing
C. Reintroducing the acl region into GPSC10-ST700 would increase its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would decrease its resistance to opsonophagocytic killing
D. Reintroducing the acl region into GPSC10-ST700 would decrease its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would increase its resistance to opsonophagocytic killing.
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A. Reintroducing the acl region into GPSC10-ST700 would reduce its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would reduce its resistance to opsonophagocytic killing.
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1. Pneumococcal polysaccharide-conjugate vaccines (PCV) target the polysaccharide capsule (CPS)
2. Current PCVs induce suboptimal protection against serotype 3 strains
3. (ST) 700–GPSC10 serotype 3 lineage is characterized by the absence of at least 6 acl genes and a distinct antimicrobial resistance (AMR) profile compared to other serotype 3 strains.
4. Accessory capsular genes (acl) regulate capsule production and shedding.
5. cpsB and cpsD are truncated homologs of acl genes, and are part of a bacterial tyrosine kinase (BYK) system that regulates capsule expression and chain length
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[{"label":"RBK Item","value":"(ST) 700–GPSC10 serotype 3 lineage is characterized by the absence of at least 6 acl genes and a distinct antimicrobial resistance (AMR) profile compared to other serotype 3 strains."},{"label":"Title","value":"Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction"},{"label":"URL","value":"https://academic.oup.com/jid/article/230/1/e189/7633460?login=false"},{"label":"Date","value":"March 26, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"cpsB and cpsD are truncated homologs of acl genes, and are part of a bacterial tyrosine kinase (BYK) system that regulates capsule expression and chain length "},{"label":"Title","value":"The bacterial tyrosine kinase system CpsBCD governs the length of capsule polymers"},{"label":"URL","value":"https://www.pnas.org/doi/full/10.1073/pnas.2103377118"},{"label":"Date","value":"November 3, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Pneumococcal polysaccharide-conjugate vaccines (PCV) target the polysaccharide capsule (CPS)"},{"label":"Title","value":"Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis"},{"label":"URL","value":"https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00665-0/fulltext"},{"label":"Date","value":"Dec 17, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Current PCVs induce suboptimal protection against serotype 3 strains"},{"label":"Title","value":"Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis"},{"label":"URL","value":"https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00665-0/fulltext"},{"label":"Date","value":"Dec 17, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Pathology
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Free-Format Question
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A hierarchy of causes of death in senescent C. elegans
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https://www.biorxiv.org/content/10.1101/2025.08.21.671442v1
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Aug 25, 2025
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Researchers tested whether uterine tumors contribute to late-life mortality in Caenorhabditis elegans in the absence of bacterial infection. Worms were grown at 20˚C on agar plates containing nematode growth media, seeded with E. coli OP50 as a food source. Nematodes at two developmental stages, L4 and D2 (defined as day 0 and day 2 of adulthood, respectively), were evaluated under the following conditions of substance administration: 50 μM floxuridine (FUDR); 50 μM FUDR + 4mM carbenicillin (Carb). Mortality was assessed every 1 - 2 days, with individuals considered as alive if any movement was observed.
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- Lifespan in days under substance administration (50 μM FUDR; 50 μM FUDR + 4mM Carb).
- Survival percentage under substance administration (50 μM FUDR; 50 μM FUDR + 4mM Carb).
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Mortality scoring was performed in Caenorhabditis elegans at two stages, L4 and D2, following administration of 50 μM floxuridine (FUDR), and 50 μM FUDR + 4mM carbenicillin (Carb), to evaluate whether uterine tumors contribute to late-life mortality when bacterial infection is inhibited. What would you expect to happen to the lifespan of C. elegans at each stage when FUDR + Carb are administered?
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In the presence of Carb and FUDR, L4 had a slightly shortened lifespan, but D2 had a significantly increased lifespan.
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- Caenorhabditis elegans is a short-lived nematode whose death results from a combination of extrinsic and intrinsic factors, with infection by its bacterial food source being one of the major extrinsic causes.
- Escherichia coli is a bacteria used as a food source for C. elegans and is the major cause of infection to which all individuals succumb in later life.
- Uterine tumors are among the most striking pathologies observed in senescent C. elegans hermaphrodites.
- 5-fluoro-2’-deoxyuridine or floxuridine (FUDR) is a drug used in the treatment of colorectal cancer that can prevent uterine tumor development.
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[{"label":"RBK Item","value":"Caenorhabditis elegans is a short-lived nematode whose death results from a combination of extrinsic and intrinsic factors, with infection by its bacterial food source being one of the major extrinsic causes."},{"label":"Title","value":"Run-on of germline apoptosis promotes gonad senescence in C. elegans"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5129915/"},{"label":"Date","value":"May 31, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Escherichia coli is a bacteria used as a food source for C. elegans and is the major cause of infection to which all individuals succumb in later life."},{"label":"Title","value":"Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation."},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC1462187/"},{"label":"Date","value":"Jul 01, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Uterine tumors are among the most striking pathologies observed in senescent C. elegans hermaphrodites."},{"label":"Title","value":"TGF-β and Insulin Signaling Regulate Reproductive Aging via Oocyte and Germline Quality Maintenance"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2955983/"},{"label":"Date","value":"Oct 15, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"5-fluoro-2’-deoxyuridine or floxuridine (FUDR) is a drug used in the treatment of colorectal cancer that can prevent uterine tumor development."},{"label":"Title","value":"MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3969279/"},{"label":"Date","value":"Feb 16, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Plant genetics
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MCQ
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DECREASE IN DNA METHYLATION 1-mediated epigenetic regulation maintains gene expression balance required for heterosis in Arabidopsis thaliana
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https://www.biorxiv.org/content/10.1101/2025.08.21.671646v1.full
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August 26, 2025.
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Researchers investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana wild-type accessions Columbia-0 (Col-0) and C24 as parental lines. Two heterozygous mutants were generated: (a) C24 (DDM1/ddm1-9), resulting from a cross between wild-type C24 and the ddm1-9 mutant line (C24 background); and (b) Col (DDM1/ddm1-1), resulting from a cross between wild-type Col-0 and the ddm1-1 mutant line (Col-0 background). The F1 generation was obtained by crossing the two heterozygous mutants, C24 (DDM1/ddm1-9) and Col (DDM1/ddm1-1). Plants were grown under controlled environmental conditions with a 16-h light / 8-h dark photoperiod at 22 °C. Seeds were sown on plastic dishes containing Murashige and Skoog (MS) agar medium supplemented with 1.0% sucrose (pH 5.7), and seedlings were transferred to soil 14 days after sowing (DAS). Rosette diameter and leaf area were measured to evaluate plant size and heterosis in F1 plants at 14, 21, and 28 DAS. Rosette diameter was defined as the maximum diameter of the rosette, measured between the two largest leaves at a given developmental stage. It depends on both the leaf blade and petiole lengths. Leaf area was calculated from photographs using image analysis with ImageJ software.
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- Rosette diameter (mm) at 14, 21, and 28 days after sowing in heterozygous and homozygous F1 lines after the cross of heterozygous mutants (C24 (DDM1/ddm1-9) x Col (DDM1/ddm1-1)).
- Leaf area at 14, 21, and 28 days after sowing in heterozygous and homozygous F1 lines after the cross of heterozygous mutants (C24 (DDM1/ddm1-9) x Col (DDM1/ddm1-1)).
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Researchers investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana wild-type accessions Columbia-0 and C24. To determine the effect of the DDM1 mutation, two heterozygous mutants, C24 (DDM1/ddm1-9) and Col (DDM1/ddm1-1), obtained from crosses with the respective wild-type accessions, were crossed to evaluate rosette diameter (mm) at 14, 21, and 28 days after sowing (DAS). At which time point after sowing is it most likely that the cross between C24 (DDM1/ddm1-9) and Col (DDM1/ddm1-1) will show the smallest statistical differences in rosette diameter among genotypes?
A. At 14 DAS.
B. At 21 DAS.
C. At 28 DAS.
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B. At 21 DAS.
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- Heterosis, also known as hybrid vigor, refers to the superior performance of the first filial generation (F1) plants compared to their parental lines.
- Epigenetics refers to mechanisms that influence gene regulatory networks without altering the underlying DNA sequence.
- Epigenetic regulation is important in the control of heterosis.
- DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeling factor that has been shown to diminish heterosis in A. thaliana.
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[{"label":"RBK Item","value":"Epigenetics refers to mechanisms that influence gene regulatory networks without altering the underlying DNA sequence."},{"label":"Title","value":"SHeterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity"},{"label":"URL","value":"https://www.pnas.org/doi/10.1073/pnas.1204464109"},{"label":"Date","value":"April 09, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Epigenetic regulation is important in the control of heterosis"},{"label":"Title","value":"Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids"},{"label":"URL","value":"https://academic.oup.com/plphys/article/176/2/1627/6117228"},{"label":"Date","value":"Dec 01, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeling factor that has been shown to diminish heterosis in A. thaliana."},{"label":"Title","value":"Role of DNA methylation in hybrid vigor in Arabidopsis thaliana"},{"label":"URL","value":"https://www.pnas.org/doi/10.1073/pnas.1613372113?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed"},{"label":"Date","value":"Oct 7, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Entomology
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MCQ
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Effects of Three Natural Dietary Compounds on Insect Pests
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https://www.biorxiv.org/content/10.1101/2025.05.23.655814v2
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May 28, 2025
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Researchers evaluated the relative efficacy of three natural compounds —neem oil, boric acid, and gallotannin acid— against larvae of three pest species: Rhynchophorus ferrugineus (red palm weevil), Plodia interpunctella (Indian meal moth), and Spodoptera exigua (beet armyworm). The larvae were reared on an optimal artificial semi‒diet composed of agar (20 g), distilled water (880 ml), brewer’s yeast (50 g), wheat germ (50 g), corn meal (50 g), ascorbic acid (4.5 g), coconut fiber (8 g), and a vitamin/amino acid additive (50 ml). The diet provided 15.0% crude protein (as a percentage of dry weight). The rearing of R. ferrugineus was conducted following the protocol established by Martin & Cabello (2006), whereas that of P. interpunctella and S. exigua followed the method of Cabello et al. (1984). The three compounds tested were boric acid (99.5%, Panreac Quimica S.L.U., Barcelona, Spain), gallotannin acid (tannic acid 99.5%, Panreac Quimica S.L.U., Barcelona, Spain), and neem oil (azadirachtin, 3.2% LS, Sipcam, Valencia, Spain). Each II-instar larva in a 20 ml Coulter vial (20 ml) was an experimental unit. Treatments included five neem oil concentrations (0, 6.3, 12.5, 25.0, 50.0 ppm), six boric acid concentrations (0, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm), and seven gallotannin acid concentrations (0, 156.3, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm). There were 20 repetitions per treatment (concentration), totaling 100 experimental units for neem oil trial, 120 for boric acid trial, and 140 for gallotannin acid trial. Larval survival was tracked at intervals: 3, 6, 9, 12, 15, and 20 days for R. ferrugineus, and 3, 6, 9, 12, and 15 days for the other species. Trials were conducted at 25±2 °C, 65±10% R.H. and photo period of 0:24 hours light: dark on R. ferrugineus and P. interpunctella species, and 16:9 hours on S. exigua species. Larval survival was analyzed by the Kaplan-Meier method with subsequent comparisons between treatments carried out via the long-rank test in each trial. These analyses were performed via IBM SPSS software, version 28. Effective median lethal concentrations (LC50) were calculated via probit analysis. If there is natural mortality in the controls, adjusted mortality is used according to Abbott’s formula.
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- Larval survival (tracked at intervals: 3, 6, 9, 12, 15, and 20 days for R. ferrugineus, and 3, 6, 9, 12, and 15 days for the other species)
- Effective median lethal concentrations (LC50) of the tested compounds (neem oil, boric acid, and gallotannin acid)
- Corrected mortality (%) across species (Rhynchophorus ferrugineus, Plodia interpunctella and Spodoptera exigua) after compound treatment (neem oil, boric acid, and gallotannin acid)
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Researchers evaluated the relative efficacy of three natural compounds —neem oil, boric acid, and gallotannin acid— against larvae of three pest species: Rhynchophorus ferrugineus, Plodia interpunctella, and Spodoptera exigua. The larvae were reared on an optimal artificial semi‒diet composed of agar (20 g), distilled water (880 ml), brewer’s yeast (50 g), wheat germ (50 g), corn meal (50 g), ascorbic acid (4.5 g), coconut fiber (8 g), and a vitamin/amino acid additive (50 ml). The diet provided 15.0% crude protein (as a percentage of dry weight). The three compounds tested were boric acid (99.5%), gallotannin acid (tannic acid 99.5%), and neem oil (azadirachtin, 3.2% LS). Each II-instar larva in a 20 ml Coulter vial (20 ml) was an experimental unit. Treatments included five neem oil concentrations (0, 6.3, 12.5, 25.0, 50.0 ppm), six boric acid concentrations (0, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm), and seven gallotannin acid concentrations (0, 156.3, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm). There were 20 repetitions per treatment (concentration), totaling 100 experimental units for neem oil trial, 120 for boric acid trial, and 140 for gallotannin acid trial. Larval survival was tracked at intervals: 3, 6, 9, 12, 15, and 20 days for R. ferrugineus, and 3, 6, 9, 12, and 15 days for the other species. Trials were conducted at 25±2 °C, 65±10% R.H. and photo period of 0:24 hours light: dark on R. ferrugineus and P. interpunctella species, and 16:9 hours on S. exigua species. Larval survival was analyzed by the Kaplan-Meier method. Effective median lethal concentrations (LC50) were calculated via probit analysis. If there is natural mortality in the controls, adjusted mortality is used according to Abbott’s formula. Which of the following outcomes is most likely?
A. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 9 or 12 days for all species
B. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 9 or 12 days for Rhynchophorus ferrugineus and Plodia interpunctella, but not for Spodoptera exigua.
C At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 12 days for Rhynchophorus ferrugineus only
D. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 15 days for all species
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A. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 9 or 12 days for all species
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- The red palm weevil Rhynchophorus ferrugineus is a pest species that affects various palm and coconut trees
- The Indian meal moth Plodia interpunctella is a species that affects mainly stored plant products
- The beet armyworm Spodoptera exigua is a pest affecting herbaceous and horticultural crops
- Boric acid and borate salts serve as active ingredients in pesticides, effectively targeting insects, spiders, mites, algae, molds, fungi, and weeds.
- Gallotannin acid, also known as tannic acid, is the most well known hydrolysable tannin.
- Azadirachtin, which is a tetranortriterpenoid, is an active ingredient of neem (Azadirachta indica A. Juss.) seed oil. It controls two hundred species of insects, including locusts, gypsy moths, cockroaches, and fall armyworms
|
[{"label":"RBK Item","value":"The red palm weevil Rhynchophorus ferrugineus is a pest species that affects various palm and coconut trees"},{"label":"Title","value":"Biología y ecología del Curculiónido rojo de la palmera, Rhynchophorus ferrugineus"},{"label":"URL","value":"https://www.researchgate.net/publication/256445857_Biologia_y_ecologia_del_Curculionido_rojo_de_la_palmera_Rhynchophorus_ferrugineus_Olivier_1790_Col_Dryophthoridae"},{"label":"Date","value":"January, 2005 "},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"The Indian meal moth Plodia interpunctella is a species that affects mainly stored plant products"},{"label":"Title","value":"Biology and management of Plodia interpunctella (Lepidoptera: Pyralidae) in stored products"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0022474X06000671?via%3Dihub"},{"label":"Date","value":"December, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"The beet armyworm Spodoptera exigua is a pest affecting herbaceous and horticultural crops"},{"label":"Title","value":"Biología, ecología y control de Spodoptera exigua (Hübner, 1808) (Lep., Noctuidae) en cultivo de pimiento en invernadero"},{"label":"URL","value":"https://digibug.ugr.es/handle/10481/55815"},{"label":"Date","value":"1994"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA, pdf available for download."},{"label":"RBK Item","value":"Boric acid and borate salts serve as active ingredients in pesticides, effectively targeting insects, spiders, mites, algae, molds, fungi, and weeds."},{"label":"Title","value":"Boric Acid Technical Fact Sheet"},{"label":"URL","value":"https://www.npic.orst.edu/factsheets/archive/borictech.html"},{"label":"Date","value":"2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Gallotannin acid, also known as tannic acid, is the most well known hydrolysable tannin."},{"label":"Title","value":"The Multifunctional Roles of Polyphenols in Plant-Herbivore Interactions"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/33535511/"},{"label":"Date","value":"Feb 01, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Azadirachtin, which is a tetranortriterpenoid, is an active ingredient of neem (Azadirachta indica A. Juss.) seed oil. It controls two hundred species of insects, including locusts, gypsy moths, cockroaches, and fall armyworms"},{"label":"Title","value":"The Toxicology and Biochemistry of Insects, 1st Edition"},{"label":"URL","value":"https://www.taylorfrancis.com/books/mono/10.1201/9781420059762/toxicology-biochemistry-insecticides-simon-yu"},{"label":"Date","value":"March 04, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Molecular Biology
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Free-Format Question
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A novel expression system enabling scalable production of glycosylated flavonoids in Escherichia coli W using a plant-derived toxic gene
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https://www.biorxiv.org/content/10.1101/2025.09.09.674713v1
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Sep 13, 2025
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Researchers compared prunin production in the SBG2339 strain, which contains the synthetic phosphate (Pi)-depletion promoter system known as Pliar, with conventional strains SBG1818 and SBG2303, which use the RhaR/Prha and XylS/Pm promoters, respectively. To evaluate the performance of this regulatory system, the E. coli platform SBG1888 was first constructed to optimize efficient UDPG biosynthesis. This strain combined the parental chassis SBG1869 with the pUDG plasmid. For consistent expression analysis and fair comparison with conventional systems, all transcriptional units were standardized using the same ribosome binding site (RBS; STD) and a low-copy origin of replication (RK2). The SbaiC7OGT gene was then expressed in SBG1888 under the control of three different regulatory systems: 1) The phosphate-responsive Pliar53 promoter, resulting in strain SBG2339; 2) The RhaR/Prha promoter, resulting in strain SBG1818; 3) The XylS/Pm promoter, resulting in strain SBG2303. All media used with the Pliar53 system were supplemented with 5 mM phosphate. Gene expression was induced only during the production phase, using phosphate-depleted M3 medium supplemented with yeast extract (YE). A concentration of 3 mM naringenin was administered as the substrate for the production of naringenin-7-O-glucoside (prunin). Flavonoid quantification was carried out using high-performance liquid chromatography (HPLC) coupled with a diode array detector (DAD).
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- Prunin concentration in different E. coli strains (SBG2339, SBG1818, and SBG2303)
- Comparison of prunin production driven by different promoter systems (Pliar53, RhaR/Prha, and XylS/Pm)
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Prunin production regulated by three different systems (Pliar53, RhaR/Prha, and XylS/Pm)was evaluated using E. coli strains SBG2339, SBG1818, and SBG2303, respectively. These strains were derived from the engineered platform SBG1888, which expresses the SbaiC7OGT gene. Prunin concentrations were measured in each strain after 24 hours of naringenin administration to enhance flavonoid production, and quantified using high-performance liquid chromatography (HPLC). What would you expect to happen to prunin production in strain SBG2303 compared to the other two strains evaluated?
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The SBG2303 strain will yield a lower prunin production than both the SBG2339 and SBG1818 strains.
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- Prunin, or naringenin-7-O-glucoside, is a flavonoid biosynthesized in plants.
- Naringenin is a substrate used for the production of prunin.
- SbaiC7OGT is a UDP-glycosyltransferase gene from Scutellaria baicalensis that catalyzes the 7-O-glycosylation of flavonoids.
- Escherichia coli is a microbial host commonly used for the heterologous expression of plant-derived molecules.
- Pliar53 is a synthetic phosphate (Pi)-depletion promoter system inspired by the bacterial phosphate (PHO) starvation response, in which low Pi concentrations activate the PHO regulon.
- XylS/Pm is a regulatory system inducible by m-toluic acid, whose derivatives are toxic and may interfere with enzymatic reactions.
- RhaR/Prha is a regulatory system inducible by L-rhamnose, whose high cost limits its application in large-scale processes.
|
[{"label":"RBK Item","value":"Naringenin is a substrate used for the production of prunin."},{"label":"Title","value":"Flavonoids naringenin chalcone, naringenin, dihydrotricin, and tricin are lignin monomers in papyrus"},{"label":"URL","value":"https://academic.oup.com/plphys/article/188/1/208/6400262"},{"label":"Date","value":"Oct 18, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"SbaiC7OGT is a UDP-glycosyltransferase gene from Scutellaria baicalensis that catalyzes the 7-O-glycosylation of flavonoids."},{"label":"Title","value":"Cloning and expression of UDP-glucose: flavonoid 7-O-glucosyltransferase from hairy root cultures of Scutellaria baicalensis"},{"label":"URL","value":"https://link.springer.com/article/10.1007/PL00008158"},{"label":"Date","value":"May, 2000"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"Escherichia coli is a microbial host commonly used for the heterologous expression of plant-derived molecules."},{"label":"Title","value":"Flavonoids, terpenoids, and polyketide antibiotics: Role of glycosylation and biocatalytic tactics in engineering glycosylation"},{"label":"URL","value":"https://doi.org/10.1016/j.biotechadv.2020.107550"},{"label":"Date","value":"May, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"Pliar53 is a synthetic phosphate (Pi)-depletion promoter system inspired by the bacterial phosphate (PHO) starvation response, in which low Pi concentrations activate the PHO regulon."},{"label":"Title","value":"Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli"},{"label":"URL","value":"https://doi.org/10.1016/j.biotechadv.2023.108154"},{"label":"Date","value":"Sep, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"XylS/Pm is a regulatory system inducible by m-toluic acid, whose derivatives are toxic and may interfere with enzymatic reactions."},{"label":"Title","value":"Modular plasmid design for autonomous multi-protein expression in Escherichia coli"},{"label":"URL","value":"https://jbioleng.biomedcentral.com/articles/10.1186/s13036-025-00483-2"},{"label":"Date","value":"Feb 10, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"RhaR/Prha is a regulatory system inducible by L-rhamnose, whose high cost limits its application in large-scale processes."},{"label":"Title","value":"Modular plasmid design for autonomous multi-protein expression in Escherichia coli"},{"label":"URL","value":"https://jbioleng.biomedcentral.com/articles/10.1186/s13036-025-00483-2"},{"label":"Date","value":"Feb 10, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Molecular Biology / Genetics
|
Free-Format Question
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Loss-of-function mutations in PLD4 lead to systemic lupus erythematosus
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https://www.nature.com/articles/s41586-025-09513-x
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September 10, 2025
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Researchers tested whether six mutations (P181L, D189E, R201Q, Y248C, A323V, G457D) in phospholipase D family member 4 (PLD4) from patients with systemic lupus erythematosus (SLE) had any effect on exonuclease activity. To evaluate the mutation, an assay was performed using lysates from reconstituted HEK293T PLD3-KO with wild-type PLD4 cells that were maintained in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 1% penicillin-streptomycin. Protein lysates were collected and purified using Flag-tag magnetic beads, then subjected to a PLD4 enzymatic activity assay (50 mM MES, pH 5.5, 150 mM NaCl, 2.5 μM substrate, 10 nM or 20 nM purified PLD4). The incubation was performed at 37 ° C for various time points (16, 35, and 50 h) and analyzed by TBE–PAGE, with nucleic acid staining conducted for 15 minutes prior to imaging.
|
- Intensity of ssDNA band fragmentation across mutants (P181L, D189E, R201Q, Y248C, A323V, G457D) at 16, 35 and 50 hours.
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Six mutations (P181L, D189E, R201Q, Y248C, A323V, G457D) in phospholipase D family member 4 (PLD4) from patients with systemic lupus erythematosus (SLE) were evaluated in cell lysates from reconstituted HEK293T PLD3-KO with wild-type PLD4 cells to evaluate the effect on exonuclease activity. Previously, cells were in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 1% penicillin-streptomycin. Protein lysates, collected and purified using Flag-tag magnetic beads, were subjected to a PLD4 enzymatic activity assay (50 mM MES, pH 5.5, 150 mM NaCl, 2.5 μM substrate, 10 nM or 20 nM purified PLD4) and incubated at 37 ° C (16, 35, and 50 h). Analysis was performed through TBE–PAGE, with nucleic acid staining conducted for 15 minutes prior to imaging. Which of the evaluated mutations are expected to show ssDNA fragmentation?
|
None of the mutants are expected to show ssDNA fragmentation
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- Systemic lupus erythematosus (SLE) is a complex multiorgan condition of variable severity.
- Phospholipase D family member 4 (PLD4) is a 5′ exonuclease that localizes in the endolysosomes and can cleave single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), thereby restricting the overactivation of TLR7 and TLR9.
|
[{"label":"RBK Item","value":"Systemic lupus erythematosus (SLE) is a complex multiorgan condition of variable severity."},{"label":"Title","value":"Genetics and pathogenesis of systemic lupus erythematosus and lupus nephritis"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25825084/"},{"label":"Date","value":"Jun, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Phospholipase D family member 4 (PLD4) is a 5′ exonuclease that localizes in the endolysosomes and can cleave single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), thereby restricting the overactivation of TLR7 and TLR9."},{"label":"Title","value":"PLD3 and PLD4 are single stranded acid exonucleases that regulate endosomal nucleic acid sensing"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC6105523/"},{"label":"Date","value":"Feb 13, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant genetics
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Free-Format Question
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ARABIDOPSIS Bsister and SEEDSTICK MADS-box transcription factors modulate maternal nutrient flow for seed development in Arabidopsis
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https://www.biorxiv.org/content/10.1101/2025.07.21.665905v1
|
July 24, 2025
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Researchers evaluated whether mutation of abs (tt16-6) and stk (stk-2) in Arabidopsis thaliana had any effect in the development of ovules and seeds by monitoring scratch accumulation. A wild-type seed (wt), and mutant seeds (abs, stk, and abs stk) were sown either directly on soil or on Murashige and Skoog (MS) medium and then moved to soil. Before sowing in germination medium, seeds were surface-sterilized with 70% ethanol for 2 minutes (min), 1% bleach for 5 min, and then washed three times with sterile water. After 10 days, the seedlings were moved to soil and grown in a growth chamber under long-day conditions (22°C, 16 h light/8 h dark).To visualize starch accumulation, pistils were isolated from flowers before anthesis. Starch staining was performed with Lugol's solution and the pistils were dissected in water to isolate the ovules. The signal was observed using a Zeiss Axiophot D1 microscope equipped with DIC optics. Images were recorded with an Axiocam MRc5 camera (Zeiss) using the Axiovision program.
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- Lugol staining intensity in mature ovules of Arabidopsis thaliana to assess starch accumulation across wild-type (WT) and mutant lines (abs, stk, and abs stk).
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Starch accumulation was determined by Lugol staining intensity in isolated ovules from dissected pistils of Arabidopsis thaliana wild-type (WT) and mutant lines (abs, stk, and abs stk). Pistils were collected from flowers prior to anthesis, from plants grown from seeds previously sown either directly in soil or initially on Murashige and Skoog (MS) medium and later transferred to soil. Before sowing on germination medium, seeds were surface-sterilized with 70% ethanol for 2 minutes, followed by 1% bleach for 5 minutes, and rinsed with sterile water. After 10 days, seedlings were transferred to soil and grown under long-day conditions in a growth chamber. Starch staining was performed using Lugol's solution, and signal detection was carried out with a Zeiss Axiophot D1 microscope equipped with DIC optics. At the final stages of ovule development in the abs mutant, based on Lugol staining intensity, which ovules sections would be expected to show higher starch accumulation?
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Higher starch accumulation is expected within the embryo sac, at the boundary between the nucellus and the chalaza, between the chalaza and the funiculus, and in the micropylar integuments.
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- Starch accumulation occurs in gamethophytic and sporophytic tissues when arabidopsis ovules behave as sink organs.
- ARABIDOPSIS Bsister/TRANSPARENT TESTA 16 (ABS/TT16) sporophytically expresses MADS-box genes that regulates the differentiation and pigmentation of the endothelium, as well as nucellus degeneration.
- Abs mutants exhibit abnormal cell morphology in the endothelium, and after fertilization, fails to accumulate proanthocyanidins (PAs) that give the typical pigmentation to the Arabidopsis seeds.
- SEEDSTICK (STK) sporophytically expresses MADS-box genes that are required for seed coat differentiation, seed size and seed abscission.
- Stk mutants are characterized by ectopic accumulation of PAs in the seed coat.
- Abs stk double mutants have ovules that are characterized by an increased accumulation of starch, lack of endothelium differentiation and division, and severe fertility defects.
|
[{"label":"RBK Item","value":"Starch accumulation occurs in gamethophytic and sporophytic tissues when arabidopsis ovules behave as sink organs."},{"label":"Title","value":"Starch Turnover and Metabolism during Flower and Early Embryo Development"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5129708/"},{"label":"Date","value":"Oct 28, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"ARABIDOPSIS Bsister/TRANSPARENT TESTA 16 (ABS/TT16) sporophytically expresses MADS-box genes that regulates the differentiation and pigmentation of the endothelium, as well as nucellus degeneration."},{"label":"Title","value":"Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5399669/"},{"label":"Date","value":"Apr 15, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Abs mutants exhibit abnormal cell morphology in the endothelium, and after fertilization, fails to accumulate proanthocyanidins (PAs) that give the typical pigmentation to the Arabidopsis seeds."},{"label":"Title","value":"Proanthocyanidin-Accumulating Cells in Arabidopsis Testa: Regulation of Differentiation and Role in Seed Development"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC280558/"},{"label":"Date","value":"Nov, 2003"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"SEEDSTICK (STK) sporophytically expresses MADS-box genes that are required for seed coat differentiation, seed size and seed abscission."},{"label":"Title","value":"SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat"},{"label":"URL","value":"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004856"},{"label":"Date","value":"Dec 18, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Stk mutants are characterized by ectopic accumulation of PAs in the seed coat."},{"label":"Title","value":"SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat"},{"label":"URL","value":"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004856"},{"label":"Date","value":"Dec 18, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Abs stk double mutants have ovules that are characterized by an increased accumulation of starch, lack of endothelium differentiation and division, and severe fertility defects. "},{"label":"Title","value":"The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04878.x"},{"label":"Date","value":"Dec 16, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant genetics / Plant biotechnology
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Free-Format Question
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Diploid gametes in maize by mutation of A-Type cyclins: a step towards apomeiosis and synthetic apomixis
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https://www.biorxiv.org/content/10.1101/2025.05.16.654085v1
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May 19, 2025
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Researchers tested whether the maize genome contains A-type cyclins similar to those found in Arabidopsis thaliana. They identified eight A-type cyclins and tested their ability to produce diploid gametes in the B104 maize variety. To determine whether the loss of function of maize A-type cyclins results in diploid gamete formation, the researchers used CRISPR-Cas9 technology to create single and multiplexed gRNAs that targeted three A-type cyclins: CYC2, CYC6, and CYC27, because those genes were more abundant in Meiosis I than the others. Edits on the target genes were confirmed by DNA sequencing (single and multiplexed (CYC2-CYC6 and CYC2-CYC27)). Diploid gamete formation was evaluated by Flow Cytometry, using WT B104 pollen grains and leaves to determine the haploid-diploid controls. To assess the penetrance of diploid gamete formation, they performed crosses using the knock-out mutants as mother or father when crossing to wild-type plants.
|
- Ploidy of male gametes and somatic cells, determined by measuring DNA content of nuclei from pollen and leaves using flow cytometry.
- Penetrance of the diploid gamete phenotype, inferred by calculating the percentage of filled, viable kernels resulting from reciprocal crosses between mutant and wild-type plants.
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Diploid gamete formation regulated by A-type cyclins in maize was evaluated by targeting three genes using CRISPR-Cas9 in a single or multiplexed fashion. Diploid gamete formation was measured by performing flow cytometry on pollen grains or leaves of edited plants. What ploidy would you expect to find in an individual derived from a self-pollinated plant edited in CYC6?
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Progeny are diploid because the single mutant produces normal haploid gametes, showing that neither male nor female meiosis was disrupted to a detectable level.
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1. A-type cyclins are required for meiosis II.
2. Unreduced gametes are gametes that did not undergo a meiotic division, resulting in 2n gametes.
3. Multiplexed gRNAs refer to constructs containing gRNAs that target more than one gene.
4. Wild-type Maize is a diploid species
|
[{"label":"RBK Item","value":"A-type cyclins are required for meiosis II."},{"label":"Title","value":"The CYCLIN-A CYCA1;2/TAM Is Required for the Meiosis I to Meiosis II Transition and Cooperates with OSD1 for the Prophase to First Meiotic Division Transition"},{"label":"URL","value":"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000989"},{"label":"Date","value":"Jun 17, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Unreduced gametes are gametes that did not undergo a meiotic division, resulting in 2n gametes."},{"label":"Title","value":"Turning Meiosis into Mitosis"},{"label":"URL","value":"https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000124"},{"label":"Date","value":"Jun 9, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
|
Plant Biotechnology, Developmental Genetics
|
Free-Format Question
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Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency
|
https://www.biorxiv.org/content/10.1101/2025.06.22.659756v1
|
June 23, 2025
|
An experiment was conducted to identify new morphogenic regulator genes that could improve maize transformation efficiency.
Researchers induced somatic embryogenesis by transforming immature maize embryos with Agrobacterium carrying vectors expressing BABY BOOM and WUSCHEL2. 1 week after transformation, transformed cells were isolated and sorted using fluorescence-activated cell sorting, yielding approx 100,000 cells for single-cell RNA sequencing (10x Genomics). After quality filtering, 6,830 cells were analyzed. Gene regulatory network inference using MINI-EX identified regulons in clusters associated with somatic embryogenesis, which were prioritized using text mining of relevant literature, yielding 60 candidate genes. These were screened by expressing each under a maize ubiquitin promoter in vectors containing a RUBY reporter (producing visible red pigment for visual confirmation). Immature B104 maize embryos were transformed via Agrobacterium, and morphogenic responses were monitored by light microscopy. Four candidates (bHLH48, EREB152, GRF4, and HB77) showed the strongest responses and were selected for validation.
For validation, each candidate was cloned into vector pG3K-Cre-AG-RUBY with a Cre/loxP auto-excision system. Immature zygotic embryos from B104 maize (11-12 days after pollination, from at least three ears) were transformed using Agrobacterium, with approximately 189-194 explants per treatment. Five treatments were tested: the four candidates plus tdTomato (negative control). At 43 days after transformation, explants with RUBY-expressing shoots were imaged using a Canon EOS 1200D camera and counted, and transformation frequency was calculated as the percentage of explants producing transgenic shoots (number of embryos with RUBY-positive shoots at 43 DAT / total embryos infected) × 100 %).
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- Transformation frequency: percentage of total explants transformed (as indicated by RUBY expression), measured using a Canon EOS 1200D camera for visual observation, across five experimental treatments: (1) tdTomato (negative control); (2) bHLH48; (3) EREB152; (4) GRF4; and (5) HB77
|
An experiment was carried out to identify new genes that could improve maize transformation efficiency. Using single-cell RNA sequencing and gene regulatory network analysis, researchers identified 60 candidate transcription factors. The four most promising candidates were validated in transformation experiments using immature B104 maize embryos transformed with vectors containing each candidate, along with a Cre/loxP auto-excision system and RUBY reporter. Transformation frequency was measured at 43 days after transformation as the percentage of explants producing transgenic shoots. Among the four newly identified candidate morphogenic regulators (bHLH48, EREB152, GRF4, and HB77), which one produced the greatest improvement in transformation efficiency compared to the negative control?
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EREB152 produced the greatest improvement.
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- Somatic embryogenesis is the process by which a somatic plant cell develops into an embryo and potentially a fertile plant. It's a critical step in generating transgenic plants, through Agrobacterium-mediated transformation and gene editing.
- Low transformation frequencies in maize pose problems for maize crop improvement, with only a fraction of transgenic events being high quality single-copy insertions.
- Expression of morphogenic regulator transcription factors such as BABY BOOM and WUSCHEL2 can induce direct somatic embryogenesis in maize explants, substantially increasing transformation efficiency.
- Although BABY BOOM and WUSCHEL2 are useful in promoting transformation efficiency, they can cause infertility and excessive callus formation, necessitating onerous interventions involving Cre/loxP auto-excision to remove them after embryo induction.
- Alternative morphogenic regulators from different transcription factor families (such as GRF-GIF fusions in wheat and maize, or WOX2A in maize) have shown promise for improving transformation while overcoming the problems with BABY BOOM and WUSCHEL2.
- Single-cell RNA sequencing enables the identification of cell-type-specific gene regulatory networks during developmental processes, pinpointing master regulator transcription factors that potentially enhance somatic embryogenesis.
|
[{"label":"RBK Item","value":"Somatic embryogenesis is the process by which a somatic plant cell develops into an embryo and potentially a fertile plant. It's a critical step in generating transgenic plants, through Agrobacterium-mediated transformation and gene editing."},{"label":"Title","value":"Rapid genotype “independent” Zea mays L. (maize) transformation via direct somatic embryogenesis"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s11627-018-9905-2"},{"label":"Date","value":"April 30, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Low transformation frequencies in maize pose problems for maize crop improvement, with only a fraction of transgenic events being high quality single-copy insertions."},{"label":"Title","value":"Use of GRF‐GIF chimeras and a ternary vector system to improve maize (Zea mays L.) transformation frequency\n"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.16880"},{"label":"Date","value":"June 23, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Expression of morphogenic regulator transcription factors such as BABY BOOM and WUSCHEL2 can induce direct somatic embryogenesis in maize explants, substantially increasing transformation efficiency."},{"label":"Title","value":"Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation"},{"label":"URL","value":"https://academic.oup.com/plcell/article/28/9/1998/6098336"},{"label":"Date","value":"September 6, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Although BABY BOOM and WUSCHEL2 are useful in promoting transformation efficiency, they can cause infertility and excessive callus formation, necessitating onerous interventions involving Cre/loxP auto-excision to remove them after embryo induction."},{"label":"Title","value":"Use of non-integrating Zm-Wus2 vectors to enhance maize transformation: Non-integrating WUS2 enhances\ntransformation"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s11627-019-10042-2"},{"label":"Date","value":"January 2, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Alternative morphogenic regulators from different transcription factor families (such as GRF-GIF fusions in wheat and maize, or WOX2A in maize) have shown promise for improving transformation while overcoming the problems with BABY BOOM and WUSCHEL2."},{"label":"Title","value":"A key to totipotency: Wuschel‐like homeobox 2a unlocks embryogenic culture response in maize ( Zea mays L.)"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.14098"},{"label":"Date","value":"June 26, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Single-cell RNA sequencing enables the identification of cell-type-specific gene regulatory networks during developmental processes, pinpointing master regulator transcription factors that potentially enhance somatic embryogenesis."},{"label":"Title","value":"MINI-EX: Integrative inference of single-cell gene regulatory networks in plants"},{"label":"URL","value":"https://www.cell.com/molecular-plant/fulltext/S1674-2052(22)00368-9"},{"label":"Date","value":"November 7, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Chemistry
|
Chemistry
|
MCQ
|
Lab-Scale Thermal Decomposition of Hydrogen Peroxide as
Green Propellant over Low-Cost Catalysts Based on Copper
Deposited on Different Supports
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https://www.mdpi.com/2226-4310/12/5/440
|
May 15, 2025
|
Researchers investigate the thermal degradation of the H2O2 green monopropellant. Three distinct catalysts—copper supported on γ-alumina, graphite, and MNC clay—were used. Conversely, a LABSYS evo-gasorption apparatus (Category: DTA/TG/DSC, Model: Setaram Instrumentation) was used to perform differential thermal analysis– thermogravimetry (DTA–TG) measurements in order to investigate the thermal breakdown of H2O2 at constant atmospheric pressure (p = 1 atm). A syringe was used to inject a 30% (w/w) H2O2 microdroplet into the metallic sample cell. It was investigated how the three different catalysts affected the H2O2 thermogram. A microdroplet of liquid H2O2 was combined with a modest amount (a few micrograms) of powdered catalyst in the
aluminum sample cell for each thermal study. Before each run, the following experimental conditions were maintained:
(i) Carrier gas: argon, with a flow rate of 50 mL·min⁻1;
(ii) Heating rate: 10 °C·min⁻1, from room temperature up to 250 °C;
(iii) The H2O2 droplet was added directly to the catalyst particles already placed in the aluminum cell.
After sealing the apparatus, a stabilization period of approximately 2 min was allowed for the system (carrier gas and sample) to equilibrate. The thermal run was then initiated to record the DTA–TG thermograms.
Experiments were run at two constant temperatures: 0 °C and 36 °C
|
- Differential pressure (ΔP, in kPa) vs time (minutes) was recorded.
- ΔP for each catalyst (Cu/γ-alumina, Cu/graphite, Cu/clay) compared to the uncatalyzed control.
- ΔP at 0 °C and 36 °C to assess temperature effects on decomposition rate.
|
Which of the following statements best describes the observed catalytic activity (as measured by differential pressure, ΔP, vs time) for the decomposition of 30 % H₂O₂ over the three copper-supported catalysts (Cu/γ-alumina, Cu/graphite, Cu/clay) compared to the uncatalyzed decomposition, at 36 °C and 0 °C?
A. At both temperatures all three catalysts produce rates almost identical to each other; the rates follow a similar trend, with 0°C just being slower than 36 °C, each gives a large increase over the uncatalyzed reaction at both temperatures.
B. At 0°C all three catalysts give a similar rate, none of them is clearly faster than another, but at 36 °C Cu/γ-alumina gives the highest rate (largest ΔP increase), followed by Cu/graphite, then Cu/clay, each significantly faster than uncatalyzed at both temperatures.
C. At 0 °C, Cu/clay a rate that is slower than the uncatalyzed reaction at the beginning, then becomes faster than the uncatalyzed reaction, while Cu/graphite, and Cu/γ-alumina have a similar rate and are higher than the uncatalyzed reaction. At 36 °C all three are faster than uncatalyzed reaction, Cu/γ-alumina is the fastest, closely followed by Cu/graphite, then Cu/clay.
D. At 0 °C all three catalysts begin slightly faster than the uncatalyzed reaction then all three become much faster, the variability being larger than the difference between the catalysts. At 36 °C the reaction with all three catalysts is much faster than the uncatalyzed reaction, with Cu/γ-alumina being much faster than Cu/graphite, then Cu/clay lags because the copper particles came off the support particles.
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C. At 0 °C, Cu/clay a rate that is slower than the uncatalyzed reaction at the beginning, then becomes faster than the uncatalyzed reaction, while Cu/graphite, and Cu/γ-alumina have a similar rate and are higher than the uncatalyzed reaction. At 36 °C all three are faster than uncatalyzed reaction, Cu/γ-alumina is the fastest, closely followed by Cu/graphite, then Cu/clay.
|
-As the world increasingly focuses on sustainable and environmentally friendly solutions, there is a growing interest in exploring greener alternative propellants that offer comparable performance while mitigating the drawbacks associated with hydrazine and its derivatives.
-The thermal decomposition of hydrogen peroxide (H2O2) as a promising green
propellant was performed over free-noble metallic-based catalysts deposited on abundant supports.
-Green monopropellants have the potential for long-term cost savings due to reduced safety measures, disposal costs, and regulatory compliance requirements associated with hazardous materials such as hydrazine
|
[{"label":"RBK Item","value":"As the world increasingly focuses on sustainable and environmentally friendly solutions, there is a growing interest in exploring greener alternative propellants that offer comparable performance while mitigating the drawbacks associated with hydrazine and its derivatives."},{"label":"Title","value":"Propulsion Systems, Propellants, Green Propulsion Subsystems and their Applications: A Review"},{"label":"URL","value":"https://ect-journal.kz/index.php/ectj/article/view/1491"},{"label":"Date","value":"March 20, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Green monopropellants have the potential for long-term cost savings due to reduced safety measures, disposal costs, and regulatory compliance requirements associated with hazardous materials such as hydrazine"},{"label":"Title","value":"Development of green propellants for future space applications"},{"label":"URL","value":"https://www.jes.or.jp/mag/stem/Vol.77/documents/Vol.77,No.5,p.105-110.pdf"},{"label":"Date","value":"June 14, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
|
Tendon Repair / Mechanotransduction
|
Numerical Values
|
GsMTx4-loaded GelMA promotes tendon regeneration and suppresses heterotopic ossification via the Apelin signaling pathway
|
https://www.sciencedirect.com/science/article/pii/S0142961225004260?via%3Dihub
|
June 19, 2025
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Researchers employed Male Sprague Dawley (SD) rats (10–12 weeks old, weighing 250–300 g) as animal model for studying tendon repair and regeneration. A central defect (1 mm in width and 5 mm in length) was created in the Achilles tendon using two parallel No.15 surgical blades. Subsequently, the skin was sutured using 4-0 Vicryl sutures. The rats received temgesic (0.3 mg/kg of body weight) for three consecutive days following the surgery to manage pain. The rats were randomly assigned to one of four groups: Achilles tendon defect (ATD) (no treatment), GelMA, GelMA + 50 μg GsMTx4, GelMA + 100 μg GsMTx4. At the time of injury, a mixture of GelMA and LAP (Lithium Phenyl-2,4,6-Trimethylbenzoylphosphinate) (20 μl), loaded with 50 or 100 μg GsMTx4 where appropriate, was placed within the ATD of treated animals and transformed into the gel state with a blue light source (3 W, 405 nm) for 30 s at a distance of 2 cm from the defect. These animals were euthanized at 2, 4, and 8 weeks post-treatment, with six rats per group per time point. The harvested Achilles tendons were fixed in 4 % paraformaldehyde at room temperature for 24 h. Following fixation, the samples were rinsed with running water and dehydrated with an ethanol gradient, and embedded in paraffin. The blocks were sectioned at 5 μm thickness using a microtome and stained with Hematoxylin and Eosin (H&E). Semi-quantitative analysis of H&E staining results was conducted according to the modified Bonar score.
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- Histologic Bonar Score (ATD, GelMA, GelMA + 50 μg GsMTx4, GelMA + 100 μg GsMTx4): 2 weeks; 4 weeks; 8 weeks.
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Researchers employed Male Sprague Dawley (SD) rats (10–12 weeks old, weighing 250–300 g) as animal model for studying tendon repair and regeneration. A central defect (1 mm in width and 5 mm in length) was created in the Achilles tendon using two parallel No.15 surgical blades. The rats were randomly assigned to one of four groups: Achilles tendon defect (ATD) (no treatment), GelMA, GelMA + 50 μg GsMTx4, GelMA + 100 μg GsMTx4. At the time of injury, a mixture of GelMA and LAP (Lithium Phenyl-2,4,6-Trimethylbenzoylphosphinate) (20 μl), loaded with 50 or 100 μg GsMTx4 where appropriate, was placed within the ATD of treated animals and transformed into the gel state with a blue light source. The animals were euthanized at 2, 4, and 8 weeks post-treatment. The harvested Achilles tendons were embedded in paraffin, sectioned using a microtome, and stained with Hematoxylin and Eosin (H&E). Semi-quantitative analysis of H&E staining results was conducted according to the modified Bonar score (BS). Based on the reported values of the BS for Achilles tendon repair and regeneration, what is the predicted difference of the BS (in points) between the GelMA and the GelMA + 100 μg GsMTx4 groups 8-weeks post treatment?
