bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Incorporation and Template‐Dependent Polymerase Inhibition are Major Determinants for the Broad‐Spectrum Antiviral Activity of Remdesivir
Authors: Gordon Calvin J. , Lee Hery W. , Tchesnokov Egor P. , Perry Jason K. , Feng Joy Y. , Bilello John P. , Porter Danielle P. , Gotte Matthias 
Published: May 2022

Remdesivir (RDV) is a direct‐acting antiviral agent that is approved in several countries for the treatment of coronavirus disease 2019 (COVID‐19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). RDV exhibits broad‐spectrum antiviral activity against positive‐sense RNA viruses, e.g. SARS‐CoV‐2 and hepatitis C virus (HCV) and non‐segmented negative‐sense RNA viruses, e.g. Nipah virus (NiV), while segmented negative‐sense RNA viruses such as influenza (Flu) virus or Crimean‐Congo hemorrhagic fever virus (CCHFV) are not sensitive to the drug. The reasons for this apparent pattern are unknown. Here, we expressed and purified representative RNA‐dependent RNA polymerases (RdRp) and studied three biochemical parameters that have been associated with the inhibitory effects of RDV‐triphosphate (TP): (i) selective incorporation of the nucleotide substrate RDV‐TP, (ii) the effect of the incorporated RDV‐monophosphate (MP) on primer extension, and (iii) the effect of RDV‐MP in the template during incorporation of the complementary UTP. The results of this study revealed a strong correlation between antiviral effects and efficient incorporation of RDV‐TP. Inhibition in primer extension reactions is heterogeneous and usually inefficient at higher NTP concentrations. In contrast, template‐dependent inhibition of UTP incorporation opposite the embedded RDV‐MP is seen with all polymerases. Molecular modeling suggests a steric conflict between the 1’‐cyano group of RDV‐MP and conserved residues of RdRp motif F. We conclude that future efforts in the development of nucleotide analogues with a broader spectrum of antiviral activities should focus on improving rates of incorporation while capitalizing on the inhibitory effects of a bulky 1’‐modification.C.J.G, H.W.L, and E.P.T contributed equally to this work
Circulating MicroRNAs in Canine Congestive Heart Failure – Why Exosomes?
Authors: Ewing Carl A. , Ewing Coralis W. , Bohan Amy 
Published: May 2022

By influencing protein translation, microRNAs (miRNAs) have emerged as powerful regulators of a wide range of biological processes. miRNAs can be found freely circulating in blood as well as in circulating exosomes. It has been speculated that evaluating the quantity of miRNAs contained in exosomes may serve as a better diagnostic and prognostic tool than those found freely circulating.A good test case for this relationship is to look at miRNA dysregulation effecting Canine Congestive Heart Failure, resulting from Myxomatous Mitral Valve Disease (MMVD), in these two contexts. In order to do this, we are assessing levels of miR‐1, miR‐126, and miR‐133a, in nine small breed, older dogs with this disorder, compared to healthy dogs, using Realtime qPCR analysis.We hypothesize that our results will confirm the assertion that exosomes reveal a more reliable indication of MMVD than by quantifying freely circulating miRNAs.
Investigating the Interaction Interface between MEK and ERK Kinase
Authors: Lin Sabrina , Naagaard Mats D. , Pham Tammy , Fera Daniela 
Published: May 2022

The mitogen‐activated protein kinase (MAPK) pathway is pertinent to various cellular processes such as cell proliferation, cell division, and cell death. Dysregulation of the MAPK pathway can therefore lead to numerous illnesses. Most notably, the dysregulation of proteins in this pathway is a significant cause of melanomas and other cancers. Due to this oncogenic potential, various drugs and inhibitors exist to regulate MAPK overexpression. As drug resistance and paradoxical activation are perpetual challenges, additional regulatory targets are needed to effectively suppress the effects of MAPK oncogenic mutations, calling for further investigation into downstream interactions such as that between MEK and ERK kinase. By identifying and characterizing the binding interface between MEK and ERK, we can identify additional drug targets that can modulate the MAPK pathway.To help map the MEK‐ERK interface, we first performed computational docking experiments to find possible interaction regions between MEK and ERK. In several trials, we found that certain MEK alpha helices interacted with ERK. We then proceeded to identify the corresponding binding partners on ERK. We introduced mutations in the most promising regions on ERK and expressed the mutant proteins using a bacterial expression system. Using biolayer interferometry and co‐elution assays, we compared the binding affinities of our mutants to that of the corresponding wild‐type.Our studies showed that introducing the K231E and K114E mutations in ERK altered the binding kinetics between MEK and ERK. Our co‐elution studies showed that a stable complex does not occur, suggesting that the interaction between MEK and ERK is either weak or transient and may need another molecule to stabilize the complex. Cross‐linking experiments are in progress, and so far, we identified 1% glutaraldehyde incubated for 5 minutes as sufficient for covalent linkage of MEK and ERK. These findings will help towards obtaining a 3D MEK‐ERK complex structure to better understand signaling in this pathway.
Immunologically active cells and infertility ‐ Quantification of uterine Natural Killer cells in endometrial samples from patients with recurrent implantation failure
Authors: Varga Ivan , Lapides Lenka , Klein Martin , Babal Pavel 
Published: May 2022