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ΔBS (GelMA - GelMA + 100 μg GsMTx4) 8-weeks post treatment = 4 - 6 points; derived from BS GelMA 8-weeks post treatment = ~ 9 points, BS GelMA + 100 μg GsMTx4 8-weeks post treatment = ~ 4 points. Note: No CI/SE/SD reported -> fallback ± 10% units (rounded) applied.
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- Tendon regeneration is highly relied on the surrounding mechanical environment.
- Studies have demonstrated the importance of Piezo1 in modulating cellular behaviors to mechanical cues, such as cell migration, differentiation, proliferation, and extracellular matrix synthesis.
- GelMA hydrogel demonstrates excellent biocompatibility and sustained release properties.
- The mechanosensitive ion channel Piezo1 is inhibited by the peptide GsMTx4
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[{"label":"RBK Item","value":"- Tendon regeneration is highly relied on the surrounding mechanical environment."},{"label":"Title","value":"In vitro loading models for tendon mechanobiology"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/10.1002/jor.23752"},{"label":"Date","value":"September 28, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Studies have demonstrated the importance of Piezo1 in modulating cellular behaviors to mechanical cues, such as cell migration, differentiation, proliferation, and extracellular matrix synthesis."},{"label":"Title","value":"Effects of mechanosensitive ion channel Piezo1 on proliferation and osteogenic differentiation of human dental follicle cells"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0940960221001734"},{"label":"Date","value":"October 20, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled source is the cited element in the paper."},{"label":"RBK Item","value":"- GelMA hydrogel demonstrates excellent biocompatibility and sustained release properties."},{"label":"Title","value":"Multifunctional GelMA platforms with nanomaterials for advanced tissue therapeutics"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S2452199X21003133"},{"label":"Date","value":"July 6, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- The mechanosensitive ion channel Piezo1 is inhibited by the peptide GsMTx4"},{"label":"Title","value":"GsMTx4: Mechanism of Inhibiting Mechanosensitive Ion Channels"},{"label":"URL","value":"https://www.cell.com/biophysj/fulltext/S0006-3495(16)31041-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0006349516310414%3Fshowall%3Dtrue"},{"label":"Date","value":"January 10, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Immunology / Microbiology
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Numerical Values
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The gut microbiota directs vitamin A flux to regulate intestinal T cell development
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https://www.biorxiv.org/content/10.1101/2025.09.08.674524v1
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Sep 10, 2025
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Researchers tested whether the intestinal microbiota influences retinoid flux through intestinal cellular pathways in five cell types: Intestinal epithelial (IE) cells, lamina propria (LP) CD11c⁺ cells, mesenteric lymph node (mLN) CD11c⁺ cells, LP CD4⁺ T cells, and mLN CD4⁺ T cells. For the study, cells from three groups of C57BL/6J wild-type mice were analyzed under different conditions: a) Conventional mice were housed under specific pathogen–free (SPF) conditions; b) Antibiotic treated mice received drinking water supplemented with Penicillin G sodium and Streptomycin sulfate for 10 days to deplete the intestinal microbiota; c) Reconventionalization mice were switched from antibiotic-treated water to untreated water for 48 hours, followed by gavage with a fecal slurry prepared from conventional donor mice. All groups were administered 10 μCi/mL ³H-retinol diluted in corn oil. For kinetic studies, mice were euthanized at 0 and 6 hours, and at 1, 2, 3, 4, 7, and 10 days post-gavage. Peyer’s patches were excised, and the tissue was flushed, washed, and then incubated for intestinal preparations. IE cells and intraepithelial lymphocytes were subsequently released by vortexing and removed by filtration through a cell strainer. The remaining tissue was washed, digested, and filtered. The digestion step was repeated once more on residual tissue to maximize immune cell yield. LP cells were enriched, collected, and then washed twice. For mLN preparations, only lymph nodes draining the small intestine were excised. CD11c⁺ myeloid cells, and CD4⁺ T cells were isolated from the LP and mLNs and subjected to magnetic enrichment. Cells were solubilized in Biosol, mixed with Bioscint scintillation cocktail, and radioactivity was measured using a liquid scintillation counter. Counts per minute (cpm) were normalized to the number of live cells.
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- Time points after ³H-retinol uptake.
- Counts per minute of ³H-retinol uptake.
- Comparison of peak ³H-retinol uptake across mice groups: conventional, antibiotic-treated and reconventionalization.
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Retinoid flux of 10 μCi/mL ³H-retinol at 0 and 6 hours, and at 1, 2, 3, 4, 7, and 10 days through intestinal epithelial (IE), lamina propria (LP) CD11c⁺, mesenteric lymph node (mLN) CD11c⁺, LP CD4⁺ T, and mLN CD4⁺ T cells was measured in three groups of C57BL/6J wild-type mice (conventional, antibiotic-treated, and reconventionalized). Based on the results, the analysis identified distinct peaks of ³H-retinol uptake across these cell types. For the three mouse groups, at which time point does the ³H-retinol peak occur in LP CD11c⁺ cells?
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0.95-1.05 days
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- Retinoids are a class of compounds derived from Vitamin A molecules.
- Retinol is a type of retinoid that is converted into retinoic acid (RA) by intestinal myeloid cells, this molecule is transferred to developing mLN T cells.
- The intestinal microbiota shapes adaptive immunity by restoring intestinal lymphocyte accumulation.
- Microbial antigens and a vitamin-A derived signal are needed to program T cell migration and maturation.
- Intestinal epithelial (IE) cells participate in the primary absorption of Vitamin A and its conversion to retinol.
- Lamina propria (LP) is the immune-rich connective tissue beneath the intestinal epithelium.
- Mesenteric lymph node (mLN) is a secondary lymph node located outside the intestinal wall, where CD4⁺ T cells are first primed.
- CD11c⁺ cells are specialized myeloid cells in the LP that convert retinol acquired from IE cells into retinoic acid.
- CD4⁺ T cells are a type of adaptive immune cell whose development in the intestine depends on signals from microbial cells.
|
[{"label":"RBK Item","value":"Retinoids are a class of compounds derived from Vitamin A molecules."},{"label":"Title","value":"Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis"},{"label":"URL","value":"https://www.cell.com/immunity/pdf/S1074-7613(18)30526-0.pdf"},{"label":"Date","value":"Dec 18, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Retinol is a type of retinoid that is converted into retinoic acid (RA) by intestinal myeloid cells, this molecule is transferred to developing mLN T cells."},{"label":"Title","value":"A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-β– and retinoic acid–dependent mechanism"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2118683/\n"},{"label":"Date","value":"Aug 06, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"The intestinal microbiota shapes adaptive immunity by restoring intestinal lymphocyte accumulation."},{"label":"Title","value":"Creating and Maintaining the Gastrointestinal Ecosystem: What We Know and Need To Know from Gnotobiology"},{"label":"URL","value":"https://journals.asm.org/doi/epub/10.1128/mmbr.62.4.1157-1170.1998"},{"label":"Date","value":"Dec 01, 1998"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Microbial antigens and a vitamin-A derived signal are needed to program T cell migration and maturation."},{"label":"Title","value":"Retinoic Acid Imprints Gut-Homing Specificity on T Cells"},{"label":"URL","value":"https://www.cell.com/action/showPdf?pii=S1074-7613%2804%2900247-X"},{"label":"Date","value":"Oct, 2004"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Intestinal epithelial (IE) cells participate in the primary absorption of Vitamin A and its conversion to retinol."},{"label":"Title","value":"Mechanisms involved in the intestinal absorption of dietary vitamin A and provitamin A carotenoids"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3525326/"},{"label":"Date","value":"Jan, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Lamina propria (LP) is the immune-rich connective tissue beneath the intestinal epithelium."},{"label":"Title","value":"Serum amyloid A delivers retinol to intestinal myeloid cells to promote adaptive immunity"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8532503/"},{"label":"Date","value":"Sep 17, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Mesenteric lymph node (mLN) is a secondary lymph node located outside the intestinal wall, where CD4⁺ T cells are first primed."},{"label":"Title","value":"Rapid Acquisition of Tissue-specific Homing Phenotypes by CD4+ T Cells Activated in Cutaneous or Mucosal Lymphoid Tissues"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2196018/"},{"label":"Date","value":"Jan 07, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"CD11c⁺ cells are specialized myeloid cells in the LP that convert retinol acquired from IE cells into retinoic acid."},{"label":"Title","value":"Serum amyloid A delivers retinol to intestinal myeloid cells to promote adaptive immunity"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8532503/"},{"label":"Date","value":"Sep 17, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"CD4⁺ T cells are a type of adaptive immune cell whose development in the intestine depends on signals from microbial cells."},{"label":"Title","value":"Rapid Acquisition of Tissue-specific Homing Phenotypes by CD4+ T Cells Activated in Cutaneous or Mucosal Lymphoid Tissues"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2196018/"},{"label":"Date","value":"Jan 07, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Pharmacology and Toxicology
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Numerical Values
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Peripheral Neuropathy After Chronic Alcohol Exposure in Mice: Impact of sex, total intake and duration and alcohol metabolism.
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https://www.biorxiv.org/content/10.1101/2025.09.02.673579v1
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Sep 7, 2025
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Researchers tested whether chronic alcohol concentration (2.5% or 5% EtOH) induces long-term, concentration- and sex-dependent mechanical hypersensitivity in mice during both the development phase (1 to 4 weeks of intake) and the recovery phase (1 to 10 weeks post-withdrawal). Adult male and female C57BL/6J mice were housed and fed control Lieber-DeCarli diet ad libitum for 7 days. After the acclimation period, mice were single housed and assigned to receive either a control Lieber-DeCarli liquid diet or a 5% (v/v) or 2.5% (v/v) alcohol Lieber-DeCarli liquid diet. For alcohol withdrawal studies, mice remained on their assigned liquid diet for four weeks and then switched back to normal pellet food and water bottles ad/libitum for ten weeks. Mechanical hypersensitivity was assessed by measuring paw withdrawal (PW) thresholds using a series of calibrated von Frey filaments (0.07-4.0 g) using the up-down method. A PW response was defined as immediate lifting, shaking or fluttering of the paw. Baseline PW thresholds were recorded before the onset of alcohol exposure.
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- Paw withdrawal thresholds across alcohol consumption stages (development and withdrawal).
- Comparison of paw withdrawal threshold across alcohol concentrations (2.5% and 5%).
- Sex-based comparison of mechanical hypersensitivity curves (female vs. male mice).
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Adult male and female C57BL/6J mice were given either a control Lieber-DeCarli liquid diet or a Lieber-DeCarli liquid diet containing 2.5% or 5% (v/v) alcohol during a 1- to 4-week development phase. After 4 weeks, the mice entered a 10-week withdrawal phase, during which they were switched back to standard pellet food and water bottles ad libitum. Based on the paw withdrawal (PW) thresholds used to evaluate mechanical hypersensitivity, what is the predicted difference (in decimal units) in PW threshold between the first and last week of alcohol withdrawal in female mice that consumed 2.5% (v/v) alcohol?
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ΔPW = (0.18-0.22) g, derived from PW(1week)= ~ 0.4 g, PW(10week) = ~ 0.6 g at [2.5% v/v EtOH in females). Note: No CI/SE/SD reported -> fallback ±0.02 g applied.
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- Chronic alcohol consumption can cause related pain phenotypes, such as alcohol-induced peripheral neuropathy (AIPN). Behavioral responses, such as somatosensory hypersensitivity, vary by sex and are influenced by the overall level of alcohol exposure.
- Alcohol-induced peripheral neuropathy (AIPN) is a progressive and prevalent somatosensory disease by which individuals present disruptions in peripheral nerve integrity and debilitating neuropathic pain.
- Mechanical sensitivity are typical assessments of sensory nociceptive changes in rodents.
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[{"label":"RBK Item","value":"Chronic alcohol consumption can cause related pain phenotypes, such as alcohol-induced peripheral neuropathy (AIPN). Behavioral responses, such as somatosensory hypersensitivity, vary by sex and are influenced by the overall level of alcohol exposure."},{"label":"Title","value":"Sex-specific differences in alcohol-induced pain sensitization"},{"label":"URL","value":"https://doi.org/10.1016/j.neuropharm.2022.109354"},{"label":"Date","value":"Mar 01, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Alcohol-induced peripheral neuropathy (AIPN) is a progressive and prevalent somatosensory disease by which individuals present disruptions in peripheral nerve integrity and debilitating neuropathic pain."},{"label":"Title","value":"Alcohol-related peripheral neuropathy: a systematic review and meta-analysis"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s00415-018-9123-1"},{"label":"Date","value":"Nov 22, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Chemistry
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Organic chemistry / Photochemistry
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MCQ
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Antioxidant and Photoprotective Capacity of Secondary Metabolites Isolated from Pseudocyphellaria berberina
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https://www.mdpi.com/1420-3049/30/18/3833
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September 22, 2025
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Researchers aimed to evaluate the photoprotective and antioxidant capacities of lichen-extracted aromatic organic compounds. Brialmontin 2 (compound 1), physciosporin (compound 2), pseudocyphellarin A (compound 3), calycin (compound 4), and 22- hydroxistictan-3-one (compound 5) were isolated from the lichen material (thalli of Pseudocyphellaria berberina). The compounds were purified by column chromatography and purity and molecular identity was confirmed by NMR spectroscopic techniques (1H-NMR and 13C-NMR). Compounds 1 to 5 were tested in vitro using DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical assay, at concentrations of 5, 50, 100, 500 and 1000 parts per million (ppm). A total of 1 mL of the sample was mixed with 3 mL of the DPPH solution (0.25 mg/L). After 30 min of reaction (at room temperature in the dark), the absorbance was measured at 517 nm in the spectrophotometer UV-VIS GENESYS 10 (Thermo Scientific, Madison, WI, USA). Free radical scavenging activity (RSA) (%) was calculated using the equation: 𝑅𝑆𝐴 (%) = 100 x (𝐴𝑏𝑙𝑎𝑛𝑘−𝐴𝑠𝑎𝑚𝑝𝑙𝑒)/(𝐴𝑏𝑙𝑎𝑛𝑘); where RSA = free radical scavenging activity, Ablank = the absorbance of the blank (solvent mixture instead of sample solution); and Asample = the absorbance of the sample.
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- DPPH free radical assay: Absorbance at 517 nm of assay reactions with compounds 1 to 5 at 5, 50, 100, 500 and 1000 ppm (UV-VIS GENESYS 10; Thermo Scientific, Madison, WI, USA).
- Free radical scavenging activity (RSA) (%): 100 x (𝐴𝑏𝑙𝑎𝑛𝑘−𝐴𝑠𝑎𝑚𝑝𝑙𝑒)/(𝐴𝑏𝑙𝑎𝑛𝑘); where RSA = free radical scavenging activity, Ablank = the absorbance of the blank (solvent mixture instead of sample solution); and Asample = the absorbance of the sample.
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Researchers aimed to evaluate the photoprotective and antioxidant capacities of lichen-extracted aromatic organic compounds. Brialmontin 2 (compound 1), physciosporin (compound 2), pseudocyphellarin A (compound 3), calycin (compound 4), and 22-hydroxistictan-3-one (compound 5) were isolated from P. berberina. Purity and molecular identity was confirmed by NMR spectroscopic techniques. Compounds 1 to 5 were tested in vitro using DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical assay, at concentrations of 5, 50, 100, 500 and 1000 parts per million (ppm). A total of 1 mL of the sample was mixed with 3 mL of the DPPH solution (0.25 mg/L). After 30 min of reaction, the absorbance was measured at 517 nm and the free radical scavenging activity (RSA) (%) was calculated using the equation: 𝑅𝑆𝐴 (%) = 100 x (𝐴𝑏𝑙𝑎𝑛𝑘−𝐴𝑠𝑎𝑚𝑝𝑙𝑒)/(𝐴𝑏𝑙𝑎𝑛𝑘); where RSA = free radical scavenging activity, Ablank = the absorbance of the blank (solvent mixture instead of sample solution); and Asample = the absorbance of the sample. What of the following outcomes is most likely?
A) Compound 5 demonstrates the highest antioxidant activity (%RSA) from all 5 tested compounds, with increasing %RSA with increasing concentrations (ppm).
B) Compound 3 demonstrates a lower antioxidant activity (%RSA) than compound 2 at all tested concentrations (ppm) except for 1000 ppm.
C) Compound 1 demonstrates the lowest antioxidant activity (%RSA) from all 5 tested compounds, with no differences in %RSA between all tested concentrations (ppm).
D) Compound 4 demonstrates a higher antioxidant activity (%RSA) than compound 5 at all tested concentrations (ppm), with increasing %RSA with increasing compound 4 concentrations (ppm).
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B) Compound 3 demonstrates a lower antioxidant activity (%RSA) than compound 2 at all tested concentrations (ppm) except for 1000 ppm.
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- Pseudocyphellaria berberina is found in open habitats with high humidity, rain, and high luminosity; being expected that it biosynthesizes photoprotective and/or antioxidant metabolites.
- DPPH (2,2-diphenyl-1-picrylhydrazyl) assay determines antioxidant activity based on measured scavenging activity towards a stable free radical
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[{"label":"RBK Item","value":"- Pseudocyphellaria berberina is found in open habitats with high humidity, rain, and high luminosity; being expected that it biosynthesizes photoprotective and/or antioxidant metabolites."},{"label":"Title","value":"Epiphytic lichens of Conguillío National Park, southern Chile (Líquenes epífitos en el Parque Nacional Conguillío, sur de Chile)"},{"label":"URL","value":"https://revistas.udec.cl/index.php/gayana_botanica/article/view/3904"},{"label":"Date","value":"June 30, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- DPPH (2,2-diphenyl-1-picrylhydrazyl) assay determines antioxidant activity based on measured scavenging activity towards a stable free radical."},{"label":"Title","value":"Statistical evaluation of DPPH, ABTS, FRAP, and Folin-Ciocalteu assays to assess the antioxidant capacity of lignins"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S0141813023003628"},{"label":"Date","value":"February 2, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
|
Analytical chemistry / Nanotechnology
|
MCQ
|
Water Permeates and Plasticizes Amorphous Carbon Dots: Unraveling the Inner Accessibility of the Nanoparticles by Glass Transition Studies
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https://advanced.onlinelibrary.wiley.com/doi/10.1002/adma.202510992
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September 22, 2025
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Researchers aimed to determine the effects of different reaction conditions on the characteristics of carbon dots. To prepare the carbon dots, β-Alanine (β-Ala) and triethylenetetramine (TETA, 97%) were dissolved in Milli-Q water (300 µL) and stirred at room temperature for 10 min in the dark. The mixture was reacted in a CEM Discover 2.0 microwave at 230 °C and 200 W for different times (3, 5, 10, 30 and 60 minutes). Samples were referred to as “CDs_time” according to the reaction times (e.g. “CDs_30” for CDs obtained with the 30 min reaction). At the end of the process, the mixtures were cooled down at room temperature, diluted with 4 mL of Milli-Q water, and filtered through 0.2 µm PTFE syringe filters. Finally, solutions were dialyzed against Milli-Q water for 3 days (MWCO of 0.5 – 1 kDa) and freeze-dried. Thermogravimetric Analysis (TGA) experiments were performed under nitrogen atmosphere (25 mL min−1 flow rate) using a TGA Discovery device (TA Instruments). The procedure used was composed of a thermal pretreatment at 120 °C for 5 min, followed by a ramp from 40 to 700 °C at 20 °C min−1. Flash Differential Scanning Calorimetry (FDSC) measurements were performed by means of a Mettler Toledo Flash DSC 1, equipped with a Huber TC100 intracooler, and operating in a temperature range between −100 and 450 °C. MultiSTaR UFS1 chip sensors were employed, after calibrating the temperature with the melting point of indium at a heating rate of 1000 K s−1. Dry samples of CDs were prepared by depositing, onto the chip's active area, a tiny particle (in the order of 100 ng) of freshly freeze-dried CDs with a single-haired brush. Samples were dried in situ by pre-treating at 180 °C for 1 min, followed by a rapid cooling at 1000 K s−1 up to −40 °C. Soon after, five consecutive heating/cooling scans were recorded, with a fixed heating/cooling rate of 1000 K s−1 between – 40 and 200 °C. The five curves were averaged before plotting for noise reduction.
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- Thermogravimetric Analysis (TGA): ramp from 40 to 700 °C at 20 °C/min for CDs_3, CDs_5, CDs_10, CDs_30 and CDs_60 (TGA Discovery; TA Instruments).
- Flash Differential Scanning Calorimetry (FDSC): temperature range between −40 and 200 °C and heating/cooling rate of 1000 K/s for CDs_3, CDs_5, CDs_10, CDs_30 and CDs_60 (Mettler Toledo Flash DSC 1).
|
To determine the effects of different reaction conditions on the characteristics of carbon dots, β-Alanine (β-Ala) and triethylenetetramine (TETA) were dissolved in Milli-Q water and stirred at room temperature for 10 min in the dark. The mixture was microwave reacted at 230 °C and 200 W for different times (3, 5, 10, 30 and 60 minutes). According to the reaction times, samples were referred to as “CDs_time” (e.g. “CDs_30” for CDs with 30 min reaction time). At the end of the process, the mixtures were cooled down at room temperature, diluted with 4 mL of Milli-Q water, and filtered through 0.2 µm PTFE syringe filters. Finally, solutions were dialyzed against Milli-Q water for 3 days (MWCO of 0.5 – 1 kDa) and freeze-dried. Thermogravimetric Analysis (TGA) experiments were performed under nitrogen atmosphere (25 mL min−1 flow rate), using a thermal pretreatment at 120 °C for 5 min, followed by a ramp from 40 to 700 °C at 20 °C/min. Flash Differential Scanning Calorimetry (FDSC) measurements were performed in a temperature range between −40 and 200 °C and at a heating/cooling rate of 1000 K/s. What of the following outcomes is the most likely?
A) The degradation temperature (Td), occurs at ≈390 ± 5 °C for all the specimens, while temperature mid-point (Tg) shifts from 112 °C for CDs_3 to 136 °C for CDs_60.
B) The degradation temperature (Td), occurs at ≈380 ± 5 °C for all the specimens except for CDs_60, while temperature mid-point (Tg) shifts from 108 °C for CDs_3 to 129 °C for CDs_60.
C) The degradation temperature (Td), occurs at ≈370 ± 5 °C for all the specimens, while the temperature mid-point (Tg) shifts from 112 °C for CDs_3 to 152 °C for CDs_60.
D) The degradation temperature (Td), occurs at ≈390 ± 5 °C for all the specimens except for CDs_3 and CDs_5, while temperature mid-point (Tg) shifts from 118 °C for CDs_3 to 134 °C for CDs_60.
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A) The degradation temperature (Td), occurs at ≈390 ± 5 °C for all the specimens, while temperature mid-point (Tg) shifts from 112 °C for CDs_3 to 136 °C for CDs_60.
|
- The core of carbon dots is generally described as hydrophobic and “inaccessible”, being highly dehydrated and composed of either amorphous, randomly cross-linked carbon or partially ordered sp2 domains (graphitic CDs).
- The diffusion of a substance like water can modify the thermodynamic variables of amorphous materials, leading to detectable changes in critical phase transition temperatures.
|
[{"label":"RBK Item","value":"- The core of carbon dots is generally described as hydrophobic and “inaccessible”, being highly dehydrated and composed of either amorphous, randomly cross-linked carbon or partially ordered sp2 domains (graphitic CDs)"},{"label":"Title","value":"The polymeric characteristics and photoluminescence mechanism in polymer carbon dots: A review"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S2468519416300933"},{"label":"Date","value":"September 23, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled source is the cited element in this paper"},{"label":"RBK Item","value":"- The diffusion of a substance like water can modify the thermodynamic variables of amorphous materials, leading to detectable changes in critical phase transition temperatures."},{"label":"Title","value":"Hydroplasticization of Polymers: Model Predictions and Application to Emulsion Polymers"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/la904211e"},{"label":"Date","value":"January 19, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled source is the cited element in this paper."}]
|
Chemistry
|
Controlled release / Nanotechnology
|
MCQ
|
Sustained Release of Antibacterial Therapeutic Elements from Functionalized Mesoporous Silica-Coated Silver Nanoparticles for Bone Tissue Engineering
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https://www.mdpi.com/2624-8549/7/5/146
|
September 10, 2025
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Researchers aimed to characterize silver (Ag)-releasing pristine and functionalized mesoporous silica-coated silver nanoparticles. For that purpose, core–shell-structured silver (Ag)-mesoporous silica nanoparticles (MSNs) (Ag@MSNs) were synthesized using a sol–gel method. An NaOH solution (2 M, 3.5 mL) was added into water (480 mL) containing CTAB (1 g) and thoroughly mixed at 80 °C for 30 min to ensure the complete dissolution of the CTAB. Afterwards, a mixture of formaldehyde (1 M, 3 mL) and a AgNO3 solution (0.1 M, 8 mL) was added dropwise with magnetic stirring. After stirring the mixture for 5 min, TEOS (5 mL) was added slowly, and it was stirred for another 2 h. The reaction temperature was kept at 80 °C for all the steps. The resultant products were collected through centrifugation and washed twice with deionized water and ethanol. The nanoparticles were then transferred to an ethanol solution (100 mL) containing NH4NO3 (0.6 g) and kept in a reflux unit at 80 °C for 24 h. Finally, the sample was washed using the same procedure and dried under vacuum to yield as-prepared Ag@MSNs. For -NH2 functionalization, Ag@MSNs (100 mg) were dispersed in isopropyl alcohol (100 mL), and 0.2 mL of APTES was added to the solution. The mixture was heated to 85 °C and stirred for 24 h. Then, the precipitates were collected through centrifugation (10,000 rpm, 5 min) and rinsed with deionized water and ethanol. Finally, the sample was dried under vacuum to yield Ag@MSNs-NH2. For -COOH functionalization, Ag@MSNs-NH2 (100 mg) were dispersed in N, N-Dimethylformamide (100 mL), and excess maleic anhydride was added to the solution. The mixture was then kept in a reflux unit at 80 °C for 24 h. The solids were collected through centrifugation (10,000 rpm, 5 min) and washed with deionized water and ethanol. Finally, the sample was dried under vacuum to yield Ag@MSNs-COOH. N2 adsorption–desorption experiments were performed to obtain the surface area and mesopore size distribution (ASAP2020 HD88, Micromeritics, Norcross, USA).
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- Specific surface (ASAP2020 HD88, Micromeritics, Norcross, USA): Ag@MSNs, Ag@MSNs-NH2 and Ag@MSNs-COOH.
- Pore diameter (ASAP2020 HD88, Micromeritics, Norcross, USA): Ag@MSNs, Ag@MSNs-NH2 and Ag@MSNs-COOH.
- Pore volume (ASAP2020 HD88, Micromeritics, Norcross, USA): Ag@MSNs, Ag@MSNs-NH2 and Ag@MSNs-COOH.
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Researchers aimed to characterize silver (Ag)-releasing pristine and functionalized mesoporous silica-coated silver nanoparticles. For that purpose, core–shell-structured silver (Ag)-mesoporous silica nanoparticles (MSNs) (Ag@MSNs) were synthesized using a sol–gel method. For -NH2 functionalization, Ag@MSNs were dispersed in isopropyl alcohol and reacted with APTES at 85 °C for 24 h under stirring, ultimately yielding Ag@MSNs-NH2. For -COOH functionalization, Ag@MSNs-NH2 were dispersed in N, N-Dimethylformamide (100 mL), and excess maleic anhydride was added to the solution, being kept in a reflux unit at 80 °C for 24 h, ultimately yielding Ag@MSNs-COOH. N2 adsorption–desorption experiments were performed to obtain the surface area and mesopore size distribution. According to the information provided, which of the following outcomes is most likely?
A) Pore diameter: Ag@MSNs > Ag@MSNs-NH2 > Ag@MSNs-COOH; Specific area: Ag@MSNs-COOH similar to Ag@MSNs-NH2
B) Pore volume: Ag@MSNs > Ag@MSNs-NH2 > Ag@MSNs-COOH; Specific area: Ag@MSNs-COOH ~1.25-fold lower than Ag@MSNs-NH2.
C) Pore volume: Ag@MSNs-COOH similar to Ag@MSNs-NH2; Specific area: Ag@MSNs-COOH similar to Ag@MSNs-NH2
D) Pore volume: Ag@MSNs-COOH < Ag@MSNs-NH2; Specific area: Ag@MSNs-COOH 1.5-fold lower than Ag@MSNs-NH2
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A) Pore diameter: Ag@MSNs > Ag@MSNs-NH2 > Ag@MSNs-COOH; Specific area: Ag@MSNs-COOH similar to Ag@MSNs-NH2
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- A change in the mesoporous silica nanoparticle (MSN) structure following surface functionalization due to substantial number of functional group grafting onto the inner surface of the MSNs, results in a narrowed pore diameter and reduced pore volume and surface area.
- The carboxylation treatment did not change the specific surface area versus -NH2 functionalization, but the pore volume was reduced by around 22%, indicating that the grafted COOH groups blocked part of the mesopore channel.
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Chemistry
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Physical Chemistry
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Free-Format Question
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Comparison of the Performance of Fluorescent, Phosphorescent and TADF Luminophores for Explosives Sensing
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https://chemrxiv.org/engage/chemrxiv/article-details/68b4a37ea94eede154c30152
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Sep 3, 2025
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Optically dilute solutions of luminophore concentrations on the order of 42 μM were prepared in toluene. Absorption spectra were recorded at room temperature on a Shimadzu UV-2600 double beam spectrophotometer using a 1 cm quartz cuvette. Steady-state emission spectra and Time Correlated Single Photon Counting (TCSPC) emission decay measurements were recorded at 298 K on either an Edinburgh Instruments FS5 or FLS980 spectrofluorometer, both
in air and under N2, the latter prepared via 3 freeze-pump-thawing cycles using a home-made Schlenk quartz cuvette. Samples were excited at 420 nm for the steady-state photoluminescence measurements in order to selectively excite the luminophore in the presence of the DNT.
375 and 379 nm picosecond pulsed diode lasers from Edinburgh Instruments were used for the time-resolved TCSPC measurements in optically diluted samples. These wavelengths correspond to the near-maximum absorbance of the emitter compounds but only the weak absorption tail of DNT. The instrument response function (IRF) was measured using a solution of Ludox (signal collected at the wavelength of the laser emission).
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-Peak value of the lowest energy absorption band for luminophores Alq3, fac-Ir(ppy)3, and 4CzIPN, as well as for 2,4-dinitrotoluene (DNT) , in nm.
-Molar absorptivity of luminophores Alq3, fac-Ir(ppy)3, and 4CzIPN, in M-1 cm-1
-Lowest energy absorption band performed at room temperature by exciting each compoundat its respective low-energy maximum lambda-abs, in nm.
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The optoelectronic characterization of Alq3, fac-Ir(ppy)3, and 4CzIPN in solution was measured before and after addition of DNT. What would you expect to happen with the absorbance after DNT addition? In which order- in terms of molar absorptivity, from the highest- would you expect the luminophores to be? In which range do you expect the ΦPL values for each luminophore analyzed?
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Once DNT is introduced, the absorbance increases due to the contribution from the absorption band of DNT (labs = 297 nm), which extends to around 400 nm.
In terms of molar absorptivity, the order of luminophores starting from the highest is 4CzIPN >Ir(ppy)3 >Alq3 .
The ΦPL values for each luminophore are as follows: Alq3 (15%-20%), Ir(ppy)3 (74%-78%), and 4CzIPN (83%-87%).
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-Nitroaromatic explosives, such as 2,4,6-trinitrotoluene (TNT) and its precursor 2,4-dini-trotoluene (DNT), are frequently found in munitions industries for military applications, landmines, and other explosive remnants of war. Consequently, detecting these compounds is essential to protect people from unwanted explosive hazards and to preserve ecosystems.
-Photoluminescence sensing is an attractive approach to detect trace concentrations of chemicals due its high sensitivity.
-Given the human cost linked to unexploded ordinances, much effort has been devoted to the development of sensors for the detection of explosives and related nitroaromatic compounds, including optical sensors.
-Organic luminophores are particularly attractive for photoluminescence sensing as many examples possess high photoluminescence quantum yield (FPL), are easy to synthesize, and their excited state and orbital energies can be readily tuned as a function of their structure.
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[{"label":"RBK Item","value":"Nitroaromatic explosives, such as 2,4,6-trinitrotoluene (TNT) and its precursor 2,4-dini-trotoluene (DNT), are frequently found in munitions industries for military applications, landmines, and other explosive remnants of war. Consequently, detecting these compounds is essential to protect people from unwanted explosive hazards and to preserve ecosystems."},{"label":"Title","value":"Distribution and Fate of Military Explosives and Propellants in Soil: A Review"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/10.1155/2012/617236"},{"label":"Date","value":"May 30, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Photoluminescence sensing is an attractive approach to detect trace concentrations of chemicals due its high sensitivity."},{"label":"Title","value":"Review—Recent Progress in Portable Fluorescence Sensors"},{"label":"URL","value":"https://iopscience.iop.org/article/10.1149/1945-7111/abd494"},{"label":"Date","value":"Jan 7, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Given the human cost linked to unexploded ordinances, much effort has been devoted to the development of sensors for the detection of explosives and related nitroaromatic compounds, including optical sensors."},{"label":"Title","value":"Aggregation induced emission based fluorenes as dual-channel fluorescent probes for rapid detection of cyanide: applications of smartphones and logic gates"},{"label":"URL","value":"https://www.sciencedirect.com/org/science/article/pii/S2046206922016680"},{"label":"Date","value":"Jun 22, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Organic luminophores are particularly attractive for photoluminescence sensing as many examples possess high photoluminescence quantum yield (FPL), are easy to synthesize, and their excited state and orbital energies can be readily tuned as a function of their structure."},{"label":"Title","value":"Principles of Fluorescence Spectroscopy"},{"label":"URL","value":"https://link.springer.com/book/10.1007/978-0-387-46312-4"},{"label":"Date","value":"Jan, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
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Chemistry
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Organic Chemistry, Electrochemistry
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MCQ
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Experimental mechanistic studies on alternating polarity electrolysis for carbon-centered radical generation
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https://chemrxiv.org/engage/chemrxiv/article-details/68d702973e708a76496df5dd
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June 5, 2025
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Researchers conducted a research on aryl radical C-P bond synthesis in a setup of two-electrode using an IKA ElectraSyn 2.0. The reaction was performed using 0.1mmol potassium 4-methoxyphenyl trifluoroborate and 0.1mmol triethyl phosphite solution ($P(OEt)_{3}$) in 4 mL of acetone with no additional salt as electrolyte. Both electrodes were made of platinum with approximately 1 cm of each electrode submerged in the above solution. Before the reaction, the solution was purged for 10 minutes with $N_{2}$ gas and maintained under an Nitrogen $N_{2}$ atmosphere. A total charge of 4 F/mol was passed through an alternating polarity square wave given. Three different conditions compared: Condition A with 20 mA current, 0.1 Hz frequency, condition B with 10 mA current, 0.5 Hz frequency, and condition C with 3 mA current, 10 Hz of frequency.
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-Crude ${}^1\text{H NMR}$ spectroscopy and ppm shift in acetone-$d_{6}$ of ($P(OEt)_{3}$) produced by electrolysis at 20 mA-0.1 Hz (A), 10 mA-0.5 Hz (B), and 3 mA-10 Hz (C).
-Integration of product peaks relative to a terephthalonitrile standard to determine product yield (%) of the resulting ($P(OEt)_{3}$) between A, B, and C.
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Researchers conducted an experiment of aryl radical C-P bond synthesis using electrolyzing potassium 4-methoxyphenyl trifluoroborate along with triethyl phosphite with platinum electrodes under an $N_{2}$ atmosphere. A total charge of 4 F/mol was passed through the cell. Three different sets of alternating polarity conditions were considered:
Condition A (20 mA, 0.1 Hz)
Condition B (10 mA, 0.5 Hz)
Condition C (3 mA, 10 Hz)
The yield of product was quantified by crude ${}^1\text{H NMR}$. Which of the following outcomes is most likely?
A. Greatest yield was achieved with Condition A (20 mA, 0.1 Hz) due to enhanced current driving reaction, but with product oxidation and side reactions due to increased applied potential.
B. Condition C (3 mA, 10 Hz) showed the greatest effectiveness, as high-frequency pulses are known to improve mass transport and reduce electrode fouling.
C. Condition B (10 mA, 0.5 Hz) produced the highest yield due to balancing of current and surface regeneration, but not full product conversion due to limited reaction driving potential.
D. All the conditions had very similar product yields.
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A. Greatest yield was achieved with Condition A (20 mA, 0.1 Hz) due to enhanced current driving reaction, but with product oxidation and side reactions due to increased potential.
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- Alternating Polarity Electrolysis is an electrochemical technique in which the polarity of the working and counter electrodes is periodically switched, used in the electrosynthesis to mitigate the electrode passivation by the incorporation of a cleaning cycle into the waveform.
- Carbon-centered radicals are unstable resulting in side reactions and reactive intermediates that result in fouling of the electrode and loss of product yield/selectivity.
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[{"label":"RBK Item","value":"- Alternating Polarity Electrolysis is an electrochemical technique in which the polarity of the working and counter electrodes is periodically switched, used in the electrosynthesis to mitigate the electrode passivation by the incorporation of a cleaning cycle into the waveform."},{"label":"Title","value":"Comprehensive Comparisons between Directing and Alternating Current Electrolysis in Organic Synthesis"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202309620"},{"label":"Date","value":"August 22, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"- Carbon-centered radicals are unstable resulting in side reactions and reactive intermediates that result in fouling of the electrode and loss of product yield/selectivity."},{"label":"Title","value":"Synthesis and Suzuki–Miyaura Cross-Coupling of Alkyl Amine-Boranes. A Boryl Radical-Enabled Strategy"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/jacs.4c07767"},{"label":"Date","value":"August 13, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Physical Chemistry, Food Chemistry
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MCQ
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Physicochemical Properties of Runner Bean and Their Starch, With a Comparison to Corn Starch
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https://ift.onlinelibrary.wiley.com/doi/full/10.1111/1750-3841.70440
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Jul 24, 2025
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The amylose content of the runner bean starches was determined using 20 mg of the starch sample was dispersed in 10 mL of 0.5 N KOH. The suspension was homogenized for 5 min. It was then transferred to a 100-mL volumetric flask and diluted to the calibration mark with distilled water. A 10-mL aliquot of the starch solution was transferred into a 50-mL volumetric flask, to which 5 mL of 0.1 N HCl and 0.5 mL of iodine reagent were then added. The volume was made up to 50 mL with distilled water, and the absorbance was read and recorded at 625 nm using a spectrophotometer (Jenway, 7305 Bibby Scientific, UK). A stock solution of pure amylose was prepared and subsequently diluted to generate working standards with absorbance values within the optimal range for spectrophotometric analysis. The standard curve was constructed using final amylose concentrations of ∼0.004, 0.008, 0.012, 0.016, and 0.020 mg mL−1.
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-Absorbances of the samples (Scarlet Emperor, White Swan, and Corn starch) in nm.
-Calculation of % of amylose using a standard curve using final amylose concentrations of ∼0.004, 0.008, 0.012, 0.016, and 0.020 mg mL−1.
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The amylose content of two runner bean starches (Scarlet Emperor and White Swan) was determined and compared to Corn starch using a spectrophotometry method. Considering that the % of amylopectin content is calculated by difference with amylose, which outcomes would you expect? Mark all the correct options:
A) Scarlet Emperor has more amylose content (in %) than White Swan and Corn starch.
B)The % of amylopectin of White swan is lower than Scarlet Emperor but higher than Corn starch.
C)The amylose content of corn starch is higher than White Swan.
D)Scarlet Emperor has more amylopectin than Corn starch.
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A) Scarlet Emperor has more amylose content (in %) than White Swan and Corn starch.
C)The amylose content of corn starch is higher than White Swan.
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-Runner bean is an underutilized legume that is a rich in protein, similar to those found in other pulses such as Bambara groundnut (15%–27%) and cowpea (16%–31%)
-The protein and starch in runner beans represent valuable ingredients with potential applications in the industry. For example, the protein isolates from pulses have reportedly showed potentials as functional foods and nutraceuticals that could be used to manage high blood pressure and combat oxidative stress.
-Despite the nutritional and potential applications of runner bean, the beans remain underutilized and poorly studied in several parts of the world.
-With the growing demand for food ingredients with novel functionality, exploring runner bean as a potential source of protein and starch requires a knowledge of their physicochemical and functional properties.
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[{"label":"RBK Item","value":"Runner bean is an underutilized legume that is a rich in protein, similar to those found in other pulses such as Bambara groundnut (15%–27%) and cowpea (16%–31%)"},{"label":"Title","value":"Enrichment of food blends with bambara groundnut flour: Past, present, and future trends"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1002/leg3.25"},{"label":"Date","value":"Jan 13, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"The protein and starch in runner beans represent valuable ingredients with potential applications in the industry. For example, the protein isolates from pulses have reportedly showed potentials as functional foods and nutraceuticals that could be used to manage high blood pressure and combat oxidative stress."},{"label":"Title","value":"Antihypertensive peptides from food proteins"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25884281/"},{"label":"Date","value":"Apr, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"Despite the nutritional and potential applications of runner bean, the beans remain underutilized and poorly studied in several parts of the world."},{"label":"Title","value":"Physicochemical and Nutritional Evaluation of Bread Incorporated with Ayocote Bean (Phaseolus coccineus) and Black Bean (Phaseolus vulgaris)"},{"label":"URL","value":"https://www.mdpi.com/2227-9717/9/10/1782"},{"label":"Date","value":"Oct 6, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"With the growing demand for food ingredients with novel functionality, exploring runner bean as a potential source of protein and starch requires a knowledge of their physicochemical and functional properties."},{"label":"Title","value":"Physicochemical properties of Bambara groundnut (Vigna subterranea) starch annealed at different temperatures"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1111/jfpp.17183"},{"label":"Date","value":"Sep 24, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Chemistry
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Material Chemistry
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Free-Format Question
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Single-Crystal Synchrotron X-ray diffraction Study Reveals Bulk Intermediate M2 phase during the VO2 Insulator-to-Metal transition
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https://chemrxiv.org/engage/chemrxiv/article-details/68c7e4b89008f1a467a158b5
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September 19, 2025
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VO₂ single crystals were prepared by synthesizing VO₂ powder from V₂O₃ and NH₄VO₃ (750 °C, 3 h, Ar), then annealing at 1200 °C for 12 h in Ar; a ~45 × 30 × 25 µm crystal that initially showed no twinning was selected.
Single-crystal synchrotron X-ray diffraction (SCXRD) was performed at SPring-8 BL02B1 (λ = 0.2463 Å) using a Pilatus3 1M CdTe detector and a nitrogen cryostream. At each temperature setpoint (300, 325, 335, 340, 345, 350, 355 K; then cooling 350, 345, 340, 335, 325 K), three 0–180° ω-scans were acquired at χ = 0°, 25°, 45°, with 0.2°/frame, 2700 frames per setpoint, 0.5 s/frame exposure, and a 600 µm Ni attenuator.
Data were converted/integrated (Bruker SAINT) with absorption/scaling corrections (SADABS/TWINABS); structures were solved with SHELXT and refined with SHELXL (independent atom model) in OLEX2. At each temperature, refinement included atomic positions and anisotropic ADPs with appropriate weighting schemes and extinction corrections; V occupancies were checked (~1) and fixed; anharmonic TDPs were evaluated (not retained); when present, a twin law was applied and twin-fraction refinements were performed.
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- For the cooling setpoints 355, 350, 345, 340, and 335 K, single-crystal X-ray diffraction (SCXRD) datasets were acquired. Acquisition parameters per setpoint: three 0–180° ω-scans at χ = 0°, 25°, 45°; 0.2°/frame; 2700 frames; 0.5 s/frame exposure; 600 µm Ni attenuator.
- From each dataset, unit-cell parameters (a, b, c, β, volume) were refined and recorded.
- Integration and refinement statistics (e.g., data completeness, R factors) were recorded for each temperature.
- Interatomic distances and angles were measured, including V–O and V–V distances and V–V–V bond angles for the vanadium coordination environments.
- Octahedral distortion parameters (Σ and Θ, via OctaDist) for V-centered octahedra were computed from the refined coordinates.
- Anisotropic atomic displacement parameters (ADPs) for vanadium (U11, U22, U33, Ueq, and principal-axis orientations) were determined at each temperature.
- Where applicable, twin-fraction refinements were performed and the refined twin domain fractions were recorded.
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A pure, untwinned VO2 crystal is heated to 355 K and then cooled to 335 K in 5 K intervals while its structure is monitored using X-ray diffraction. In this cooling sequence, what phases, including the intermediate phases, would be observed at each temperature?
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355 K: R (P4₂/mnm). 350 K: R (P4₂/mnm). 345 K (cooling): Mostly R, with M2 (C2/m) appearing transiently in frames 1–36, 708, and 709 (intermediate phase). 340 K: M2 (C2/m). 335 K: M1 (P2₁/c).
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- VO₂ IMT & phases: VO₂ exhibits a reversible insulator-to-metal transition near ~340 K (~67 °C) between M1 (monoclinic, P2₁/c) and R (tetragonal rutile, P4₂/mnm).
- An intermediate monoclinic M2 (C2/m) phase can emerge in bulk VO₂ during the transition (thermal-path dependent), so phase identification may involve R ↔ M2 ↔ M1.
- Single-crystal synchrotron X-ray diffraction distinguishes these phases via their symmetry/Bragg patterns and enables per-temperature phase assignment and unit-cell refinement.
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[{"label":"RBK Item","value":"VO₂ IMT & phases: VO₂ exhibits a reversible insulator-to-metal transition near ~340 K (~67 °C) between M1 (monoclinic, P2₁/c) and R (tetragonal rutile, P4₂/mnm). "},{"label":"Title","value":"Control of the metal–insulator transition in vanadium dioxide by modifying orbital occupancy"},{"label":"URL","value":"https://www.nature.com/articles/nphys2733"},{"label":"Date","value":"Sep 22, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Chemistry
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Analytical Chemistry
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Free-Format Question
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Refining Nature's Defense: Production and Evaluation of Mosquito Repellents from Ocimum tenuiflorum L. (Krishna and Rama Subtypes) and Ocimum gratissimum L. Essential Oils
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https://chemrxiv.org/engage/chemrxiv/article-details/68b28477a94eede1548681bb
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Sep 12, 2025
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The effectiveness of the mosquito repellent sprays (each one formulated with one active component: O. tenuiflorum L.subtype Krishna, O. tenuiflorum L.subtype Rama, and O. gratissimum L.) was evaluated using the following method. Equal numbers of adult male and female volunteers between the ages of 18 and 55 were selected for the testing. All of them were in good physical health so that the possible variation could be minimized. They avoided alcohol and fragrance products for at least twelve hours before, and during, the test.
Laboratory-reared, 3-10 days old, 200 blood-starved adult female Ae. albopictus (Skuse) mosquitoes were placed in 45 cm3 laboratory cages 1 hr before the test. Prior to the test, the forearm and hand of the human volunteers were cleansed with unscented soap, rinsing thoroughly, and allowing them to dry for 10 min before the repellent solution was applied. A 5 cm2 area on each forearm (between the wrist and elbow) of those volunteers was marked with a permanent marker. Approximately 0.1 mL of the repellent spray was uniformly applied to the marked area on one forearm, while the other forearm was treated with ethanol as a control. Both forearms were covered with sleeves during the test, leaving the marked areas exposed. Then both arms were simultaneously placed in the cage. An attempted bite by a mosquito was considered a confirmed bite. For each volunteer, only one repellent was tested per day. After 30 min of the repellent application, the participant’s forearm was exposed to the mosquitoes in the test cage for 3 min.
This procedure was repeated for a 3 hr period at 30 min intervals. The time between repellent application and the first confirmed bite was recorded as the complete protection time (CPT). If the mosquitoes did not attempt to bite the control arm during the 3 hr period, the trial was terminated without recording data. It was repeated with a new batch of
mosquitoes to ensure that the absence of bites was due to repellency and not because the mosquitoes were not actively seeking a blood meal at the time. DEET was used as the positive control and applied to one arm, instead of the repellent spray and the above procedure was followed. Each experiment was conducted three times in separate cages, with different male and female volunteers to eliminate any effects of skin differences on repellency. The percentage protection (%p) was calculated as the reduction in landings by the treatment when compared to the negative control over all exposures.
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-Percentage protection (%p), calculated as the reduction in landings by the treatment when compared to the negative control over all exposures using equation %p = ((C−T)/C)X100, where T is the average number of mosquito bites on the surface per minute on the test arm and C is the average number of mosquito bites per minute on the control arm.
--%p was calculated every 30 min until 180 min.
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The effectiveness of the mosquito repellent sprays (each one formulated with one active component: O. tenuiflorum L.subtype Krishna, O. tenuiflorum L.subtype Rama, and O. gratissimum L.) was evaluated through the calulation of percentage protection (%p) every 30 min. What values of %p would you expect each different repellent spray after 150 min to have? What about the positive control after the same time?
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After 150 min, the O. tenuiflorum L. subtype Krishna repellent spray had a %p of 87.9±14.3, the O. tenuiflorum L.subtype Rama spray had a %p of 88.6±4.5, and the O. gratissimum L one had a %p of 88.6±4.1. The positive control (DEET) showed a %p of 90.7±6.9.
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-Mosquito-borne diseases, such as malaria, dengue fever, chikungunya, and Zika, pose major global health threats and are responsible for more than 700,000 deaths annually .
-With climate change favorable for the pathogens and their resistance evolving, there is an urgent need for sustainable vector control strategies worldwide.
-The overuse of chemical insecticides has been proven to lead to insecticide resistance in mosquitoes, harm to non-target species, and environmental pollution. This underscores the importance of exploring natural product-based mosquito repellents as safer alternatives that are environmentally appropriate and ecologically sustainable.
-Basil (Ocimum spp.) is an aromatic plant native to Sri Lanka that is commonly used as a traditional mosquito repellent.
|
[{"label":"RBK Item","value":"Mosquito-borne diseases, such as malaria, dengue fever, chikungunya, and Zika, pose major global health threats and are responsible for more than 700,000 deaths annually."},{"label":"Title","value":"Vector-borne diseases"},{"label":"URL","value":"https://www.who.int/news-room/fact-sheets/detail/vector-borne-diseases"},{"label":"Date","value":"Sep 26, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"With climate change favorable for the pathogens and their resistance evolving, there is an urgent need for sustainable vector control strategies worldwide."},{"label":"Title","value":"A critical assessment of mosquito control and the influence of climate change on mosquito-borne disease epidemics"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s10668-021-01792-4"},{"label":"Date","value":"Sep 1, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"The overuse of chemical insecticides has been proven to lead to insecticide resistance in mosquitoes, harm to non-target species, and environmental pollution This underscores the importance of exploring natural product-based mosquito repellents as safer alternatives that are environmentally appropriate and ecologically sustainable."},{"label":"Title","value":"Plant-Based Bioinsecticides for Mosquito Control: Impact on Insecticide Resistance and Disease Transmission"},{"label":"URL","value":"https://www.mdpi.com/2075-4450/13/2/162"},{"label":"Date","value":"Feb 3, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Basil (Ocimum spp.) is an aromatic plant native to Sri Lanka that is commonly used as a traditional mosquito repellent."},{"label":"Title","value":"Exploration, Conservation, and Utilization of Ethnobotanical Knowledge: Sri Lankan Perspective"},{"label":"URL","value":"https://link.springer.com/chapter/10.1007/978-3-030-55494-1_19"},{"label":"Date","value":"Mar 27, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
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Chemistry
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Electrochemistry.
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Numerical Values
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Time-resolved photo-electrochemical measurements to study band bending of BiVO4 photoanodes.
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https://chemrxiv.org/engage/chemrxiv/article-details/68b1a2e2728bf9025e19a17e?
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Sep 05, 2025.
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Thin-film BiVO₄ photoanodes were investigated in a three-electrode photo-electrochemical RRDE cell under chopped AM 1.5G illumination. Light switch-ON/OFF transients were recorded over 0–2.5 V vs RHE, and the disk photocurrent during switch-ON was fit with exponentials to isolate the fast space-charge reorganization time constant (τ\_fast) (along with slower components).
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- Disk photocurrent transients** at light switch-ON/OFF (current vs time) across 0–2.5 V vs RHE.
- Exponential fits of transients to extract characteristic time constants (including τ\_fast) in seconds; report the average τ\_fast (switch-ON) over the potential window.
- Steady-state J–E curves** under illumination.
- RRDE ring current** (Pt ring) vs time/potential for O₂ detection/validation.
- Assignment of τ\_fast to space-charge reorganization based on transient behavior.
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Thin-film BiVO₄ photoanodes were tested in a three-electrode photo-electrochemical RRDE cell under chopped AM 1.5G illumination. During light “switch-ON” steps over 0–2.5 V vs RHE, the disk photocurrent transients were fit with exponentials to isolate the fast space-charge reorganization process (τ\_fast).
At these conditions, what is the average value of τ\_fast in seconds (s) for the switch-ON process?
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0.0022±0.002 s.
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- BiVO₄ is a semiconductor photoanode used for oxygen evolution under illumination; its behavior is probed in a three-electrode photoelectrochemical cell.
- Band bending at the semiconductor/electrolyte interface creates a space-charge region that governs carrier separation and the early transient response.
- Time-resolved photoelectrochemistry with chopped AM 1.5G illumination measures photocurrent transients at light on/off to extract characteristic time constants.
- A rotating ring–disk electrode (RRDE) uses a Pt ring to detect dissolved O₂ produced at the disk, distinguishing disk photocurrent from ring current.
- The flat-band potential is the potential where band bending vanishes and is estimated from cyclic-voltammetry features; potentials are reported vs RHE.
- Exponential fitting of transients yields τ\_fast and slower components that reflect interfacial charge reorganization and reaction kinetics.
|
[{"label":"RBK Item","value":"- BiVO₄ is a semiconductor photoanode used for oxygen evolution under illumination; its behavior is probed in a three-electrode photoelectrochemical cell."},{"label":"Title","value":"A Novel Aqueous Process for Preparation of Crystal Form-Controlled and Highly Crystalline BiVO4 Powder from Layered Vanadates at Room Temperature and Its Photocatalytic and Photophysical Properties"},{"label":"URL","value":"https://pubs.acs.org/doi/abs/10.1021/ja992541y"},{"label":"Date","value":"Nov 24, 1999"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"- Band bending at the semiconductor/electrolyte interface creates a space-charge region that governs carrier separation and the early transient response."},{"label":"Title","value":"Energy-Band Alignment of BiVO4 from Photoelectron Spectroscopy of Solid-State Interfaces"},{"label":"URL","value":"https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.8b06241"},{"label":"Date","value":"Agus 21, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"- A rotating ring–disk electrode (RRDE) uses a Pt ring to detect dissolved O₂ produced at the disk, distinguishing disk photocurrent from ring current."},{"label":"Title","value":"Rotating Ring–Disk Electrode Study of Oxygen Evolution at a Perovskite Surface: Correlating Activity to Manganese Concentration"},{"label":"URL","value":"https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.6b07654"},{"label":"Date","value":"Nov 15, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"The flat-band potential is the potential where band bending vanishes and is estimated from cyclic-voltammetry features; potentials are reported vs RHE."},{"label":"Title","value":"Flat band potential determination: avoiding the pitfalls"},{"label":"URL","value":"https://pubs.rsc.org/en/content/articlehtml/2019/ta/c9ta09569a"},{"label":"Date","value":"Nov 8, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Materials Science / Materials Chemsitry
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Free-Format Question
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Distributed direct air capture by carbon nanofiber air filters
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https://chemrxiv.org/engage/chemrxiv/article-details/68c21cac9008f1a467b779dd
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September 01, 2025
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Researchers investigated the CO2 capture properties of carbon nanofiber (CNF) nonwoven prepared by electrospinning of 8wt% polyacrylonitrile (PAN) in DMF at 8kV and 1mL/hr flow rate. This was followed followed by calcination at 250C in air for 5hr and pyrolysis under argon between 600C-900C for 2hr to obtain conductive CNFs. CNFs were then impregnated with branched polyethylenimine (PEI) at mass loadings between 1-20wt% in methanol for 5s and dried ambiently to form a PEI–CNF direct-air-capture (DAC) filter with PEI mass loadings between 16-78 wt%.
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-In situ Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectra during heating from 27 °C to 105 °C.
-CO2 breakthrough analysis under dry and humid conditions with 400 ppm CO2/N2 mixture, measuring downstream CO2 concentration.
-Adsorption capacity retention and PEI weight loss over temperature-swing cycles using in situ thermogravimetric analysis (TGA).
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Researchers prepared PEI–CNF direct-air-capture (DAC) filters with pyrolyzed between 600-900C and PEI mass loadings between 16-78% for CO2 capture experiments. Fibers with varying PEI loading were subject to breakthrough experiments under dry and humid conditions with 400 ppm CO2/N2 mixture, measuring downstream CO2 concentration. FTIR-ATR spectra during heating from 27 °C to 105 °C were collected to monitor CO2 desorption. Adsorption capacity retention and PEI weight loss over temperature-swing cycles using in situ TGA were investigated for a representative PEI-CNF DAC filter. What does the FTIR peak that forms at 3347cm-1 at 105C indicate about CO2 binding, and how is this reflected in the breakthrough and in-situ TGA experiments?
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The FTIR peak at 3347cm-1 is from amine stretching from free surface sites after CO2 desorption. As the CO2 adsorption is based on amine binding, breakthrough times (and consequently capacity) increase with PEI content and humidity. For the same reason, in-situ TGA confirms recoverable cyclic capacity fades with PEI mass.
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- Reversible amine - CO₂ binding governs capture and regeneration. CO₂ binds to PEI amine sites on the CNF filter during adsorption, and heating releases (desorbs) CO₂ to restore capacity.
- At low temperatures, captured CO₂ remains bound. Without heating, there is no desorption; the adsorbed CO₂ stays on the amine sites until the filter is warmed to the regeneration temperature.
- CO2 adsorption is enhanced in the presence of humidity as nucleophiles like water promote chemisorption.
|
[{"label":"RBK Item","value":"Reversible amine - CO₂ binding governs capture and regeneration. CO₂ binds to PEI amine sites on the CNF filter during adsorption, and heating releases (desorbs) CO₂ to restore capacity."},{"label":"Title","value":"Polyethylenimine Applications in Carbon Dioxide Capture and Separation: From Theoretical Study to Experimental Work"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1002/ente.201600694"},{"label":"Date","value":"Feb 22, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"CO2 adsorption is enhanced in the presence of humidity as nucleophiles like water promote chemisorption"},{"label":"Title","value":"A Unified Approach to CO2–Amine Reaction Mechanisms"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/acsomega.0c03727"},{"label":"Date","value":"October 1, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Catalysts / Materials Science
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Numerical Values
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Enhanced Amitriptyline Degradation by Electrochemical Activation of Peroxydisulfate: Mechanisms of Interfacial Catalysis and Mass Transfer
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https://doi.org/10.3390/molecules30183835
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September 22, 2025
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Carbon-encapsulated zinc oxide nanocomposites (C@ZnO) were synthesized using a hydrothermal–calcination method. Specifically, 0.5, 1.0, 2.0, and 4.0 g of ZnO were mixed with equal amounts of polyvinylpyrrolidone (PVP) in 300 mL of ultrapure water. Then, 19.8 g of glucose was added to the above suspension. After 24 h of stirring, the suspension was hydrothermally treated at 180 °C for 4 h, washed with ethanol, and dried at 60 °C. The resulting powder was calcined under N2 at 600 °C (10 °C/min ramp, 4 h hold), yielding dark grey solid powder. This powder was ground and sieved through a 60-mesh nylon sieve to ensure uniform particle size. Through this process, amorphous carbon-encapsulated ZnO composites were obtained, with ZnO masses of 50 mg, 100 mg, 200 mg, and 400 mg incorporated during synthesis. These were designated as 50 C@ZnO, 100 C@ZnO, 200 C@ZnO, and 400 C@ZnO, respectively. The surface morphology of the material samples were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) and BET/BJH analysis of N2 adsorption–desorption isotherms were performed to determine surface area and pore volume.
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- Surface morphology: scanning electron microscopy (SEM) and transmission electron microscopy (TEM) of 50 C@ZnO, 100 C@ZnO, 200 C@ZnO, and 400 C@ZnO.
- Surface area and pore volume: BET/BJH analysis of N2 adsorption–desorption isotherms of 50 C@ZnO, 100 C@ZnO, 200 C@ZnO, 400 C@ZnO, and pristine ZnO.
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Researchers aimed to fabricate amorphous carbon-encapsulated zinc oxide modified anodes as catalysts for amitriptyline degradation. Carbon-encapsulated zinc oxide nanocomposites (C@ZnO) were synthesized using a hydrothermal–calcination method. Through this process, amorphous carbon-encapsulated ZnO composites were obtained, with ZnO masses of 50 mg, 100 mg, 200 mg, and 400 mg incorporated during synthesis. These were designated as 50 C@ZnO, 100 C@ZnO, 200 C@ZnO, and 400 C@ZnO, respectively. The surface morphology of the material samples were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) and BET/BJH analysis of N2 adsorption–desorption isotherms were performed to determine surface area and pore volume. What is the predicted difference in BET surface area (m^2/g) between 50 C@ZnO and 400 C@ZnO groups?
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Δ BET surface area [50 C@ZnO - 400 C@ZnO] (m^2/g): 247 - 302; derived from 443.44 (50 C@ZnO) - 169.20 (400 C@ZnO). Note: no CI reported → fallback ±10 % applied
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• Antibiotics and compounds such as amitriptyline (AMT) are detected in wastewater and natural waters, reaching high concentrations and causing negative ecological impacts.
• Various methods are being investigated to remove AMT and other PPCPs, with particular emphasis on the use of carbon materials and metal oxides
• Although these techniques demonstrate high efficiency, the toxicity of the byproducts generated is still unknown, and efforts are being made to improve the efficiency and sustainability of the processes, especially under natural water conditions.
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[{"label":"RBK Item","value":"Antibiotics and compounds such as amitriptyline (AMT) are detected in wastewater and natural waters, reaching high concentrations and causing negative ecological impacts."},{"label":"Title","value":"Antibiotics and antibiotic resistance genes in landfills: A review."},{"label":"URL","value":"https://www.researchgate.net/publication/354913786_Antibiotics_and_antibiotic_resistance_genes_in_landfills_A_review"},{"label":"Date","value":"September 28, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Various methods are being investigated to remove AMT and other pharmaceuticals and personal care products (PPCPs), with particular emphasis on the use of carbon materials and metal oxides. \n"},{"label":"Title","value":"UV-driven removal of tricyclic antidepressive drug amitriptyline using TiO2 and TiO2/WO3 coatings"},{"label":"URL","value":"https://www.researchgate.net/publication/349023269_UV-driven_removal_of_tricyclic_antidepressive_drug_amitriptyline_using_TiO2_and_TiO2WO3_coatings"},{"label":"Date","value":"January 20, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Physics
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Applied Physics
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MCQ
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Reducing Temperature Swing and Rectifying Radiative Heat Transfer for Passive Dynamic Space Thermal Control with Variable-Emittance Coatings
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https://arxiv.org/abs/2509.13794
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September 17, 2025
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An experiment was conducted to measure the thermal rectification of a dynamic, thermochromic $\text{VO}_{2}$ coating in a high-vacuum ($<1\times 10^{-3} \,\text{Pa}$) cryostat. The coating, consisting of a 55-nm $\text{VO}_{2}$, 500-nm silicon, and 200-nm aluminum thin film stack, was fabricated on a 1-inch-squared silicon wafer. This sample was attached to a polyimide thin-film heater and mounted on a 5 mm thick acrylic carrier plate with a thermistor for temperature measurement. The experiment operated in two distinct modes with the sample spaced $\sim 2 \,\text{mm}$ from a temperature-controlled surface. One is Forward-biased, in which the $\text{VO}_{2}$ sample was heated to various steady-state temperatures, and its radiative heat flux ($q_{\text{fwd}}$) to the surface held at a constant $25^{\circ}\text{C}$ was measured. Second is Reverse-biased, in which the $\text{VO}_{2}$ sample was maintained at a constant $25^{\circ}\text{C}$, while the surface was heated to various temperatures ($20^\circ\text{C}$ to $100^\circ\text{C}$) to create a hot environment radiating towards the sample, and the radiative heat flux ($q_{\text{rev}}$) was measured. The radiative thermal tests were conducted under high vacuum ($< 1 \times 10^{-3}$ Pa) inside a cryostat (Janis VPF-800) equipped with a cold finger and a custom-made sample mount. A test sample along with a heat flux sensor (FluxTeq, PHFS-01) of $ \pm 5 \% $ accuracy and a polyimide thin-film heater (OMEGA Engineering, KHLVA-101/10-P) was first attached to the $ 5 \text{mm} $-thick acrylic carrier plate, all in $ 1 \text{-inch-squared} $ size. A thermistor (Mouser Electronics, SC30F103VN) with an accuracy of $ \pm 0.1^{\circ} \text{C} $ was buried in the thermal paste between the sample and the heat flux sensor for measuring the sample temperature. After the acrylic carrier plate was pinned onto the brackets with about $ 2 \text{-mm} $ spacing between the sample and the coldfinger, the cryostat was then brought down to high vacuum followed by liquid nitrogen (LN2) filling to cool down the coldfinger to $ 80 \, \text{K} $, which mimics the cold space thermal environment.
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- Measuring radiative heat flux (in KW/m2) against temperature from 25 °C to 100 °C, forward-biased scenarios in both heating and cooling cycles.
- Measuring radiative heat flux (in KW/m2) against temperature from 25 °C to 100 °C, reversed-biased scenarios in both heating and cooling cycles.
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An experiment was conducted to measure the thermal rectification of a dynamic, thermochromic $\text{VO}_{2}$ coating in a high-vacuum cryostat. The coating consists of a silicon and aluminum thin film stack. This sample was attached to a polyimide thin-film heater and mounted on a 5 mm thick acrylic carrier plate with a thermistor for temperature measurement. The experiment operated in two distinct modes. One is Forward-biased, in which the $\text{VO}_{2}$ sample was heated to various steady-state temperatures ($20^\circ\text{C}$ to $100^\circ\text{C}$), and its radiative heat flux ($q_{\text{fwd}}$) to the surface held at a constant $25^{\circ}\text{C}$ was measured. Second is Reverse-biased, in which the $\text{VO}_{2}$ sample was maintained at a constant $25^{\circ}\text{C}$, while the surface was heated to various temperatures to create a hot environment radiating towards the sample, and the radiative heat flux ($q_{\text{rev}}$) was measured. Consider the two scenarios when the temperature difference ($\Delta T$) between the $\text{VO}_{2}$ sample and the external object is identical ($\Delta T = 55^{\circ}\text{C}$). How does the measured forward heat flux ($q_{\text{fwd}}$) compare to the reverse heat flux ($q_{\text{rev}}$)?
a) The forward heat flux is approximately equal to the reverse heat flux at low temperature and significantly larger at higher temperatures, and radiative heat flux shows a nearly constant thermal conductance for the forward-biased scenario, and linearly dependent thermal conductance for the reversed-biased scenario.
b) Both forward heat flux and reverse heat flux don't depend upon temperature, have the same value at any given temperature measured in this experiment, and radiative heat flux shows a nearly constant thermal conductance for the reversed-biased scenario.
c) The forward heat flux is significantly larger than the reverse heat flux at low temperatures and approximately equal at higher temperatures, and radiative heat flux shows a nearly constant thermal conductance for the forward-biased scenario, and linearly dependent thermal conductance for the reversed-biased scenario.
d) The forward heat flux is approximately equal to the reverse heat flux at low temperature and significantly larger at higher temperatures, and the radiative heat flux shows a nearly constant thermal conductance for the reversed-biased scenario.
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d) The forward heat flux is approximately equal to the reverse heat flux at low temperature and significantly larger at higher temperatures, and the radiative heat flux shows a nearly constant thermal conductance for the reversed-biased scenario.
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- VO2 has a phase transition, which could occur within a narrow 20°C temperature range around 68°C.
- The total hemispherical emittance of the VO2FP emitter in the metallic phase is reduced by 10% from the total normal emittance, while it remains the same in the insulating phase without excitation of FP resonance.
- Radiative heat transfer from a body around 300 K to a heat sink at either 80 K or 3 K is almost the same, with only a 0.5% difference due to ~T4 dependence
|
[{"label":"RBK Item","value":"VO2 has a phase transition, which could occur within a narrow 20°C temperature range around 68°C."},{"label":"Title","value":"Highly transparent smart thermal emitter realized by thin vanadium dioxide"},{"label":"URL","value":"https://pubs.aip.org/aip/jap/article/137/8/085302/3337032/Highly-transparent-smart-thermal-emitter-realized"},{"label":"Date","value":"Feb 24, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Open-access, this is cited as reference 13 in the paper"}]
|
Physics
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Applied Physics
|
Free-Format Question
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Thermal Endurance of Suspended Thin-Film Lithium Niobate up to 800 °C
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https://arxiv.org/abs/2509.13568
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September 16, 2025
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An experiment was conducted to study the thermal endurance of suspended thin-film lithium niobate (LN) acoustic resonators. The devices were fabricated on a 600 nm thick stoichiometric X-cut LN film on 1 µm amorphous silicon (a-Si) on 500 µm high-resistivity silicon wafer, with interdigitated electrodes made of 40 nm of platinum (Pt) on a 5 nm titanium (Ti) adhesion layer. Release windows were etched through the LN and a-Si sacrificial layer by argon gas ion milling, and the Ti and Pt layers were deposited by electron beam evaporation. A second 40 nm Pt layer was applied to the probe pads in a second deposition round. The unwanted metal was removed with a liftoff process after each round, and the devices were released or suspended by a XeF2 etch.
A variety of common resonator designs were implemented by varying the anchor designs (one, two or no anchors), the in-plane rotation, and the number and width of the electrodes. A meandering line structure is designed alongside the resonators using the same metal stack and thickness. To test the devices, these were subjected to a series of annealing rounds starting from 250°C to 550°C in increments of 50°C. The ramp rate for heating and cooling was selected to avoid the pyroelectric effects of LN (100°C). The target temperature was maintained for 10 hours and after each round, the devices were cooled to room temperature for characterization.
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- Electrode metal resistivity obtained with DC probes on the meandering line resistivity structures initially and after each annealing round
- Physical changes to the device structure via optical microscopy, including the observation of anchor breakage at elevated temperatures
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Researchers studied the thermal endurance of suspended thin-film lithium niobate (LN) acoustic resonators. The devices were fabricated on a 600 nm thick stoichiometric X-cut LN film on a 1 µm amorphous silicon (a-Si) sacrificial layer on 500 µm high-resistivity silicon wafer, with interdigitated electrodes made of 40 nm of platinum (Pt) on a 5 nm titanium (Ti) adhesion layer. Meandering line structures were deposited alongside the resonators using the same metal stack and thickness to test electrode metal resistivity. The resonators were subjected to annealing rounds starting from 250°C to 550°C in 50°C increments. In each round, the target temperature was maintained for 10 hours, after which the samples were cooled to room temperature for characterization. Measurements of the electrode metal resistivity were conducted by applying a DC probe applied to the meandering line resistivity structure parallel to the resonators. This was done before the initial annealing and after each round. How did resistivity change, qualitative, from its initial value and after each subsequent round below 450°C?
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Resistivity decreased after the first anneal at 250°C, and increased with subsequent annealing rounds in that range.
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- Lithium niobate possesses a high Curie temperature of 1200 °C, which has potential for use in harsh thermal environments.
- The LN quality can degrade when heated because lithium atoms can diffuse out of the LN, and can form Li-poor LiNb$_3$O$_8$ phases in the LN film.
- The metal, LN, and support substrate all have different coefficients of thermal expansion (CTEs) and are expected to crack when heated to and cooled from high temperatures. However, suspended LN devices have demonstrated operability at 500 °C.
|
[{"label":"RBK Item","value":"The LN quality can degrade when heated because lithium atoms can diffuse out of the LN, and can form Li-poor LiNb$_3$O$_8$ phases in the LN film."},{"label":"Title","value":"Effect of the annealing treatment on the physical and structural properties of LiNbO3 thin films deposited by radio-frequency sputtering at room temperature"},{"label":"URL","value":"https://doi.org/10.1016/j.tsf.2021.138660"},{"label":"Date","value":"May 31, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [9] in the main article."},{"label":"RBK Item","value":"The metal, LN, and support substrate all have different coefficients of thermal expansion (CTEs) and are expected to crack when heated to and cooled from high temperatures. However, suspended LN devices have demonstrated operability at 500 °C."},{"label":"Title","value":"A Laterally Vibrating Lithium Niobate MEMS Resonator Array Operating at 500 °C in Air"},{"label":"URL","value":"https://doi.org/10.3390/s21010149"},{"label":"Date","value":"Dec 29, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA, cited as reference [30] in the main article."}]
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Physics
|
Physics/Atomic physics
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Free-Format Question
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Compact Continuous Cold Atomic Beam from a Single Cell with 3D Cooling and Ultra-low Light Shift
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https://arxiv.org/abs/2510.13126
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October 15, 2025
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Researchers investigated a compact single-cell source of a continuous cold-atom beam (⁸⁷Rb) that achieves simultaneous 3D cooling by integrating a two-dimensional magneto-optical trap (2D MOT) with an off-axis moving optical molasses (OM). A vapor-cell apparatus (overall length ≈170 mm) provided transverse MOT cooling with circularly polarized beams detuned by ΔMOT = −4Γ from the F = 2 → F′ = 3 D₂ transition and a cylindrical quadrupole field (≈10 G cm⁻¹), where Γ is the natural linewidth. Longitudinal cooling and velocity control were realized with two pairs of lin⊥lin OM beams oriented 20° to the extraction axis, detuned by ΔOM = −5Γ and symmetrically shifted by ±δOM to set the mean atomic speed (≈5–20 m s⁻¹) over an OM interaction length lOM ≈ 50 mm. Custom in-vacuum mirrors formed the off-axis geometry and incorporated a 0.8 mm output aperture to collimate the beam (cooling length lc ≈ 50 mm) while suppressing near-resonant stray light. The setup included permanent-magnet field generation, state-preparation “plug” lasers 40 mm downstream for sharp time-of-flight (TOF) edges, and fluorescence detection at 294 mm with a calibrated photomultiplier tube (PMT) to extract longitudinal temperature, velocity, and flux. For coherence diagnostics, two π/2 Raman beams separated by L = 100 mm in a magnetically shielded region produced spatial-domain Raman–Ramsey fringes, enabling quantification of decoherence and ultra-low light shift (typ. −0.51 Hz) under operating MOT power.
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- Time-of-flight (TOF) time series and distribution obtained from the emitted fluorescence from the atoms in F=2 state, collected with imaging optics and recorded by a calibrated PMT at a primary detection distance of 294 mm.
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Researchers investigated the longitudinal temperature and atomic flux of a continuous cold ⁸⁷Rb beam using a time-of-flight (TOF) method. The temperature was extracted from the FWHM of the TOF distribution, while the flux was obtained from the integrated spectral density. Based on measurements for a saturation intensity of 1.67 mW/cm2, what outcome would researchers expect for the change in longitudinal temperature and atomic flux when the MOT power is increased?
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Increasing MOT power raises the flux but affects the temperature only weakly.
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- Combining a 2D MOT with an off-axis moving OM yields a high-flux beam with significantly reduced longitudinal temperature compared to conventional MOT-based sources.
- Continuous operation of cold-atom beam sources eliminates the dead time inherent to pulsed sources and thus suppresses aliasing noise from undersampling.
|
[{"label":"RBK Item","value":"Continuous operation of cold-atom beam sources eliminates the dead time inherent to pulsed sources and thus suppresses aliasing noise from undersampling."},{"label":"Title","value":"Improvement of the frequency stability below the dick limit with a continuous atomic fountain clock"},{"label":"URL","value":"https://ieeexplore.ieee.org/document/6156823"},{"label":"Date","value":"Feb 27, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled, but cited in the main paper as reference [1]."}]
|
Physics
|
Condensed Matter Physics
|
Numerical Values
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Role of non-reciprocity in spin-wave channeling
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https://arxiv.org/pdf/2505.07401
|
May 12, 2025
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The study employed patterned synthetic antiferromagnetic (SAF) films composed of Co40Fe40B20 (17 nm)/Ru(0.7 nm)/Co40Fe40B20 (17 nm). The films were shaped into 5 μm-wide stripes acting as spin-wave conduits and insulated by a 150 nm Si3N4 layer. A 1.8 μm-wide, 160 nm-thick microwave antenna was fabricated on top to generate a radio-frequency magnetic field perpendicular to an externally applied static field Hx. Brillouin light scattering (BLS) microscopy was employed to image the dynamic magnetization with a spatial resolution of roughly 350 nm and 200 × 200 nm² pixel size. The antenna was driven by a monochromatic RF source (3–10 GHz), exciting mainly the acoustic branch of spin waves. Measurements were performed for several field strengths (27–100 mT). The experiments shall analyze the magnetization response when feeding the antenna with an RF source.
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- Frequency of the uniform acoustic mode measured from microfocused BLS spectra patterned synthetic antiferromagnetic (SAF) films.
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The study employed patterned synthetic antiferromagnetic (SAF) films composed of Co40Fe40B20 (17 nm)/Ru(0.7 nm)/Co40Fe40B20 (17 nm). Brillouin light scattering (BLS) microscopy was employed to image the dynamic magnetization. The antenna was driven by a monochromatic RF source (3–10 GHz), which primarily excited the acoustic branch of spin waves. Measurements were performed for several field strengths (27–100 mT). The experiments shall analyze the magnetization response when feeding the antenna with an RF source. Predict the frequency of uniform modes for the acoustic mode.
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The frequency of uniform modes for the acoustic mode at a field strength of 50 mT is 6.14 - 6.54 GHz. (No CI/SE/SD is mentioned, fallback ±0.2 GHz)
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- Recognizing that the experiment uses patterned synthetic antiferromagnetic (SAF) stripes (5 µm wide) with a microwave antenna (1.8 µm wide) to excite spin waves.
- Recognizing that the antenna’s coverage fraction affects excitation uniformity and hence influences the detected Brillouin Light Scattering (BLS) signal.
- In past studies of the SWs in confined geometries, it has often been possible to understand the nature of the modes by using the dispersion relation in the corresponding unbounded films and applying some quantification of the transverse wavevector according to specific boundary conditions. The BLS images could then be understood from overlap integrals of the antenna r.f. field and the profiles of the few allowed modes.
|
[{"label":"RBK Item","value":"Recognizing that the experiment uses patterned synthetic antiferromagnetic (SAF) stripes (5 µm wide) with a microwave antenna (1.8 µm wide) to excite spin waves."},{"label":"Title","value":"Exchange energies in CoFeB/Ru/CoFeB synthetic antiferromagnets."},{"label":"URL","value":"https://doi.org/10.1103/PhysRevMaterials.7.044404"},{"label":"Date","value":"April, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled, but this is cited as reference 9 in the paper"},{"label":"RBK Item","value":"Recognizing that the antenna’s coverage fraction affects excitation uniformity and hence influences the detected Brillouin Light Scattering (BLS) signal."},{"label":"Title","value":"Analytical expression of the magneto-optical Kerr effect and Brillouin light scattering intensity arising from dynamic magnetization"},{"label":"URL","value":"https://arxiv.org/abs/1006.1906"},{"label":"Date","value":"June, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Open-access, this is cited as reference 32 in the paper"},{"label":"RBK Item","value":"In past studies of the SWs in confined geometries, it has often been possible to understand the nature of the modes by using the dispersion relation in the corresponding unbounded films and applying some quantification of the transverse wavevector according to specific boundary conditions. The BLS images could then be understood from overlap integrals of the antenna r.f. field and the profiles of the few allowed modes."},{"label":"Title","value":"Magnonic Waveguides Studied by Microfocus Brillouin Light Scattering"},{"label":"URL","value":"https://ieeexplore.ieee.org/document/7001083"},{"label":"Date","value":"Jan 1, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled, but this is cited as reference 27 in the paper"}]
|
Physics
|
Physics
|
Free-Format Question
|
Improving the lifetime of aluminum-based superconducting qubits through atomic layer etching and deposition
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https://arxiv.org/pdf/2506.17474
|
June 20, 2025
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Researchers investigate the effect of a post-fabrication surface treatment combining atomic layer etching (ALE) and atomic layer deposition (ALD) on aluminum-based superconducting quantum devices. The device is comprised of λ/4 coplanar waveguide (CPW) resonators and planar trasmon qubits (24 µm-wide capacitor plates with 30 µm gaps and 200 nm-long Josephson junctions), both fabricated using 100 nm thick Al films on high-resistivity (> 20 kΩ · cm) silicon substrates (trace and gap widths of 30 μm). The ALE process was performed at 300 °C using 50 cycles of alternating exposures of HF-pyridine (4 ± 0.5 hPa) and trimethylaluminum (TMA, 1.7 ± 0.2 hPa), with a dose-purge sequence of 1–10–1–10 s, achieving an etch rate of 0.5 Å/cycle. This was followed in situ by 10 cycles of ALD using TMA and H₂O (2.3 ± 0.2 hPa), with a 0.2–10–0.2–10 s sequence, yielding a ~1 nm Al₂O₃ capping layer. The entire process was conducted in a Picosun/AMAT R-200 reactor under 11 hPa base pressure with 300 sccm N₂ carrier gas. The treatment was applied to fully fabricated devices, including both top and sidewall surfaces, without breaking vacuum. Each chip contained 12 resonators with frequencies from 5.2 to 6.2 GHz. Five chips (4 transmons each) were measured before and after treatment, along with six untreated control chips and one annealed-only chip. Measurements were performed in a dilution refrigerator (DR) at 10 mK using a vector network analyzer (VNA). Instruments used for measurements were X-ray photoelectron spectroscopy (XPS) (Al Kα X-ray source (1486.6 eV)) and photo-induced force infrared microscopy (PiFM).
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- PiFM spectra averaged across Si and Al regions for ALE+ALD-treated transmon qubit chips (a.u vs. cm^-1).
- PiFM spectra averaged across Si and Al regions for untreated transmon qubit chips (a.u vs. cm^-1).
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A dry surface treatment that combines atomic layer etching and deposition (ALE and ALD) for dielectric loss in fully fabricated quantum devices formed from aluminum thin films on silicon is applied to coplanar waveguide resonators and planar transmon quibits. When comparing the area-normalized PiFM spectra averaged across Si and Al regions measured on the untreated and ALE+ALD-treated transmon qubit chips, what is the observed change in behavior of the area-normalized photo-induced force (a.u) between the ALE+ALD treated resonator (Al trace) and the Untreated resonator (Al and Si) for a wavenumber range of 1000-800 cm^-1?
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The untreated resonator (Al and Si) exhibits a monotonic decay in area-normalized photo-induced force, while the ALE+ALD treated resonator (Al trace) exhibits higher values across the range, with a large peak around the 950 cm^-1 wavenumber and smaller peaks decreasing after that.
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- Atomic layer etching (ALE) is a technique used to remove material with atomic level precision using sequential, self-limiting surface reactions.
- Atomic layer deposition (ALD) is a chemical vapor deposition technique based on sequential self-terminating gas–solid reactions used for manufacturing inorganic material layers with very small thicknesses.
- A coplanar waveguide (CPW) is a transmission line consisting of a conductor and two ground planes on a substrate that is mainly used for high-frequency signals.
- Transmon qubits are a specific type of superconducting quantum bit (qubit) used for quantum computing.
- A dilution refrigerator (DR) is a specialized refrigerator that provides continuous cooling reaching extremely low temperatures, mainly using elements such as 3He or 4He.
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[{"label":"RBK Item","value":"Atomic layer etching (ALE) is a technique used to remove material with atomic level precision using sequential, self-limiting surface reactions."},{"label":"Title","value":"Competition between Al2O3 atomic layer etching and AlF3 atomic layer deposition using sequential exposures of trimethylaluminum and hydrogen fluoride"},{"label":"URL","value":"https://pubs.aip.org/aip/jcp/article/146/5/052819/75040/Competition-between-Al2O3-atomic-layer-etching-and"},{"label":"Date","value":"January 4, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Atomic layer deposition (ALD) is a chemical vapor deposition technique based on sequential self-terminating gas–solid reactions used for manufacturing inorganic material layers with very small thicknesses."},{"label":"Title","value":"Surface chemistry of atomic layer deposition: A case study for the trimethylaluminum/water process "},{"label":"URL","value":"https://pubs.aip.org/aip/jap/article-abstract/97/12/121301/893976/Surface-chemistry-of-atomic-layer-deposition-A?redirectedFrom=fulltext"},{"label":"Date","value":"June 30, 2005"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled (Referenced by original paper)"},{"label":"RBK Item","value":"A coplanar waveguide (CPW) is a transmission line consisting of a conductor and two ground planes on a substrate that is mainly used for high-frequency signals."},{"label":"Title","value":"Determining Interface Dielectric Losses in Superconducting Coplanar-Waveguide Resonators\n"},{"label":"URL","value":"https://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.12.014012"},{"label":"Date","value":"July 8, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled (Referenced by original paper)"},{"label":"RBK Item","value":"Transmon qubits are a specific type of superconducting quantum bit (qubit) used for quantum computing."},{"label":"Title","value":"Merged-Element Transmons: Design and Qubit Performance\n"},{"label":"URL","value":"https://journals.aps.org/prapplied/abstract/10.1103/PhysRevApplied.16.024023"},{"label":"Date","value":"August 13, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled (Referenced in original paper)"},{"label":"RBK Item","value":"A dilution refrigerator (DR) is a specialized refrigerator that provides continuous cooling reaching extremely low temperatures, mainly using elements such as 3He or 4He."},{"label":"Title","value":"Principles and methods of dilution refrigeration\n"},{"label":"URL","value":"https://journals.aps.org/ppf/abstract/10.1103/PhysicsPhysiqueFizika.4.1"},{"label":"Date","value":"August 1, 1968"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Physics
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Physics/Medical Physics
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Numerical Values
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In vivo solid stress is associated with poor patient survival in glioma
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https://arxiv.org/abs/2510.00009
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September 15, 2025
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Researchers tested whether tumor growth caused increased displacement field magnitude. Seven female C57BL/6 mice (10 ± 2 weeks old) were investigated at 13 and 22 days following GBM implantation. Implantation was done by injection of 20,000 GL261 tumor cells into the right striatum (2 mm lateral, 1 mm anterior, and 3 mm deep from the bregma) using a 1 μL Hamilton syringe over a 15-minute period. Mice were anesthetized with ketamine/xylazine (ketamine-hydrochloride + 1 mg xylazine per 100 g bodyweight) during the procedure. An additional group of twelve female C57BL/6 mice (12 weeks old) were used as healthy controls. Imaging was performed on a preclinical 7T MRI scanner (BioSpec 70/20 USR, Bruker, Germany and Paravision 6.0.1 Software) using a 20-mm diameter volume coil (RAPID Biomedical, Rimpar, Germany). The mice were anesthetized with isoflurane (1.0–1.5%, CP Pharma, Burgdorf, Germany) diluted in a mixture of 30% O2 and 70% N2O and placed inside the scanner. To assess tumor volume in GBM-bearing mice, 32 contiguous axial image slices were acquired using a T2-weighted (T2w) rapid acquisition with refocused echoes (RARE) sequence (repetition time (TR) = 4200 ms, echo time (TE) = 36 ms, field of view (FoV) = 19.2 x 19.2 mm², matrix size = 192 x 192, resolution = 0.1 x 0.1 x 0.5 mm$^3$). Nine contiguous slices were acquired in healthy mice (TR = 1800 ms, TE = 54 ms, FoV = 20 x 20 mm², matrix size = 256 x 256, resolution = 0.078 x 0.078 x 1 mm$^3$).
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● Tumour volume over time (day 13 vs day 22)
● Displacement field magnitude by MRI (healthy mice vs glioblastoma mice)
● Solid stress and deformation measurements (shear wave speed, volumetric strain, octahedral shear strain, shear modulus) using multifrequency MRE with 3D MRI and diffeomorphic image registration.
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Female C57BL/6 mice (10 ± 2 weeks old) were investigated by 7T MRI at 13 and 22 days following GBM cell implantation and compared to healthy controls. Based on tumor growth rate and aggressiveness, what is the mean displacement field magnitude, in mm, of the GBM mice at day 22 when compared to healthy control mice?
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GBM mean displacement field magnitude = [2.1 - 3.1] mm at day 22, based on 95% confidence intervals
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● Gliomas are the most common malignant brain tumors with glioblastoma (GBM) being the most prevalent and lethal subtype, accounting for 54% of newly diagnosed gliomas.
● In vivo magnetic resonance elastography (MRE) has revealed that gliomas exhibit unusual soft solid properties compared to the typically highly viscous brain parenchyma.
● Solid stress – defined as the sum of mechanical shear and compressive forces acting on tissue - has been suggested as a key driver of tumor aggressiveness by influencing cell signaling.
● Directly measuring tumor solid stress in patients is difficult as spatially resolved force fields are typically inaccessible through non-invasive imaging techniques.
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[{"label":"RBK Item","value":"Gliomas are the most common malignant brain tumors with glioblastoma (GBM) being the most prevalent and lethal subtype, accounting for 54% of newly diagnosed gliomas."},{"label":"Title","value":"CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2006-2010"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3798196/"},{"label":"Date","value":"November 1, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA; this is reference 1 in the paper."},{"label":"RBK Item","value":"In vivo magnetic resonance elastography (MRE) has revealed that gliomas exhibit unusual soft solid properties compared to the typically highly viscous brain parenchyma."},{"label":"Title","value":"High-Resolution Mechanical Imaging of Glioblastoma by Multifrequency Magnetic Resonance Elastography"},{"label":"URL","value":"https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110588"},{"label":"Date","value":"October 22, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA; this is reference 12 in the paper."},{"label":"RBK Item","value":"Solid stress – defined as the sum of mechanical shear and compressive forces acting on tissue - has been suggested as a key driver of tumor aggressiveness by influencing cell signaling."},{"label":"Title","value":"Compression stiffening of brain and its effect on mechanosensing by glioma cells"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC4380293/"},{"label":"Date","value":"July 04, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA; this is reference 21 in the paper."},{"label":"RBK Item","value":"Directly measuring tumor solid stress in patients is difficult as spatially resolved force fields are typically inaccessible through non-invasive imaging techniques."},{"label":"Title","value":"Quantifying solid stress and elastic energy from excised or in situ tumors"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC6546092/"},{"label":"Date","value":"April 19, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA; this is reference 27 in the paper."}]
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Physics
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Physics/Nuclear Experiment
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Numerical Values
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Beta-decay Half Lives beyond Ca-54: A Systematic Survey of Decay Properties approaching the Neutron Dripline
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https://arxiv.org/abs/2510.19757#:~:text=Uthayakumaar%2C%20W.%20B.%20Walters%2C%20S.,of%20single%2Dparticle%20neutron%20states.
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October 22, 2025
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Researchers investigated β-decay half-lives of neutron-rich nuclei near ⁵⁴Ca to study shell evolution toward the neutron dripline.
The experiment was conducted at the Facility for Rare Isotope Beams (FRIB) using the FRIB Decay Station initiator (FDSi). A 215 MeV/nucleon, 10-kW ⁸²Se primary beam bombarded a 5-mm carbon target, producing neutron-rich fragments around ⁵⁴Ca. The Advanced Rare Isotope Separator (ARIS) selected isotopes with two magnetic rigidity settings (Bρ = 5.2642 Tm for ⁵⁵Ca and 5.3613 Tm for ⁵⁴K).
Particle identification was achieved using the ΔE–TOF method with a Si PIN detector and parallel-plate avalanche counter. The separated isotopes were implanted into a segmented YSO detector at the first focal plane of the FDSi, surrounded by HPGe, LaBr₃, and VANDLE detectors for β and γ detection.
This configuration enabled correlated measurement of β-decay electrons, γ-rays, and β-delayed neutrons, allowing precise determination of half-lives for nuclei with Z = 17–22.
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- β-decay half-lives of neutron-rich isotopes near ⁵⁴Ca were measured using correlated β–γ–neutron detection at the FRIB Decay Station initiator (FDSi).
- Particle identification was obtained from ΔE–TOF measurements using an MSX100 Si PIN detector and a parallel-plate avalanche counter.
- Implantation and decay timing were recorded with a segmented YSO detector coupled to a position-sensitive photomultiplier.
- Measurements of γ-ray and β-delayed neutron signals with HPGe, LaBr₃, and VANDLE detectors to identify decay channels.
- Beam energy (215 MeV/nucleon) and separator rigidity (Bρ = 5.26–5.36 Tm) were controlled to maintain stable fragment selection
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Researchers investigated β-decay half-lives of neutron-rich isotopes near ⁵⁴Ca to explore changes in nuclear structure beyond the N = 34 shell closure. Based on the experimental data, what is the predicted half-life of ⁵⁹Sc obtained from decay curve fitting using the Markov Chain Monte Carlo (MCMC) method?
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Half-life(59Sc) = 5.5–9.5 ms (from MCMC decay-curve fitting).
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- Understanding of β-decay processes and how half-lives reflect nuclear shell structure and stability near the neutron dripline.
- Knowledge of the experimental techniques such as ΔE–TOF particle identification and implantation–decay correlation analysis.
- Knowledge of how γ-ray and β-delayed neutron detections are used to identify decay pathways and determine isotopic lifetimes.
- Understanding of the use of Monte Carlo or MCMC methods for statistical fitting of decay curves and uncertainty evaluation.
- Basic understanding of the Facility for Rare Isotope Beams (FRIB) setup, including the FRIB Decay Station initiator (FDSi) and ARIS separator operation
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[{"label":"RBK Item","value":"Understanding of β-decay processes and how half-lives reflect nuclear shell structure and stability near the neutron dripline."},{"label":"Title","value":"Global description of 𝛽− decay in even-even nuclei with the axially-deformed Skyrme finite-amplitude method"},{"label":"URL","value":"https://journals.aps.org/prc/abstract/10.1103/PhysRevC.93.014304"},{"label":"Date","value":"January 11, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled\n(There are no open-access alternatives; that is the flagship publication regarding the subject matter in the field)."},{"label":"RBK Item","value":"Knowledge of the experimental techniques such as ΔE–TOF particle identification and implantation–decay correlation analysis."},{"label":"Title","value":"Commissioning of the Advanced Rare Isotope Separator ARIS at FRIB"},{"label":"URL","value":"linkinghub.elsevier.com/retrieve/pii/S0168583X23001556"},{"label":"Date","value":" March 2, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled\n(There are no open-access alternatives; that is the flagship publication regarding the subject matter in the field)."},{"label":"RBK Item","value":"Understanding of the use of Monte Carlo or MCMC methods for statistical fitting of decay curves and uncertainty evaluation."},{"label":"Title","value":"emcee: The MCMC Hammer"},{"label":"URL","value":"https://iopscience.iop.org/article/10.1086/670067"},{"label":"Date","value":"January 9, 2013 "},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Knowledge of how γ-ray and β-delayed neutron detections are used to identify decay pathways and determine isotopic lifetimes."},{"label":"Title","value":"Development of a Reference Database for Beta-Delayed Neutron Emission"},{"label":"URL","value":"https://arxiv.org/abs/2102.01165"},{"label":"Date","value":"February 1, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Basic understanding of the Facility for Rare Isotope Beams (FRIB) setup, including the FRIB Decay Station initiator (FDSi) and ARIS separator operation"},{"label":"Title","value":"Isotope Harvesting at FRIB: Additional opportunities for scientific discovery\n"},{"label":"URL","value":"https://arxiv.org/abs/1812.03984"},{"label":"Date","value":"December 7, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Plant biotechnology
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Numerical Values
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Induction of synthetic apomixis in two sorghum hybrids enables seed yield and genotype preservation over multiple generations
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https://www.biorxiv.org/content/10.1101/2025.07.02.662806v1
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July 5, 2025.
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Researchers sought to induce a process similar to natural apomixis in Sorghum bicolor, a sexually reproducing species. They identified three genes—SPO11, REC8, and OSD1—that control the meiotic process. Using CRISPR-Cas9, the researchers targeted these genes, evoking a mitotic-like division and producing unreduced, non-recombinant gametes (MiMe mutant).
The researchers then used a two-step approach to combine the MiMe with parthenogenesis to produce sorghum self-reproducing hybrids. In the first step, a characterized Tx430 transgenic line with the maize DD45 promoter:ASGR-BBML2 coding gene sequences was crossed with a wild-type Tx623 sorghum line to generate a F1 hybrid. In the second step, immature embryos from this cross were used in a secondary transformation to introduce CRISPR/Cas9 together with MiMe gRNA.
To confirm the successful production of synthetic apomictic clonal sorghum progeny, estimate the system's penetrance was estimated in the T2/3/4 generations by assessing heterozygosity maintenance using SNP marker sequencing. 104 polymorphic SNP markers were chosen across the 10 chromosomes of sorghum for analysis. These SNP markers were compared between mother and offspring plants to calculate a percentage of conserved SNPs. SNP marker genotyping was performed using TaqMan SNP genotyping assays (ThermoFisher) with sorghum leaf samples, as previously described (Ye et al., 2024).
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- 104 SNP markers of the mother plant compared to its T3 offspring.
- Percentage of SNP conservation between the mother plant and its T3 offspring.
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Maintenance of heterozygosity was assessed in a sorgum T2 hybrid progeny derived from a T2 transgenic plant that contained triple homozygous knockout edits for SPO11, REC8, and OSD1 genes, resulting in a Mitotic-like division (MiMe), with the ectopic expression of the BBM gene that induces parthenogenesis. What would be the percentage of heterozygosity maintenance of the progeny of T3 trasgenic offspring, based on the results of SNP analysis?
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88%-98%
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-Some species can form seed asexually via apomixis where the maternal genotype is preserved in the progeny.
-Introduction of apomixis from natural species to sexual relatives by plant breeding has generally proved inefficient or unsuccessful with respect to clonal seed production.
-Two broad categories of apomictic mechanisms are sporophytic and gametophytic apomixis.
-Meiotic avoidance, or apomeiosis, can be achieved through mutagenesis to induce the Mitosis instead of Meiosis, or MiMe phenotype.
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[{"label":"RBK Item","value":"Some species can form seed asexually via apomixis where the maternal genotype is preserved in the progeny"},{"label":"Title","value":"Gametophytic Apomixis"},{"label":"URL","value":"https://link.springer.com/chapter/10.1007/978-3-642-69302-1_10"},{"label":"Date","value":"January, 1984"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Introduction of apomixis from natural species to sexual relatives by plant breeding has generally proved inefficient or unsuccessful with respect to clonal seed production"},{"label":"Title","value":"Apomixis: Its Identification and Use in Plant Breeding"},{"label":"URL","value":"https://acsess.onlinelibrary.wiley.com/doi/epdf/10.2135/cropsci1987.0011183X002700060010x"},{"label":"Date","value":"November 1, 1987"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Two broad categories of apomictic mechanisms are sporophytic and gametophytic apomixis"},{"label":"Title","value":"The Genetic Control of Apomixis: Asexual Seed Formation"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC4063905/"},{"label":"Date","value":"June 1, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Meiotic avoidance, or apomeiosis, can be achieved through mutagenesis to induce the Mitosis instead of Meiosis, or MiMe phenotype"},{"label":"Title","value":"Turning Meiosis into Mitosis"},{"label":"URL","value":"https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000124"},{"label":"Date","value":"June 9, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Microbiology
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MCQ
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Inhibition of Enterotoxigenic Escherichia coli adhesion via aptamers prevents infection in IPEC-J2 cells
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https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-025-04233-8
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August 25, 2025
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Scientists tested whether two aptamers could reduce Enterotoxigenic Escherichia coli (ETEC) K88 adhesion and cytotoxicity in vitro in IPEC-J2 cells (intestinal porcine epithelial cells derived from neonatal piglet jejunum). Two aptamers, K88-Apt A04 (fimbrial-specific aptamer) and K88-Apt 37 (cell-targeting aptamer), were first applied in 200 µL of binding buffer at 37 °C to ETEC K88 with FAM-labels to determine binding affinity by measuring fluorescence intensity. Unbound ssDNA was removed with 1 mL of PBS. The adhesion rate of ETEC to IPEC-J2 cells was calculated by infecting the cells with ETEC K88 at MOIs of 1, 10, 10^2, 10^3, and 10^4 at 37 °C and 5% CO2 for one hour to allow for bacterial adhesion. Cells were further tested every hour for 5 hours after infection at the optimal MOI.
Aptamer adherence assays were completed under three conditions. Aptamer inhibition assays (Apt + K88 + cell) included a control and treatment group with aptamer concentrations of 0, 20, 50, 100, and 200 nM and ETEC K88 (MOI of 10). The aptamer + bacteria suspension was incubated at 37 °C for 1.5 hours, then added to IPEC-J2 cell cultures and incubated at 37 °C with 5% CO2 for 1.5 hours. Unattached bacteria were removed and washed twice with PBS. Adherence prevention assays (Apt + cell + K88) were also conducted by aptamer concentrations of 0, 20, 50, 100, and 200 nM co-incubated with IPEC-J2 cells at 37 °C and 5% CO2 for 1.5 hours. ETEC K88 (MOI 10) was added to the pretreated aptamers at the same conditions for 1.5 hours. Unattached bacteria were removed and washed twice with PBS. Treatment assays (K88 + cell + Apt) included treatment with aptamers at concentrations of 0, 20, 50, 100, and 200 nM at 37 °C for 1.5 hours after IPEC-J2 cells were exposed to ETEC K88 at 37 °C, 5% CO2 for 1.5 hours. After each adhesion assay, the cells were stained with crystal violet to visualize cell morphology and detect apoptosis. Triton X-100 lysis, CFU plating, and flow cytometry were used to quantify adherent bacteria. Cytotoxicity was measured using a lactate dehydrogenase test kit. ELISA was also used to measure protein expression levels of TNF-alpha and IL-8, and qPCR was used to measure mRNA expression of TLR6, NOD1, NOD2, IL-6, IL-8, and TGFβ1.
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- Quantification of adherent bacteria via CFU counts after Triton X-100 lysis and plating (comparison across MOIs, incubation times and aptamer concentrations).
- Morphology/apoptosus after crystal violet staining and microscopy.
- Cytotoxicity measured by LDH assay (492/620 nm), expressed as % cytotoxicity relative to control.
- ELISA quantification of TNF-alpha and IL-8 from culture supernatant
- Gene expression (mRNA) for TLR6, NOD1, NOD2, IL-6, IL-8, and TGFβ1 by qPCR, normalized to beta-actin.
- Aptamer-bacteria binding affinity of FAM-labeled aptamers incubated with ETEC K88 using fluorescence spectrometry (Kd values).
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Researchers tested whether two DNA aptamers, K88-Apt 37 (cell-targeting) and K88-Apt A04 (fimbrial-targeting), could reduce the adhesion of Enterotoxigenic Escherichia coli (ETEC) K88 to porcine intestinal epithelial IPEC-J2 cells. Aptamers were tested in three conditions: adherence inhibition (aptamer + bacteria, then cells), adherence prevention (aptamer + cells, then bacteria), and treatment (cells + bacteria, then aptamer). Which of the following is the most likely outcome?
A. K88-Apt 04 tended to show stronger adhesion inhibition than K88-Apt 37 with lower cytotoxicity.
B. Both K88-Apt 37 and K88-Apt A04 demonstrated the best anti-adhesion effect when mixed with the bacteria first.
C. The adherence-prevention group demonstrated the highest cytotoxicity.
D. Pre-treating cells with aptamers results in maximum inhibition.
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B. Both K88-Apt 37 and K88-Apt A04 demonstrated the best anti-adhesion effect when mixed with the bacteria first.
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- Entertoxigenic Escherichia coli (ETEC) K88 is a pathogenic strain causing diarrhea in post-weaned piglets that begins with adhesion to intestinal epithelial cells via fimbriae (K88 adhesin).
- Aptamers are short single-stranded DNA or RNA sequences that bind to target molecules.
- K88-Apt A04 binds ETEC K88 fimbriae.
- K88- Apt 37 binds host cell surface molecules involved in ETEC adhesion.
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[{"label":"RBK Item","value":"Entertoxigenic Escherichia coli (ETEC) K88 is a pathogenic strain causing diarrhea in post-weaned piglets that begins with adhesion to intestinal epithelial cells via fimbriae (K88 adhesin).\n"},{"label":"Title","value":"Both flagella and F4 fimbriae from F4ac + enterotoxigenic Escherichia coli contribute to attachment to IPEC-J2 cells in vitro"},{"label":"URL","value":"https://link.springer.com/article/10.1186/1297-9716-44-30"},{"label":"Date","value":"May 13, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Aptamers are short single-stranded DNA or RNA sequences that bind to target molecules. "},{"label":"Title","value":"Current perspectives on aptamers as diagnostic tools and therapeutic agents."},{"label":"URL","value":"https://www.mdpi.com/1999-4923/12/7/646"},{"label":"Date","value":"July 9, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"K88-Apt A04 binds ETEC K88 fimbriae."},{"label":"Title","value":"Rapid fluorescent detection of enterotoxigenic Escherichia coli (ETEC) K88 based on graphene oxide-dependent nanoquencher and Klenow fragment-triggered target cyclic amplification."},{"label":"URL","value":"https://journals.sagepub.com/doi/10.1366/15-07881?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed"},{"label":"Date","value":"October 1, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"K88- Apt 37 binds host cell surface molecules involved in ETEC adhesion."},{"label":"Title","value":"Aptamer selection for the detection of Escherichia coli K88."},{"label":"URL","value":"https://cdnsciencepub.com/doi/10.1139/w11-030?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed"},{"label":"Date","value":"May 31, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Chemical Ecology / Animal Behavior
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MCQ
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A male-derived volatile sex pheromone in Caenorhabditis nematodes identified through its mimicry by a predator
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https://www.biorxiv.org/content/10.1101/2025.09.12.675966v1.full
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September 17, 2025
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Researchers used solid phase microextraction (SPME) to sample headspace volatiles present above live cultures of C. remanei and C. elegans adult males, as well as those of females and hermaphrodites from both species, respectively. Focusing on methyl 3-methyl-2-butenoate (MMB), a compound produced by a predacious fungi Arthrobotrys oligospora, known for its strong attractive potential that was highly female- and hermaphrodite-specific within several Caenorhabditis species, including C. remanei and C. elegans, suggesting that MMB might function as a mimic of an endogenous, male-produced, volatile sex pheromone (VSP) within these species.
Nematode preparation for solid-phase microextraction (SPME) sampling in C. elegans and C. remanei N2, JK574 (fog-2) and CB1490 (him-5) strains of C. elegans and the EM464 strain of C. remanei were used for headspace sampling. The nematodes were propagated on NGM plates that had been seeded with Escherichia coli OP50 at 20°C. The nematodes were synchronized by bleaching and at the fourth larval stage (L4) the hermaphrodites/females and males were sorted and transferred onto new OP50 plates. The following day, 1000 each of the nematodes (C. elegans young adult N2 hermaphrodites, fog-2 females, him-5 males or C. remanei EM464 males) were picked into 1 ml of M9 buffer in 4 ml clear glass vials which were sealed with PTFE/silicone septa and immediately subjected to SPME sampling. Sperm depleted N2 hermaphrodites were prepared by transferring to a fresh OP50 plate every day until no more eggs were laid, at which point 250 of the sperm-depleted, old hermaphrodites in 250 µl of M9 buffer were subjected to headspace sampling as described above. Mated fog-2 females were prepared by overnight incubation with 1-3 of N2 males on an OP50 plate, following which 250 mated females with confirmed egg laying were used for the headspace sampling. Solid phase microextraction(SPME) was used to sample volatiles present in the headspace above worm cultures prepared in sealed 4 mL vials as described above. All SPME fibers (divinylbenzene/carboxen/polydimethylsiloxane, 50/30 mm; Supelco, Bellefonte, PA) were pre-conditioned for 10 min in the GC injector (250°C) prior to use. For a typical collection, each fiber was inserted through the vial septa and exposed for a time period of 16 hr at room temperature. Fibers were either immediately analyzed or sealed in SPME fiber assembly storage devices (Supelco) to await analysis. For quantitative analyses, standard dilutions of MMB prepared as 1 mL aliquots in sealed 4 mL vials were sampled by SPME for 16 hrs and immediately analyzed by GC-MS. Analyses of SPME samples were carried out using both comprehensive two-dimensional gas chromatographic mass spectrometry (GC x GC-MS), as well as one-dimensional gas chromatography mass-spectrometry (GC-MS). Methyl 3-methyl-2-butenoate (MMB) was positively identified based on a comparison of its electron-impact mass spectrum and gas-chromatographic retention time with those of an authentic sample purchased from Sigma Aldrich. Comprehensive two-dimensional gas-chromatographic mass-spectral analyses (GC x GC-MS) were carried out using a Pegasus 4D (Leco Corp., ST. Joseph, MI) equipped with a Restek Rxi-5 Sil MS primary column (5% diphenyl/95% dimethyl polysiloxane; 30m length x 0.25 mm i.d. x 0.25 -μm film thickness). Two different secondary columns were used during the course of this work. A Restek Rxi-5 Sil MS secondary column (5% diphenyl/95% dimethyl polysiloxane; 1.3 m length x 0.18 mm i.d. x 0.18 -μm film thickness) and an SGE Analytical Science BPX50 secondary column (50% diphenyl/50% dimethyl polysiloxane; 1.0 m length x 0.1 mm i.d. x 0.10 -μm film thickness). An injector temperature of 250 °C with splitless injection was used, with the split valve opening at 20 seconds. The primary column oven temperature was held at 40 °C for 1 min, then increased at a rate of 3 °C/min to a temperature of 126°C, after which it was increased at a rate of 12 °C/min to a final temperature of 275°C. The secondary column oven followed a temperature program that maintained a +15°C offset from the primary column oven. A 3.5 s modulation period (0.80 hot pulse; 0.95 cold pulse) was used with a modulator temperature program that maintained a +15 °C offset from the secondary column oven. The carrier gas flow rate was 1.3 mL/min. Data processing was carried out using LECO ChromaTOF software with a signal-to-noise threshold of 30 for peak detection. Additional analyses, including quantitative measurements, were carried out a Shimadzu QP2010 plus gas chromatograph mass spectrometer equipped with a Restek Rxi-5Sil MS column (5% diphenyl/95% dimethyl polysiloxane; 30m length x 0.25 mm i.d. x 0.25 -μm film thickness). An injector temperature of 250 °C with splitless injection was used, with the split valve opening at 0.52 minutes. A column temperature program was used that remained at 50°C for the first minute, increased at a rate of 6 °C per min to a temperature of 200 °C, and then increased at a rate of 20 °C per min to a final temperature of 280 °C. The carrier gas flow rate was 1.22 mL/min. Chemotaxis assays were performed to evaluate the attractiveness of either worm-conditioned media (WCM) or prepared solutions of authentic methyl 3-methyl-2-butenoate (MMB). Two types of chemotaxis assays were conducted. The WCM-based chemotaxis assays tested whether adult females of C. remanei or hermaphrodites of C. elegans are attracted to WCM derived from adult males of either species. The worm-conditioned media (WCM) (20 worms/10 µL) containing the native sex pheromone from C. elegans males and C. remanei males in M9 buffer was prepared and used for the chemotaxis assay according to the method in Leighton et al.,10 and applied to the inside lid of a 6-cm Petri dish prepared with chemotaxis media (2.0% agar, 1 mM MgSO4, 1 mM CaCl2, 25 mM KH2PO4, pH 6.0). A 10 µL aliquot of WCM was pipetted above one sodium azide spot, and 10 µL of M9 buffer was pipetted to the opposite side as a control. The plate was then placed in a small box to eliminate the influence of light. The assay was run at least for 1 hr. If >20% of nematodes were still alive after 1 hr, we extended the incubation time until >80% of nematodes tested were dead, as determined by periodic checking. This took between 1 hr and 4 hrs. Pairwise comparisons were performed using a two-tailed Student’s t-test, with p < 0.05 considered statistically significant. The MMB-based chemotaxis assays tested the attraction of C. remanei females to various concentrations of synthetic MMB. A dilution series ranging in concentration from 3.8 × 10-4 M to 3.8 × 10-9 M was prepared from a 50% (v/v) stock solution of MMB in ethanol. A 100 µL aliquot of each dilution was placed in the inverted cap of a microcentrifuge tube and positioned on the inside lid of a 10-cm Petri dish above one sodium azide spot. Approximately 100 synchronized C. remanei females were placed at the center of the plate. The plate was then placed in a small box to eliminate the influence of light. The assay was run for at least 1 hr. If >20% of nematodes were still alive after 1 hr, we extended the incubation time until >80% of nematodes tested were dead, as determined by periodic checking. This took between 1 hr and 4 hrs. Differences among concentrations were analyzed using one-way ANOVA followed by Tukey’s multiple comparison test (p < 0.01). In both types of assays, worms were bleached and synchronized, and L4 stage males/hermaphrodites/females were manually picked to ensure sexual purity. Worms were allowed to mature for an additional 24 hours before use. Worms were washed twice in M9 buffer and twice in ddH2O before being transferred to assay plates. The chemotaxis index (CI) was calculated as {(number of nematodes at test cue zone) - (number of nematodes at the control zone)} /{(number of nematodes at test cue zone) + (number of nematodes at the control zone)}. All chemotaxis assays were repeated at least three times.
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- GC x GC-MS chromatograms obtained for SPME headspace sampling for both species, as well as for an authentic sample of methyl 3-methyl-2-butenoate (MMB)
- GC x GC-MS mass spectra obtained for SPME headspace sampling for both species, as well as for an authentic sample of methyl 3-methyl-2-butenoate (MMB)
- Chemotaxis index (CI) evaluating both species' attractiveness for worm-conditioned media (WCM)
- Chemotaxis index (CI) evaluating both species' attractiveness for prepared solutions of authentic methyl 3-methyl-2-butenoate (MMB)
- MMB concentration across different WCM samples.
|
Researchers used solid phase microextraction (SPME) to sample headspace volatiles present above live cultures of C. remanei and C. elegans adult males, as well as those of females and hermaphrodites from both species, respectively. Focusing on methyl 3-methyl-2-butenoate (MMB), a compound produced by a predacious fungi Arthrobotrys oligospora, known for its strong attractive potential that was highly female- and hermaphrodite-specific within several Caenorhabditis species, including C. remanei and C. elegans, suggesting that MMB might function as a mimic of an endogenous, male-produced, volatile sex pheromone (VSP) within these species.
Which of the following outcomes is most likely?
A. The compound methyl 3-methyl-2-butenoate (MMB) was found to be produced by both C. remanei males and females; and C. elegans males and hermaphrodites.
B. The compound methyl 3-methyl-2-butenoate (MMB) was found to be produced by C. remanei and C. elegans males only.
C. The compound methyl 3-methyl-2-butenoate (MMB) was found to be produced by C. remanei males only.
D. The compound methyl 3-methyl-2-butenoate (MMB) was found to be produced by C. elegans males only.
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C. The compound methyl 3-methyl-2-butenoate (MMB) was found to be produced by C. remanei males only.
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- The nematode-trapping fungus Arthrobotrys oligospora has shown a remarkable instance of chemical mimicry wherein the fungus secretes a mixture of volatile compounds, including those representing olfactory cues of food, to lure prey nematodes
- The strong attraction elicited by methyl 3-methyl-2-butenoate (MMB), was highly female- and hermaphrodite-specific within several Caenorhabditis species, including C. remanei and C. elegans
- The existence of female- and hermaphrodite-derived volatile sex pheromones (VSPs), which are attractive to males, is well documented within C. elegans and related species. By contrast, evidence for the existence of a male-derived VSP that is attractive to females or hermaphrodites has been less clear.
|
[{"label":"RBK Item","value":"The nematode-trapping fungus Arthrobotrys oligospora has shown a remarkable instance of chemical mimicry wherein the fungus secretes a mixture of volatile compounds, including those representing olfactory cues of food, to lure prey nematodes"},{"label":"Title","value":"Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey"},{"label":"URL","value":"https://elifesciences.org/articles/20023"},{"label":"Date","value":"January 18, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"The existence of female- and hermaphrodite-derived volatile sex pheromones (VSPs), which are attractive to males, is well documented within C. elegans and related species. By contrast, evidence for the existence of a male-derived VSP that is attractive to females or hermaphrodites has been less clear."},{"label":"Title","value":"C. elegans males optimize mate-preference decisions via sex-specific responses to multimodal sensory cues"},{"label":"URL","value":"https://www.cell.com/current-biology/fulltext/S0960-9822(24)00178-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982224001787%3Fshowall%3Dtrue"},{"label":"Date","value":"March 11, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Entomology
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MCQ
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Envenomation leads to venom protein reduction and recovery delay in bumblebee workers
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https://www.biorxiv.org/content/10.1101/2025.07.25.666811v1.full
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July 31, 2025
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Researchers investigated proteomic changes in the venom sac, the primary reservoir for venom storage, of Bombus terrestris workers over a short time-course post-envenomation. Bombus terrestris colonies (n=5) were obtained from Koppert Biological Systems (Netherlands) and kept under constant conditions at 28°C and under red light illumination. Sugar water (APlinvert, Germany) and pollen (Biobest, Belgium) were provided ad libitum. To control for age, they collected callows (within 48h post-eclosion) and transferred each to a box (15cm x 15cm x 15cm) consisting of four related mature workers (distinguishable due to clipped wings), brood, and sugar water for approximately 72h to allow for maturation. To induce envenomation, they used parafilm-covered 0.2ml tubes filled with 100µl autoclaved phosphate buffered saline (PBS). For each collection, they temporarily restrained the bee and placed the collection tube close to the aculeus. They visually confirmed stinging by the presence of a hole in the parafilm. Control bees experienced the same handling procedure, but no venom was collected. Post-envenomation, workers were returned to their boxes and remained until a designated sampling time-point, which was either 1h, 24h or 168h(one week) after procedure. At each designated collection time-point, workers were transferred into individual cryotubes, snap-frozen in liquid nitrogen, and stored at -80°C before being dissected. In total, they collected 25 workers (Envenomation group: 1h (n=5), 24h (n=4) and 168h (one week, n=3); Control group: 1h (n=5), 24h (n=4) and 168h (n=4)). Individuals, one each from a different colony, were used for each treatment group and time-point. They also assessed the collected venom for protein content using the Qubit protein assay kit. For each bee, the venom sac was extracted and subsequently homogenised in PBS. To determine differently abundant proteins, an EASY-nLC 1000 system (Thermo Scientific) and a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Scientific) were used. MS/MS data were analysed using MaxQuant.
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- Protein content of the venom samples
- Proteome changes in the venom sac at different timings post-evenomation
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Researchers investigated proteomic changes in the venom sac, the primary reservoir for venom storage, of Bombus terrestris workers over a short time-course post-envenomation. To induce envenomation, researchers used parafilm-covered 0.2ml tubes filled with 100µl autoclaved phosphate buffered saline (PBS). For each collection, they temporarily restrained the bee and placed the collection tube close to the aculeus. Control bees experienced the same handling procedure, but no venom was collected. Post-envenomation, workers were returned to their boxes and remained until a designated sampling time-point, which was either 1h, 24h or 168h (one week) after procedure. At each designated collection time-point, workers were transferred into individual cryotubes, snap-frozen in liquid nitrogen, and stored at -80°C before being dissected. They also assessed the collected venom for protein content using the Qubit protein assay kit. For each bee, the venom sac was extracted and subsequently homogenised in PBS. To determine differently abundant proteins, an EASY-nLC 1000 system (Thermo Scientific) and a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Scientific) were used. Which of the following outcomes is most likely?
A. Researchers found that nearly all reduced and elevated SDAPs (significantly differentially abundant proteins) were unique to individual time-points.
B. Researchers found that nearly all reduced and elevated SDAPs (significantly differentially abundant proteins) were not unique to individual time-points.
C. Researchers found that nearly all reduced SDAPs (significantly differentially abundant proteins) were not unique to individual time-points, while nearly all elevated SDAPs were unique to individual time-points.
D. Researchers found that nearly all reduced SDAPs (significantly differentially abundant proteins) were unique to individual time-points, while nearly all elevated SDAPs were not unique to individual time-points.
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A. Researchers found that nearly all reduced and elevated SDAPs (significantly differentially abundant proteins) were unique to individual time-points.
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- The venom sac acts as a reservoir for the storage of venom proteins that are primarily produced in the connected tubular venom glands.
- Changes in the venom sac proteome can provide an insight into the molecular response and recovery post-envenomation.
- Venom regeneration is potentially costly
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[{"label":"RBK Item","value":"The venom sac acts as a reservoir for the storage of venom proteins that are primarily produced in the connected tubular venom glands."},{"label":"Title","value":"The venom gland of queens of Apis mellifera (Hymenoptera, Apidae): morphology and secretory cycle"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0968432806000278?via%3Dihub"},{"label":"Date","value":"March 29, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Venom regeneration is potentially costly "},{"label":"Title","value":"The venom optimization hypothesis revisited"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0041010112008173?via%3Dihub"},{"label":"Date","value":"December 22, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Changes in the venom sac proteome can provide an insight into the molecular response and recovery post-envenomation."},{"label":"Title","value":"The venom gland of queens of Apis mellifera (Hymenoptera, Apidae): morphology and secretory cycle"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0968432806000278?via%3Dihub"},{"label":"Date","value":"March 29, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Behavioral Ecology / Entomology
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MCQ
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Male bumblebees adapt foraging to environmental conditions to sustain mate-seeking efforts
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https://www.biorxiv.org/content/10.1101/2025.09.08.674615v1.full
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September 11, 2025
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Researchers investigated how the spatial arrangement of nectar and scent-marking sites, along with nectar availability, influence male Bombus terrestris movement patterns. They manipulated the distribution of feeders (artificial flowers) and scent-marking locations (branches), and varied nectar delivery rates, to assess effects on foraging, scent-marking, and patrolling. They used high-resolution 3D video tracking of the spatial movement in a controlled flight cage environment, examining how males navigate trade-offs between feeding and reproductive efforts.
Experiments were conducted in a flight cage (300 cm L × 300 cm W × 150 cm H) within a controlled laboratory environment. The cage was enclosed with white tulle fabric, a fine mesh material with an estimated pore size of c.a. 0.5mm. Environmental conditions were maintained at 21.8 ± 0.02 °C and 46.2 ± 0.3% relative humidity, recorded continuously using a digital sensor. They used male B. terrestris from ten commercial colonies (each containing a queen and 40–50 workers) and from additional male-only boxes (∼ 50 males per box). Colonies were housed in wooden nest boxes (28 × 16 × 11 cm) lined with cat litter to regulate moisture levels. A 25% (w/w) sucrose solution was provided via feeders, and nests were provided with Natupol pollen (Koppert, Suffolk, UK) twice weekly. To simulate a realistic environment for foraging, scent-marking, and patrolling, they arranged six Cotoneaster horizontalis branches and six artificial flowers in the flight cage. C. horizontalis is a shrub whose flowers are naturally visited by bumblebees (Corbet and Westgarth-Smith, 1992) and was used as a substrate for male scent-marking behaviour. Branches were selected to have minimal lateral branching and measured approximately 15 cm, providing a relatively uniform and accessible structure for landing and marking. Each branch was mounted on a 3D-printed white tripod (10 cm high) to ensure stability and consistent presentation across trials. The artificial flowers were designed to deliver controlled amounts of nectar substitute (BIOGLUC®, Biobest, Belgium). Artificial flowers were automatically refilled every hour using Tempatron AM24 drive motors and a gear kit-controlled cam sequencer system (RS Components, Corby, UK). The refill system was active for 15 minutes at the start of each hour, followed by a 45-minute pause, repeating this cycle continuously throughout the day. Two different sucrose delivery rates were implemented to simulate conditions of high and low nectar availability. Under the high-rate condition, nectar was delivered at 4.64 ± 0.16 μl/min, resulting in 69.6 ± 0.16 μl per flower over each 15-minute refill period. In contrast, under the low-rate condition, nectar was dispensed at 1.63 ± 0.23 μl/min, yielding 24.4 ± 0.23 μl per flower per refill cycle. Two spatial configurations were tested, representing contrasting resource distributions: a clumped array and a dispersed array. In the clumped array, items (branches and artificial flowers) were arranged at regular intervals (52 cm) within a 135 cm x 135 cm area (c.a. 1.82 m2), creating a dense, uniformly spaced layout that mimicked a tightly packed patch of vegetation. In the dispersed array, items were placed at irregular distances across a 208 cm x 208 cm area (c.a. 4.33 m2), guided by a 5 × 5 placement grid to achieve a heterogeneous layout with variable spacing between items. A total of 51 males were tested across the spatial and nectar availability conditions: 12 in the dispersed array with low nectar availability, 12 in the clumped array with low nectar, 12 in the clumped array with high nectar, and 15 in the dispersed array with high nectar. Male bees were released into the flight cage at c.a. 15:30 on the day prior to testing. The cage operated under a light-dark regime of 8 hours of light and 16 hours of darkness, with lights on from c.a. 09:00 to 17:00. Following release, bees experienced c.a. 1.5 hours of light (from 15:30 to 17:00), during which they began initial exploration and familiarisation with the new environment. On the day of testing, males were observed until at least one individual had scent-marked a branch, fed from an artificial flower, and demonstrated sustained flight. Once a suitable bee was identified, individual testing began. Only one bee was tested at a time to eliminate social interference. All other bees were removed and returned to the training box. The focal bee was then recorded for six hours, from 09:30 to 15:30, using two Basler GenICam cameras for 3D tracking. Since the behaviours they were interested in (feeding and scent-marking) can involve a range of movement speeds they treated all walking and sitting movement as the same for the purposes of further behavioural classification. Feeding was defined as any instance in which a bee was recorded walking or sitting within 20 cm of a flower and no more than 5.5 cm above or below the flower platform. To ensure interactions were specific to the flower platform, body movement had to be predominantly horizontal, with a horizontal-to-vertical movement ratio exceeding 1.5. Scent-Marking was characterised by a bee walking or sitting within a 20 cm radius of an item at a height of no more than 1 cm above it, where vertical body movement was predominant (horizontal-to-vertical movement ratio below 1). They used the term Patrolling to describe flight behaviour near flowers or branches involving slow, highly manoeuvrable movement, consistent with environmental inspection in search of mates. A patrolling bout began when a bee entered a 20 cm radius around a flower or branch and flew no more than 10 cm above it, while maintaining a flight speed below 50 cm/s and an angular velocity (i.e., rate of change in heading direction) above 125°/s. These thresholds were chosen to distinguish patrolling from faster, straighter transit flights, capturing the characteristic tight turning and hovering-like motion typical of inspection behaviour. A patrolling event was considered to have ended when the bee: (1) landed on a branch, the cage floor, or netting; (2) ascended more than 45 cm above the level of the items (suggesting transition to exploratory flight); or (3) went more than 5 seconds without meeting the criteria for further inspections.
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- Behavior frequency variability (foraging, scent-marking, and patrolling) across different combinations of spatial resource distribution (clumped vs. dispersed) and nectar availability (low vs. high)
- Total time spent performing each behavior across different combinations of spatial resource distribution (clumped vs. dispersed) and nectar availability (low vs. high)
- Duration of individual behavioral events in response to changes in spatial resource distribution (clumped vs. dispersed) and nectar availability (low vs. high)
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Researchers investigated how the spatial arrangement of nectar and scent-marking sites, along with nectar availability, influence male Bombus terrestris movement patterns. They manipulated the distribution of feeders (artificial flowers) and scent-marking locations (branches), and varied nectar delivery rates, to assess effects on foraging, scent-marking, and patrolling. They used high-resolution 3D video tracking of the spatial movement in a controlled flight cage environment, examining how males navigate trade-offs between feeding and reproductive efforts. Which of the following outcomes is most likely?
A. Nectar availability had significant effects on foraging, scent-marking, and patrolling event frequencies.
B. Nectar availability had minimal effects on patrolling and scent-marking event frequencies, but significant effects on foraging event frequencies.
C. Nectar availability had minimal effects on foraging event frequencies but significant effects on patrolling and scent-marking event frequencies.
D. Nectar availability had minimal effects on foraging, scent-marking, and patrolling event frequencies.
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D. Nectar availability had minimal effects on foraging, scent-marking, and patrolling event frequencies.
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- Animals adjust how they allocate time and energy – for example, balancing foraging with reproductive behaviors – based on both internal conditions (such as energy reserves) and external cues (such as resource availability, competition, and predation risk)
- Bumblebee workers (Bombus spp.) learn sequences of flower visits that they adjust in response to changes in spatial layout and nectar availability
- A key component of male reproductive behaviour in many Bombus species involves scent-marking patrol circuits during which they deposit pheromones on substrates such as branches, leaves, or stems as they establish regular flight paths to attract receptive queens
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[{"label":"RBK Item","value":"Animals adjust how they allocate time and energy – for example, balancing foraging with reproductive behaviors – based on both internal conditions (such as energy reserves) and external cues (such as resource availability, competition, and predation risk) "},{"label":"Title","value":"Meta-analysis reveals that animal sexual signalling behaviour is honest and resource based"},{"label":"URL","value":"https://www.nature.com/articles/s41559-021-01409-z"},{"label":"Date","value":"March 15, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Bumblebee workers (Bombus spp.) learn sequences of flower visits that they adjust in response to changes in spatial layout and nectar availability"},{"label":"Title","value":"Habitat structure and animal movement: the behaviour of bumble bees in uniform and random spatial resource distributions"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s004420050329"},{"label":"Date","value":"June 30, 1997"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"A key component of male reproductive behaviour in many Bombus species involves scent-marking patrol circuits during which they deposit pheromones on substrates such as branches, leaves, or stems as they establish regular flight paths to attract receptive queens"},{"label":"Title","value":"Patrolling and scent-marking behavior in Japanese bumblebee Bombus ardens ardens males: alternative mating tactic?"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s13592-017-0534-2"},{"label":"Date","value":"August 12, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant genetics
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MCQ
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ALFIN-LIKE Proteins Orchestrate H3K4me3-H3K27me3 Crosstalk to Regulate Plant Embryogenesis
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https://www.biorxiv.org/content/10.1101/2025.04.08.647773v1
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April 8, 2025
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Researchers studied the antagonistic interplay between H3K27me3 and H3K4me3 during Arabidopsis embryogenesis. They identified a developmentally specific interaction between the FIS-PRC2 complex and ALFIN-LIKE (AL) proteins. AL proteins are a family of plant-specific PHD domain proteins that recognize H3K4me3. The Arabidopsis genome contains seven AL protein-coding genes. Researchers examined self-pollinated siliques at the globular stage of embryo development in triple (al4/5/7), quadruple (al4/5/6/7 and al3/4/5/7), quintuple (al1/4/5/6/7 and al3/4/5/6/7), and sextuple (al1/3/4/5/6/7) mutants of ALFIN-LIKE genes to determine if loss-of-function of AL genes results in seed abortion or is related to embryo-defective phenotypes. The siliques were fixed overnight in an ethanol and acetic acid solution (9:1), transferred to 70% ethanol, and dissected. The seeds/ovules were then cleared in a chloral hydrate solution for several hours or overnight. Then, the seeds/ovules were imaged using a Zeiss DMR microscope with DIC filters and a Leica Flexacam C3 LSR camera. The researchers quantified the percentage of embryo defects classified as mild or severe for each combination of mutant lines.
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- Embryos defect at the globular stage (%) of wild type vs mutants of the alfin genes (triple, quadruple, quintuple, and sextuple).
- Embryos defect at the heart stage (%) of wild type vs mutants of the alfin genes (triple, quadruple, quintuple, and sextuple).
- Confocal images of seeds/ovules from wild type vs mutants of the alfin genes (triple, quadruple, quintuple, and sextuple).
- Quantification of embryo elongation at the one-cell stage in wild-type and al sextuple mutant.
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Researchers evaluated embryo development at the globular stage in wild-type and al mutant seeds (triple, quadruple, quintuple, and sextuple) from self-pollinated plants based on clearing analysis. Confocal images were taken and embryo defects were measured in both wild-type and al mutants, and classified as either mild or severe. Suppose researchers observed altered flowering time, slow development, reduced plant height, fewer branches, longer internodes, and fewer flowers with disrupted phyllotaxis. Mark all the al mutants you would expect to exhibit this characteristic observed?
A. Four (quadruple) mutant.
B. Three (triple) mutants.
C. Five (quintuple) mutants.
D. Six (sextuple) mutants.
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C, D. Five (quintuple) mutants and Six (sextuple) mutants.
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- The MEA-PRC2 (also called FIS-PRC2) complex functions specifically in the female gametophyte, early embryo, and endosperm, a placental-like tissue that fills the seed cavity and provides nutrients to the growing embryo.
- ALFIN-LIKE (ALs), is a class of plant-specific PHD domain proteins that bind H3K4me3.
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[{"label":"RBK Item","value":"- The MEA-PRC2 (also called FIS-PRC2) complex functions specifically in the female gametophyte, early embryo, and endosperm, a placental-like tissue that fills the seed cavity and provides nutrients to the growing embryo."},{"label":"Title","value":"Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development\n\n"},{"label":"URL","value":"https://doi.org/10.1093/emboj/cdg444\n"},{"label":"Date","value":"September 15, 2003"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- ALFIN-LIKE (ALs), is a class of plant-specific PHD domain proteins that bind H3K4me3."},{"label":"Title","value":"Involvement of Alfin-Like Transcription Factors in Plant Development and Stress Response\n"},{"label":"URL","value":"https://doi.org/10.3390/genes15020184"},{"label":"Date","value":"January 29, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant genetics
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Free-Format Question
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AtSDR4L and its paralog DIG2 repress somatic embryogenesis during post-embryonic development in Arabidopsis
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https://www.biorxiv.org/content/10.1101/2025.09.19.677292v1
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September 21, 2025
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Researchers evaluated whether mutation of genes SEED DORMANCY 4-LIKE (Atsdr4l-5) and its paralog DYNAMIC INFLUENCER of GENE EXPRESSION 2 (dig2), had any effect in preventing the expression of positive regulators of somatic embryogenesis in seedlings of Arabidopsis thaliana and thus repressing somatic embryogenesis. To visualize if there is an influence of Atsdr4l-5 dig2 on the development of somatic embryogenesis, they induced callus formation by using Wildtype (Col-0) and double mutant (Atsdr4l-5 dig2) sterilized seeds that were inoculated in half-strength Murashige and Skoog (MS) medium (M0404, Sigma Aldrich) with 1% sucrose and 5 µM 2,4 D (D70724, Sigma Aldrich) and incubated at 4°C in the dark for 2 days (minimal condition). The seeds were shaken under light for 7 days at 130 rpm and were subjected to a 2,4 D-free half-strength Murashige and Skoog (MS) medium with 1% sucrose and 0.7 % phytogar for two weeks. The seedlings were then stained with Sudan Red 7B for 40 minutes and underwent two rounds of wash with water, followed by five rounds of 70 % ethanol wash. The formation of somatic embryos was observed and acquired using a Leica M205 FCA Fluorescence stereo microscope. Acquired images were processed with Fiji software v1.54k.
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- Development of callus tissue on wild-type and the double mutant (Atsdr4l-5 dig2) after auxin treatment.
- Development of somatic embryos on wild-type and the double mutant (Atsdr4l-5 dig2) after transferring the callus to an auxin-free medium.
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Somatic embryo development was assessed by microscopical observation in wild-type (WT) and double mutant (Atsdr4l-5 dig2) seeds of Arabidopsis thaliana. Seeds were inoculated in half-strength Murashige and Skoog (MS) medium (M0404, Sigma Aldrich) with 1% sucrose and 5 µM 2,4 D (D70724, Sigma Aldrich) and incubated at 4°C in the dark for 2 days. The seeds were shaken under light for 7 days at 130 rpm and were subjected to 2,4 D-free half-strength Murashige and Skoog (MS) medium with 1% sucrose and 0.7 % phytogar for two weeks. Seedlings were then stained with Sudan Red 7B for 40 minutes and underwent two rounds of wash with water, followed by five rounds of 70 % ethanol wash. The formation of somatic embryos was observed and acquired using a Leica M205 FCA Fluorescence stereo microscope. Acquired images were processed with Fiji software v1.54k. Based on microscopical observations, which genotype was able to induce somatic embryos under a minimal condition medium?
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In a minimal condition that can induce the callus formation in Col-0 seedlings without a subsequent formation of somatic embryos from calli, Atsdr4l-5 dig2 seedlings exhibited the formation of embryo-like structures from calli
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- Somatic embryogenesis is the capability to form asexual embryos arising from somatic cells, independent of fertilized gametes.
- SEED DORMANCY 4-LIKE (AtSDR4L) is a transcriptional corepressor from Arabidopsis thaliana that is an accessory to the Polycomb Repressive Complex.
- Atsdr4l loss-of-function mutants exhibit several developmental defects, including delayed germination, seedlings with swollen hypocotyls accompanied by the overaccumulation of fatty acids in this region, as well as growth arrest with a lack of true leaves and roots.
- DYNAMIC INFLUENCER of GENE EXPRESSION 2 (dig2) is a paralog of AtSDR4L.
|
[{"label":"RBK Item","value":"Somatic embryogenesis is the capability to form asexual embryos arising from somatic cells, independent of fertilized gametes."},{"label":"Title","value":"'Open minded' cells: how cells can change fate"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/17194589/"},{"label":"Date","value":"Mar, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"SEED DORMANCY 4-LIKE (AtSDR4L) is a transcriptional corepressor from Arabidopsis thaliana that is an accessory to the Polycomb Repressive Complex."},{"label":"Title","value":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8454663/"},{"label":"Date","value":"Jul 1, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Atsdr4l loss-of-function mutants exhibit several developmental defects, including delayed germination, seedlings with swollen hypocotyls accompanied by the overaccumulation of fatty acids in this region, as well as growth arrest with a lack of true leaves and roots."},{"label":"Title","value":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8454663/"},{"label":"Date","value":"Jul 1, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"DYNAMIC INFLUENCER of GENE EXPRESSION 2 (dig2) is a paralog of AtSDR4L."},{"label":"Title","value":"Co-repressors AtSDR4L and DIG1 interact with transcription factor VAL2 and promote Arabidopsis seed-to-seedling transition"},{"label":"URL","value":"https://watermark02.silverchair.com/kiae225.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAA1owggNWBgkqhkiG9w0BBwagggNHMIIDQwIBADCCAzwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM2Ni5hVm7Zma-e5-TAgEQgIIDDdiwsgULDJrKfgXG_P8GVwat-2naSSVZcHCT0ur75kJbNLY7lKTAxDRHzAqImBxnwVUf1lRCKWF0_9bsjFKBuve6H5Ie_UADUaqZ0odmmfDZErpXKTFrUhtwPqmVNJpg7Z9wz0YWZagoOc0F4tTt1DBnTdgPQJcac1aY6xrdALT7QfyTGYmFmFVGKUdIGCEF6Vak9An1val2w1z9J_FW3sDNu8wvHl_4eMgNnNgTzMNbJXg8PPinmx9XTvqOE8wocJp4Yk4-qPG8oaJt1Xzd5L1inxPX1Sq2t88M1rjRNV1Ebs3ygm2AV13xWyWFheCLh_U-DfH8z3jAyJJiMIno44ALj61dqDHAnj9U9DcybX_6yK-6gcD-elAZoI3syFOYZun3xDLw6trxGnFyHqr7gCi0n2GxrEd2Lu1mlIXs0qbfTLUrWBpm2CLGfI95_TXa9-0FttN8AE3b-aAWdbow7Q0wW5_3Qk7QTxIzJErSPVHamflUGPkjGqOOAxdPrh5oeZX06-kgNJHI-sKZmj97vv7kZsvw_v1G5sBsKDul-t7kbcO3Fk1EJPAUYo73Z21Z2rSdJ-uksVj7CzZHUTKwJ7WaQF5SMXOiqhkfcJjOF9O7DaBr6MHMqrTtBTHjsXFoIPF5nb4yHKUtQv5CmPCXjxG3Rp-9uGhFpFukHYA1O6z4b10CPPKqaGw3N_pnPlOW5g0P0Sv53dUhFKIQOy0Tx4a10BUB1ehbPvWEX2bEuLgAG09V1S-NJqE_7Sy12vlSobSVxUrw8bVqc_3nRXe_e9jcf4IAr_-c3IiEUg2LtPJgr02g1ebF3fPlsKAYmjcz3A7V9zBCrP9Ds83IjfqbD09MsVSzRVcFUgceKaJrUwjNHzzMk8B9_8R1n-Eout0soJHLlqN5peGbAZaYDxB-jDEidlm512WRBF59GH-7QE1HVj3PCe-lTSeowAjK8TDIv261WGqd9A8xGghCSCF8t2AJkF2XPoRwJJmgse9DeX72yqo-UyRnBDFWejXHH8xnm6_Epzs-ho4p0Z3BXMc"},{"label":"Date","value":"Apr 23, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Biology / Zoology
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Free-Format Question
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The genitals of rhinoceros beetles: a general overview of the endophallus in the tribe Agaocephalini (Coleoptera: Scarabaeidae: Dynastinae)
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https://www.biorxiv.org/content/10.1101/2025.09.18.677223v1
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September 21, 2025
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Researchers investigated the male genital structures (endophalli) of rhinoceros beetles in the tribe Agaocephalini. Selected specimens were softened by immersion in hot water for 10-20 minutes, and the abdomen was removed to extract the aedeagus. The tissues were digested in 10% KOH at room temperature for 6-24 hours depending on specimen condition, then transferred to distilled water, allowing partial eversion of the endophallus. Structures were washed in 70% ethanol and preserved in glycerol. To facilitate observation, endophalli were mounted in 2.5% carboxymethyl cellulose; specimens difficult to observe due to transparency were stained with 10% Nigrosin for contrast. For inflation, 2.5% carboxymethyl cellulose was injected through the phallobase using a 15 g oral zonde needle. Prepared structures were examined under Nikon SMZ645 stereoscope and Eclipse 50i microscope systems, photographed with a Nikon D5200 camera using macro lenses, and image stacks were processed with Zerene Stacker and retouched using Adobe Photoshop. A total of 93 specimens representing Agaocephalini and other comparative Dynastinae tribes were analyzed.
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-Extent of endophallus eversion after KOH digestion and water immersion.
-Visibility and contrast of endophalli with and without Nigrosin staining.
-Morphological characters of the endophallus (temones, lobes, endophalliculi, raspulae, endophallites) observed under stereoscope and microscope.
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Researchers prepared and examined the endophalli (male intromittent organs) of 93 rhinoceros beetle specimens representing Agaocephalini and comparative Dynastinae tribes. Specimens were digested in 10% KOH, washed, preserved in glycerol, and mounted in 2.5% carboxymethyl cellulose; some were stained with 10% Nigrosin or inflated for improved visibility. Endophallus morphology was then analyzed under stereoscope and microscope, with imaging performed using macro photography and image stacking. What would be the expected shape to result from the joining of the temones?
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A ring-like structure
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- The endophallus is a membranous sac encased inside the aedeagus, specifically within the median lobe, is composed of two sclerotized temones, a lobe (or lobes), and a number of spine-like endophallites.
- The aedeagus is the external sclerotized structure of the male genitalia, composed of a bilobed tegmen and a phallobase.
|
[{"label":"RBK Item","value":"The endophallus is a membranous sac encased inside the aedeagus, specifically within the median lobe, is composed of two sclerotized temones, a lobe (or lobes), and a number of spine-like endophallites."},{"label":"Title","value":"Morphology and terminology of dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae) male genitalia"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/26176150/"},{"label":"Date","value":"Jan, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"The aedeagus is the external sclerotized structure of the male genitalia, composed of a bilobed tegmen and a phallobase."},{"label":"Title","value":"The terminalia of the superfamily Scarabaeoidea (Coleoptera): specific glossary, dissecting methodology, techniques and previously unrecorded sexual dimorphism in some difficult groups"},{"label":"URL","value":"https://academic.oup.com/zoolinnean/article-abstract/191/4/1001/5879902?redirectedFrom=fulltext&login=false"},{"label":"Date","value":"Aug 03, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Animal Behavior, Behavioral Ecology
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Free-Format Question
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Vocally mediated coordination during a cooperative task in parrots
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https://www.biorxiv.org/content/10.1101/2025.10.10.681640v1
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October 11, 2025
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Researchers investigated whether peach-fronted conures (small parrots) use vocal communication to coordinate during a cooperative string-pulling task. Four individuals (two males, two females) were tested in all six pairwise combinations. The apparatus consisted of an out-of-reach sliding board with food rewards, featuring two eyelets through which a wool string passed into the birds' individual cages. To retrieve food, both birds had to pull their string ends simultaneously; solo pulling caused the string to slip without reward. Birds were separated by a remotely operated trap door, with a cardboard barrier providing visual isolation in some conditions.
Each pair was tested under four conditions differing only in visual access and release timing: (1) 'Cooperative' (visual contact, simultaneous release), (2) 'Delayed' (visual contact, staggered release with Bird 1 waiting for Bird 2), (3) 'Blind' (visual barrier, simultaneous release), and (4) 'Blind delayed' (visual barrier, staggered release). In delayed conditions, Bird 1's door opened first; after a 5-second delay, Bird 2's door opened. Each bird completed 20 trials per condition in each pairing role (Bird 1 or Bird 2 in delayed conditions).
Vocalizations were recorded using a free-field microphone positioned 15 cm above the cages and digitized at 16-bit/44.1 kHz. Video footage from two synchronized webcams (25 fps) allowed matching each vocalization to its caller by observing beak opening. Calls were classified into nine distinct types (aggressive, contact, contact soft, high harmonics, intense, soft, soft harmonics, soft intense, readiness-call) using hierarchical cluster analysis (hclust function, R stats package) based on peak frequency, peak pressure, and first quartile acoustic features.
The critical coordination window was defined from when Bird 1 reached the string until trial completion. Trial outcomes (success or failure) were recorded via video analysis. Fisher's exact tests determined statistical associations between specific call types and trial outcomes in each condition.
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- Vocalization type per call: Units: Categorical (9 types: aggressive, contact, contact soft, high harmonics, intense, soft, soft harmonics, soft intense, readiness-call), determined by hierarchical cluster analysis (hclust, R stats package) applied to audio recordings; recorded across all trials over four experimental conditions (Cooperative, Delayed, Blind, Blind delayed) for all six parrot pairs
- Trial outcome per trial: Units: Binary (success or failure), determined by visual observation of synchronized video footage (two webcams, 25 fps), recorded across all trials over four experimental conditions (Cooperative, Delayed, Blind, Blind delayed) for all six parrot pairs
- Call occurrence during critical coordination window per call: Units: Binary (present during window or not), determined by temporal synchronization of audio recordings with video timestamps; recorded across all trials over four experimental conditions (Cooperative, Delayed, Blind, Blind delayed) for all six parrot pairs
- Caller identity per call. Units: Categorical (four labelled individuals), determined by visual observation via video analysis, recorded across all trials over four experimental conditions (Cooperative, Delayed, Blind, Blind delayed) for all six parrot pairs
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An experiment investigated whether peach-fronted conures (small parrots) use vocal communication to coordinate during a cooperative string-pulling task. The task required each pair to pull the two ends of a loose string at the same time. If either bird acted alone the string slipped and no reward was obtained (trial failure). Birds were tested in four conditions: (1) 'Cooperative' (visual contact, simultaneous release), (2) 'Delayed' (visual contact, staggered release with Bird 1 waiting for Bird 2), (3) 'Blind' (visual barrier, simultaneous release), and (4) 'Blind delayed' (visual barrier, staggered release). The critical coordination window was defined as the time from when Bird 1 arrived at the string, continuing until success or failure. Vocalizations were recorded continuously and classified into nine distinct call types: aggressive, contact, contact soft, high harmonics, intense, soft, soft harmonics, soft intense, and readiness-call. The researchers analyzed which specific call types were associated with successful versus unsuccessful coordination in each condition, using Fisher's exact tests to determine statistical associations between individual call types and trial outcomes.
During the critical coordination window in the Blind delayed condition, which call type(s), if any, showed significant associations with trial failure?
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High harmonics and Intense calls showed significant associations with trial failure.
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- Communication is a social event where an emitter produces a signal to be received by a listener with the purpose of influencing the listener’s behavior; communication has occurred when the listener receives and responds to the emitted signal.
- In many animal species, vocalizations play a crucial role in coordinating group behaviors
- Vocalizations not only help coordinate group activities but also enable cooperation to accomplish shared tasks to achieve common goals
- Parrots show many cognitive abilities similar to those observed in large-brained mammals such apes and dolphins
- Parrots rely heavily on vocal communication, since their gestural repertoire is limited
|
[{"label":"RBK Item","value":"Communication is a social event where an emitter produces a signal to be received by a listener with the purpose of influencing the listener’s behavior; communication has occurred when the listener receives and responds to the emitted signal."},{"label":"Title","value":"Signalers and receivers in animal communication"},{"label":"URL","value":"https://www.annualreviews.org/content/journals/10.1146/annurev.psych.54.101601.145121"},{"label":"Date","value":"September 17, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"In many animal species, vocalizations play a crucial role in coordinating group behaviors."},{"label":"Title","value":"Sneeze to leave: African wild dogs (Lycaon pictus) use variable quorum thresholds facilitated by sneezes in collective decisions"},{"label":"URL","value":"https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0347"},{"label":"Date","value":"September 06, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Vocalizations not only help coordinate group activities but also enable cooperation to accomplish shared tasks to achieve common goals"},{"label":"Title","value":"Evidence that bottlenose dolphins can communicate with vocal signals to solve a cooperative task"},{"label":"URL","value":"https://royalsocietypublishing.org/doi/10.1098/rsos.202073"},{"label":"Date","value":"March 17, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Parrots show many cognitive abilities similar to those observed in large-brained mammals such apes and dolphins"},{"label":"Title","value":"Cognitive and communicative abilities of grey parrots"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0168159106001055"},{"label":"Date","value":"June 27, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Parrots rely heavily on vocal communication, since their gestural repertoire is limited"},{"label":"Title","value":"Gestural communication in a new world parrot"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0376635714000680"},{"label":"Date","value":"March 12, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Microbiology
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Free-Format Question
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Thyme essential oil potentials as a bactericidal and biofilm-preventive agent against prevalent bacterial pathogens
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https://www.nature.com/articles/s41598-025-16485-5
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August 27, 2025
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Researchers evaluated the antibacterial activity of nine essential oils (ginger oil, basil oil, thyme oil, peppermint oil, clove oil, sage oil, geranium oil, lavender oil, and garlic oil) against gram-positive and gram-negative pathogens (Staphylococcus aureus ATCC 25,923, Methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43,300, Bacillus cereus ATCC 33,018, Listeria innocua ATCC 33,090, Listeria monocytogenes ATCC 19,115, Pseudomonas aeruginosa ATCC 35,032, Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14,028, Shiga toxin-producing Escherichia coli (STEC) wild type strain 93111, and Escherichia coli O157:H7 ATCC 700,728). Bacterial strains were cultured overnight (TGY broth medium). 100 µl of bacterial broth culture (108 CFU/ml, 0.5 McFarland standard) were seeded on MH agar with 6.0mm diameter wells. Essential oils were applied (100 mg/mL in DMSO and 60 µl of each oil transferred into a well in triplicate). DMSO only was used as a negative control, and gentamicin (Gram+) and ampicillin (Gram -) as positive controls. The diameter of the zone of inhibition was measured after incubation at optimal temperatures (30-37 °C) for 24 hours.
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- Zone of inhibition (mm) of essential oils (ginger oil, basil oil, thyme oil, peppermint oil, clove oil, sage oil, geranium oil, lavender oil, and garlic oil) against bacterial srains (Staphylococcus aureus ATCC 25,923, Methicillin-resistant Staphylococcus aureus MRSA ATCC 43,300, Bacillus cereus ATCC 33,018, Listeria innocua ATCC 33,090, Listeria monocytogenes ATCC 19,115, Pseudomonas aeruginosa ATCC 35,032, Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14,028, Shiga toxin-producing Escherichia coli (STEC) wild type strain 93111, and Escherichia coli O157:H7 ATCC 700,728).
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Researchers tested nine essential oils (ginger, basil, thyme, peppermint, clove, sage, geranium, lavender, and garlic) against both Gram-positive and Gram-negative pathogenic bacteria (Staphylococcus aureus ATCC 25923, Methicillin-resistant Staphylococcus aureus MRSA ATCC 43300, Bacillus cereus ATCC 33018, Listeria innocua ATCC 33090, Listeria monocytogenes ATCC 19115, Pseudomonas aeruginosa ATCC 35032, Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028, Shiga toxin-producing Escherichia coli (STEC) wild type strain 93111, and Escherichia coli O157:H7 ATCC 700728) using an agar well diffusion assay. The bacteria were cultured overnight, and then 100 µl of bacterial broth culture (10^8 CFU/ml, 0.5 McFarland standard) was seeded on MH agar. Afterward, 6.0mm diameter wells were introduced into the agar. Essential oils were applied (100 mg/mL in DMSO), and 60 µl of each oil was transferred into a well in triplicate. DMSO only was used as a negative control, and gentamicin (Gram+) and ampicillin (Gram -) as positive controls. The plates were incubated at 30-37 °C for 24 hours before measuring inhibition zone (mm). Predict which essential oil will produce the smallest inhibition zone against Bacillus cereus ATCC 33018.
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Sage oil and Geranium oil will produce the smallest inhibition zone against Bacillus cereus ATCC 33018
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- Plant essential oils (EOs) have low molecular weights and are lipophilic, allowing them to penetrate tissues quickly and efficiently.
- EOs are considered antimicrobial.
- EOs can interact with the lipid bilayer of bacterial cell membranes and disrupt function (cell cycle, protein synthesis, DNA replication, motility, QS activity, cell adhesion, and EPS formation).
|
[{"label":"RBK Item","value":"Plant essential oils (EOs) have low molecular weights and are lipophilic, allowing them to penetrate tissues quickly and efficiently.\n"},{"label":"Title","value":"Antioxidant, antimicrobial, and antibiofilm properties of essential oils extracted from Dialium guineense."},{"label":"URL","value":"https://www.tandfonline.com/doi/full/10.1080/10942912.2023.2236322#abstract"},{"label":"Date","value":"November 28, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"EOs are considered antimicrobial."},{"label":"Title","value":"Essential oils: A promising eco-friendly food preservative. Food Chem. "},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0308814620311304"},{"label":"Date","value":"November 15, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"EOs can interact with the lipid bilayer of bacterial cell membranes and disrupt function (cell cycle, protein synthesis, DNA replication, motility, QS activity, cell adhesion, and EPS formation).\n"},{"label":"Title","value":"Anti-biofilm mechanisms of action of essential oils by targeting genes involved in quorum sensing, motility, adhesion, and virulence: A review."},{"label":"URL","value":"https://www.mdpi.com/2079-6382/14/5/503"},{"label":"Date","value":"May 13, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
|
Cancer Biology
|
Numerical Values
|
Mitochondria-targeting polymer cLipG/CuET activates the cGAS/STING pathway to enhance cholangiocarcinoma immunotherapy
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https://pmc.ncbi.nlm.nih.gov/articles/PMC12512424/
|
Oct 09, 2025
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Researchers evaluated whether cLipG/CuET alone or in combination with αCTLA-4 exhibits anti-cancer activity in a cholangiocarcinoma (CCA) mouse (C57BL/6J) model. To establish the CCA model, each mouse received a hydrodynamic tail-vein injection containing 25 µg of KRAS^G12D and 10 µg of sgP19 plasmids together with Sleeping Beauty (SB) transposase. CCA-bearing mice were randomly divided into four groups: saline control, cLipG/CuET monotherapy, αCTLA-4 monotherapy, and combined cLipG/CuET + αCTLA-4 treatment. For the cLipG/CuET group, mice received tail-vein injections every two days throughout the 21-day study period. The αCTLA-4 group received intraperitoneal injections three times per week. Body weight was measured at each treatment point to monitor general health. After 21 days of treatment, mice were sacrificed under approved ethical protocols, and livers were excised and weighed to assess tumor burden.
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- Body weight (g) of mice recorded throughout the 21-day treatment period after different treatments (saline, cLipG/CuET, αCTLA-4, and cLipG/CuET + αCTLA-4)
- Liver weight (g) measured at necropsy of mice to assess tumor burden after different treatments (saline, cLipG/CuET, αCTLA-4, and cLipG/CuET + αCTLA-4).
- Liver weight/body weight in mice after different treatments (saline, cLipG/CuET, αCTLA-4, and cLipG/CuET + αCTLA-4)
|
Researchers treated cholangiocarcinoma (CCA) model mice with cLipG/CuET alone, αCTLA-4 alone, or a combination of cLipG/CuET and αCTLA-4 for 21 days. The cLipG/CuET was administered intravenously every other day, and αCTLA-4 was administered intraperitoneally three times per week. After the 21-day treatment, mice were sacrificed, and tumor growth, body weight and liver weight were measured. What would be the expected body weight of CCA model mice on day 6 after treatment with αCTLA-4?
|
Weight = [19.44 - 23.76] g , derived from body weight ~21.60 g after treatment with αCTLA-4 in CCA model mice on day 6. Note: No CI/SE/SD reported -> fallback ±2.16 g applied.
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- CTLA-4-positive are lymphocytes that are more enriched in Intrahepatic cholangiocarcinoma (ICC) tissues than in peritumoral liver tissues.
- cLipo is modified with disulfiram copper (CuET) to form nanoparticles (Lipo@CuET, cLipo/CuET) with a stronger anti-cancer efficacy.
- CuET is a novel copper ethylthiocarbamate complex formed by the drug disulfiram (DSF), primarily used for treating alcohol addiction in combination with copper. Due to the presence of copper, CuET greatly enhances the anti-cancer property of DSF.
|
[{"label":"RBK Item","value":"CTLA-4-positive are lymphocytes that are more enriched in Intrahepatic cholangiocarcinoma (ICC) tissues than in peritumoral liver tissues.\n"},{"label":"Title","value":"Reprogramming the Intrahepatic Cholangiocarcinoma Immune Microenvironment by Chemotherapy and CTLA-4 Blockade Enhances Anti–PD-1 Therapy"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10985468/"},{"label":"Date","value":"Jan 22, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"CuET is a novel copper ethylthiocarbamate complex formed by the drug disulfiram (DSF), primarily used for treating alcohol addiction in combination with copper. Due to the presence of copper, CuET greatly enhances the anti-cancer property of DSF."},{"label":"Title","value":"Alcohol-abuse drug disulfiram targets cancer via p97 segregase adaptor NPL4"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5730499/"},{"label":"Date","value":"Dec 6, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
|
Infectious Disease
|
Numerical Values
|
Therapeutic potential of greenly synthesized selenium nanoparticles against experimental cyclosporiasis
|
https://www.nature.com/articles/s41598-025-15238-8
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August 17, 2025
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Researchers studied the therapeutic potential of greenly synthesized selenium nanoparticles (SeNPs) in the treatment of Cycolospora cayetanensis infection. Swiss albino mice (male, 4-6 weeks, weighing 23+/- 2 g) were rendered immunocompromised by weekly intraperitoneal injections of cyclophosphamide (70 mg/kg) and orally infected with 10,000 Cycolospora oocysts (sporulated, 48 h after 2nd immunosuppression dose, 10^4 oocysts/0.1mL of PBS per mouse) isolated and purified from heavily infected HIV patients. SeNPs were synthesized by incubating the cell-free filtrate of Alcaligenes faecalis with sodium selenite to form stable nanoparticles. The mice (n=42) were divided into four groups: healthy uninfected untreated controls (n=6), infected untreated controls (n=12), infected mice treated with cotrimoxazole (CMX; 5 mg/kg trimethoprim + 25 mg/kg sulfamethoxazole daily for 7 days)(n=12), and infected mice treated with SeNPs (10 mg/kg orally for 7 consecutive days beginning on day 6 post-infection)(n=12). Half of the mice were sacrificed for evaluations on day 14 post infection for assessment of the efficacy of therapy, and the other half on day 30 for assessment of recurrence. Serum reduced glutathione (GSH) and malondialdehyde (MDA) levels were measured in sera of mice in all studied groups on the 14th day post infection using a colorimetric kit according to the manufacturer’s instructions.
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- Serum levels of malondialdehyde (MDA) (mol/mL) across groups (healthy uninfected untreated, infected untreated, infected mice treated with cotrimoxazole, and infected mice treated with SeNPs) on day 14 post-infection.
- Serum levels of reduced glutathione (GSH) (mg/dL) across groups (healthy uninfected untreated, infected untreated, infected mice treated with cotrimoxazole, and infected mice treated with SeNPs) on day 14 post-infection.
|
Researchers studied the therapeutic potential of greenly synthesized selenium nanoparticles (SeNPs) in the treatment of Cycolospora cayetanensis infection. Swiss albino mice (male, 4-6 weeks, weighing 23+/- 2g) were rendered immunocompromised by weekly intraperitoneal injections of cyclophosphamide (70 mg/kg). Mice (n=42) were divided into four groups: healthy uninfected untreated controls (n=6), infected untreated controls (n=12), infected mice treated with cotrimoxazole (n=12), and infected mice treated with SeNPs. Infected mice were orally administrated with 10,000 Cycolospora oocysts (sporulated, 48 h after 2nd immunosuppression dose, 10^4 oocysts/0.1mL of PBS per mouse). On day 6 post-infection, infected treated groups were administrated for 7 days with either cotrimoxazole (5 mg/kg trimethoprim + 25 mg/kg sulfamethoxazole daily) or SeNPs (10 mg/kg orally). On day 14 post-infection, serum markers of oxidative stress, reduced glutathione (GSH) and malondialdehyde (MDA) were measured using a colorimetric kit. What is the expected mean serum reduced glutathione (GSH) level (mg/dL) in the SeNP-treated group on day 14 post-infection?
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MeanGSH = [4.30 – 5.22] mg/dL. Fallback ±0.46 SD.
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- Cyclospora cayetanensis is a protozoan parasite that causes diarrheal disease in immunosuppressed individuals.
- Cotrimoxazole (TMP-SMX) is the standard drug for cyclosporiasis infections.
- Selenium nanoparticles (SeNPs) are experimental, eco-friendly nanotherapeutics that exhibit high metabolic stability, membrane permeability, and low toxicity.
- Redox imbalance during intracellular coccidian infection dominates due to the upsurge of malondialdehyde (MDA) levels and subsequent depletion of endogenous glutathione (GSH), leading to tissue pathology and damage.
|
[{"label":"RBK Item","value":"- Cyclospora cayetanensis is a protozoan parasite that causes diarrheal disease in immunosuppressed individuals. "},{"label":"Title","value":"Cyclospora Cayetanensis Cyclosporiasis: Update Microorganisms "},{"label":"URL","value":"https://www.mdpi.com/2076-2607/7/9/317"},{"label":"Date","value":"September 4, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Cotrimoxazole (TMP-SMX) is the standard drug for cyclosporiasis infections."},{"label":"Title","value":"Isatin-1,2,3-triazole derivatives: synthesis, molecular Docking and evaluation against acute experimental toxoplasmosis. "},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0001706X24003528?via%3Dihub"},{"label":"Date","value":"December, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Selenium nanoparticles (SeNPs) are experimental, eco-friendly nanotherapeutics that exhibit high metabolic stability, membrane permeability, and low toxicity."},{"label":"Title","value":" Recent research progress on the synthesis and biological effects of selenium nanoparticles"},{"label":"URL","value":"https://www.frontiersin.org/journals/nutrition/articles/10.3389/fnut.2023.1183487/full"},{"label":"Date","value":"May 15, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Redox imbalance during intracellular coccidian infection dominates due to the upsurge of malondialdehyde (MDA) levels and subsequent depletion of endogenous glutathione (GSH), leading to tissue pathology and damage."},{"label":"Title","value":"Biogenic selenium nanoparticles: trace element with promising anti-toxoplasma effect"},{"label":"URL","value":"https://www.tandfonline.com/doi/full/10.1080/20477724.2023.2186079"},{"label":"Date","value":"Mar 05, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Chemistry
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Organic Synthesis
|
MCQ
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Selective Nitration and Nitrosation of ArylBoronic Acid Derivatives with N-Nitrososulfonamides
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https://pmc.ncbi.nlm.nih.gov/articles/PMC12332795/
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May 15, 2025
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Researchers performed the selective nitrosation of arylboronic acids using a controlled solution-phase method under mild, metal-free conditions. In a typical experiment, arylboronic acid (0.1 mmol) was combined with nitrosating reagent NO-1 (1.0 equiv) in dichloromethane (1 mL, 0.1 M) at room temperature (25 °C). Acetic acid (10 mol%) was added as a catalyst to promote the nitrosation process. The mixture was stirred under air for a defined reaction time (24 h) to ensure complete conversion. After the reaction, the mixture was directly analyzed without further oxidation steps. Product structures were confirmed by ¹H NMR (400 MHz), ¹³C NMR (100 MHz), and mass spectrometry (MS) to verify the formation of nitrosoarenes.
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- Product yield (%) measured by chromatographic isolation to quantify the conversion efficiency of arylboronic acids or aryltrifluoroborates to nitroso or nitroarenes.
- Product identity and purity verified using ¹H NMR (400 MHz) and ¹³C NMR (100 MHz) spectroscopy.
- Electronic substituent effects (σp values) analyzed to correlate substituent electron-withdrawing/donating strength with product selectivity.
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A mild, metal-free protocol was established for the nitration and nitrosation of arylboronic acids and aryltrifluoroborates using the nitrosating reagent NO-1 in dichloromethane (0.1 M, 25 °C). The effects of acid catalysts (AcOH, HCl), reaction time, and substituent electronics were systematically examined to control product selectivity.
At what range of Hammett constant (σp) values for the 4-position substituent will the direct nitrosation/nitration of arylboronic acids begin to exclusively favor the NO₂ product (nitration)?
A. Highly negative, approximately -0.40
B. Highly positive, approaching +0.80
C. In the range of approximately 0.20 to 0.40
D. Exactly 0.00 (unsubstituted arene)
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C. In the range of approximately 0.20 to 0.40
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- 3,3-dimethyl-2-nitroso-2,3-dihydrobenzo[d]isothiazol-1,1-dioxide is a source of nitroso groups, however is only able to achieve nitrosation via ipso substitution.
- Aryl substitution products and rates can often be rationalised through the use of Hammett constants which is a measure of the electronic effect a functional group has on the system.
|
[{"label":"RBK Item","value":"3,3-dimethyl-2-nitroso-2,3-dihydrobenzo[d]isothiazol-1,1-dioxide is an electrophilic source of nitroso groups"},{"label":"Title","value":"Versatile New Reagent for Nitrosation under Mild Conditions"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/acs.orglett.1c00637?ref=PDF"},{"label":"Date","value":"April 12, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, no OA paper available."},{"label":"RBK Item","value":"Aryl substitution products and rates can often be rationalised through the use of Hammett constants"},{"label":"Title","value":"A survey of Hammett substituent constants and resonance and field parameters"},{"label":"URL","value":"https://pubs.acs.org/doi/abs/10.1021/cr00002a004?ref=PDF"},{"label":"Date","value":"March 1, 1991"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, common paper on the subject"}]
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Biology
|
Microbiology
|
Numerical Values
|
Indolicidin derivatives as potent dual-action antifungal and antibacterial agents for the treatment of skin infections: A comprehensive study from in vitro to in vivo evaluation
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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0331796
|
September 5, 2025
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Researchers evaluated a novel antimicrobial peptide (AMP), synthesized from Indolicidin (IND-4, 11K), for antimicrobial efficacy against Gram-positive bacteria, Gram-negative bacteria, and Candida albicans. IND-4, 11K was designed by replacing proline at positions 3 and 10 with lysine (via solid-phase peptide synthesis) for in vitro testing against the parent peptide (IND). S. aureus, P. aeruginosa, S. epidermidis, E. coli, K. pneumoniae, Enterococcus, and Candida albicans strains were prepared from ATCC stocks, revived on nutrient media and prepped for testing (adjusted to 0.5 McFarland, diluted to 10^6 CFU/mL, then 1:100 in Brain-Heart Infusion (BHI) broth to 10⁴ CFU/mL). Serial twofold dilutions of peptides IND and IND-4, 11K (1280-80 µM) were prepared in 96-well plates in triplicate with Muller-Hinton broth and inoculated with microbial suspension (37 °C for 24 h). MIC (minimum inhibitory concentration) was measured as the lowest concentration with no growth (OD620), and MBC (minimum bactericidal concentration) was measured by subculturing from MIC and higher wells onto MH agar (observe colony formation after 24h). Controls included streptomycin (Gram -), penicillin (Gram +), and nystatin (fungal) with PBS as a negative control.
|
- Minimum inhibitory concentration (MIC) (µM) across strains (S. aureus, P. aeruginosa, S. epidermidis, E. coli, K. pneumoniae, Enterococcus, and Candida albicans) after administration of serial twofold dilutions of peptides IND and IND-4, 11K (1280-80 µM)
- Minimum bactericidal concentration (MBC) (µM) across strains (S. aureus, P. aeruginosa, S. epidermidis, E. coli, K. pneumoniae, Enterococcus, and Candida albicans) after administration of serial twofold dilutions of peptides IND and IND-4, 11K (1280-80 µM)
|
In an in vitro antimicrobial study, researchers tested a novel peptide (IND-4,11K), derived from Indolicidin, against several bacterial and fungal pathogens. Pseudomonas aeruginosa ATCC strains were revived on nutrient media, adjusted to ~10⁴ CFU/mL, and inoculated into 96-well plates containing Müller–Hinton broth. Peptides IND and IND-4,11K were prepared in twofold serial dilutions from 1280 µM down to 80 µM, and the plates were incubated at 37 °C for 24 hours. The minimum inhibitory concentration (MIC) was defined as the lowest peptide concentration at which no visible microbial growth was observed, measured by optical density at OD₆₂₀.
Predict the minimum inhibitory concentration (MIC) of IND-4,11K against Pseudomonas aeruginosa?
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116-140 µM
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- AMPs (antimicrobial peptides) are short peptides that exhibit broad-spectrum activity by targeting bacterial membranes or inhibiting intracellular processes.
- IND-4, 11K is an indolicidin derivative, replacing prolines at positions 3 and 10 with lysine.
|
[{"label":"RBK Item","value":"AMPs (antimicrobial peptides) are short peptides that exhibit broad-spectrum activity by targeting bacterial membranes or inhibiting intracellular processes. "},{"label":"Title","value":"Antimicrobial host defence peptides: functions and clinical potential"},{"label":"URL","value":"https://www.nature.com/articles/s41573-019-0058-8"},{"label":"Date","value":"Feb 27, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":" IND-4, 11K is an indolicidin derivative, replacing prolines at positions 3 and 10 with lysine."},{"label":"Title","value":"Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis. Nature protocols."},{"label":"Date","value":"May 12, 2011"},{"label":"URL","value":"https://www.nature.com/articles/nprot.2011.324"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Chemistry
|
Analytical Chemistry
|
Free-Format Question
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Olfactory Experiments with Cotton or Viscose Pads: Major Chemical Confounders Detected by GCxGC-QTOF
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/68418f361a8f9bdab5ea55d6/original/olfactory-experiments-with-cotton-or-viscose-pads-major-chemical-confounders-detected-by-g-cx-gc-q-tof.pdf
|
June 10, 2025
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Researchers used two pad types to evaluate volatile emissions under controlled conditions: Dermatess (10 × 10 cm, 67% viscose / 33% polyester; Pietrasanta Pharma, Italy) and Cutisorb (10 × 10 cm, 100% cotton; BSN Medical, Germany). Water (Arium Pro, Sartorius) was evenly dosed to simulate sweat. For 25 °C dynamic headspace (DHS), pads received 0, 100, 200, 300, 500 µL with four replicate per condition and no thermal pre-treatment. For 60 °C DHS, pads received 0, 100, 150, 200, 300, 500 µL with five replicate per pad type; an additional set was pre-baked at 150 °C for 20 min before dosing. DHS was performed in a Markes µ-Chamber: stainless chambers were conditioned at 150 °C for 20 min under Nitrogen flow of 150 mL min⁻¹ (LNI Swissgas NG EOLO10L), cooled to 25 °C, purge off, then fitted with Tenax-GR sorbent tubes (120 mg; poly-2,6-diphenylphenylene oxide with 23% carbon; 60/80 mesh; mean particle size 0.5 µm). On-line thermal desorption used a Markes Centri platform with two-stage desorption to enable refocusing and flow compatibility (TD 25–75 mL min⁻¹; capillary GC 0.5–5 mL min⁻¹). GC×GC analysis employed an Agilent 7890B with capillary-flow modulator, a DB-5MS first dimension (30 m × 0.25 mm × 0.25 µm) and DB-INNOWAX second dimension (5 m × 0.25 mm × 0.15 µm), helium 5.0 in constant-flow mode (0.5 mL min⁻¹ in 1D; 18 mL min⁻¹ in 2D), and a 2 seconds modulation period. Identification used spectral similarity > 750, LRI proximity ≤ 50 units, and elemental-formula spectral accuracy < 10 ppm.
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• Measurement of VOC release from cotton and viscose-polyester pads.
• Comparison of VOC release across different water volumes (0, 100, 150, 200, 300, 500 µL).
• Comparison of VOC release at different extraction temperatures (25°C and 60°C).
• Measurement of the effect of thermal pre-treatment (150°C for 20 minutes) on VOC release.
• Quantification of the fold change in peak volume for individual VOCs upon water addition.
• Determination of the statistical significance (p-value) of changes in VOC release.
• Estimation of extracted VOC amounts relative to an internal standard (d₅-chlorobenzene).
• Analysis of VOC release patterns (exponential vs. linear) in response to water addition.
• Identification of VOCs using criteria for spectral similarity, linear retention index, and mass accuracy.
|
The effects of water load and extraction temperature (0–500 µL; 25 °C and 60 °C) were evaluated using Dermatess pads (10 × 10 cm, 67% viscose/33% polyester) and Cutisorb pads (10 × 10 cm, 100% cotton). Pads were extracted by dynamic headspace in a Markes µ-Chamber (N₂ 150 mL min⁻¹ conditioning), and analytes collected on Tenax-GR sorbent tubes. VOC concentrations were measured immediately after extraction by on-line thermal desorption (Markes Centri) coupled to GC×GC–QTOF-MS (Agilent 7890B; DB-5MS × DB-INNOWAX; Helium constant-flow; 2 seconds modulation), and compounds were identified using spectral similarity > 750, LRI proximity ≤ 50 units, and elemental-formula spectral accuracy < 10 ppm.
Beyond simply increasing the amount of VOCs released, how did the fundamental emission pattern differ between cotton and viscose-polyester pads as more water was added?
|
The VOC release from cotton pads followed a consistent exponential trend, whereas the release from viscose-polyester pads was biphasic, starting exponentially at lower water volumes and then transitioning to a more linear increase at higher volumes.
|
-VOCs are volatile organic compounds that are highly spontaneous and readily react in air through several physical and chemical reactions. VOCs are released when moisture or heat interacts with materials like cotton and viscose-polyester
- Thermal desorption (TD) is a physical remediation method used to treat contaminants, particularly for volatile and semi-volatile contaminants
|
[{"label":"RBK Item","value":"VOCs are volatile organic compounds that are highly spontaneous and readily react with the particles of ambiance and produce a polluted atmosphere through several physical and chemical reactions. VOCs are released when moisture or heat interacts with materials like cotton and viscose-polyester\n"},{"label":"Title","value":"Environmental and human health impacts of volatile organic compounds: A perspective review"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0045653522039820"},{"label":"Date","value":"February, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Thermal desorption (TD) is a physical remediation method used to treat contaminants, particularly for volatile and semi-volatile contaminants "},{"label":"Title","value":"Thermal desorption for remediation of contaminated soil: A review"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0045653519300797"},{"label":"Date","value":"April, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
|
Physics
|
Mesoscale and Nanoscale Physics
|
MCQ
|
Giant Spin-to-Charge Conversion by Tailoring Magnetically Proximitized Topological Dirac Semimetal
|
https://arxiv.org/abs/2507.17639
|
July 23, 2025
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Researchers investigated the influence of the magnetic proximity effect (MPE) on spin-to-charge conversion efficiency in ferromagnet/topological Dirac semimetal (TDS) bilayers. A series of Fe (4 nm)/α-Sn (tₛₙ = 0, 9, 25, 32.5, and 35 nm)/InSb heterostructures were fabricated using molecular beam epitaxy (MBE) on InSb (001) substrates. The substrates were annealed at 400°C to remove oxide layers, followed by the growth of a 100-200 nm InSb buffer layer at 500 nm h⁻¹ to achieve an atomically flat surface. For α-Sn thicknesses between 9 nm and 32.5 nm, the InSb surface was terminated by an In-rich reconstruction. The α-Sn and Fe layers were then deposited at rates of 1 nm min⁻¹ and 0.25 nm min⁻¹, respectively, and capped with a 3-5 nm Al layer to prevent oxidation. Frequency-dependent ferromagnetic resonance (FMR) spectroscopy was carried out on Fe (4 nm) / α-Sn (tₛₙ = 0 – 35 nm) / InSb heterostructures at room temperature using a coplanar waveguide and Keysight vector network analyzer (VNA).
|
- The frequency dependence of the peak to peak linewidth of the resonant field is measured against tₛₙ in 0 – 35 nm range from FMR spectrum.
|
Researchers investigated the influence of the magnetic proximity effect (MPE) on spin-to-charge conversion efficiency in ferromagnet/topological Dirac semimetal (TDS) bilayers. A series of Fe (4 nm)/α-Sn (tₛₙ = 0, 9, 25, 32.5, and 35 nm)/InSb heterostructures were fabricated using molecular beam epitaxy (MBE). Frequency-dependent ferromagnetic resonance (FMR) spectroscopy was carried out on Fe (4 nm) / α-Sn (tₛₙ = 0 – 35 nm) / InSb heterostructures at room temperature using a coplanar waveguide and Keysight vector network analyzer (VNA). Predict which is correct for the Gilbert damping constant α measured from the frequency dependence of the peak-to-peak linewidth of the resonant field against tₛₙ.
a) A pronounced increase in α is observed as the α-Sn layer thickness increases from tₛₙ = 0 nm to tₛₙ = 35 nm.
b) A pronounced increase in α is observed as the α-Sn layer thickness increases from tₛₙ = 0 nm to tₛₙ = 25 nm, and then remains almost constant as tₛₙ exceeds 25 nm.
c) A pronounced decrease in α is observed as the α-Sn layer thickness increases from tₛₙ = 0 nm to tₛₙ = 25 nm, followed by an increase as tₛₙ exceeds 25 nm.
d) A pronounced increase in α is observed as the α-Sn layer thickness increases from tₛₙ = 0 nm to tₛₙ = 25 nm, followed by a decrease as tₛₙ exceeds 25 nm.
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d) A pronounced increase in α is observed as the α-Sn layer thickness increases from tₛₙ = 0 nm to tₛₙ = 25 nm, followed by a decrease as tₛₙ exceeds 25 nm.
|
- It has been shown that spin-charge interconversion is absent at the interface of Fe and topological insulator (TI) α-Sn thin film (5 nm), and an Fe/Ag (2 nm)/α-Sn (5 nm) heterostructure exhibited a very high efficiency of spin-charge conversion, which was quantified as an inverse Edelstein length (λIEE) of 2.1 nm.
- TDSs represent a rare class of topological materials characterized by linear band dispersions (Dirac cones), and these Dirac cones are composed of spin-degenerate linear bands, exhibiting strong coupling between spin, orbital, and momentum degrees of freedom.
- The α-Sn, have promising preliminary results to exhibit highly
efficient spin-charge interconversion and magnetization reversal.
|
[{"label":"RBK Item","value":"It has been shown that spin-charge interconversion is absent at the interface of Fe and topological insulator (TI) α-Sn thin film (5 nm), and an Fe/Ag (2 nm)/α-Sn (5 nm) heterostructure exhibited a very high efficiency of spin-charge conversion, which was quantified as an inverse Edelstein length (λIEE) of 2.1 nm."},{"label":"Title","value":"Spin to Charge Conversion at Room Temperature by Spin Pumping into a New Type of Topological Insulator: 𝛼-Sn Films"},{"label":"URL","value":"https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.096602"},{"label":"Date","value":"Mar 1, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 7 in the paper"},{"label":"RBK Item","value":"TDSs represent a rare class of topological materials characterized by linear band dispersions (Dirac cones), and these Dirac cones are composed of spin-degenerate linear bands, exhibiting strong coupling between spin, orbital, and momentum degrees of freedom. "},{"label":"Title","value":"Classification of stable three-dimensional Dirac semimetals with nontrivial topology"},{"label":"URL","value":"https://www.nature.com/articles/ncomms5898"},{"label":"Date","value":"Sep 15, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 14 in the paper"},{"label":"RBK Item","value":"The α-Sn, have promising preliminary results to exhibit highly\nefficient spin-charge interconversion and magnetization reversal."},{"label":"Title","value":"Switching of a Magnet by Spin-Orbit Torque from a Topological Dirac Semimetal"},{"label":"URL","value":"https://advanced.onlinelibrary.wiley.com/doi/abs/10.1002/adma.202005909"},{"label":"Date","value":"May 3, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 20 in the paper"}]
|
Chemistry
|
Organic Chemistry
|
Numerical Values
|
Activation Energies Reveal Unusual Temperature Sensitivity in Mechanochemical Reactions
|
https://chemrxiv.org/engage/chemrxiv/article-details/68daa4513e708a7649cca588
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Sep 17, 2025
|
The Diels–Alder cycloaddition reaction between anthracene (1) and maleic anhydride (2) was investigated under solution, ball milling, and RAM conditions. The reaction under solid-state conditions was done using NaCl as a bulk material and toluene as a liquid-assisted grinding (LAG) additive (η = 0.025 µL/mg). Milling was performed in a custom-made stainless-steel vessel with a single stainless-steel ball (10 mm) at 30 Hz in a MM400 mill equipped with a temperature-controlled heating jacket and direct thermocouple monitoring for precise control of the reaction temperature.
the reaction was studied under media-free conditions using RAM, adjusting the NaCl filler to compensate for the absence of a ball.
Finally, the amount of toluene additive was systematically varied, spanning neat grinding (η = 0 µL·mg-1 ) to solution-like conditions (η = 0.58 µL·mg-1).
|
- Conversion was quantified by 1H nuclear magnetic resonance (NMR) spectroscopy of the crude mixture.
- Kinetic measurements were conducted across reaction times from 0 to 10,800 s and temperatures between 323–343 K.
|
Knowing that the reported value for the Diels–Alder cycloaddition reaction between anthracene and maleic anhydride in solution is 14.9 kcal·mol-1, what is the expected activation energy for this reaction obtained in ball milling, under the following conditions: ball milling using NaCl as a bulk material and toluene as a liquid-assisted grinding additive (η = 0.025 µL/mg)?
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Activation energy under ball milling conditions was determined as 28.9 kcal·mol⁻¹. Note: The fallback applied is +/-10%, so any energy value inside the following range is also acceptable: [26.0 kcal·mol⁻¹, 31.8 kcal·mol⁻¹].
|
- Mechanochemistry involves the initiation or
acceleration of reactions through mechanical energy typically imparted by grinding, milling, or shearing forces.
- RAM stands for resonant acoustic mixing, which address some limitations of mechanochemistry and does not use milling balls.
|
[{"label":"RBK Item","value":"- Mechanochemistry involves the initiation or\nacceleration of reactions through mechanical energy— typically imparted by grinding, milling, or shearing forces."},{"label":"Title","value":"Mechanochemistry for Synthesis"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/abs/10.1002/ange.201906755"},{"label":"Date","value":"July 11, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"- RAM stands for resonant acoustic mixing, which address some limitations of mechanochemistry and does not use milling balls."},{"label":"Title","value":"Direct mechanocatalysis by resonant acoustic mixing (RAM)"},{"label":"URL","value":"https://pubs.rsc.org/en/content/articlepdf/2023/sc/d3sc01591b"},{"label":"Date","value":"May 18, 2023"}]
|
Physics
|
Optic Physics
|
MCQ
|
Spacetime-disorder-induced localization of light in non-Hermitian quasicrystals
|
https://arxiv.org/abs/2505.04205
|
May 07, 2025
|
An experiment was conducted using an optical synthetic quasicrystal to study wave packet dynamics. The setup consists of two coupled fiber loops of unequal lengths connected by a variable beamsplitter, forming a 1+1D mesh lattice. This initiates each run by injecting a single 50 ns pulse into a longer fibre loop, which is connected to a shorter fibre loop through a VBS. The input pulse is cut out of a continuous wave signal from a tunable laser with an AOM with a 40 dB suppression ratio. Pulses traveling through the shorter loop are advanced in time, whereas those in the longer loop are delayed. And its propagation is tracked over 80 time steps. A Mach-Zehnder modulator introduces a static, incommensurate imaginary potential g(n) on one of the loops. The MZM in the longer loop modulates pulse amplitudes to simulate disordered dissipation. A phase modulator on the same loop is used to introduce uncorrelated spacetime disorder by applying random phase shifts at each position n and time step m. Single-mode fibres are used to extend the propagation time for each loop to approximately 50 μs. By adding a fibre optic patch cable in one of the loops, a propagation time difference of 158 ns is created, distinguishing the long and short loops. An erbium-doped fibre amplifier in each loop compensates for propagation losses and allows us to maintain a high optical signal-to-noise ratio. For optical gain clamping, high-power continuous wave laser signals at 1,535 nm are injected into the amplifiers via an OC. All fibre components are designed for operation at 1,550 nm wavelength and employ standard single-mode fibres. The polarization needs to be aligned in front of polarization-sensitive components to obtain a high interference contrast. Arbitrary waveform generators generate all electrical signals that drive the modulators. The system is prepared with a coupling ratio of $\beta = 0.4\pi$. For this value of $\beta$, in the absence of spacetime disorder ($\phi = 0$), the system is known to be in a delocalized phase where all eigenstates are extended.
|
- The normalized intensity distribution $|\psi_{n}(m)|^{2}$ of the optical pulse at each position n and time step m.
- The second moment, $M_{2}(m)$, of the pulse distribution, calculated from the intensity profile at each time step to quantify its spatial spreading.
- The Inverse Participation Ratio (IPR) of the wave packet's final intensity distribution at time step m=80.
|
In an optical synthetic quasicrystal with a non-Hermitian, incommensurate imaginary potential, a wave packet is prepared from a single-site excitation. The system's coupling ratio is fixed at $\beta = 0.4\pi$, a value for which the system is in a delocalized phase under coherent dynamics. Given this initial condition, what is the most likely outcome for the spreading dynamics of the wave packet when a strong, uncorrelated spacetime disorder ($\phi = 2\pi$) is introduced via random phase shifts at each lattice site and time step?
A) The wave packet's spreading will transition from ballistic to diffusive, and its second moment will grow linearly with time.
B) The wave packet will become strongly localized at its initial position, and its second moment will quickly saturate at a small, bounded value.
C) The wave packet's spreading will remain delocalized and ballistic, as the non-Hermitian potential protects the system from the dephasing effects of the disorder.
D) The wave packet will become localized, but its second moment will continue to grow at a slow, sub-diffusive rate.
|
B) The wave packet will become strongly localized at its initial position, and its second moment will quickly saturate at a small, bounded value.
|
- Anderson localization is a wave phenomenon where destructive interference of scattered waves in a disordered medium prevents their propagation, leading to the confinement of the wave packet.
- A quasicrystal, such as one described by the Aubry-Andre (AA) model, is a structure that is ordered but lacks strict periodicity.
- A non-Hermitian system is one that does not conserve energy which usually involves physical mechanisms like site-dependent gain or loss, which can be modeled with an imaginary potential.
- Spacetime disorder refers to a potential that is random in both space and time, which is usually implemented experimentally using uncorrelated random phase shifts and acts as a dephasing mechanism.
- The second moment, $M_{2}(m)$, of a wave packet's intensity distribution quantifies its spatial spread. Ballistic spreading corresponds to $M_{2}(m) \sim m^{2}$, while diffusive spreading corresponds to $M_{2}(m) \sim m$.
|
[{"label":"RBK Item","value":"Anderson localization is a wave phenomenon where destructive interference of scattered waves in a disordered medium prevents their propagation, leading to the confinement of the wave packet."},{"label":"Title","value":"Absence of Diffusion in Certain Random Lattices"},{"label":"URL","value":"https://journals.aps.org/pr/abstract/10.1103/PhysRev.109.1492"},{"label":"Date","value":"March 01, 1958"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [1] in the report."},{"label":"RBK Item","value":"A quasicrystal, such as one described by the Aubry-Andre (AA) model, is a structure that is ordered but lacks strict periodicity."},{"label":"Title","value":"Analyticity breaking and Anderson localization in incommensurate lattices"},{"label":"URL","value":"https://www.researchgate.net/publication/265502988_Analyticity_breaking_and_Anderson_localization_in_incommensurate_lattices"},{"label":"Date","value":"January, 1980"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [29] in the report."},{"label":"RBK Item","value":"The second moment, $M_{2}(m)$, of a wave packet's intensity distribution quantifies its spatial spread. Ballistic spreading corresponds to $M_{2}(m) \\sim m^{2}$, while diffusive spreading corresponds to $M_{2}(m) \\sim m$."},{"label":"Title","value":"What Determines the Spreading of a Wave Packet?"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevLett.79.1959"},{"label":"Date","value":"September 15, 1997"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [44] in the report."}]
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Physics
|
Optical Physics
|
Free-Format Question
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Digital holographic imaging of superfluid helium free surfaces
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https://www.arxiv.org/abs/2509.10235
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September 12, 2025
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The free surface of superfluid helium was visualized using off-axis digital holography in two distinct cryogenic systems to compare the characteristics of noise-driven surface waves. System A consisted of a helium bath (wet) cryostat. The wet cryostat consists of two double-walled glass Dewar flasks. The inner vessel contains liquid helium and is partially immersed in an open bath of liquid nitrogen (nitrogen jacket). This fully transparent configuration reaches a base temperature of approximately 1.55 K. Researchers mounted optical components required for DH on a breadboard above the cryostat. A fiber-coupled CW laser beam first passes through a beam expander, which increases its waist to approximately 17 mm. A 50:50 beam splitter splits the expanded beam into a reference and a probe beam. The reference beam reflects off a static mirror. In contrast, the probe beam (approximately 2 mW incident power) enters the cryostat, traverses the superfluid sample, and reflects off another mirror before recombining with the reference beam at the beam splitter. This design results in a Michelson interferometer with a probe-to-reference arms aspect ratio of approximately 30:1. The experimental region of interest is a cylindrical enclosure filled with superfluid helium. This experimental cell is suspended from the cryostat lid on fiberglass rods with low thermal conductivity and fitted with evenly spaced annular baffles. Researchers aligned the optical scheme for off-axis DH by mounting the room-temperature components on three-adjuster kinematic mounts, thereby eliminating the need to adjust the mirror inside the cryostat finely. With adjustments in the reference mirror, they introduced a relative tilt between the optical paths of the reference and probe beams, as crucially required by off-axis DH. The resulting hologram, which captures information about the fluctuating superfluid interface, is recorded by a high-speed CMOS camera with a camera sensor from the Phantom VEO 640L. The researchers acquired 20.48-second datasets of 4096 images with a resolution of 1536 × 1536 pixels, sampled at 200 frames per second. The spatially averaged PSDs were computed using Welch’s method, with 10 long Hann windows overlapped every 4 s. To extract the time series of the individual modes, they employed fifth-order Butterworth bandpass filters centered around each of the peaks. The experimental cell has a diameter of 54 mm. System B consisted of a cryogen-free (dry) refrigerator with a design of closed-cycle loops containing a thin superfluid helium film with a thickness of approximately $578~\mu\mathrm{m}$, which formed on a sapphire optical flat. The cooling power in the sample region is typically delivered through a cascade of cooling stages, the first of which is a cryocooler that operates by cyclically compressing and expanding gaseous helium. Researchers used a commercial dry system comprising four cooling stages, reaching a base temperature around $300~\mathrm{mK}$. A key characteristic of this setup is the presence of substantial, low-frequency mechanical vibrations generated by its $2~\mathrm{Hz}$ mechanical cryocooler. As the system cools to its base temperature, the helium condenses and enters the superfluid phase, forming a relatively thick superfluid film that coats the cell’s internal surfaces. Optical access along the cell’s axis of symmetry is achieved through a set of sapphire flats, enabling DH in a Mach-Zehnder interferometric configuration. A collimated laser beam is split into a reference beam and a probe beam by a beam splitter. Each beam is independently expanded, and the beams are later recombined at the beam splitter. As in the System A setup, the resulting hologram is recorded by a high-speed camera. In this configuration, the probe beam (incident power on the order of 100 µW) may traverse the superfluid film twice, as the film coats each optical port. To avoid this, researchers heated the top of the cell to (1.999 ± 0.001) K, a temperature sufficient to remove the top superfluid coating, allowing the laser beam to interact with only a single superfluid layer. Here, they also acquired 20-second-long datasets of 4000 images with 1024×1024 pixels, sampled at 200 frames per second. The spatially averaged PSDs and the frequency filtering required for the normal mode analysis were computed using the same algorithms and parameters as for the helium bath cryostat.
|
- Recording a time series of off-axis digital holograms using a high-speed CMOS camera of system A consisted of a helium bath (wet) cryostat.
- Recording a time series of off-axis digital holograms using a high-speed CMOS camera of system B consisted of a cryogen-free (dry) refrigerator
|
The free surface of superfluid helium was visualized using off-axis digital holography in two distinct cryogenic systems to compare the characteristics of noise-driven surface waves. System A consisted of a helium bath (wet) cryostat. The wet cryostat consists of two double-walled glass Dewar flasks. The inner vessel contains liquid helium and is partially immersed in an open bath of liquid nitrogen (nitrogen jacket). This fully transparent configuration reaches a base temperature of approximately 1.55 K. Researchers mounted optical components required for DH on a breadboard above the cryostat. A fiber-coupled CW laser beam first passes through a beam expander, which increases its waist to approximately 17 mm. A 50:50 beam splitter splits the expanded beam into a reference and a probe beam. The reference beam reflects off a static mirror. In contrast, the probe beam enters the cryostat, traverses the superfluid sample, and reflects off another mirror before recombining with the reference beam at the beam splitter. This design results in a Michelson interferometer with a probe-to-reference arms aspect ratio of approximately 30:1. This experimental cell is suspended from the cryostat lid on fiberglass rods with low thermal conductivity and fitted with evenly spaced annular baffles. The resulting hologram, which captures information about the fluctuating superfluid interface, is recorded by a high-speed CMOS camera. System B consisted of a cryogen-free (dry) refrigerator with a design of closed-cycle loops containing a thin superfluid helium film with a thickness of approximately $578~\mu\mathrm{m}$, which formed on a sapphire optical flat. The cooling power in the sample region is typically delivered through a cascade of cooling stages, the first of which is a cryocooler that operates by cyclically compressing and expanding gaseous helium. As the system cools to its base temperature, the helium condenses and enters the superfluid phase, forming a relatively thick superfluid film that coats the cell’s internal surfaces. Optical access along the cell’s axis of symmetry is achieved through a set of sapphire flats, enabling DH in a Mach-Zehnder interferometric configuration. A collimated laser beam is split into a reference beam and a probe beam by a beam splitter. Each beam is independently expanded, and the beams are later recombined at the beam splitter. As in the System A setup, the resulting hologram is recorded by a high-speed camera. Predict whether the wave amplitude in System B will be larger, smaller, or similar to that in System A.
|
The wave amplitude in System B will be smaller than in System A.
|
- Surface waves induce variations in the optical path of the probe beam, producing local phase shifts encoded in the recorded digital hologram. Reconstructing these phase shifts directly yields the topography of the evolving surface, obtained by scaling them with a constant factor proportional to the refractive index contrast ∆n between the sample and free space.
- In a Helium bath cryostat, the temperature, starting at 4.2 K (boiling point at normal atmospheric pressure), can be further reduced through evaporative cooling by lowering the pressure above the bath, resulting in the cooling power on the order of 1 W.
- Off-axis digital holography provides the quantitative retrieval of phase shifts encoded within holograms created by the interference of two beams.
|
[{"label":"RBK Item","value":"Surface waves induce variations in the optical path of the probe beam, producing local phase shifts encoded in the recorded digital hologram. Reconstructing these phase shifts directly yields the topography of the evolving surface, obtained by scaling them with a constant factor proportional to the refractive index contrast ∆n between the sample and free space."},{"label":"Title","value":"Diffraction phase microscopy: principles and applications in materials and life sciences"},{"label":"URL","value":"https://opg.optica.org/aop/abstract.cfm?uri=aop-6-1-57"},{"label":"Date","value":"Mar 26, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as a reference 19 in the paper"},{"label":"RBK Item","value":"In a Helium bath cryostat, the temperature, starting at 4.2 K (boiling point at normal atmospheric pressure), can be further reduced through evaporative cooling by lowering the pressure above the bath, resulting in the cooling power on the order of 1 W"},{"label":"Title","value":"A continuously-cooled 3He/4He phase separation refrigerator\n"},{"label":"URL","value":"https://arxiv.org/abs/2503.10754"},{"label":"Date","value":"March 13, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Off-axis digital holography provides the quantitative retrieval of phase shifts encoded within holograms created by the interference of two beams."},{"label":"Title","value":"Digital Holography and Digital Image Processing\n"},{"label":"URL","value":"https://link.springer.com/book/10.1007/978-1-4757-4988-5"},{"label":"Date","value":"November 30, 2003"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but referenced in the paper as ref [16]"}]
|
Physics
|
Optics
|
MCQ
|
Nonlocal Metasurface Lens for Long-Wavelength Infrared Radiation
|
https://arxiv.org/abs/2505.04856
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May 07, 2025
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An experiment was conducted to characterize a nonlocal metalens fabricated from a $1.45 \,\mu\text{m}$ thick germanium film on a 0.5-inch diameter zinc-selenide substrate. The metalens was square-shaped, with side length equal to $900 \,\mu\text{m}$, and had a hyperboloidal geometric phase profile. The proposed metalens design was characterized by a constant lattice of “unperturbed” crosses with spatially varying perturbed crosses at the interstitial sites. The perturbation was realized by displacing the horizontal rod along the x axis, and/or the vertical one along the y axis. The lens was designed to convert incoming right-circularly polarized (RCP) light into a focused, left-circularly polarized (LCP) beam at its resonant wavelength of $10.31 \,\mu\text{m}$. In the experiment, the metalens was illuminated with RCP light at this resonant wavelength. The transmitted light was then passed through a rotating linear polarizer before being imaged by a camera. The total light intensity was measured separately for two regions: the area of the focal spot and the surrounding unfocused background area, as a function of the linear polarizer's rotation angle.
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- Integrated light intensity within the focal spot area as a function of the linear polarizer's rotation angle.
- Integrated light intensity of the unfocused background area as a function of the linear polarizer's rotation angle.
- Reflectance spectrum of the metalens measured with unpolarized light.
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A nonlocal metalens designed to convert right-circularly polarized (RCP) light to a focused left-circularly polarized (LCP) spot is illuminated with RCP light at its resonant wavelength of $10.31 \,\mu\text{m}$. The proposed metalens design has a constant lattice of “unperturbed” crosses with spatially varying perturbed crosses at the interstitial sites. The
perturbation is realized by displacing the horizontal rod along the x axis, and/or the vertical one along the y axis. The transmitted light passes through a rotating linear polarizer, and a camera records the intensity. The intensity patterns (intensity vs. polarizer angle) are generated for both the focused spot and the unfocused background. What is the most likely relationship between these two intensity patterns?
A) The focused spot will show a constant intensity regardless of the polarizer's angle, while the background intensity will follow a sinusoidal pattern.
B) The intensity pattern of the focused spot will be phase-shifted by 90° with respect to the intensity pattern of the unfocused background.
C) Both the focused spot and the unfocused background will show identical sinusoidal intensity patterns that are in phase with each other.
D) The intensity pattern of the focused spot will be phase-shifted by 45° with respect to the intensity pattern of the unfocused background.
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B) The intensity pattern of the focused spot will be phase-shifted by 90° with respect to the intensity pattern of the unfocused background.
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- A nonlocal metalens is an ultrathin, patterned optical component that uses extended lattice resonances (quasi-bound states in the continuum or q-BICs) to manipulate light.
- q-BICs can arise from chiral perturbations that allow for arbitrary polarization states via geometric phase engineering.
- For circularly polarized incident light matching the q-BIC resonance, two projections of the polarization basis are necessary to analyze the outgoing signal.
|
[{"label":"RBK Item","value":"A nonlocal metalens is an ultrathin, patterned optical component that uses extended lattice resonances (quasi-bound states in the continuum or q-BICs) to manipulate light."},{"label":"Title","value":"Diffractive Nonlocal Metasurfaces"},{"label":"URL","value":"https://doi.org/10.1002/lpor.202100633"},{"label":"Date","value":"July 03, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [1] in the paper."},{"label":"RBK Item","value":"q-BICs can arise from chiral perturbations that allow for arbitrary polarization states via geometric phase engineering."},{"label":"Title","value":"Chiral Quasi-Bound States in the Continuum"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevLett.126.073001"},{"label":"Date","value":"February 17, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference [13] in the paper."},{"label":"RBK Item","value":"For circularly polarized incident light matching the q-BIC resonance, two projections of the polarization basis are necessary to analyze the outgoing signal."},{"label":"Title","value":"Selection rules for quasibound states in the continuum"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevB.102.035434"},{"label":"Date","value":"July 24, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference [2] in the paper."}]
|
Physics
|
Optics
|
Free-Format Question
|
Ablation of black-Si by (Gauss-)Bessel femtosecond laser beams
|
https://arxiv.org/abs/2505.05263
|
May 08, 2025
|
An experiment is conducted to study the laser machining of black-silicon (b-Si), a surface-nanotextured form of silicon. A femtosecond Gauss-Bessel (GB) laser beam (wavelength 1030 nm, pulse duration 201 fs, repetition rate of 602.7 kHz) is used for the ablation. The GB-beam is focused onto the b-Si sample, producing a central, high-intensity core with a measured diameter of approximately $2.6 \,\mu\text{m}$. A series of linear grooves is machined into the b-Si surface by scanning the beam. Each groove is created using a different, progressively increasing laser pulse energy $E_p$ from $1 \,\mu\text{J}$ to $13.6 \,\mu\text{J}$. The final morphology and dimensions of these ablated grooves are then imaged and measured using a scanning electron microscope (SEM).
|
- Pulse energy ($E_p$) of the Gauss-Bessel beam for each ablated groove
- Top-view scanning electron microscope images of the ablated grooves
- Width of the central ablated groove as a function of the incident laser pulse energy
- Depth and aspect ratio of the ablated grooves
|
An experiment investigates the machining of black-silicon using a femtosecond Gauss-Bessel (GB) laser beam with a wavelength, pulse duration, and repetition rate of 1030 nm, 201 fs, and 602.7 kHz, respectively. A series of grooves are ablated, with each groove created using a progressively higher pulse energy ($E_p$), varied from $1 \,\mu\text{J}$ to $13.6 \,\mu\text{J}$. The final width of the central groove is then measured. Describe the relationship between the incident laser pulse energy ($E_p$) and the measured width of the central ablated groove, particularly when moving from intermediate to high pulse energies.
|
As the pulse energy increases to high levels, the measured width of the central opening becomes narrower due to the formation of a very high-aspect-ratio central groove, which leads to the redeposition and oxidation of material around the entrance of the opening.
|
- Black-Silicon (b-Si) is a form of silicon with a surface modified to have a random nano-needle pattern, which makes it highly absorbent to light and appear black.
- Laser Ablation is a process where material is removed from a solid surface by irradiating it with a high-intensity laser beam.
- A Gauss-Bessel (GB) beam is a specialized, non-diffracting type of laser beam that maintains a narrow, high-intensity central core over a much longer distance than a conventional Gaussian beam.
- For Gaussian beams, the Liu method shows that the dependence of the width of the ablated pit W on the pulse energy $E_p$ follows $W^2(ln(E_p))$.
|
[{"label":"RBK Item","value":"Black-Silicon (b-Si) is a form of silicon with a surface modified to have a random nano-needle pattern, which makes it highly absorbent to light and appear black."},{"label":"Title","value":"Improved broadband and quasi-omnidirectional anti-reflection properties with biomimetic silicon nanostructures"},{"label":"URL","value":"https://www.nature.com/articles/nnano.2007.389"},{"label":"Date","value":"December 02, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [1] in the report."},{"label":"RBK Item","value":"Laser Ablation is a process where material is removed from a solid surface by irradiating it with a high-intensity laser beam."},{"label":"Title","value":"Ablation of solids by femtosecond lasers: Ablation mechanism and ablation thresholds for metals and dielectrics"},{"label":"URL","value":"https://doi.org/10.1063/1.1447555"},{"label":"Date","value":"March 01, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [52] in the report."},{"label":"RBK Item","value":"A Gauss-Bessel (GB) beam is a specialized, non-diffracting type of laser beam that maintains a narrow, high-intensity central core over a much longer distance than a conventional Gaussian beam."},{"label":"Title","value":"Bessel and annular beams for materials processing"},{"label":"URL","value":"https://doi.org/10.1002/lpor.201100031"},{"label":"Date","value":"January 17, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [34] in the report."},{"label":"RBK Item","value":"For Gaussian beams, the Liu method shows that the dependence of the width of the ablated pit W on the pulse energy $E_p$ follows $W^2(ln(E_p))$."},{"label":"Title","value":"Simple technique for measurements of pulsed Gaussian-beam spot sizes"},{"label":"URL","value":"https://doi.org/10.1364/OL.7.000196"},{"label":"Date","value":"May 1, 1982"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [43] in the report."}]
|
Physics
|
Applied Physics
|
Free-Format Question
|
Control of nanomechanical resonances by an electron beam
|
https://www.arxiv.org/abs/2509.10302
|
September 12, 2025
|
An electrically isolated nanomechanical cantilever was studied inside a CamScan3600 scanning electron microscope (SEM) chamber at a pressure of 3 $\mu\text{bar}$. The cantilever, measuring 32 $\mu\text{m}$ in length, 800 $\text{nm}$ in width, and 150 $\text{nm}$ in thickness, was composed of a silicon nitride base with successive 50 $\text{nm}$ coatings of gold and gallium nitride. A piezoelectric actuator drove the cantilever's in-plane oscillations with a 500 $\text{mV}_{pp}$ sinusoidal voltage. The actuator was driven by the signal output of a Zurich Instruments UHFLI 600 MHz lock-in amplifier. The SEM's electron beam was held stationary at a distance of 100 $\text{nm}$ from the cantilever's edge, operating with a constant acceleration voltage of 10 $\text{kV}$. The beam current $(I_{e})$ was adjusted through six steps: 500 $\text{pA}$; 1.0 $\text{nA}$; 1.5 $\text{nA}$; 2.0 $\text{nA}$; 2.5 $\text{nA}$; and 3.0 $\text{nA}$.
|
- The oscillation amplitude of the isolated cantilever as a function of the driving frequency for each discrete value of electron beam current.
- The cantilever's fundamental resonance frequency, determined from the peak of the frequency response curve at each electron beam current setting.
|
The resonance frequency of an electrically isolated nanomechanical cantilever is measured while the current $(I_{e})$ of a nearby electron beam is increased from $500 , \text{pA}$ to $3.0 , \text{nA}$. The interaction between the electron beam and the charge that accumulates on the cantilever results in a frequency shift $(\Delta f_{o})$. What is the expected functional dependence of this resonance frequency shift on the beam current?
|
The resonance frequency shift exhibits a superlinear dependence on the electron beam current, increasing more rapidly than a quadratic relationship would predict. While a simple electrostatic model predicts a quadratic shift, the size of the electron beam itself can expand at larger currents, which further contributes to charging the cantilever and causes the resonance frequency to shift faster with respect to $I_e$.
|
- An electron beam can cause significant electron beam charging, which is the accumulation of negative charge on samples that are electrically isolated or poorly conductive.
- The mechanical resonance frequency of an oscillator is determined by its effective mass and spring constant; an increase in this constant (stiffening) causes the resonance frequency to increase in what is known as a blue-shift.
- A repulsive Coulomb force between a charged object and a nearby charge source can cause electrostatic stiffening, an effect that acts against the object's motion to increase its effective spring constant and resonance frequency.
- The principle of charge-current proportionality suggests that the amount of charge accumulating on a sample from an electron beam is expected to be proportional to the beam's current.
- Electron beam expansion is a phenomenon where the effective size of an electron beam spot can expand at higher currents, increasing its interaction with a nearby sample and enhancing charge accumulation beyond simple proportionality.
|
[{"label":"RBK Item","value":"An electron beam can cause significant electron beam charging, which is the accumulation of negative charge on samples that are electrically isolated or poorly conductive. "},{"label":"Title","value":"Charging effect induced by electron beam irradiation: a review"},{"label":"URL","value":"https://doi.org/10.1080/14686996.2021.1976597"},{"label":"Date","value":"November 11, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA, this is reference 24 in the manuscript"},{"label":"RBK Item","value":"A repulsive Coulomb force between a charged object and a nearby charge source can cause electrostatic stiffening, an effect that acts against the object's motion to increase its effective spring constant and resonance frequency. "},{"label":"Title","value":"Frequency Tuning of Nanowire Resonator Using Electrostatic Spring Effect"},{"label":"URL","value":"https://ieeexplore.ieee.org/document/4815997"},{"label":"Date","value":"April 17, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference 39 in the paper."}]
|
Physics
|
Optics Physics
|
Numerical Values
|
A sub-volt near-IR lithium tantalate electro-optic modulator
|
https://arxiv.org/abs/2505.00906
|
May 01, 2025
|
Researchers fabricated a TFLT MZM operating at a near-IR wavelength of 737 nm. The fabricated unbalanced MZM consists of a directional coupler as an input beamsplitter and a L = 5 mm long electrode in the ground-signal-ground configuration, followed by another directional coupler at the output. Grating couplers are used to couple light on and off the chip to near-IR single-mode fibers. The optical layer of the device is defined using 150 keV electron-beam lithography with 500 nm-thick ma-N2405 resist on top of a 200 nm-thick x-cut TFLT-on-SiO2 layer. The waveguide width is designed to be 600 nm. The SiO2 layer is 2 µm-thick and is on a Si substrate. The TFLT is etched by 100 nm using an Ar+-based inductively coupled plasma reactive ion etching. Etch-induced re-deposition is removed using a high-pH solution. The devices are then annealed in an O2 atmosphere at 520°C for 2 h to mitigate etch-induced imperfections. For the MZMs, an 800 nm-thick SiO2 cladding layer is then deposited by plasma-enhanced chemical vapor deposition. The DC bias stability of two electro-optic Mach-Zehnder modulators is compared. The first modulator is fabricated using thin-film lithium tantalate (TFLT), and the second, serving as a counterpart, is fabricated with a similar process using thin-film lithium niobate (TFLN). For the test, each modulator is subjected to a constant on-chip optical power of 4.3 dBm at a wavelength of 737 nm. A DC step voltage is applied to each device to set its operating point at quadrature bias. The output optical power from the modulator is then monitored over 16 minutes in ambient conditions to measure any drift from this bias point. To measure the DC bias stability of MZM over long timescales. First, it applied a 0.1 Hz-frequency square wave to the modulator using an on-chip optical power, and measured the modulator response with a photodetector.
|
- The output optical power as a function of time over 16 minutes for the TFLT modulator.
- The output optical power as a function of time over 16 minutes for the TFLN modulator.
- The total DC bias drift, in decibels (dB), for the TFLT modulator.
- The total DC bias drift, in decibels (dB), for the TFLN modulator.
|
An experiment compares the long-term stability of two Mach-Zehnder modulators, one made from thin-film lithium tantalate (TFLT) and a counterpart from thin-film lithium niobate (TFLN). Both are operated with 4.3 dBm of on-chip optical power at 737 nm and biased at quadrature. The output power is monitored for 16 minutes to quantify the DC bias drift. To measure the DC bias stability of MZM over long timescales. First, it applied a 0.1 Hz-frequency square wave to the modulator using an on-chip optical power, and measured the modulator response with a photodetector. Based on the experimental results, what is the total measured DC bias drift, in decibels (dB), for the thin-film lithium niobate (TFLN) modulator?
|
Δ DC bias drift = [7.2–8.8] dB at 16 min for the TFLN modulator operated at 4.3 dBm optical power (737 nm). No CI/SE/SD reported → fallback ±0.8 dB applied.
|
- In particular, the relaxation rate will increase with more applied optical power and can be exacerbated with applied DC or RF field. This effect reduces the DC stability of electro-optic circuits, such as Mach-Zehnder modulators (MZMs), and has been one of the main challenges faced by TFLN photonics
|
[{"label":"RBK Item","value":"In particular, the relaxation rate will increase with more applied optical power and can be exacerbated with applied DC or RF field. This effect reduces the DC stability of electro-optic circuits, such as Mach-Zehnder modulators (MZMs), and has been one of the main challenges faced by TFLN photonics"},{"label":"Title","value":"Relaxation of the electro-optic response in thin-film lithium niobate modulators"},{"label":"URL","value":"https://opg.optica.org/oe/fulltext.cfm?uri=oe-32-3-3619"},{"label":"Date","value":" Jan 19, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Open-access, this is cited as reference 22 in the paper"}]
|
Physics
|
Physics/Applied Physics
|
Numerical Values
|
Kilovolt-Class $\beta$-Ga$_2$O$_3$ Field-Plated Schottky Barrier Diodes with MOCVD-Grown Intentionally $10^{15}\,\text{cm}^{-3}$ Doped Drift Layers
|
https://arxiv.org/pdf/2509.14403
|
September 17, 2025
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Field-plated Schottky barrier diodes (FP-SBDs) were fabricated to test the electrical performance of a homoepitaxially grown $\beta$-Ga$_2$O$_3$ epilayer. The process began with the Metal-Organic Chemical Vapor Deposition (MOCVD) of a $10\,\mu\text{m}$ thick drift layer on a conductive (010) Sn-doped $\beta$-Ga$_2$O$_3$ substrate. This drift layer was intentionally doped with silane to achieve a target net donor concentration of $6.5 \times 10^{15}\,\text{cm}^{-3}$. The diode fabrication involved depositing a Ni/Au/Ni Schottky anode, followed by a $120\,\text{nm}$ TiO$_2$/Al$_2$O$_3$ nanolaminate dielectric layer. A field plate was then patterned to overlap the dielectric by $10\,\mu\text{m}$. Finally, a Ti/Au ohmic contact was deposited on the backside of the substrate to serve as the cathode. The final device chosen for high-voltage testing had a circular anode diameter of $60\,\mu\text{m}$. High voltage breakdown measurements were performed on a Keysight B1505a parameter analyzer using Fluorinert as a dielectric fluid to prevent air breakdown induced arcing during measurement.
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- Current density (A/cm$^2$) as a function of the reverse bias voltage (kV) for the FP-SBD.
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A 60~$\mu$m diameter field-plated Schottky barrier diode is fabricated on a 10~$\mu$m thick MOCVD-grown $\beta$-Ga$_2$O$_3$ drift layer with an intentional net donor concentration of $6.5 \times 10^{15}$~cm$^{-3}$. Given these material and device parameters, what is the predicted maximum reverse breakdown voltage ($V_{\rm BR}$) in kilovolts (kV)?
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The predicted maximum reverse breakdown voltage is in the range of 1.35 kV - 1.65 kV.
Note: No CI/SE/SD reported by the authors -> a ±10% fallback policy was applied to the value reported by the authors, 1.50 kV.
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- A Schottky Barrier Diode (SBD) is a type of semiconductor diode formed by the junction of a semiconductor with a metal, known for its fast switching speed and low forward voltage drop.
- $\beta$-Ga$_2$O$_3$ (Beta Gallium Oxide) is an ultra-wide bandgap semiconductor material prized in power electronics for its ability to withstand very high electric fields before breaking down.
- A drift layer is a thick, lightly doped epitaxial layer in a power semiconductor device specifically designed to support the high voltage in the device's off-state.
- Breakdown Voltage ($V_{\rm BR}$) is the minimum reverse voltage applied to a diode that causes it to break down and conduct a large current.
- A field plate is an electrode structure in a semiconductor device designed to reshape the electric field, reducing its peak value at sensitive locations (like a contact edge) to increase the overall breakdown voltage.
|
[{"label":"RBK Item","value":"A Schottky Barrier Diode (SBD) is a type of semiconductor diode formed by the junction of a semiconductor with a metal, known for its fast switching speed and low forward voltage drop."},{"label":"Title","value":"Fundamentals of Power Semiconductor Devices"},{"label":"URL","value":"https://doi.org/10.1007/978-3-319-93988-9"},{"label":"Date","value":"September 28, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [70] in the report."},{"label":"RBK Item","value":"$\\beta$-Ga$_2$O$_3$ (Beta Gallium Oxide) is an ultra-wide bandgap semiconductor material prized in power electronics for its ability to withstand very high electric fields before breaking down."},{"label":"Title","value":"β-Gallium oxide power electronics"},{"label":"URL","value":"https://doi.org/10.1063/5.0060327"},{"label":"Date","value":"February 07, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"A drift layer is a thick, lightly doped epitaxial layer in a power semiconductor device specifically designed to support the high voltage in the device's off-state."},{"label":"Title","value":"Fundamentals of Power Semiconductor Devices"},{"label":"URL","value":"https://doi.org/10.1007/978-3-319-93988-9"},{"label":"Date","value":"September 28, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [70] in the report."},{"label":"RBK Item","value":"Breakdown Voltage ($V_{\\rm BR}$) is the minimum reverse voltage applied to a diode that causes it to break down and conduct a large current."},{"label":"Title","value":"Fundamentals of Power Semiconductor Devices"},{"label":"URL","value":"https://doi.org/10.1007/978-3-319-93988-9"},{"label":"Date","value":"September 28, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [70] in the report."},{"label":"RBK Item","value":"A field plate is an electrode structure in a semiconductor device designed to reshape the electric field, reducing its peak value at sensitive locations (like a contact edge) to increase the overall breakdown voltage."},{"label":"Title","value":"High-k Oxide Field-Plated Vertical (001) β-Ga₂O₃ Schottky Barrier Diode With Baliga's Figure of Merit Over 1 GW/cm²"},{"label":"URL","value":"10.1109/LED.2021.3089945"},{"label":"Date","value":"June 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [72] in the report."}]
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Biology
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Reproductive Biology
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MCQ
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Seminal F2-IsoP and RvD1 Levels in Idiopathic Infertile Men
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https://www.mdpi.com/2079-7737/14/4/450
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April 21, 2025
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Researchers investigated whether idiopathic male infertility is associated with altered levels of F₂-isoprostanes (F₂-IsoPs) and Resolvin D1 (RvD1) in seminal plasma. Semen samples for were procured from 77 men (age range: 29–39 years) experiencing infertility (i.e. inability to achieve conception following a minimum of two years of regular, unprotected intercourse, with exclusion of female factor infertility), and classified as having idiopathic male infertility. Semen samples were collected following a period of sexual abstinence of 3–5 days. Standard semen parameters were evaluated according to the WHO guidelines. Specifically, sperm motility was assessed and categorized as rapid progressive, slow progressive, non-progressive, or immotile. Sperm morphology was evaluated using pre-stained Testsimplets® slides (Origio, Firenze, Italy). Sperm vitality was determined using the eosin staining technique, employing 0.5% Eosin Y (Thermo Fisher Scientific, Waltham, MA, USA) in a 0.9% aqueous sodium chloride solution. The established lower reference limit for sperm vitality is ≥54%. Following routine semen analysis, samples were aliquoted for subsequent assays. For immunolocalization studies, 100 μL aliquots were washed with phosphate-buffered saline (PBS) and subsequently smeared onto microscope slides. Total F2-IsoP concentrations in seminal plasma were quantified following established methodologies. Initially, samples underwent basic hydrolysis. Subsequently, acidified water and an internal standard, deuterated prostaglandin F2α (PGF2α−d4), were added to each sample. Purification was performed using sequential solid-phase extraction. Samples were first loaded onto an octadecylsilane (C18) cartridge (WAT043395, Sep-Pak® Vac C18, 500 mg, Waters, Milford, MA, USA). The eluate from the C18 cartridge was then applied to an aminopropyl (NH2) cartridge (WAT054560, Sep-Pak® Vac NH2, 500 mg, Waters, Milford, MA, USA). Following purification, chemical derivatization was performed. The carboxylic acid group of F2-IsoPs was converted to its pentafluorobenzyl ester derivative, while the hydroxyl groups were converted to trimethylsilyl ethers. Final quantification was achieved using gas chromatography coupled with negative ion chemical ionization tandem mass spectrometry (GC/NICI-MS/MS) utilizing a TRACE GC and PolarisQ Ion Trap system (Thermo Finnigan, San Jose, CA, USA). F2-IsoPs were quantified by monitoring the specific precursor-to-product ion transition for 8−iso−PGF2α (Cayman Chemical, Ann Arbor, MI, USA), the most abundant F2-IsoP isomer, specifically targeting the fragment ion at m/z 299. Results were expressed as ng/mL. Concentrations RvD1 in seminal plasma were determined using a commercial double-antibody sandwich Enzyme-Linked Immunosorbent Assay (ELISA) kit (MyBioSource, San Diego, CA, USA). This assay employed microtiter plate wells pre-coated with an anti-RvD1 monoclonal capture antibody and utilized a biotin-conjugated polyclonal antibody for detection, and was performed according to the manufacturer’s protocol. RvD1 concentrations in the samples were interpolated from a standard curve and expressed in pg/mL. Patients were divided into two groups according to the levels of F2-IsoPs (Group 1 ≤ 29.96 ng/mL and Group 2 > 29.96 ng/mL). Immunofluorescence analysis was performed in 10 patients of Group 1 and 10 patients of Group 2 to evaluate the localization of F2-IsoPs. The smeared slides prepared as previously described were fixed in methanol at −20 °C for 20 min, followed by acetone at −20 °C for 5 min, and rehydrated in PBS for 10 min at room temperature before the reaction. Then, the slides were treated with PBS-bovine serum albumin (BSA) 1% and 5% of normal goat serum (NGS) for 20 min and incubated overnight at 4 °C with a rabbit polyclonal anti-8-iso-PGF2α antibody (Abcam, Cambridge, UK), diluted 1:100 in PBS-BSA 0.1% and NGS 1%. The reaction was detected using a goat anti-Rabbit IgG Secondary Antibody Alexa Fluor™ 488 (Thermo Fisher Scientific, Waltam, MA, USA) diluted 1:500 in PBS-BSA 0.1% and NGS 1%. Specificity of binding was confirmed by the negative staining using the diluent (PBS-BSA 0.1% and NGS 1%) and omitting the primary antibody. Sperm nuclei were stained with 4,6-diamidino-2-phenylindole (DAPI) solution (Vysis, Downers Grove, IL, USA) diluted 1:20,000 in PBS for 10 min at room temperature. Finally, the slides were rinsed in PBS and mounted with 1,4-diazabicyclo [2.2.2] octane (Sigma-Aldrich, St. Louis, MO, USA). The slides were observed and evaluated with a Leica DMI 6000 Fluorescence Microscope (Leica Microsystems, Wetzlar, Germany), and the images were acquired by the Leica AF6500 Integrated System for Imaging and Analysis (Leica Microsystems, Wetzlar, Germany). Spearman’s rank correlation coefficient (ϱ) was utilized to evaluate the associations between the variables under investigation.
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- Sperm motility: for all 77 patients (according to the WHO guidelines).
- Sperm morphology: for all 77 patients (pre-stained Testsimplets® slides).
- Sperm vitality: for all 77 patients (eosin staining technique).
- F₂-isoprostanes (F₂-IsoPs) concentration in seminal plasma (mg/mL): for all 77 patients (GC/NICI-MS/MS).
- Resolvin D1 (RvD1) concentration in seminal plasma (pg/mL): for all 77 patients (sandwich ELISA).
- Immunolocalization of F2-IsoPs: for patients from group 1 (n = 10) and group 2 (n = 10) (Leica DMI 6000 Fluorescence Microscope).
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Idiopathic male infertility may correlate with oxidative stress and inflammation markers in seminal plasma. To evaluate this, 77 men classified as having idiopathic male infertility were recruited into a study. Researchers measured standard semen parameters (according to the WHO guidelines) in semen samples from all patients, and F₂-isoprostanes (F₂-IsoPs) and Resolvin D1 (RvD1) concentrations in all seminal plasma samples from all patients. For Immunolocalization of F2-IsoPs, patients were divided into two groups according to the levels of F2-IsoPs (Group 1 ≤ 29.96 ng/mL (n = 10) and Group 2 > 29.96 ng/mL (n = 10)). Which of the following outcomes is most likely?
A. A significant correlation was observed between the F2-IsoPs levels and progressive sperm motility and sperm viability.
B. The percentage of spermatozoa showing a faint F2-IsoPs immunolabeling signal in the tail was significantly higher in Group 1 than in Group 2.
C. A significant correlation was observed between the RvD1 levels and sperm normal morphology and progressive motility.
D. The majority of spermatozoa in Group 2 not displayed any F2-IsoPs immunolabeling in the acrosomal region.
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B. The percentage of spermatozoa showing a faint F2-IsoPs immunolabeling signal in the tail was significantly higher in Group 1 than in Group 2.
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- Idiopathic male infertility is defined as abnormality in at least one semen parameter, with no previous history of diseases affecting fertility.
- F2-Isoprostanes (F2-IsoPs) are formed via free-radical-mediated peroxidation of polyunsaturated fatty acids (PUFAs) esterified in membrane phospholipids. These compounds have been established as powerful markers of in vivo lipid peroxidation (LPO).
- Resolvin D1 (RvD1), derived from docosahexaenoic acid, and it is linked to inflammatory male infertility and reduced sperm quality.
|
[{"label":"RBK Item","value":"Idiopathic male infertility is defined as abnormality in at least one semen parameter, with no previous history of diseases affecting fertility."},{"label":"Title","value":"Is There a Relevant Clinical Impact in Differentiating Idiopathic versus Unexplained Male Infertility?"},{"label":"URL","value":"https://wjmh.org/DOIx.php?id=10.5534/wjmh.220069"},{"label":"Date","value":"September 02, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"F2-Isoprostanes (F2-IsoPs) are formed via free-radical-mediated peroxidation of polyunsaturated fatty acids (PUFAs) esterified in membrane phospholipids. These compounds have been established as powerful markers of in vivo lipid peroxidation (LPO)."},{"label":"Title","value":"The isoprostanes—25 years later"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S1388198114002169?via%3Dihub"},{"label":"Date","value":"October 30, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled version is the cited RBK element in this paper"},{"label":"RBK Item","value":"Resolvin D1 (RvD1), derived from docosahexaenoic acid, and it is linked to inflammatory male infertility and reduced sperm quality."},{"label":"Title","value":"Role of isoprostanes in human male infertility"},{"label":"URL","value":"https://www.tandfonline.com/doi/full/10.1080/19396368.2020.1793032"},{"label":"Date","value":"August 25, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Physics
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Optics
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Numerical Values
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Fabrication of highly uniform laser-induced periodic structures on polycarbonate via UV femtosecond pulses
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https://arxiv.org/abs/2505.02477
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May 5, 2025
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A polycarbonate (PC) surface is irradiated in ambient air using a 258 nm, 170 fs pulsed laser source. The laser beam is focused on the surface by a plano-convex, achromatic spherical lens with a focal length of 100 mm. The polarization is set to circular using a quarter-wave plate to investigate the formation of 2D nanostructures. The experiment systematically varies the laser fluence and the effective number of pulses ($N_{eff}$) to study their impact on the resulting topography. A specific set of irradiations is performed at a constant fluence of 130 mJ/c^2, while $N_{eff}$ is varied. The resulting surface structures are visualized with a scanning electron microscope (SEM), and their features are quantified using image analysis software.
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- The morphology of surface topographies produced using circularly polarized light.
- The size distribution of the radii of the protruded nanostructures as a function of the effective number of pulses.
- The mean radius of the nanospheres for the specific condition of a fluence of 130 mJ/cm^2 and an effective number of 100 pulses.
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A polycarbonate surface is structured using circularly polarized 258 nm femtosecond laser pulses at a constant fluence of 130 mJ/cm^2. This process results in the formation of protruding, nanosphere-like structures. Based on the experimental results, what is the mean radius, in nanometers, of the nanospheres formed after irradiating the surface with an effective number of 100 pulses?
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The mean radius of the nanospheres is in the range of 75 - 99 nm.
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- Laser-Induced Periodic Surface Structures (LIPSS) are microscopic, self-organized patterns that can form on the surface of a material when it is irradiated with laser pulses.
- The polarization of a laser beam describes the orientation of its electric field's oscillation. Linear polarization means the field oscillates along a single line, while circular polarization means the field vector rotates in a circle.
- In LIPSS formation, linear polarization typically results in one-dimensional (1D) ripples. Circular polarization, which has no single preferred direction, often leads to the formation of two-dimensional (2D) patterns, such as dot-like or nanosphere-like structures.
- Fluence is the laser pulse energy delivered per unit area (e.g., J/cm^2) , while the effective number of pulses (Neff) accounts for the cumulative dose on a given spot from overlapping pulses during scanning.
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[{"label":"RBK Item","value":"Laser-Induced Periodic Surface Structures (LIPSS) are microscopic, self-organized patterns that can form on the surface of a material when it is irradiated with laser pulses."},{"label":"Title","value":"Maxwell Meets Marangoni—A Review of Theories on Laser-Induced Periodic Surface Structures"},{"label":"URL","value":"https://doi.org/10.1002/lpor.202000215"},{"label":"Date","value":"August 31, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Laser-Induced Periodic Surface Structures (LIPSS) are microscopic, self-organized patterns that can form on the surface of a material when it is irradiated with laser pulses."},{"label":"Title","value":"Self-organized pattern formation upon femtosecond laser ablation by circularly polarized light"},{"label":"URL","value":"https://doi.org/10.1016/j.apsusc.2005.08.120"},{"label":"Date","value":"April 30, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference [43] in the report."}]
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Biology
|
Biochemistry
|
MCQ
|
Neuroblastoma-associated ALK variants have distinct cellular and biochemical activities
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https://www.biorxiv.org/content/10.1101/2025.09.25.677354v1
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September 25, 2025
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Researchers investigated whether neuroblastoma-associated ALK (Anaplastic Lymphoma Kinase) variants differ in their ability to bind to Glycogen Synthase Kinase 3 isoforms (GSK3α and GSK3β) in cells. HEK293T cells were transfected using Lipofectamine 2000 with plasmids expressing ALK^WT (wild-type), ALK^F1174L, ALK^R1275Q, or the kinase-dead ALK^I1250T, together with GSK3α- or GSK3β-FLAG constructs. After 24 h, cells were lysed in GST (Glutathione S-Transferase; 50 mM Tris-HCl pH 7.4, 200 mM NaCl, 1 % NP-40, 2 mM MgCl₂, 10 % glycerol) buffer containing protease and phosphatase inhibitors. Protein complexes were isolated with Anti-FLAG M2 magnetic beads (10µl beads with 200µg protein), then pulled-down samples were analyzed by Western blotting using XCell SureLock™ Mini-Cell and XCell II™ Blot Module Electrophoresis System with antibodies against ALK, GSK3α, and GSK3β (primary dilution 1:1000). For total lysate, 10µg protein was added and 5 μl of Precision Plus Protein Dual Color Standards as protein ladder. Band intensities for ALK+GSK3α/β were quantified in ImageJ (three biological replicas).
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- Relative ALK–GSK3 binding intensity across ALK variants (ALK^WT, ALK^F1174L, ALK^R1275Q, ALK^I1250T) and GSK3 isoforms (GSK3α, GSK3β).
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Researchers investigated whether neuroblastoma-associated ALK (Anaplastic Lymphoma Kinase) variants differ in their ability to bind to Glycogen Synthase Kinase 3 isoforms (GSK3α and GSK3β) in cells. HEK293T cells were transfected using Lipofectamine 2000 with plasmids expressing ALK^WT (wild-type), ALK^F1174L, ALK^R1275Q, or the kinase-dead ALK^I1250T, together with GSK3α- or GSK3β-FLAG constructs. After 24 h, cells were lysed in GST (Glutathione S-Transferase; 50 mM Tris-HCl pH 7.4, 200 mM NaCl, 1 % NP-40, 2 mM MgCl₂, 10 % glycerol) buffer containing protease and phosphatase inhibitors. Protein complexes were isolated with Anti-FLAG M2 magnetic beads (10µl beads with 200µg protein), then pulled-down samples were analyzed by Western blotting with antibodies against ALK, GSK3α, and GSK3β (primary dilution 1:1000). Band intensities for ALK+GSK3α/β were quantified in ImageJ (three biological replicates).
Given these experimental conditions, which of the following outcomes is most likely for the binding interactions between the ALK variants and GSK3 isoforms?
A. The ALK^F1174L variant showed the highest binding affinity for GSK3α and GSK3β, compared to the other variants.
B. The ALK^R1275Q variant showed the highest binding affinity for GSK3α and GSK3β, compared to the other variants.
C. The ALK^WT variant showed similar affinity to GSK3α and GSK3β as ALK^R1275Q & ALK^F1174L variants
D. The ALK^F1174L and ALK^R1275Q variants showed similar binding affinity for GSK3β and GSK3α, both higher than ALK^WT
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A. The ALK^F1174L variant showed the highest binding affinity for GSK3α and GSK3β, compared to the other variants.
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- Anaplastic Lymphoma Kinase (ALK) is a tyrosine kinase receptor that is frequently mutated in neuroblastoma, a childhood cancer derived from neural crest cells.
- In neuroblastoma, 85% of ALK mutations are found at three distinct positions in its kinase domain: F1174, F1245, R1275.
- Glycogen Synthase Kinase 3 (GSK3) is a serine/threonine kinase that regulates neural crest cell migration.
|
[{"label":"RBK Item","value":"- Anaplastic Lymphoma Kinase (ALK) is a tyrosine kinase receptor that is frequently mutated in neuroblastoma, a childhood cancer derived from neural crest cells. "},{"label":"Title","value":"Genomic ALK alterations in primary and relapsed neuroblastoma"},{"label":"URL","value":"https://www.nature.com/articles/s41416-023-02208-y"},{"label":"Date","value":"February 17, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- In neuroblastoma, 85% of ALK mutations are found at three distinct positions in its kinase domain: F1174, F1245, R1275"},{"label":"Title","value":"Genomic ALK alterations in primary and relapsed neuroblastoma"},{"label":"URL","value":"https://www.nature.com/articles/s41416-023-02208-y"},{"label":"Date","value":"February 17, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Glycogen Synthase Kinase 3 (GSK3) is a serine/threonine kinase that regulates neural crest cell migration."},{"label":"Title","value":"Glycogen synthase kinase 3 controls migration of the neural crest lineage in mouse and Xenopus"},{"label":"URL","value":"https://www.nature.com/articles/s41467-018-03512-5"},{"label":"Date","value":"March 19, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
|
Animal Behavior, Toxicology, Pharmacology
|
MCQ
|
Ivermectin Reduces Withdrawal-Induced Alcohol Intake via CeA GABAergic Enhancement
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https://www.biorxiv.org/content/10.1101/2025.10.14.682432v1
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Oct 15, 2025
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Researchers evaluated whether ivermectin attenuates escalated ethanol self-administration in dependent heterogeneous stock (HS) rats. 32 HS rats (16 males, 16 females) were trained to self-administer 10% (v/v) ethanol under a fixed ratio 1 schedule. Dependence was induced using chronic intermittent ethanol (CIE) vapor exposure (14 h on / 10 h off daily) from week 4 to week 10, during which blood alcohol levels (collecting 0.1 ml of tail blood, centrifuge to separate plasma and then analyzed using gas chromatography or an Analox AM1 Alcohol Analyser) were measured twice weekly to maintain an average of approximately 180 mg/dl. After dependence was established, rats underwent 2-hour post-vapor self-administration sessions during acute withdrawal (7–10 h after vapor cessation). Self-administration sessions used an apparatus with two retractable levers positioned on the right wall, with a sipper cup containing two wells situated between them. Both levers were accessible throughout the session. Each equipped with a syringe that delivered ethanol and water solutions, respectively (0.1mL/reinforcer). Post-vapor self-administration Ivermectin was freshly dissolved in 0.9% saline with 5% Tween 80 and administered intraperitoneally four hours before testing different doses (0, 1, 2.5, 5, 10 mg/kg) in a Latin square design. Ethanol intake (g/kg body weight) was recorded for each dose condition, and data were analyzed for dose- and sex-dependent effects.
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-Ethanol intake (g/kg body weight) during post-vapor self-administration sessions at each ivermectin dose (0, 1, 2.5, 5, 10 mg/kg) between male and female HS rats.
-Blood alcohol levels (mg/dL) during vapor exposure to confirm the dependence state in male and female HS rats.
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Ivermectin is hypothesized to modulate GABAergic signaling in the central amygdala (CeA) and reduce alcohol intake during withdrawal. Researchers evaluated whether ivermectin attenuates escalated ethanol self-administration in male and female dependent HS rats. Rats underwent operant training for 10% ethanol self-administration, followed by chronic intermittent ethanol vapor exposure to induce dependence, verified by blood alcohol levels of approximately 180 mg/dl. During withdrawal, ivermectin (0, 1, 2.5, 5, 10 mg/kg, i.p.) was administered 4–6 hours prior to 2-h post-vapor ethanol self-administration sessions and ethanol intake was measured (g/kg). Data were plotted as intake versus dose for males and females, and both. Which of the following outcomes is more likely to occur?
A) Ivermectin dose-dependently reduced ethanol intake, but only males showed a significant decrease at 5 and 10 mg/kg.
B) Ivermectin reduced ethanol intake only from dose 5mg/kg in both sexes.
C) Ivermectin dose-dependently reduced ethanol intake in both sexes, females being more sensitive.
D) Ivermectin dose-dependently reduced ethanol intake, with females showing slightly higher reduction than males at 5 and 10mg/kg doses.
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A) Ivermectin dose-dependently reduced ethanol intake, but only males showed a significant decrease at 5 and 10 mg/kg.
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- Heterogeneous stock (HS) rats display broad phenotypic variation in ethanol drinking and related behaviors.
- P2X4 receptor (P2X4R), encoded by the gene P2rx4, a ligand-gated ion channel highly expressed in the central nervous system that facilitates ATPmediated calcium influx and modulates GABAergic, glutamatergic, glycinergic, and cholinergic neurotransmission.
- Ivermectin (IVM) is an antiparasitic agent and well-characterized positive allosteric modulator of P2X4Rs that antagonizes ethanol's inhibitory effect on the receptor.
|
[{"label":"RBK Item","value":"Heterogeneous stock (HS) rats display broad phenotypic variation in ethanol drinking and related behaviors.\n"},{"label":"Title","value":"A Preclinical Alcohol Biobank: Samples from Behaviorally Characterized HS Rats for AUD Research"},{"label":"URL","value":"https://www.eneuro.org/content/12/9/ENEURO.0207-25.2025"},{"label":"Date","value":"September 12, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"P2X4 receptor (P2X4R), encoded by the gene P2rx4, a ligand-gated ion channel highly expressed in the central nervous system that facilitates ATPmediated calcium influx and modulates GABAergic, glutamatergic, glycinergic, and cholinergic neurotransmission."},{"label":"Title","value":"Activation and Regulation of Purinergic P2X Receptor Channels"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3141880/"},{"label":"Date","value":"Sep, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Ivermectin (IVM) is an antiparasitic agent and well-characterized positive allosteric modulator of P2X4Rs that antagonizes ethanol's inhibitory effect on the receptor. \n"},{"label":"Title","value":"Avermectins differentially affect ethanol intake and receptor function: Implications for developing new therapeutics for alcohol use disorders"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC4209915/"},{"label":"Date","value":"Jan 22, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
|
Physiology / Neuroscience
|
Free-Format Question
|
APOE4 carriers resistant to cognitive decline show unique relationships between cerebrovascular response to exercise and dual-task cognitive-balance performance
|
https://www.biorxiv.org/content/10.1101/2025.09.30.679544v1
|
October 1, 2025
|
Researchers investigated the relationship between cerebrovascular response and cognitive-motor dual-task performance in cognitively-normal APOE4 (Apolipoprotein E4) carriers who maintain preserved function. Cognitively-normal older adults (76±4 years, 8 APOE4 carriers [3 females, 5 males], 22 noncarriers [16 females, 6 males]) with absence of neurologic or orthopedic disability preventing independent standing and walking, completed clinical balance testing under dual-task conditions. Exclusion also included insulin dependence, peripheral neuropathy, and active coronary artery disease/congestive heart failure. Participants completed extensive neuropsychological testing and Clinical Dementia Rating (CDR) assessment. Only individuals with normal cognitive status (CDR=0) and APOE genotyping (classified as APOE carrier in the presence of 1 or 2 APOE4 alleles determined by Taqman single-nucleotide polymorphism (SNP) allelic discrimination assay by two APOE-defining SNPs, rs429358 [C_3084793_20] and rs7412 [C_904973_10]) were included in this analysis. The clinical balance testing consisted of a walking task across a 16-foot long narrow beam (3.5-inch width) (1-inch height to minimize postural threat). Participants were instructed to fold their arms across their chest and walk as far as they could across the beam, but did not receive instructions on walking speed. Trials ended when the participant stepped off the beam, walked sideways, or unfolded their arms, and their initial ground foot placement position was marked. In the dual-task beam walk, participants had to perform a cognitive task that required them to verbally count backward by 3s, starting at a random integer between 20 and 100, as stated by the experimenter immediately following the cue to begin the beam walk. The beam distance traversed was recorded in feet.
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- Distance traversed (feet) in APOE4 carriers vs. non-carriers under dual-task walking conditions (16-ft-long, 3.5 in-wide beam; arms folded; verbally count by 3's starting at a random integer between 20 and 100 given by the experimenter immediately following the cue to begin walking).
|
Researchers investigated the relationship between cerebrovascular response and cognitive-motor dual-task performance in cognitively-normal APOE4 (Apolipoprotein E4) carriers who maintain preserved function. Cognitively-normal older adults (76±4 years, 8 APOE4 carriers [3 females, 5 males], 22 noncarriers [16 females, 6 males]) with absence of neurologic or orthopedic disability preventing independent standing and walking, completed clinical balance testing under dual-task conditions. Exclusion also included insulin dependence, peripheral neuropathy, and active coronary artery disease/congestive heart failure. Participants completed extensive neuropsychological testing and Clinical Dementia Rating (CDR) assessment. Only individuals with normal cognitive status (CDR=0) and APOE genotyping (classified as APOE carrier in the presence of 1 or 2 APOE4 alleles determined by Taqman single-nucleotide polymorphism (SNP) allelic discrimination assay by two APOE-defining SNPs, rs429358 [C_3084793_20] and rs7412 [C_904973_10]) were included in this analysis. The clinical balance testing consisted of a walking task across a 16-foot long narrow beam (3.5-inch width) (1-inch height to minimize postural threat). Participants were instructed to fold their arms across their chest and walk as far as they could across the beam, but did not receive instructions on walking speed. Trials ended when the participant stepped off the beam, walked sideways, or unfolded their arms, and their initial ground foot placement position was marked. In the dual-task beam walk, participants had to perform a cognitive task that required them to verbally count backward by 3s, starting at a random integer between 20 and 100, as stated by the experimenter immediately following the cue to begin the beam walk. The beam distance traversed was recorded in feet.
Predict the relative difference (higher, lower, no difference) in average beam distance traversed of cognitively-normal older adults with APOE4 compared to noncarriers conducted under dual-task conditions.
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Cognitively-normal older adults with APOE4 showed no differences in balance performance, measured as average beam distance traversed, compared to noncarriers in dual-task conditions.
|
- Apolipoprotein E4 (APOE4) allele is the strongest known genetic risk factor for Alzheimer’s disease
- The emergence of cognitive interference in balance and walking over the course of aging is one of the most prevalent clinical phenomena that emerges with aging
- Greater degradation of balance and gait performance under cognitive loading is an early and sensitive indicator of behavioral dysfunction in older adults and can predict future dementia and falls
|
[{"label":"RBK Item","value":"Apolipoprotein E4 (APOE4) allele is the strongest known genetic risk factor for Alzheimer’s disease"},{"label":"Title","value":"The Neurobiology and Age-Related Prevalence of the ε4 Allele of Apolipoprotein E in Alzheimer’s Disease Cohorts"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5531868/"},{"label":"Date","value":"August 06, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"The emergence of cognitive interference in balance and walking over the course of aging is one of the most prevalent clinical phenomena that emerges with aging"},{"label":"Title","value":"Stance perturbation-evoked potentials in old people with poor gait and balance"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S1388245799001959"},{"label":"Date","value":"November 08, 1999"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Greater degradation of balance and gait performance under cognitive loading is an early and sensitive indicator of behavioral dysfunction in older adults and can predict future dementia and falls"},{"label":"Title","value":"Gait and Cognition: A Complementary Approach to Understanding Brain Function and the Risk of Falling"},{"label":"URL","value":"https://agsjournals.onlinelibrary.wiley.com/doi/10.1111/j.1532-5415.2012.04209.x"},{"label":"Date","value":"October 30, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Pathology
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MCQ
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Alkalinized Filtered Water Induces Changes in the Gut Microbiome in Inflammatory Bowel Disease
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https://www.biorxiv.org/content/10.1101/2025.09.19.677298v1
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September 21, 2025
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A three-month, two-arm, randomized intervention study involving 46 patients with IBD in remission was conducted. Volunteers were asked to drink filtered water for three months, and received filtering jars containing either active filters (Alkanatur® Drops SLU, Milladoiro-Ames, A Coruña, Spain) or mock filters (Tap). Blood samples were collected before and after the intervention. Circulating levels of cytokines IL-1b, IL-4, IL-6, TNF-a, and IL-10 in plasma were analyzed by cellular cytometry using Multiplex Cytokine Assays (Pro-cartaPlex Immunoassays, ThermoFisher Scientific) at the CNB (CSIC) Flow Cytometry Unit.
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• Circulating cytokine levels (IL-1β, IL-4, IL-6, IL-10, TNF-α) in plasma, in pg/mL
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Researchers tested the effects of alkalinized filtered water in patients with IBD in remission through a threemonth intervention study. Participants were divided into two groups: one consumed filtered water from an active filtering device, and the control group consumed water from a mock device. Blood samples were collected before and after the intervention. Circulating cytokine levels (IL-1b, IL-4, IL-6, TNF-a, and IL-10 ) were assessed from plasma. Which of the following outcomes are most likely? Mark all the correct options:
A) Subjects drinking alkalinized filtered water exhibited significant lower levels of IL-4 than controls.
B) Subjects drinking alkalinized filtered water exhibited a significant, decrease in circulating IL-1b than controls.
C) Subjects drinking alkalinized filtered water exhibited a consistent, albeit not statistically significant, decrease in circulating IL-1b than controls.
D) Subjects drinking alkalinized filtered water exhibited a consistent, albeit not statistically significant, decrease in circulating IL-4 than controls.
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A) Subjects drinking alkalinized filtered water exhibited significant lower levels of IL-4 than controls.
C) Subjects drinking alkalinized filtered water exhibited a consistent, albeit not statistically significant, decrease in circulating IL-1b than controls.
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• Inflammatory Bowel Disease (IBD) includes Crohn’s disease and ulcerative colitis, characterized by chronic gut inflammation and dysbiosis.
• The gut microbiome plays a key role in IBD pathogenesis, and certain bacterial groups like Bacteroides fragilis can have dual roles (pro- or anti-inflammatory) depending on context.
• Alkalinized filtered water has been shown in preclinical models to reduce inflammation and modulate gut microbiota.
• qPCR targeting 16S rRNA genes is a common method for quantifying specific bacterial groups in fecal samples.
|
[{"label":"RBK Item","value":"•\tInflammatory Bowel Disease (IBD) includes Crohn’s disease and ulcerative colitis, characterized by chronic gut inflammation and dysbiosis."},{"label":"Title","value":"Inflammatory Bowel Diseases (IBD) and the Microbiome-Searching the Crime Scene for Clues"},{"label":"URL","value":"https://doi.org/10.1053/j.gastro.2020.09.056"},{"label":"Date","value":"May 5, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"•\tThe gut microbiome plays a key role in IBD pathogenesis, and certain bacterial groups like Bacteroides fragilis can have dual roles (pro- or anti-inflammatory) depending on context."},{"label":"Title","value":"The Gut Microbiome and Inflammatory Bowel Diseases"},{"label":"URL","value":"https://doi.org/10.1146/annurev-med-042320-021020"},{"label":"Date","value":"Mars 14, 2023 "},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"•\tAlkalinized filtered water has been shown in preclinical models to reduce inflammation and modulate gut microbiota."},{"label":"Title","value":"Intestinal Effects of Filtered Alkalinized Water in Lean and Obese Zucker Rats"},{"label":"URL","value":"https://doi.org/10.3390/microorganisms12020316"},{"label":"Date","value":"February 2, 2024 "},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"•\tqPCR targeting 16S rRNA genes is a common method for quantifying specific bacterial groups in fecal samples."},{"label":"Title","value":"Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard"},{"label":"URL","value":"https://doi.org/10.1002/mbo3.977"},{"label":"Date","value":" January 11, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Cell Biology
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Free-Format Question
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Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies
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https://www.biorxiv.org/content/10.1101/2025.09.17.676148v3
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September 17, 2025
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Researchers tested whether the small molecule SH6 had any effect in the degradation of ZBTB7A in HUDEP-2 cells. Cells were cultured in StemSpan SFEM II media (Stem Cell Technologies) supplemented with 50 ng/mL human stem cell factor, 3 U/mL erythropoietin, 1 μM dexamethasone, and 1 μg/mL doxycycline. Cells were treated with SH6 at different concentrations (0.25, 0.5, 1, 2.5, 5 μM) or DMSO for 24 hours and harvested in quadruplicates using RIPA buffer (Sigma) per the manufacturer’s instructions. Cells were lysed in RIPA buffer supplemented with protease inhibitors. Lysates were resolved on 4-12% Bis-Tris gels, transferred to PVDF membranes, and probed with antibodies against ZBTB7A (CST, 50565) and β-actin (Santa Cruz, sc-47778). Blots were developed using Biorad Chemidoc MP Imaging system. Quantification of WB signal performed by ImageJ (v1.54p).
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- Protein levels in SH6- (0.25, 0.5, 1, 2.5, 5 μM) and DMSO- treated HUDEP-2 cells
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Protein levels of ZBTB7A were measured from HUDEP-2 cells after SH6 treatment to evaluate the effect of the addition of this molecule. To assess the protein levels, a cells were cultured in StemSpan SFEM II media (Stem Cell Technologies) supplemented with 50 ng/mL human stem cell factor, 3 U/mL erythropoietin, 1 μM dexamethasone, and 1 μg/mL doxycycline. Then, cells were treated with SH6 at different concentrations (0.25, 0.5, 1, 2.5, 5 μM) or DMSO for 24 hours and harvested in quadruplicates using RIPA buffer (Sigma) per the manufacturer’s instructions. Cells were lysed in RIPA buffer supplemented with protease inhibitors. Lysates were resolved on 4-12% Bis-Tris gels, transferred to PVDF membranes, and probed with antibodies against ZBTB7A (CST, 50565) and β-actin (Santa Cruz, sc-47778). Blots were developed using Biorad Chemidoc MP Imaging system. Quantification of WB signal performed by ImageJ (v1.54p). What would be the expected SH6 concentration in which ZBTB7A protein levels will start to drop compared to β-actin in HUDEP-2 cells?
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ZBTB7A protein levels will start to drop at 0.25 μM SH6, instead β-actin protein levels will stay the same in the different concentrations.
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- ZBTB7A, also known as leukemia/lymphoma-related factor or LRF, is a transcription factor that is a critical repressor of γ-globin expression during the fetal-to-adult hemoglobin switch.
- SH6 is a novel small molecule non-iMID that targets ZBTB7A for CRBN-dependent proteasomal degradation.
|
[{"label":"RBK Item","value":"ZBTB7A, also known as leukemia/lymphoma-related factor or LRF, is a transcription factor that is a critical repressor of γ-globin expression during the fetal-to-adult hemoglobin switch. "},{"label":"Title","value":"Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin"},{"label":"URL","value":"https://www.science.org/doi/10.1126/science.aad3312"},{"label":"Date","value":"Jan 15, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Microbiology
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Free-Format Question
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Studies on the antibacterial activity of the antimicrobial peptide Mastoparan X against methicillin-resistant Staphylococcus aureus
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https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1552872/full
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May 28, 2025
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Scientists investigated the antibacterial activity of Mastoparan X (MPX), an antimicrobial peptide, against methicillin-resistant Staphylococcus aureus (MRSA). The MRSA USA300 strain was resuscitated from frozen stock and cultured overnight at 37 °C, in Trypticase Soy Broth (TSB) with continuous shaking (200 rpm). The overnight culture was diluted (1:10,000) in fresh TSB medium and incubated for 4-6 hours until reaching the exponential growth phase. Logarithmic-phase MRSA USA300 cultures were adjusted to 5 × 10^6 CFU/mL in Mueller-Hinton broth (MHB). MPX was synthesized (solid-phase N-9-fluoromethoxycarbonyl chemistry, high-performance liquid chromatography purification to purity ≥95%), then dissolved in DMSO to prepare a 25 mg/mL stock solution. MPX was serially diluted (1–256 μg/mL) in 200 μL MHB within 96-well plates. Controls include MHB containing MRSA USA300 without MPX (positive control), MHB containing MPX without MRSA USA300 (negative control), and MHB only (blank control). After 24 h incubation at 37 °C, the minimum inhibitory concentration (MIC) was determined as the lowest concentration preventing a resazurin (0.1% dye) color change (blue to pink).
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- Minimum inhibitory concentration (MIC) of Staphylococcus aureus (MRSA) after exposure to serial two-fold dilution of Mastoparan X (1, 2, 4, 8, 16, 32, 64, 128, 256 μg/mL)
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Researchers investigated the antibacterial activity of Mastoparan X (MPX), an antimicrobial peptide, against methicillin-resistant Staphylococcus aureus (MRSA). The minimum inhibitory concentration (MIC) of MPX against S. aureus MRSA USA300 was determined by broth microdilution. Cultures adjusted to 5 × 10⁶ CFU/mL in Mueller-Hinton broth were incubated with serial two-fold dilutions of MPX (1–256 μg/mL) in 96-well plates at 37°C for 24 hours. After adding 0.1% resazurin dye, the MIC was defined as the lowest concentration at which no color change occurred (blue, indicating inhibited metabolism).
Predict the resazurin color outcome in the 16 μg/mL well after 24 h.
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Resazurin in the 16 μg/mL well will turn pink after 24 hours.
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- Antimicrobial peptides (AMPs) are a class of small-molecule peptides produced by the body’s innate immune system that can penetrate bacterial cell membranes and transport proteins.
- Mastoparan X (MPX) is an AMP shown to exhibit antimicrobial activity against Gram+ + bacteria, Gram - bacteria, and fungal pathogens (Candida albicans).
|
[{"label":"RBK Item","value":"Antimicrobial peptides (AMPs) are a class of small-molecule peptides produced by the body’s innate immune system that can penetrate bacterial cell membranes and transport proteins. "},{"label":"Title","value":"Antimicrobial mechanisms and clinical application prospects of antimicrobial peptides."},{"label":"URL","value":"https://www.mdpi.com/1420-3049/27/9/2675"},{"label":"Date","value":"April 21, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Mastoparan X (MPX) is an AMP shown to exhibit antimicrobial activity against Gram+ + bacteria, Gram - bacteria, and fungal pathogens (Candida albicans)."},{"label":"Title","value":"The antimicrobial peptide mastoparan X protects against enterohemorrhagic Escherichia coli O157:H7 infection, inhibits inflammation, and enhances the intestinal epithelial barrier."},{"label":"URL","value":"https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.644887/full"},{"label":"Date","value":"June 9, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Microbiology
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Free-Format Question
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Role of NaCl and Glutamine on Biofilm Production from Pseudomonas aeruginosa
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https://www.mdpi.com/2076-2607/13/9/2198#:~:text=aeruginosa%20Pc%2C%20pyocyanin%2Dproducing),In%20P
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September 19, 2025
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Scientists investigated how nutritional shifts affect the function of Pseudomonas aeruginosa strains. P. aeruginosa ATCC 27853 was used as a standard reference against two clinical isolates: pyorubrin producer (Pr) and pyocyanin producer (Pc). The three strains were overnight culture to a turbidity equivalent to 0.5 McFarland. A concentration of 10⁷ CFU/mL was inoculated and incubated at 37°C with 150 rpm for 24 h in three cultured medias: Luria–Bertani (LB) broth as a control, LB without NaCl (LB-NaCl) prepared with only tryptone and yeast extract, and LB broth with yeast extract replaced by 10 mM glutamine (LB-YE/GLn). 200 µL of bacterial suspension were dispensed and incubated under static conditions (37°C, 48 h and 72 h) in flat-bottom 96-well, in triplicate for each condition. Non-adherent bacteria were washed three times (300 µL of phosphate-buffered saline). Incubation in the dark (37°C for 3 h) took place after the addition of 200 µL of PBS and 50 µL XTT solution. At 48 h and 72 h, absorbance was measured at 490 nm, after agitation, using a Perkin Elmer Wallac 1420 Victor2 Microplate Reader and corrected by subtracting the background levels of the corresponding uninoculated media. Biofilm reduction was calculated with the equation Br =[(A-B)/A] x 100, where A and B are the OD490 reads from the control culture (LB) and varied cultural conditions LB-NaCl or LB-YE/GLn)
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- Absorbance at 490 nm of biofilm formed by Pseudomonas aeruginosa strains (P. aeruginosa ATCC 27853, Pr, and Pc) under different culture media (LB, LB-NaCl, and LB-YE/GLn).
- Biofilm reduction by Pseudomonas aeruginosa strains (P. aeruginosa ATCC 27853, Pr, and Pc) under different culture media (LB, LB-NaCl, and LB-YE/GLn).
- Percentage of biofilm production by Pseudomonas aeruginosa strains (P. aeruginosa ATCC 27853, Pr, and Pc) under different culture media (LB, LB-NaCl, and LB-YE/GLn).
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The nutritional shift caused by NaCl depletion and glutamine supplementation in biofilm production of Pseudomonas aeruginosa strains was evaluated. Scientists cultured 10⁷ CFU/mL of three P. aeruginosa strains (ATCC 27853; clinical Pr—pyorubrin-producing; clinical Pc—pyocyanin-producing), previously grown overnight to a turbidity of 0.5 McFarland, into three media types: Luria–Bertani (LB) broth as control, LB without NaCl (LB-NaCl), and LB with yeast extract replaced by 10 mM glutamine (LB-YE/Gln). All cultures were incubated at 37°C. For biofilm formation, 200 µL of bacterial suspension was dispensed into flat-bottom 96-well plates and incubated under static conditions at 37°C for 48 and 72 hours. After incubation, non-adherent bacteria were washed off. Then, 200 µL of PBS and 50 µL of XTT solution were added to each well and incubated in the dark at 37°C for 3 hours. Absorbance was measured at 490 nm using a Perkin Elmer Wallac 1420 Victor2 Microplate Reader at both time points. What would be the expected strain that will have the lowest biofilm production percentage when growing in a culture without NaCl?
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Pseudomonas aeruginosa Pr
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- Pseudomonas aeruginosa (P. aeruginosa), an opportunistic pathogen capable of establishing persistent infections and classified among the ESKAPE pathogens due to its high levels of antibiotic resistance.
- Biofilms are complex, three-dimensional microbial communities encased in a self-produced extracellular matrix.
- Biofilm formation by P. aeruginosa is a well-documented contributor to its virulence and resistance mechanisms.
- Glutamine is an aminoacid that plays a pivotal role in regulating biofilm formation and virulence in P. aeruginosa.
|
[{"label":"RBK Item","value":"Pseudomonas aeruginosa (P. aeruginosa), an opportunistic pathogen capable of establishing persistent infections and classified among the ESKAPE pathogens due to its high levels of antibiotic resistance."},{"label":"Title","value":"Antimicrobial resistance of Pseudomonas aeruginosa: navigating clinical impacts, current resistance trends, and innovations in breaking therapies"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11026690/"},{"label":"Date","value":"Apr 05, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Biofilms are complex, three-dimensional microbial communities encased in a self-produced extracellular matrix."},{"label":"Title","value":"Pseudomonas aeruginosa Biofilms"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7698413/"},{"label":"Date","value":"Nov 17, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Biofilm formation by P. aeruginosa is a well-documented contributor to its virulence and resistance mechanisms."},{"label":"Title","value":"Pseudomonas aeruginosa Biofilm Formation and Its Control"},{"label":"URL","value":"https://www.mdpi.com/2673-8449/1/3/19"},{"label":"Date","value":"Oct 15, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Glutamine is an aminoacid that plays a pivotal role in regulating biofilm formation and virulence in P. aeruginosa."},{"label":"Title","value":"Utilization of L-glutamate as a preferred or sole nutrient in Pseudomonas aeruginosa PAO1 depends on genes encoding for the enhancer-binding protein AauR, the sigma factor RpoN and the transporter complex AatJQMP"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7962211/"},{"label":"Date","value":"Mar 15, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
|
Microbiology
|
Free-Format Question
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Pyrazinamide kills Mycobacterium tuberculosis via pH-driven weak-acid permeation and cytosolic acidification
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https://www.biorxiv.org/content/10.1101/2025.09.26.678883v1
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Sep 27, 2025
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Researchers evaluated the bactericidal activity of Pyrazinamide (PZA) in two non-replicating Mycobacterium tuberculosis (Mtb) strains to determine whether the acidification caused by PZA could induce bacterial cell death independently of the panCD locus. Two recombinant strains, Mtb H37Ra (ATCC 25177) and Mtb mc²6230, both expressing pH-GFP, were generated by electroporation and subsequently selected on 7H11 agar medium supplemented with 10% OADC and 50 mg/L Hygromycin B. To test the effect of PZA, exponentially growing cultures of Mtb H37Ra pH-GFP and Mtb mc²6230 pH-GFP were centrifuged, the supernatants were removed, and the pellets were washed and resuspended in phosphate-citrate buffer adjusted for Mtb H37Ra to pH 7 and pH 5.5, and for Mtb mc²6230 to pH 5.5. The media were supplemented with 50 mg/L Hygromycin B to obtain a final OD600 of 0.1. PZA was added at final concentrations of 0, 50, 200, or 500 mg/L. Monensin (MON) or rifampicin (RIF) was used as an internal positive control for growth inhibition. When required, 25 mg/L of pantothenate (Panto) was also added to the medium. At each time point (day 0, 2, 7, and 14), 200 μL of the undiluted culture (10⁰) was sampled. From this, serial dilutions were prepared ranging from 10⁻¹ to 10⁻⁵. Then, 10 μL of each dilution was spotted onto 7H10 agar plates supplemented with 10% (v/v) OADC, 50 mg/L Hygromycin B, and 25 mg/L Panto to facilitate recovery of Mtb cells. The plates were incubated for 21 days at 37 °C. Plates were scanned using a ChemiDoc™ MP Imaging System (Bio-Rad), with bacterial spot imaging performed using the ‘White Epi Illumination’ setting combined with the ‘Standard Filter’. Experiments were performed on two independent occasions and are representative of one biological replicate.
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- Colony Forming Unit (CFU) counts of serially diluted (10⁻¹ to 10⁻⁵) Mtb strains at different pH conditions (H37Ra pH 7, H37Ra pH 5.5, and mc²6230 pH 5.5) across increasing concentrations of PZA (0, 50, 200, and 500 mg/L), in the presence or absence of 25 mg/L pantothenate.
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The acidification effect of pyrazinamide (PZA) on bacterial cell death, independently of the panCD locus, was evaluated in two non-replicating Mycobacterium tuberculosis (Mtb) strains: Mtb H37Ra (ATCC 25177) and Mtb mc²623, using a spot colony-forming unit (CFU)-based assay. Exponentially growing Mtb cultures were previously washed several times, normalized, and incubated in phosphate-citrate buffer (PCB) at pH 7.0 (H37Ra) or pH 5.5 (H37Ra and mc²623), supplemented with 50 mg/L Hygromycin B to a final OD600 of 0.1. Strains were exposed to increasing concentrations of PZA (0, 50, 200, or 500 mg/L), in the presence or absence of 25 mg/L pantothenate (Panto). Serial dilutions (10⁻¹ to 10⁻⁵) were prepared and 10 µL of each dilution was spotted onto 7H10 agar plates supplemented with 10% (v/v) OADC, 50 mg/L Hygromycin B, and 25 mg/L pantothenate. Plates were incubated for 21 days at 37 °C. Monensin (MON) or rifampicin (RIF) was used as an internal positive control for growth inhibition. Bacterial spots were visualized by scanning the plates using a ChemiDoc™ MP Imaging System (Bio-Rad). What would be the expected concentration of PZA that will show an approximately 3-log¹⁰ reduction in Mtb H37Ra bacterial viability on day 7?
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All concentrations (50, 200, or 500 mg/L) shows an approximately 3-log¹⁰ reduction in Mtb H37Ra bacterial viability on day 7
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- Pyrazinamide (PZA) is a cornerstone drug in tuberculosis (TB) treatment with a strong bactericidal activity in vivo on both active and non-replicating bacterial subpopulations.
- PZA antimicrobial activity is related to the release of protons inside Mycobacterium tuberculosis (Mtb) cytoplasm which causes a decrease in the intrabacterial pH (IBpH) and membrane potential.
- panD is a gene that encodes for the aspartate decarboxylase PanD, involved in Coenzyme A (CoA) synthesis.
- panD gene mutation has been analyzed in Mtb low-level resistant mutants to pyrazinoate anion (POA⁻)/pyrazinoic acid (HPOA).
- H37Ra (ATCC 25177) is a recombinant prototrophic Mtb strain expressing pH-GFP.
- mc²623 is a recombinant pantothenate auxotrophic Mtb mutant strain lacking the panCD locus and expressing pH-GFP.
|
[{"label":"RBK Item","value":"PZA antimicrobial activity is related to the release of protons inside Mycobacterium tuberculosis (Mtb) cytoplasm which causes a decrease in the intrabacterial pH (IBpH) and membrane potential. "},{"label":"Title","value":"Role of Acid pH and Deficient Efflux of Pyrazinoic Acid in Unique Susceptibility of Mycobacterium tuberculosis to Pyrazinamide"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC93615/"},{"label":"Date","value":"Apr, 1999"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"panD is a gene that encodes for the aspartate decarboxylase PanD, involved in Coenzyme A (CoA) synthesis. "},{"label":"Title","value":"Mutations in panD encoding aspartate decarboxylase are associated with pyrazinamide resistance in Mycobacterium tuberculosis"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3697303/"},{"label":"Date","value":"Jun 12, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"panD gene mutation has been analyzed in Mtb low-level resistant mutants to pyrazinoate anion (POA⁻)/pyrazinoic acid (HPOA)."},{"label":"Title","value":"Mutations in panD encoding aspartate decarboxylase are associated with pyrazinamide resistance in Mycobacterium tuberculosis"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3697303/"},{"label":"Date","value":"Jun 12, 2013"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
|
Pharmacology and Toxicology
|
Free-Format Question
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Comparative study on the protective effect of dexrazoxane and blueberry extract against doxorubicin-induced cardiotoxicity in rats
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https://www.nature.com/articles/s41598-025-19853-3
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September 23, 2025
|
Researchers evaluated the protective effects of Dexrazoxane (DEX) and blueberry extract (BB) on Doxorubicin (DOX)-induced cardiomyopathy in rats. 56 male Wistar albino rats, aged 6–8 weeks and weighing 175 ± 25 g, were housed under a 12:12-hour light–dark cycle at 24 ± 2 °C and 50 ± 10% relative humidity, with ad libitum access to food and water for 14 days. The rats were randomly assigned to seven treatment groups: Control, DOX, BB, DEX, DOX+BB, DOX+DEX, and BB+DOX+DEX. For Control rats received an intraperitoneal (IP) injection of normal saline (1 ml/kg) on day 11. DOX group was administered with DOX as a single IP injection (18 mg/kg) on day 11. BB group was administered orally daily with BB extract dissolved in olive oil (80 mg/kg) for 14 days and an IP injection with a normal saline (18 mg/kg) on day 11. DEX group was administered with DEX (180 mg/kg in 5% DMSO) IP injection on day 11. BB+DOX group received the oral BB daily dose (80 mg/kg, for 14 days) and an IP injection of DOX (18 mg/kg) on day 11. DEX+DOX group received a single IP injection of DEX (180 mg/kg) 30 minutes before an IP injection of DOX (18 mg/kg) on day 11. BB+DEX+DOX group received an oral BB daily dose (80 mg/kg) for 14 days, and on day 11 an IP injection of DEX (180 mg/kg) 30 minutes before an IP injection of DOX (18 mg/kg). Rats were euthanized 24 hours after the final injection using isoflurane inhalation anestesia (4–5% for induction, 1–2% for maintenance) via a precision vaporizer, followed by decapitation. Cardiac tissues were collected, washed with saline, and homogenized. Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Germany, Cat. No. 217004), converted to cDNA, and amplified by quantitative real-time PCR (qRT-PCR) with SYBR Green chemistry to measure gene expression of miR-140-5p, Nrf2, and Sirt2.
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- Expression levels (fold change) of miR-140-5p in cardiac tissue of rats across treatment conditions (control, DOX, BB, DEX, DOX+BB, DOX+DEX, and BB+DOX+DEX).
- Expression levels (fold change) of Sirt2 in cardiac tissue of rats across treatment conditions (control, DOX, BB, DEX, DOX+BB, DOX+DEX, and BB+DOX+DEX).
- Expression levels (fold change) of Nrf2 in cardiac tissue of rats across treatment conditions (control, DOX, BB, DEX, DOX+BB, DOX+DEX, and BB+DOX+DEX).
|
To study the protective effects of Dexrazoxane (DEX) and blueberry extract (BB) against Doxorubicin (DOX)-induced cardiomyopathy in rats, researchers measured the expression of 3 molecular markers (miR-140-5p, Sirt2, and Nrf2) in Wistar albino rats cardiac tissue from seven treatment groups: a) Group I, intraperitoneal (IP) normal saline injection (1 ml/kg) on day 11; b) Group 2, DOX (18 mg/kg) IP injection on day 11; c) Group 3, daily oral administration of BB extract in olive oil (80 mg/kg) for 14 days and IP normal saline injection (18 mg/kg) on day 11; d) Group 4, DEX (180 mg/kg in 5% DMSO) IP injection on day 11; e) Group 5, daily oral administration of BB extract in olive oil (80 mg/kg) for 14 days and IP DOX injection (18 mg/kg) on day 11; f) Group 6, single IP DEX injection (180 mg/kg) 30 minutes before an IP DOX injection (18 mg/kg) on day 11; g) Group 7, daily oral administration of BB extract in olive oil (80 mg/kg) for 14 days, and a single IP DEX injection (180 mg/kg) 30 minutes before an IP DOX injection (18 mg/kg) on day 11. Rats were euthanized and cardiac tissues were collected. Total RNA was extracted, converted to cDNA, and amplified by qRT-PCR to measure gene expression (miR-140-5p, Nrf2, and Sirt2). What would be the expected group that will have the highest Sirt2 expression compared to the control?
|
Group 3, blueberry extract
|
- Doxorubicin (DOX): A chemotherapeutic drug effective against various cancers but can potentially cause acute or chronic cardiotoxicity.
- Dexrazoxane (DEX): A derivative of ethylenediaminetetraacetic acid (EDTA) that acts as an intracellular iron chelator, providing cardioprotective effects by reducing reactive oxygen species.
- Blueberry (Vaccinium corymbosum L.): A natural source of anthocyanins, which function as antioxidant compounds that help reduce oxidative stress and inflammation.
|
[{"label":"RBK Item","value":"Doxorubicin (DOX): A chemotherapeutic drug effective against various cancers but can potentially cause acute or chronic cardiotoxicity."},{"label":"Title","value":"Doxorubicin-induced cardiotoxicity and risk factors"},{"label":"URL","value":"https://doi.org/10.1016/j.ijcha.2023.101332"},{"label":"Date","value":"Feb, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Dexrazoxane (DEX): A derivative of ethylenediaminetetraacetic acid (EDTA) that acts as an intracellular iron chelator, providing cardioprotective effects by reducing reactive oxygen species."},{"label":"Title","value":"Chemical, Biological and Clinical Aspects of Dexrazoxane and Other Bisdioxopiperazines"},{"label":"URL","value":"http://dx.doi.org/10.2174/0929867305666220314194045"},{"label":"Date","value":"1998"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Blueberry (Vaccinium corymbosum L.): A natural source of anthocyanins, which function as antioxidant compounds that help reduce oxidative stress and inflammation."},{"label":"Title","value":"Blueberry Anthocyanins-Enriched Extracts Attenuate Cyclophosphamide-Induced Cardiac Injury"},{"label":"URL","value":"https://doi.org/10.1371/journal.pone.0127813"},{"label":"Date","value":"July 2, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
|
Developmental biology / Cryobiology
|
Numerical Values
|
Cryopreservation of Platynereis dumerilii larvae
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https://www.biorxiv.org/content/10.1101/2025.07.31.667934v2
|
August 2, 2025
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Researchers developed a cryopreservation protocol for Platynereis dumerilii larvae. Animals were kept in a 50/50 mix of natural seawater (NSW, from the North Sea) and artificial sea water (ASW, Tropic Marin Pro Reef Salt), adjusted to a salinity of 35 ppt. pH is maintained between pH 7.9 and 8.2, general culture rooms are maintained at 18-20 °C for optimum growth rate and a 16:8 light/dark cycle. Adults are kept in 6L acrylic boxes containing 1.5 L of ASW and water changes are conducted every 2 weeks. Culture boxes containing juvenile worms less than 2 months of age are not water-changed. Original Standard feeding regime: new batches are not fed until after they are cultured at 7-13 days old. The original standard diet begins with feeding larvae < 1 month old twice a week with Tetraselmis marina . Once they begin forming tubes, they are fed twice a week: the first feeding consists of finely chopped organic spinach (denree Blattspinat or similar), and the second feeding consists of PlanktoMarin (a diatom-based liquid food, GROTECH GmBH) or, alternatively, a mixture of powdered Tetramine (Tetra) and Spirulina spec. Improved feeding regime: in further experiments that ultimately resulted in successful survival (up to maturing worms) the starter food for the thawed larvae was modified such that only 50% of the mixture consists of Tetraselmis marina, the other 50% are 1:1 mixture of diatoms Grammatophora marina (Lyngbye). Initially, f/2 was used for growing diatoms. However, we subsequently started using a set of commercial components from CORALAXY. 6-day cultures with a final concentration of ~1.6–1.8 x 10 cells/ml are used for feeding. In addition to this live algal diet fed twice a week, larvae were also fed once per week with the commercial food Planktomarin (GROTECH GmBH). After the worms began forming tubes, they were fed with approximately one small chopped organic spinach leaf per worm. Cryoprotectant agents (CPAs) used along the experiments were dimethyl sulfoxide (Me2SO), ethylene glycol (EG), propylene glycol (PG), Glycerol (Gly), Sucrose (SUC) from Sigma Aldrich. To test the sensitivity to different CPAs, 8 days post-fertilization larvae were exposed for 3 minutes to 1.4M of each permeating CPA (Me2SO, EG, PG and Gly), then carefully filtered (40 µm mesh) and transferred to clean sea water for observation. In a second phase, combinations of cryoprotecting agents were tested by reducing Me2SO content and supplementing it with glycerol and/or sucrose and proceeded as above. For cryopreservation, larvae were exposed to 0.25 ml straws (IMV technologies), with a 1:1 mix of larvae and different concentrations of Me2SO. Larvae were incubated for ca. 3,10,30 and 60 min in the cryoprotecting solution. Straws were sealed with colored sealing powder (IMV technologies) and cooled down from 20°C to -35°C at 2.5min -1, Straws were transferred immediately into liquid nitrogen. Thawing of each straw was done in a water bath at 18°C by immersion for 20-30 seconds. Thawed larvae were rinsed in filtered NSW. The morphology of the larvae was documented before and after each trial with a stereomicroscope, and in some cases with a compound microscope. Mortality rates were obtained from counts of damaged and seemingly healthy larvae. Histological analysis was done using haematoxylin and eosin (H&E).
|
- Survival (%) of larvae measured immediately and longitudinally over days as a function of CPA composition and equilibration time (min).
-Survival post-thaw (%) of larvae measured immediately and longitudinally over days after cooling/thaw protocol with different CPA composition.
- External morphology after thaw (presence/absence of deformities) assessed by microscopy.
-Histological tissue integrity post-thaw (H&E sections; normal vs disrupted structures).
-Growth and development after thaw: number of segments/tube formation; maturation status (male/female) and lifespan (months).
-Growth rate of survivors (% increase over time) under optimized post-thaw husbandry.
|
In the cryopreservation assay with 8-day-post-fertilization Platynereis dumerilii larvae, animals were equilibrated in 1.4 M Me₂SO (CPA) for a set time, loaded into 0.25-mL straws, cooled at 2.5 °C·min⁻¹ from 20 °C to −35 °C, plunged into liquid nitrogen, then thawed at 18 °C. What is the most likely immediate post-thaw survival (%) for the 60-min equilibration condition (exposure + cryopreservation)?
|
Immediate post-thaw survival₆₀min = 13.7–23.7 %, derived from the reported mean 18.7 % for 8-dpf larvae exposed to 1.4 M Me₂SO and cryopreserved after a 60-min equilibration (Figure 2). Note: Numeric CI/SE/SD not provided → fallback tolerance ±5 pp applied.
|
- Successful cryopreservation protocols for Polychaete have been established only for the larvae of Nereis virens
- Although rapid warming is generally associated with improved survival outcomes in some cases, thawing at temperatures closer to the organism’s physiological range yields better results
|
[{"label":"RBK Item","value":"Successful cryopreservation protocols for Polychaete have been established only for the larvae of Nereis virens"},{"label":"Title","value":"Cryopreservation of Nereis virens(Polychaeta, Annelida) Larvae: The Mechanism of Cryopreservation of a Differentiated Metazoan"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S001122409792006X?via%3Dihub"},{"label":"Date","value":"May, 1997"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Although rapid warming is generally associated with improved survival outcomes in some cases, thawing at temperatures closer to the organism’s physiological range yields better results"},{"label":"Title","value":"Cryopreservation of sea urchin embryos (Paracentrotus lividus) applied to marine ecotoxicological studies"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0011224009001369?via%3Dihub"},{"label":"Date","value":"September 26, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
|
Chemistry
|
Electrochemical catalysis
|
MCQ
|
Highly active hydrogen evolution reaction (HER) catalysts formed by energetic Ptn cluster deposition: Deposition dynamics and the HER mechanism
|
https://chemrxiv.org/engage/chemrxiv/article-details/68c471f19008f1a46720baa5
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Sep 17, 2025
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Size-selected platinum clusters (Ptₙ⁺; n = 2, 4, 7) were deposited onto highly oriented pyrolytic graphite (HOPG) under ultrahigh vacuum with controlled kinetic energies spanning 1–50 eV per atom and a uniform flux of 1.5 × 10¹⁴ Pt atoms cm⁻² (≈0.1 monolayer referenced to Pt(111)). Pt sticking and the fraction of Pt on the surface were characterized by X-ray photoelectron spectroscopy (XPS) and low-energy He⁺ ion scattering (ISS), respectively, and clusters were imaged using scanning transmission
electron microscopy (S/TEM), cryo-S/TEM, and cryo-TEM. Hydrogen evolution reaction (HER) activity was measured in 0.1 M HClO₄ by cyclic voltammetry after initial stabilization, using background-subtracted currents (iₚₜ = i − 0.9·i_{HOPG}), and performance was compared systematically as a function of deposition energy and cluster size, enabling direct correlation between deposition dynamics and catalytic behavior.
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-Sticking probability of Ptₙ on HOPG (fraction or %) as a function of deposition energy (~1–50 eV atom⁻¹) for n = 2, 4, 7; assay: XPS/ISS.
-Fraction of Pt exposed at the surface versus subplanted (fraction) versus deposition energy and cluster size (n = 2, 4, 7); assay: ISS/XPS ratio; initial fraction determined from the second ISS scan.
-HER current, i_Pt, in 0.1 M HClO₄, measured after stabilization (CV cycles 4–6), compared across deposition energies (~1–50 eV atom⁻¹) and cluster sizes (n = 2, 4, 7); definition: i_Pt = i − 0.9·i_HOPG.
-Tafel slope (mV dec⁻¹) obtained from tangent lines to Tafel plots built from CV-derived currents
-Change in i_Pt before versus after scans to oxidizing upper potentials, assessed at representative deposition energies with follow-up CVs.
|
Size-selected platinum clusters (Ptₙ⁺, n ≤ 7) were deposited onto highly oriented pyrolytic graphite (HOPG) under ultrahigh vacuum at controlled kinetic energies ranging from 1 to 50 eV/atom, with a total deposition flux of 1.5 × 10¹⁴ Pt atoms/cm² (~0.1 monolayer of Pt(111)). The resulting Ptₙ/HOPG electrodes were characterized using X-ray photoelectron spectroscopy (XPS), low-energy He⁺ ion scattering (ISS), and electron microscopy to determine sticking probability, surface vs. subplanted Pt fractions, and defect formation. Electrochemical hydrogen evolution reaction (HER) activity was evaluated in 0.1 M HClO₄ using cyclic voltammetry. Based on the primary outcomes of the Ptₙ/HOPG study, which of the following statements are correct?( mark all the correct answers).
A) The activities for Ptₙ/HOPG are substantially higher than those for Ptₙ/FTO, and one contributing factor is transport.
B) The higher activity of the surface layer atoms in hard-landed Ptₙ/HOPG is a structural effect.
C) The cluster size effects in this system are relatively weak.
D) Electrolyte composition was the main factor determining HER activity.
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A) The activities for Ptₙ/HOPG are substantially higher than those for Ptₙ/FTO, and one contributing factor is transport.
B) The higher activity of the surface layer atoms in hard-landed Ptₙ/HOPG is a structural effect.
C) The cluster size effects in this system are relatively weak.
|
-HER proceeds via the Volmer–Heyrovsky/Tafel sequence within the CHE framework, and the apparent activity reflects the availability of electrolyte-accessible H* adsorption sites.
-On HOPG, sticking depends strongly on impact energy and sufficiently energetic impacts can break C–C bonds and drive subplantation.
-Soft-landed clusters on HOPG tend to diffuse/aggregate, whereas higher-energy deposition can pin clusters
-HOPG, highly oriented pyrolytic graphite, is a model sp²-carbon electrode used to interpret support/transport effects.
|
[{"label":"RBK Item","value":"HER proceeds via the Volmer–Heyrovsky/Tafel sequence within the CHE framework, and the apparent activity reflects the availability of electrolyte-accessible H* adsorption sites.\n"},{"label":"Title","value":"Modeling the electrified solid–liquid interface"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S0009261408013754"},{"label":"Date","value":"Nov 24, 2008"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, cited by the article"},{"label":"RBK Item","value":"On HOPG, sticking depends strongly on impact energy and sufficiently energetic impacts can break C–C bonds and drive subplantation."},{"label":"Title","value":"Energy-controlled depositions of size-selected silver nanoparticles on HOPG substrates."},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S000926149900891X"},{"label":"Date","value":"Oct 1, 1999"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, cited by the article"},{"label":"RBK Item","value":"Soft-landed clusters on HOPG tend to diffuse/aggregate, whereas higher-energy deposition can pin clusters"},{"label":"Title","value":"The impact of size-selected Ag clusters on graphite: an STM study"},{"label":"URL","value":"https://iopscience.iop.org/article/10.1088/0953-8984/8/41/025"},{"label":"Date","value":"Aug 12, 1996"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, cited by the article"},{"label":"RBK Item","value":"HOPG, highly oriented pyrolytic graphite, is a model sp²-carbon electrode used to interpret support/transport effects."},{"label":"Title","value":"Nanoscale Electrochemistry of sp2 Carbon Materials: From Graphite and Graphene to Carbon Nanotubes"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/acs.accounts.6b00301"},{"label":"Date","value":"Aug 8, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, cited by the article"}]
|
Biology
|
Synthetic Biology, Molecular Biology
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Numerical Values
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Adverse Effects of UV-Exposure on DNA Strand Displacement Reactions
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https://www.biorxiv.org/content/10.1101/2025.09.27.673911v1
|
September 28, 2025
|
The researchers examined the impact of UV-shadowing in the presence of impurities that disrupt circuit behaviour, for DNA strand displacement-based circuits.
DNA samples were annealed at concentrations of 50–100 μM in volumes of 50–100 μL, depending on the experimental requirements, with top strands in 50% excess to ensure that only the purest top strands participated in hybridization; all non-four-way DSD reporters were annealed with a 120% top strand excess. Annealing was carried out by heating to 90°C, holding at 90°C for 5 minutes, and then cooling to 20°C, at a cooling rate of 1°C/min.
3wDSD reaction kinetics were monitored by fluorescent reporter reactions (a fluorophore is attached to the dsDNA reporter, when a signal DNA displaces the top strand of the reporter, the fluorophore is separated from the quencher and begins emitting fluorescence). By measuring the fluorescence, a researcher can quantify the amount of signal present in the system by calibrating fluorescence against known signal concentrations. In this experiment, fluorescence from the reporters was captured using a BioTek Synergy H1 plate reader with the following settings:
* excitation wavelength, 490 nm
* emission wavelength, 525 nm
* optic position, bottom
* gain, 75
* isothermal set-point temperature, 25◦C.
The experiments were conducted in Corning 284-well black clear-bottom plates. To all experimental wells, 5 μM (2 μM for the four-way experiments) PolyT20 (an oligonucleotide consisting of 20 consecutive thymine bases) was added before adding any DNA to minimize adsorption of DNA to the well walls.
For all experiments, reporter strands were added first, and their fluorescence values were recorded to measure the background fluorescence as a baseline. Calibration experiments were conducted alongside each experiment by adding known concentrations of signal DNA to the reporter and measuring the resulting fluorescence. The fluorescence values were baseline-corrected by subtracting their corresponding averaged baseline values (i.e., the self-fluorescence of the unactivated reporter). The correlation between known signal concentrations and baseline-corrected fluorescence was fitted to a second-order polynomial at each time point. During data processing, experimental fluorescence data were also baseline-corrected by subtracting their corresponding averaged baseline values. These baseline-corrected fluorescence values were then converted to reported signal concentration values using the time-dependent calibration curve.
3wDSD experiments were run at signal concentrations of 0, 12.5, 25, 37.5, and 50 nM, using both UV-exposed and UV-free signal strands, together with 75 nM of their complimentary UV-free dsDNA reporters.
Relative fluorescence was calculated using the absolute result for the UV-exposed signal vs. the absolute result for the UV-free signal of the same concentration, as a percentage.
|
* Fluorescence at equilibrium (Eq. Fluorescence; excitation wavelength, 490 nm; emission wavelength, 525 nm).
* UV-exposed and UV-free signal strands.
* Different signal concentrations (0, 12.5, 25, 37.5, and 50 nM).
|
The researchers examined the impact of UV-shadowing (exposure to UV light) in the presence of impurities that disrupt circuit behaviour, for DNA strand displacement (DSD)-based circuits.
Three-way DNA strand displacement (3wDSD; a single-stranded DNA (ssDNA) signal invades a double-stranded DNA (dsDNA) reporter) are the most widely used DSD architecture.
The impact of UV-shadowing in 3wDSD was analyzed, using two types of signal sequences, pyrimidine-pair-rich (PP-rich) and pyrimidine-pair-poor (PP-poor), to investigate sequence dependent defects. For each sequence type, signal concentrations of 0, 12.5, 25, 37.5, and 50 nM were used, considering both UV-exposed (3 minutes) and UV-free signal strands, together with 75 nM of their complimentary UV-free reporters. The baseline-corrected equilibrium fluorescence values of the reporting reactions were obtained and plotted.
In the experiment with UV-exposed and UV-free signals, considering the average across the different signal concentrations used, how much did the percent yield (aproximate to the closest integer, range +/-5%) drop for the pyrimidine-rich UV-exposed signals vs. the UV-free signals?
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The yield for UV-exposed signals decreased by aproximately 48% (valid range of 43-53%).
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* DNA strand displacement (DSD) reactions are basic tools for molecular computation and programmable self-assembly. These reactions can execute complex information-processing tasks.
* DSD circuits are DNA-based structures capable of binding to and manipulating physical materials, to enable the algorithmic control over matter, from the molecular to the macroscopic scale.
* Three-way DNA strand displacement (3wDSD; a single-stranded DNA (ssDNA) signal invades a double-stranded DNA (dsDNA) reporter) is the most widely used form of DSD architecture.
* Fluorescence reporters, with a fluorophore attached to the dsDNA reporter, are used to measure yield (reaction). When a signal DNA displaces the top strand of the reporter, the fluorophore is separated from the quencher and begins emitting fluorescence.
* PAGE is a standard method for purifying double-stranded complexes in DSD systems. Such purification protocols commonly include the use of UV light (200–290 nm, referred to as UV-shadowing) to visualize DNA bands and is known to damage nucleic acids.
|
[{"label":"RBK Item","value":"DNA strand displacement (DSD) reactions are basic tools for molecular computation and programmable self-assembly. These reactions can execute complex information-processing tasks."},{"label":"Title","value":"Enzyme-Free Nucleic Acid Logic Circuits"},{"label":"URL","value":"https://www.science.org/doi/10.1126/science.1132493"},{"label":"Date","value":"December 8, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"DSD circuits are DNA-based structures capable of binding to and manipulating physical materials, to enable the algorithmic control over matter, from the molecular to the macroscopic scale."},{"label":"Title","value":"Controlling Matter at the Molecular Scale with DNA Circuits"},{"label":"URL","value":"https://www.annualreviews.org/content/journals/10.1146/annurev-bioeng-060418-052357"},{"label":"Date","value":"June, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Fluorescence reporters are used to measure yield (reaction). In the reporter, a fluorophore is attached to the dsDNA reporter. When a signal DNA displaces the top strand of the reporter, the fluorophore is separated from the quencher and begins emitting fluorescence."},{"label":"Title","value":"Two novel “release-on-demand” fluorescent biosensors for probing UV-induced DNA damage induced in single stranded and double stranded DNA: Comparative study"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0141813022013769"},{"label":"Date","value":"August 31, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"PAGE is a standard method for purifying double-stranded complexes in DSD systems. Such purification protocols commonly include the use of UV light (200–290 nm) to visualize DNA bands to locate and excise them. This gel monitoring method is referred to as UV-shadowing and is known to damage nucleic acids."},{"label":"Title","value":"Individual Determination of the Yield of the Main UV-Induced Dimeric Pyrimidine Photoproducts in DNA Suggests a High Mutagenicity of CC Photolesions"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/bi0022543"},{"label":"Date","value":"February 2, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
|
Biology
|
Microbiology
|
Numerical Values
|
Antibacterial activity of a conventional hydrogel and a nanoparticle based hydrogel containing Satureja khuzestanica essential oil.
|
https://pmc.ncbi.nlm.nih.gov/articles/PMC12215506/
|
July 1, 2025
|
Researchers compared the antibacterial efficacy of two hydrogel formulations containing Satureja khuzestanica essential oil (EO): an alginate/CMC hydrogel (H-Alg/CMC-EO) and an alginate nanoparticle-CMC hydrogel (H-AlgNP/CMC-EO). EO (0.25% w/v) was emulsified with Tween 20 (0.25–1.0% w/v) at 2000 rpm for 3 min, then mixed with 0.5% sodium alginate. Crosslinking was achieved using CaCl₂ (0.04% or 0.1% w/v) for 40 minutes, resulting in the formation of nanoparticles. The optimal formulation (<200 nm particle size) was selected. H-AlgNP/CMC-EO was prepared by combining the selected EO-loaded AlgNPs with 3.5% carboxymethyl cellulose (CMC) and stirring for 24 hours. A conventional hydrogel (H-Alg/CMC-EO) was prepared by emulsifying EO (0.25% w/v) with Tween 20 (0.25–1.0% w/v) in a 0.5% alginate solution. Distilled water was added during alginate blending to prevent nanoparticle formation. 3.5% CMC was added and stirred (24h, room temperature). Blank formulations (H-Alg/CMC and H-AlgNP/CMC) were prepared as controls. Experimental groups included evaluation against S. aureus and P. aeruginosa: control (untreated bacteria), H-Alg/CMC, H-Alg/CMC-EO, H-AlgNP/CMC, and H-AlgNP/CMC-EO at concentrations of 310, 625, and 1250 µg/mL. Bacterial suspensions (1.5x10⁸ CFU/mL) were treated with 0.25, 0.5, and 1 g of hydrogel formulations (37 °C for 24 h). 10 µL of each treated culture was then applied to Mueller-Hinton agar (MHA), incubated at 37 °C for 24 h, after which colony-forming units (CFU) were quantified for the control and treated samples. Antibacterial efficacy was expressed as % reduction in CFUs compared to the untreated control group.
|
- Colony-forming unit (CFU) counts of Staphylococcus aureus and Pseudomonas aeruginosa after treatment with hydrogel formulations H-Alg/CMC, H-Alg/CMC-EO, H-AlgNP/CMC, and H-AlgNP/CMC-EO at 310, 625, and 1250 µg/mL.
- Bacterial growth (%) of Staphylococcus aureus and Pseudomonas aeruginosa after treatment with hydrogel formulations (H-Alg/CMC, H-Alg/CMC-EO, H-AlgNP/CMC, and H-AlgNP/CMC-EO) at different concentrations (310, 625, and 1250 µg/mL).
|
In an antibacterial assay of hydrogel formulations containing Satureja khuzestanica essential oil (EO), researchers treated P. aeruginosa suspensions (1.5 x 10^8 CFU/mL) with 310, 625, and 1250 µg/mL concentrations of an alginate nanoparticle-CMC hydrogel loaded with essential oil (H-AlgNP/CMC-EO). The hydrogel and bacteria were incubated at 37 °C for 24 h. Colony-forming units were quantified by plating 10 µL of the treated bacterial suspension onto Mueller-Hinton agar at 37 °C for 24h. An untreated control was included for comparison. Antibacterial efficacy was expressed as bacterial growth (%) reduction in CFUs compared to the untreated control group. Based on this experimental setup, what is the expected bacterial growth (%) for the P. aeruginosa group treated with 625 µg/mL of H-AlgNP/CMC-EO?
|
27%-33%
|
- Satureja khuzestanica is a medicinal plant exhibiting antimicrobial properties.
- Hydrogels (three-dimensional polymeric networks capable of retaining large amounts of water) are candidate platforms for encapsulation and delivery of bioactive compounds.
- Carboxymethyl cellulose's (CMC) biocompatibility, tunable viscosity, water retention, and chemical stability make it a good candidate for drug delivery systems.
- Alginate nanoparticles (AlgNPs) enhance antimicrobial efficacy by facilitating wound penetration and protecting active agents (sustained drug release).
|
[{"label":"RBK Item","value":"Satureja khuzestanica is a medicinal plant exhibiting antimicrobial properties."},{"label":"Title","value":"Essential oil constituents and antimicrobial activities of Iranian Satureja khuzestanica"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/10.1002/fsn3.1871"},{"label":"Date","value":"September 17, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Hydrogels (three-dimensional polymeric networks capable of retaining large amounts of water) are candidate platforms for encapsulation and delivery of bioactive compounds.\n"},{"label":"Title","value":"Hydrogels in the clinic: An update"},{"label":"URL","value":"https://aiche.onlinelibrary.wiley.com/doi/10.1002/btm2.10680"},{"label":"Date","value":"May 16, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Carboxymethyl cellulose's (CMC) biocompatibility, tunable viscosity, water retention, and chemical stability make it a good candidate for drug delivery systems."},{"label":"Title","value":"Carboxymethyl cellulose-based oral delivery systems."},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0141813019306415?via%3Dihub"},{"label":"Date","value":"July 15, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Alginate nanoparticles (AlgNPs) enhance antimicrobial efficacy by facilitating wound penetration and protecting active agents (sustained drug release).\n"},{"label":"Title","value":"Alginate nanoparticles for drug delivery and targeting. "},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/31465282/"},{"label":"Date","value":"2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"The original article is not available online; paywalled."}]
|
Chemistry
|
Materials Chemistry
|
MCQ
|
Luminescent chiral molecular glasses by melt-quenching enantiopure BINAP
|
https://chemrxiv.org/engage/chemrxiv/article-details/68ba9100728bf9025e89c155
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Sep 18, 2025
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A researcher prepares chiral molecular glasses from enantiopure BINAP (R-BINAP or S-BINAP). Microcrystalline BINAP (verified by solution ^1H/^31P NMR and PXRD) is loaded in hermetically sealed Al pans under inert gas and subjected to cyclic DSC: heat from RT to 320 °C at 10 °C min⁻¹ (N₂ flow) to pass the sharp melt near 244 °C for the enantiomers, then cool at −10 °C min⁻¹ to vitrify; repeat scans confirm a clear glass transition at ~98 °C without recrystallization for the enantiopure forms. The racemate, by contrast, recrystallizes on cooling (exotherm ≈ 218 °C) and shows no glass transition on reheating.
The resulting glass is then sent for optical characterizations including steady-state photoluminescence and circularly polarized luminescence (CPL) analysis. Together, these data confirm successful melt-quenching of enantiopure BINAP into a kinetically stable, homochiral glass (T_g ≈ 98 °C), and provide the basis for understanding the observed enhancement of both the radiative rate constant (k_F) and CPL dissymmetry factor (g_lum) due to the rigid, isotropic glass environment.
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-Steady-State Excitation and Emission Spectra – recorded in the solid state at room temperature, comparing glassy vs crystalline BINAP;
-Stokes Shift Analysis – derived from excitation (~380 nm) and emission (~430 nm) maxima to assess reduced excited-state relaxation in the glass.
-Time-Correlated Single-Photon Counting (TCSPC) – performed at room temperature, yielding τ ≈ 1.1 ns for g-R-BINAP vs 0.8 ns in crystal.
- Photoluminescence quantum yield (PLQY) measured under identical excitation conditions for crystalline and glassy samples; radiative rate constant 𝑘𝐹 estimated from the PLQY and lifetime measurements.
- Circularly polarized luminescence (CPL) spectra in the solid state at room temperature for crystalline and glassy samples of both enantiomers; left- and right-circularly polarized intensities (IL, IR).
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During the melt-quenching study of enantiopure BINAP, a ~30% increase in the radiative rate constant (kₓ) and an order-of-magnitude enhancement in the circularly polarized luminescence (CPL) dissymmetry factor (gₗᵤₘ) were observed in the glassy state compared to the crystalline state.
What rationalizes this unusual dual enhancement?
A. The glassy matrix restricts molecular motion and strengthens π···π interactions, leading to enhanced Franck–Condon factors and improved overlap between electric and magnetic dipole moments.
B. The rigid, amorphous glass environment minimizes intermolecular coupling and conformational averaging, thereby enhancing Franck–Condon factors and increasing μ–m dipole alignment.
C. The isotropic and kinetically trapped glass reduces structural relaxation and intermolecular interactions, resulting in stronger Franck–Condon transitions and improved μ–m dipole overlap.
D. The vitrified state imposes structural rigidity and isotropy, limiting molecular reorganization and enhancing Franck–Condon factors while promoting greater μ–m transition overlap.
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B. The rigid, amorphous glass environment minimizes intermolecular coupling and conformational averaging, thereby enhancing Franck–Condon factors and increasing μ–m dipole alignment.
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-Franck–Condon Principle and Radiative Rate (kₓ): The Franck–Condon principle governs electronic transitions is essential. A stiffer molecular environment (like a glass) reduces vibrational relaxation, leading to stronger vertical transitions and higher oscillator strength, thereby increasing the radiative rate constant (kₓ).
-Electric–Magnetic Dipole Interaction in CPL (μ–m Overlap):
Circularly polarized luminescence (CPL) is required, particularly how electric (μ) and magnetic (m) transition dipole moments** interact. Improved μ–m overlap in a rigid, isotropic glass enhances the luminescence dissymmetry factor (gₗᵤₘ), yielding stronger chiral emission.
-Effect of Structural Rigidity and Isotropy on Photophysics:
Glass formation alters molecular packing is key — the rigid, amorphous structure suppresses intermolecular π–π coupling and conformational averaging, enabling enhanced kₓ and gₗᵤₘ simultaneously, an uncommon outcome compared to flexible or crystalline environments.
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[{"label":"RBK Item","value":"-Effect of Structural Rigidity and Isotropy on Photophysics:\nGlass formation alters molecular packing is key — the rigid, amorphous structure suppresses intermolecular π–π coupling and conformational averaging, enabling enhanced kₓ and gₗᵤₘ simultaneously, an uncommon outcome compared to flexible or crystalline environments."},{"label":"Title","value":"Intriguing Room Temperature Phosphorescence in Crystalline Porous Organic Frameworks"},{"label":"URL","value":"https://advanced.onlinelibrary.wiley.com/doi/10.1002/adfm.202308096"},{"label":"Date","value":"Sep 13, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Chemistry
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Inorganic Chemistry
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Free-Format Question
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Accessibility and Reactivity of Pentavalent Plutonium Under Alkaline Conditions
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https://chemrxiv.org/engage/chemrxiv/article-details/68cd7dc623be8e43d623d226
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April 07, 2025
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Researchers analyse the crystallography of crystals of the Pu(V) hydroxides K₂[PuᵛO₂(OH)₃].2H₂O, Na[PuᵛO₂(OH)₂(H₂O)].2.5H₂O and Na₂[PuᵛO₂(OH)₃] ·2H₂O. The crystals were synthesized and placed directly into Parabar 10312 (Hampton Research) cryoprotective immersion oil. A high-quality single crystal of each compound was isolated in the fast-drying epoxy and secured on the tip of a glass fiber mounted on a Bruker Quazar single-crystal diffractometer equipped with a microfocus X-ray beam (Mo Kα; λ = 0.71073 Å) and an Apex II detector. The crystallographic frames were collected at 100K (Oxford Cryosystems Cryostream 700) with the Bruker APEXII software package. Peak intensities were corrected for Lorentz, polarization, background effects, and absorption effects using the APEX6 software. The initial structure solution was determined by intrinsic phasing and refined on the basis of F^2 for all unique data using the SHELXL version 5 program.
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-Isolation of a high-quality single crystal of K₂[PuO₂(OH)₃].2H₂O, Na[PuO₂(OH)₂(H₂O)].2.5H₂O and Na₂[PuO₂(OH)₃] ·2H₂O in fast-drying epoxy
-Collection of crystallographic frames at 100K using a Bruker Quazar single-crystal diffractometer equipped with a microfocus X-ray beam (Mo Kα; λ = 0.71073 Å) and an Apex II detector.
-Correction of peak intensities, for Lorentz, polarization, background effects, and absorption effects using the APEX6 software
-Determination of initial structure by intrinsic phasing
-Refinement on the basis of F^2 for all unique data using the SHELXL version 5 program
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A crystallographic analysis of the Pu(V) hydroxides K₂[PuO₂(OH)₃].2H₂O, Na[PuO₂(OH)₂(H₂O)].2.5H₂O and Na₂[PuO₂(OH)₃] ·2H₂O was made. In what range (in ANgstromS) would the Pu=Oyl bond distance be for these compounds?
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1.85-1.88 Angstrom
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- Pu(V) (PuO₂⁺) is important for its solubility in aqueous media, but its chemistry is poorly studied due to the difficulty of obtaining pure solutions and its tendency toward redox disproportionation.
-In neutral or basic media, Pu(V) can be stabilized, but its behavior in strongly alkaline solutions is still poorly understood.
-Pu(VI) and Pu(V) are known to have low solubilities in slightly alkaline media, but much higher solubilities in highly concentrated hydroxide solutions, probably due to the formation of soluble hydroxylated complexes.
-To date, only a few crystal structures of Pu(V) complexes are known.-PuO2+ species are the predominant and most soluble species of plutonium in aqueous environments.
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[{"label":"RBK Item","value":"Pu(V) (PuVO₂⁺) is important for its solubility in aqueous media, but its chemistry is poorly studied due to the difficulty of obtaining pure solutions and its tendency toward redox disproportionation."},{"label":"Title","value":"Solubility of plutonium hydroxides/hydrous oxides under reducing conditions and in the presence of oxygen"},{"label":"URL","value":"https://comptes-rendus.academie-sciences.fr/chimie/item/10.1016/j.crci.2007.02.011.pdf"},{"label":"Date","value":"February 7, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"In neutral or basic media, Pu(V) can be stabilized, but its behavior in strongly alkaline solutions is still poorly understood."},{"label":"Title","value":"Alkaline Chemistry of Transuranium Elements and Technetium and the Treatment of Alkaline Radioactive Wastes"},{"label":"URL","value":"https://www.osti.gov/servlets/purl/92064"},{"label":"Date","value":"May 1, 1995"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Pu(VI) and Pu(V) are known to have low solubilities in slightly alkaline media, but much higher solubilities in highly concentrated hydroxide solutions, probably due to the formation of soluble hydroxylated complexes."},{"label":"Title","value":"Aquatic Chemistry of Pentavalent Plutonium: Determination of the First Hydrolysis Constant"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/36877636/"},{"label":"Date","value":"March 6, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"To date, only a few crystal structures of Pu(V) complexes are known.-PuO2+ species are the predominant and most soluble species of plutonium in aqueous environments."},{"label":"Title","value":"Pu(VI) hydrolysis: further evidence for a dimeric plutonyl hydroxide and contrasts with U(VI) chemistry"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/ic051760j"},{"label":"Date","value":"January 13, 2006"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Chemistry
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Materials Chemistry
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MCQ
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Multidentate Macrocyclic Salphen-Based 2D Conjugated Metal-Organic Framework
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https://chemrxiv.org/engage/chemrxiv/article-details/6871f6a743bc52e4ec925712
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Jul 15, 2025
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A researcher aimed to construct a Cu-based 2D conjugated metal–organic framework (SM-MOF-Cu) using a multidentate salphen macrocyclic ligand (SM-6OH). The SM-6OH ligand was first synthesized under an inert argon atmosphere by dispersing SM-6OMe (447.1 mg, 0.5 mmol) in anhydrous CH₂Cl₂ (20 mL). Then, BBr₃ (1.0 M in CH₂Cl₂, 9 mL, 9 mmol) was added dropwise at 0 °C, and the mixture was stirred at room temperature for 72 h. After quenching with water and filtration, the resulting solid was washed and dried under vacuum to afford SM-6OH as a black powder (90% yield).
For MOF fabrication, SM-6OH (16.2 mg, 0.02 mmol) was dispersed in DMF (0.75 mL) and sonicated for 15 min. Aqueous NH₄OH (100 µL, 25–28%) was then added to deprotonate the phenolic groups, and the mixture was sonicated again for 15 min. Subsequently, a solution of Cu(C₅H₄F₃O₂)₂ (37.0 mg, 0.1 mmol) in MeOH (1.0 mL) was introduced, followed by brief sonication (3 min). Finally, 1.0 mL of water was added, and the sealed vial was heated at 85 °C for 72 h. After cooling, the precipitate was collected by filtration, thoroughly washed with DMF, water, and acetone, and dried under vacuum to yield SM-MOF-Cu as a black powder (93% yield). Optimization studies confirmed that NH₃·H₂O was the preferred base over NaOH (which formed Cu₂O impurities) and that DMF/MeOH/H₂O = 0.75 / 0.25 / 1.0 mL offered optimal crystallinity
For FTIR analysis, the researcher recorded solid-state ATR spectra on a Bruker Alpha spectrometer over 400–4000 cm⁻¹ at room temperature.
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- For FTIR analysis, the researcher recorded solid-state ATR spectra on a Bruker Alpha spectrometer over 400–4000 cm⁻¹ at room temperature. Samples of SM-6OH, SM-MOF-Cu, and the Cu(II) precursor were analyzed.
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A researcher synthesized a Cu-based two-dimensional conjugated metal–organic framework (SM-MOF-Cu) using a multidentate salphen macrocyclic ligand (SM-6OH) containing phenolic –OH groups. During FTIR analysis, the spectrum of the MOF revealed a new absorption band at approximately 494 cm⁻¹, which was absent in the free ligand.
What does the emergence of this new peak indicate? Mark all the correct options.
A. Appearance of low-frequency modes associated with weak Cu···N interactions or lattice vibrations, without the formation of direct Cu–N coordination bonds in the framework.
B. Development of vibrational bands arising from Cu–O coordination between Cu²⁺ centers and phenolic oxygen atoms, indicating that nitrogen atoms are not involved in metal–ligand bonding at this frequency.
C. Formation of Cu–N coordination vibrations associated with direct bonding between Cu²⁺ centers and nitrogen donors of the ligand.
D. Emergence of Cu–N stretching modes corresponding to coordination linkages established between copper ions and nitrogen atoms in the framework.
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C. Formation of Cu–N coordination vibrations associated with direct bonding between Cu²⁺ centers and nitrogen donors of the ligand.
D. Emergence of Cu–N stretching modes corresponding to coordination linkages established between copper ions and nitrogen atoms in the framework.
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- Two-dimensional conjugated metal-organic frameworks (2D c-MOFs), characterized by inplane extended π- conjugated structures and out-of-plane π-π stacking interactions between layers, have emerged as a prominent class of crystalline porous materials.
- Their unique structural and electronic properties have garnered significant research interest due to potential applications in electrocatalysis, supercapacitors, metal-ion batteries, and chemiresistive sensing, among others.
- The strategic integration of macrocyclic building blocks (e.g., phthalocyanines, porphyrins, and tribenzocyclynes) into 2D c-MOFs has introduced well-defined inner cavities with tailored functionalities, demonstrating promising applications in tandem catalysis and ion-selective adsorption.
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[{"label":"RBK Item","value":"Two-dimensional conjugated metal-organic frameworks (2D c-MOFs), characterized by inplane extended π- conjugated structures and out-of-plane π-π stacking interactions between layers, have emerged as a prominent class of crystalline porous materials."},{"label":"Title","value":"Electrically Conductive Metal–Organic Frameworks"},{"label":"URL","value":"https://pubs.acs.org/doi/full/10.1021/acs.chemrev.9b00766"},{"label":"Date","value":"April 10, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Their unique structural and electronic properties have garnered significant research interest due to potential applications in electrocatalysis, supercapacitors, metal-ion batteries, and chemiresistive sensing, among others."},{"label":"Title","value":"Hierarchical Tuning of the Performance of Electrochemical Carbon Dioxide Reduction Using Conductive Two-Dimensional Metallophthalocyanine Based Metal–Organic Frameworks"},{"label":"URL","value":"https://pubs.acs.org/doi/abs/10.1021/jacs.0c07041"},{"label":"Date","value":"December 11, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Chemistry
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Materials Chemistry
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Free-Format Question
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Tailored Phosphate Leaving Groups Direct Pathway-Dependent Self-Assembly
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https://chemrxiv.org/engage/chemrxiv/article-details/68e6bdc4dfd0d042d182cf7d
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Oct 13, 2025
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Researchers synthesized N-terminally protected phenylalanine-derived aminoacyl phosphate esters (FEP, FPP, FNP, and FDDP) bearing ethyl, phenyl, naphthyl, and dodecyl phosphate leaving groups to study pathway-dependent self-assembly. Reactions were conducted by mixing each acyl phosphate ester (10 mM) with amino acid amide nucleophiles-arginine, leucine, phenylalanine, and tryptophan amides (10 mM)-in 0.6 M borate buffer (pH 9.1) at room temperature (~25 °C) in a total volume of 1 mL. Reaction parameters including buffer concentration (0.6 M), pH (9.1), temperature (25 °C), molar ratio (1:1), and stirring rate (0–800 rpm) were controlled to observe differences in assembly behavior. Structural and kinetic characterization was performed using ultra-performance liquid chromatography (UPLC) to monitor hydrolysis and product formation, confocal microscopy to visualize supramolecular structures, and transmission electron microscopy (TEM) to examine nanoscale morphology. Rheological measurements (storage and loss moduli) were used to assess gel mechanical properties, while dye-partitioning assays using Alexa Fluor 488 and Nile Red determined internal polarity of the formed assemblies. All reactions and measurements were performed at 25 °C under controlled pH and concentration conditions to ensure reproducibility.
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- Time-dependent absorbance (turbidity) was measured using a spectrophotometer for reactions in 0.6 M borate buffer at pH 9.1 and 25 °C.
- Microscopic morphology was observed using confocal microscopy (with a 10 µm scale bar) for samples in 0.6 M borate buffer, pH 9.1.
- Nanoscale structure was characterized using Transmission Electron Microscopy (TEM) for assemblies formed in 0.6 M borate buffer, pH 9.1.
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N-terminally protected phenylalanine-derived aminoacyl phosphate esters (FEP, FPP, FNP, and FDDP) were synthesized to investigate pathway-dependent self-assembly driven by variations in phosphate leaving groups. Each ester (10 mM) was reacted with amino acid amide nucleophiles in 0.6 M borate buffer (pH 9.1, 25 °C) under controlled stirring and stoichiometry. Assembly kinetics and structures were analyzed using UPLC, confocal microscopy, TEM, and rheology, while dye-partitioning assays probed internal polarity, enabling correlation between molecular reactivity and supramolecular organization.
How will the supramolecular structures of the dipeptide Boc-FR-NH2 differ when synthesized using Boc-FDDP compared to Boc-FEP and Boc-FPP?
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Boc-FR-NH2 from Boc-FEP and Boc-FPP remained soluble, while the product from Boc-FDDP underwent self-assembly into large spherical aggregates, originating from vesicular structures.
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-In peptide-based systems, differences in amino acid side chains or protecting groups are known to drive the formation of distinct structures by modulating noncovalent interactions.
-Structures of reactive intermediates formed in water impact supramolecular organization.
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[{"label":"RBK Item","value":"In peptide-based systems, differences in amino acid side chains or protecting groups are known to drive the formation of distinct structures by modulating noncovalent interactions. \n\n\n\n"},{"label":"Title","value":"Selective peptide bond formation via side chain reactivity and self-assembly of abiotic phosphates\n\n\n\n"},{"label":"URL","value":"https://www.nature.com/articles/s41467-025-56432-6\n"},{"label":"Date","value":"Feb 03, 2025\n\n\n"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA\n\n\n"},{"label":"RBK Item","value":"Structures of reactive intermediates formed in water could impact supramolecular organization."},{"label":"Title","value":"Peptide self-assembly through liquid-liquid phase separation"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S2451929423002413"},{"label":"Date","value":"Sep 14, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Photochemistry, Physical chemistry
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Free-Format Question
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Comparison of the Performance of Fluorescent, Phosphorescent and TADF Luminophores for Explosives Sensing
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https://chemrxiv.org/engage/chemrxiv/article-details/68b4a37ea94eede154c30152
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03 September, 2025
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Researchers performed Tris(8-hydroxyquinolato)aluminum(III) (Alq3), factris(2-phenylpyridinato)iridium(III) (fac-Ir(ppy)3), and 1,2,3,5-tetrakis(carbazol-9-yl)-4,6-dicyanobenzene (4CzIPN) in solution. Alq3 was purchased from Sigma-Aldrich (sublimed grade, 99.995%). fac-Ir(ppy)3 and 4CzIPN were synthesized according to the literature. Optically dilute solutions of luminophore concentrations on the order of 42 μM were prepared in toluene. Absorption spectra were recorded at room temperature on a Shimadzu UV2600 double-beam spectrophotometer using a 1 cm quartz cuvette. Steady-state emission spectra and Time Correlated Single Photon Counting (TCSPC) emission decay measurements were recorded at 298 K on either an Edinburgh Instruments FS5 or FLS980 spectrofluorometer, both in air and under N2, the latter prepared via 3 freeze-pump-thawing cycles using a home-made Schlenk quartz cuvette. Samples were excited at 420 nm for the steady-state photoluminescence measurements. 375 and 379 nm picosecond pulsed diode lasers from Edinburgh Instruments were used for the time-resolved TCSPC measurements in optically diluted samples. These wavelengths correspond to the near-maximum absorbance of the emitter compounds. The instrument response function (IRF) was measured using a solution of Ludox (signal collected at the wavelength of the laser emission).
Time-resolved photoluminescence measurements were fitted using the Fluoracle software (Edinburgh Instruments) to a sum of exponentials decay model, with chi-squared (𝜒A) values of between 1 and 2. Each component of the decay is assigned a weight (𝑤J), which is the contribution of the emission from each component to the total emission.
Photoluminescence quantum yields (ΦPL) of solutions were determined using the optically dilute method in which four sample solutions with absorbances between 0.1 and 0.01 were used.
fac-Ir(ppy)3 and 4CzIPN were degassed before emission measurements. The Beer-Lambert law was found to remain linear at the concentrations of the solutions. For each sample, linearity between absorption and emission intensity was verified through linear regression analysis with the Pearson regression factor (R2 ) for the linear fit of the data set surpassing 0.9. Individual relative FPL values were calculated for each solution, and the values reported represent the slope obtained from the linear fit of these results. The ΦPL was determined from the equation: ΦPL= ΦR * (Ar/As * Is/It * ns^2/nr^2) where A stands for the absorbance at the excitation wavelength, I is the integrated area under the corrected emission curve, and n is the refractive index of the solvent with the subscripts “s” and “r” representing sample and reference, respectively. ΦR is the absolute quantum yield of the external reference quinine sulfate (ΦR = 54.6% in 1 N H2SO4). The experimental uncertainty in the ΦPL is conservatively estimated to be 10%, though they have found that statistically they can reproduce ΦPL values to 3% relative error.
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- Preparation and optical measurements: Dilute solutions of Alq₃, fac-Ir(ppy)₃, and 4CzIPN at ~42 μM in toluene.
- Absorption spectra: Collected on a Shimadzu UV-2600 double-beam spectrophotometer using a 1 cm quartz cuvette.
- Stationary emission and TCSPC decay measured at 298 K in air and under N₂ (freeze-pump-thaw cycles). Excitation at 420 nm (stationary emission) and 375–379 nm (TCSPC).
- Decay analysis: Fitting using a sum-of-exponentials model with Fluoracle software (χ² between 1 and 2). Relative weights were assigned to each decay component.
- Quantum-yield measurement (relative Φ_PL): Determined by the optically dilute method using four solutions with absorbance 0.1–0.01; λ_exc = 365 nm for the relative Φ_PL determination; emission areas integrated and referenced to quinine sulfate (Φ_R = 54.6% in 1 N H₂SO₄) with refractive-index correction per the stated procedure.
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Given Alq₃, fac-Ir(ppy)₃, and 4CzIPN solutions, at ~42 μM in toluene (Ir(ppy)₃ and 4CzIPN degassed). The solutions were excited at 420 nm for stationary emission and 375–379 nm for TCSPC. In what order do you expect the photoluminescence quantum yield (ΦPL) of these compounds?
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ΦPL 4CzIPN > ΦPL fac-Ir(ppy)₃> ΦPL Alq₃
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-Photoluminescence detection is an attractive method for detecting trace concentrations of chemicals due to its high sensitivity.
-Organic luminophores are ideal due to their high quantum efficiency, ease of synthesis, and the ability to tune their electron levels through molecular design.
-The interaction of a luminophore with an explosive molecule is a bimolecular interaction that often results in photoluminescence quenching, as electron-poor nitroaromatics possess very deep lowest unoccupied molecular orbitals (LUMOs) and therefore typically act as photoinduced electron transfer (PET) acceptors.
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[{"label":"RBK Item","value":"Photoluminescence detection is an attractive method for detecting trace concentrations of chemicals due to its high sensitivity."},{"label":"Title","value":"Recent Progress in Portable Fluorescence Sensors"},{"label":"URL","value":"https://iopscience.iop.org/article/10.1149/1945-7111/abd494/meta"},{"label":"Date","value":"January 7, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Environmental Chemistry / Analytical Chemistry
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Free-Format Question
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Geospatial assessment of heavy metal contamination and metal-resistant bacteria in Qarun Lake, Egypt
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https://enveurope.springeropen.com/articles/10.1186/s12302-025-01152-3
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June 21, 2025
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To conduct a geospatial analysis of heavy metal contamination, researchers used Flame Atomic Absorption Spectrophotometry (Model: PerkinElmer AAnalyst 400, USA) to measure the levels of heavy metals (Pb, Cd, Ni, and Cr) in water samples. The materials were acidified with HNO₃ to achieve a pH of less than 2, followed by filtration using Whatman No. 42 filter paper prior to analysis. Standard solutions obtained from credible reference materials were utilized for system calibration. The concentrations of lead (Pb), cadmium (Cd), nickel (Ni), and chromium (Cr) were quantified at their specific wavelengths.
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-Lead, Cadmium, Nickel and Chromium concentrations using Flame Atomic Absorption Spectrophotometry
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To determine the concentration of lead (Pb), cadmium (Cd), nickel (Ni), and chromium (Cr) in surface water samples from Lake Qarun, Egypt, researchers used Flame Atomic Absorption Spectrophotometry. They acidified the materials with HNO₃ to achieve a pH<2, followed by filtration prior to analysis, and then they quantified the metals at their specific wavelengths. Which of the heavy metals Pb, Ni, Cd or Cr has the highest concentration in this samples?
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Lead
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Lead (Pb), cadmium (Cd), chromium (Cr), and nickel (Ni) are heavy metals of particular concern due to their environmental persistence, propensity for bioaccumulation in animals, and toxicity.
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[{"label":"RBK Item","value":"Lead (Pb), cadmium (Cd), chromium (Cr), and nickel (Ni) are heavy metals of particular concern due to their environmental persistence, propensity for bioaccumulation in animals, and toxicity."},{"label":"Title","value":"Heavy Metal Toxicity and the Environment."},{"label":"URL","value":"https://doi.org/10.1007/978-3-7643-8340-4_6"},{"label":"Date","value":"January 01, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Physics
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Physics/Atomic Physics
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MCQ
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High-sensitivity molecular spectroscopy of SrOH using magneto-optical trapping
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https://www.arxiv.org/abs/2509.09786
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September 11, 2025
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A strontium target inside a $2.4\,\mathrm{K}$ copper cell was ablated by a pulsed Nd:YAG laser. Water vapor was introduced into the cell reacting with the strontium atoms released in ablation to form strontium monohydroxide (SrOH) molecules. Helium introduced via a separate fill line thermalized with the cold walls of the cell and cooled the SrOH. The SrOH was extracted by hydrodynamic flow into a cryogenic buffer-gas beam (CBGB). The CBGB of SrOH was laser-slowed and directed into a 3D magneto-optical trap (MOT). Molecules captured in the trap were cooled to approximately 1 mK within 20 ms. The setup included a multi-laser (12 frequency) optical-cycling system addressing $\mathrm{\bar{X}^2\Sigma^+ \leftrightarrow \bar{A}/\bar{B}}$ bands to repump different vibrational modes, and magnetic quadrupole coils for confinement. To ensure high scattering rates, repumpers were broadened to $\sim 350\,\mathrm{MHz}$ by an over-driven electro-optic modulator. Some molecules fell out of the primary optical cycle into vibrationally excited dark states that were not addressed by the cooling lasers. These molecules remained in the MOT region for $\sim 10\,\mathrm{ms}$. During this free-flight duration, a separate weak $5\,\mathrm{mW}$ probe laser was overlapped with the trapping cloud. The frequency of this probe laser was scanned over a wide range of candidate repumping frequencies to find a transition that returned them to the main optical cycle. Cold (∼4 K) SrOH is created in a cryogenic buffer gas beam source. Then, spectroscopy is performed 1 inch from the cell aperture using a retro-reflected probe laser traveling perpendicular to the molecular beam axis. The fluorescence from the molecules is collected by a lens and a curved mirror, after which the resulting MOT fluorescence is recorded using a Czerny-Turner spectrometer and an EMCCD camera, thus identifying decay frequencies and vibronic assignments.
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- The baseline MOT fluorescence signal was measured using the EMCCD optical imaging system. This provides the steady-state fluorescence proportional to the trapped molecular number before depletion.
- The MOT fluorescence signal after depletion into the dark state was measured using the EMCCD camera. This is the depleted reference for recovery spectroscopy.
- The MOT fluorescence signal after probe-induced recovery was measured using the EMCCD camera.
- The probe laser frequency (scanned over several GHz) was monitored by a calibrated wavemeter.
- The probe laser intensity / power in mW was measured with an optical power meter before MOT.
- The MOT lifetime and free-flight time in ms was recorded with the optical imaging system after switching lasers. The free-flight time defines the effective interaction time for repumper spectroscopy.
- The recovered signal linewidth was derived from MOT fluorescence and probe frequency scans.
- MOT fluorescence was collimated using an invacuum lens and imaged on the EMCCD to determine the number of molecules.
- The molecular temperature was measured using time-of-flight expansion.
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An experiment uses a MOT to perform repumper spectroscopy on SrOH molecules. After molecules are moved into a dark state, a probe laser is scanned to find the recovery transition. Based on the principles of laser spectroscopy, what is the defining characteristic of the measured recovery signal as a function of the probe laser's frequency?
A) The recovery signal is a significantly broadened peak, with a width primarily determined by power broadening from the probe laser.
B) The recovery signal exhibits a highly asymmetric, Fano-like line shape, indicative of interference between the repumping pathway and background scattering processes.
C) The recovery signal is a sharp, symmetric Lorentzian peak with a spectral width on the order of the natural linewidth of the transition (~10 MHz).
D) The recovery signal is observed over an extremely broad frequency range of several GHz, hundreds of times larger than the natural linewidth of the transition.
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D) The recovery signal is observed over an extremely broad frequency range of several GHz, hundreds of times larger than the natural linewidth of the transition.
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- With the precise knowledge of the state energy from this work, we determine that many energy spacings between low-lying rotational levels in the band lie in the 1–100 GHz range.
- A longer interaction time during spectroscopic measurements allows for low-probability, off-resonance events to accumulate. In systems with exceptionally long interaction times, this can generate a measurable signal over a frequency range much broader than the natural linewidth.
|
[{"label":"RBK Item","value":"With the precise knowledge of the state energy from this work, we determine that many energy spacings between low-lying rotational levels in the band lie in the 1–100 GHz range, confirming the viability of a proposed UDM search using temporal variations of µ."},{"label":"Title","value":"Enhanced sensitivity to ultralight bosonic dark matter in the spectra of the linear radical SrOH"},{"label":"URL","value":"https://journals.aps.org/pra/abstract/10.1103/PhysRevA.103.043313"},{"label":"Date","value":"Apr 8, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference 1 in the report."},{"label":"RBK Item","value":"A longer interaction time during spectroscopic measurements allows for low-probability, off-resonance events to accumulate. In systems with exceptionally long interaction times, this can generate a measurable signal over a frequency range much broader than the natural linewidth."},{"label":"Title","value":"The Theory of Coherent Atomic Excitation."},{"label":"URL","value":"https://www.science.org/doi/10.1126/science.250.4987.1603.a"},{"label":"Date","value":"December 14, 1990"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"This paper is paywalled but is cited as reference 45 in the report."}]
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Chemistry
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Radiopharmacy
|
Numerical Values
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A single-step radiolabeling strategy for PET, SPECT, and therapeutic radionuclides using nanoparticles as a universal chelator
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https://chemrxiv.org/engage/chemrxiv/article-details/68a4302423be8e43d6e15c5d
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Jul 16, 2025
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In this experiment, the researchers employed a microwave-assisted (MW) synthesis to obtain small ¹¹¹In radiolabeled nanoparticles with a core size of ~3 nm. The general protocol for the synthesis and radiolabeling of the nanoparticles was as follows: in a 0.5 – 2 mL MW vial with a suitable magnetic stirrer, 540 µL of milli Q water, 150 µL of a 50 mg/mL solution of iron (III) chloride hexahydrate, and 160 µL of a 50 mg/mL sodium citrate were added, and then 50 µL of ¹¹¹In (III) chloride solution (0.01 M HCl) and 100 µL of hydrazine hydrate were added to the vial. The vial was closed with a septum cap and stirred under MW at 100 ºC for 10 min. After this time, the reaction was cooled down with pressurized air to 50 ºC and then purified using a size exclusion Sephadex G-25 prepacked column.
Using this protocol, they synthesized ¹¹¹In-IONT, where IONT (iron oxide nanotracers) denotes the nanoparticles formed by a maghemite core coated with citrate molecules.
The average (N=3) hydrodynamic size of the obtained compound was measured by DLS in water, after its decay.
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- Dynamic light scattering (DLS) measurement of the hydrodynamic diameter of ¹¹¹In-IONT in water, after radioactivity decay (N = 3).
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Small radiolabeled nanoparticles of ¹¹¹In-IONT were synthesized using a microwave-assisted vial with a suitable magnetic stirrer. Milli Q water, 50 mg/mL solution of iron (III) chloride hexahydrate, and 50 mg/mL sodium citrate were added. Then, ¹¹¹In (III) chloride solution (0.01 M HCl) and hydrazine hydrate were added to the vial. The average hydrodynamic size was determined by DLS in water. What is the average hydrodynamic size obtained for ¹¹¹In-IONT (in nm)?
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¹¹¹In-IONT average hydrodynamic size= [10.7-11.5] nm
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• There is no universal chelator that meets: binds rapidly and completely at very low concentrations of the radiometal, maintains high in vivo stability, allows easy bioconjugation with vector molecules, and functions with different radioisotopes for diagnosis and therapy.
• Depending on the radioisotope, chelators may have specific problems.
• Nanoparticles are proposed to replace traditional chelators. Chelator-free techniques offer greater stability, although each system exhibits distinct properties and in vivo behavior.
|
[{"label":"RBK Item","value":"There is no universal chelator that meets: binds rapidly and completely at very low concentrations of the radiometal, maintains high in vivo stability, allows easy bioconjugation with vector molecules, and functions with different radioisotopes for diagnosis and therapy."},{"label":"Title","value":"Thrombo-Tag, an in Vivo Formed Nanotracer for the Detection of Thrombi in Mice by Fast Pre-Targeted Molecular Imaging"},{"label":"URL","value":"https://pubs.rsc.org/en/content/articlelanding/2020/nr/d0nr04538a"},{"label":"Date","value":"October 8, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Depending on the radioisotope, chelators may have specific problems."},{"label":"Title","value":"An Overview of PET Radiochemistry, Part 2: Radiometals"},{"label":"URL","value":"https://jnm.snmjournals.org/content/59/10/1500"},{"label":"Date","value":"May 10, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Nanoparticles are proposed to replace traditional chelators. Chelator-free techniques offer greater stability, although each system exhibits distinct properties and in vivo behavior."},{"label":"Title","value":"Results of a randomized phase-III trial to evaluate the efficacy of strontium-89 adjuvant to local field external beam irradiation in the management of endocrine resistant metastatic prostate cancer"},{"label":"URL","value":"https://www.redjournal.org/article/0360-3016(93)90309-J/abstract"},{"label":"Date","value":"April 2, 1993"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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