BackgroundDespite enormous advancements of reproductive medicine, recurrent implantation failure and habitual abortion remain an ongoing issue. One of the most important aspects of successful implantation is the intricate immune regulation necessary for the acceptance of the hemiallogenic embryo. The most numerous immune cells in the decidua are uterine Natural Killer (uNK) cells. Studies suggest that changes in the uNK cells count and physiology may be responsible for the aforementioned conditions. Thus, the uNK cells testing may provide valuable insights into their pathogenesis.MethodsWe compared Pipelle endometrial sampling with conventional curettage to find out whether the less invasive Pipelle method is a viable alternative of tissue collection.ResultsWe examined tissue samples from 9 patients obtained by both methods. The average size of tissue samples obtained with pipelle was 10,27 mm2, samples obtained with curettage had on average 18,74 mm2. Using immunohistochemical visualization of CD56 (NK cells) and granzyme B antigens (serine protease‐expressing activation state of NK cells), we found out that the average total count of CD56 / mm2 was for pipelle 90,13 and 84,04 for curettage. We also proved a correlation between granzyme B positivity and identification of NK cells clusters. The results showed that Pipelle endometrial sampling is a suitable method of tissue harvesting for the purpose of uNK cells examination. Discussion: Pipelle endometrial sampling is safe, cost‐effective and can be performed on an outpatient basis without the need of anaesthesia or analgesia. Several issues remain to be solved: how to standardize the subsequent uNK cells testing, how to interpret the results and finally yet importantly, how to use this knowledge in personalized treatment protocols.
Orchidectomy exacerbates respiratory instability induced by intermittent hypoxia in C57BL6/J mice
Authors: Ganouna‐Cohen Gauthier , Marcouiller François , Joseph Vincent 
Published: May 2022

IntroductionSleep apnea (SA) is characterized by obstructions of the airways or cessation of breathing during sleep leading to intermittent hypoxia (IH). In rodents, exposure to IH induces strong oxidative stress in the peripheral chemoreceptors (the main oxygen sensors inducing cardiorespiratory responses to IH), which increase their activity leading to instability of the respiratory control system, ultimately increasing the frequency of apnea during sleep. In human, patients with SA have low circulating testosterone levels and the severity of SA in overweight patients is negatively correlated with testosterone levels. However, testosterone can reduce oxidative stress in certain animal and clinical models. We therefore tested the hypothesis that testosterone modulates the respiratory instability induced by HI.MethodWe used intact (Sham) or orchidectomized (ORX) C57BL/6J male mice exposed for 14 days to IH (12h / day, 10 cycles / h, 6% nadir oxygen) or in normoxia (Nx). We used whole body plethysmography on freely behaving and non‐anesthetized mice to measure the frequency of apneas and sighs as well as the length of the apneas during sleep. The antioxidant activity of superoxide dismutase (SOD), catalase and glutathione peroxidase (GPx) were then measured in plasma.ResultsIH increases the frequency of post‐sigh apneas as well as the length of post‐sigh and spontaneous apneas in Sham and ORX mice. In ORX‐IH mice, the length of post‐sigh apneas was further increased, and there was a higher proportion of multiple apneas after a single sigh. In Nx mice, GPx activity was increased by ORX, this effect was not present in mice exposed to IH.ConclusionThe lack of testosterone in ORX mice amplifies the effects of IH on respiratory stability during sleep and alters the regulation of GPx activity in plasma. Further studies are needed to better understand the underlying mechanism
Fundamentals of Biochemistry, a free and new LibreText book for Undergraduate Courses
Authors: Jakubowski Henry , Flatt Patricia , Agnew Henry , Larsen Delmar 
Published: May 2022

We are developing a new fee online biochemistry text, Fundamentals of Biochemistry, within the LibreTexts project (Libretexts.org) as part of a Department of Education funded grant to produce textbooks for all chemistry courses required for a four‐year ACS certified degree. This text covers a full year sequence of biochemistry and will be available in Fall 2022. The book could serve traditional, ASBMB‐certified and ACS‐certified majors, as well as students taking a one‐semester course. Adopting instructors could create a custom text from the content. Characteristic of all LibreText books, Fundamentals of Biochemistry will be open to everyone via the internet and completely free, as all should have access to knowledge. It is comprehensive and topical, as new materials are easily added. It has and will be constructed with a community of active collaborators. The LibreText collections of books have served 223 million students and saved them $31 million, an undue burden for our students and society.Some of the features of Fundamentals of Biochemistry include

Interactive 2D mathematical graphs with sliders that allow change of constants with immediate update of graphs;
Interactive molecular models using iCn3D (https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html) that allows students to view and interact with rendered structures;
Imbedded VCell (https://vcell.org/) models that allow users to display time course graphs for simple to complex reactions;
Animations to accompany the VCell progress curve graphs;
Chapter sections on metabolic control analyses that will include Vcell models;
Addition of new materials such as RNA glycans, SARS‐CoV‐2 structures, etc.
The text will be available for adoption by Fall 2022. We continue to need help in writing key features and in a continual process of updating, especially in these areas:

end‐of‐chapter and chapter‐imbedded problems (hopefully based on research literature)
mechanisms of your favorite enzymes or topics you feel not presented well in other texts
inclusive and diverse content
climate change, health disparities, addiction, etc.
The Effect of Cold and Warm Water Ingestion Prior to and During Passive Heating on Local Sweat Rate
Authors: Leach Caileigh , Newhouse Douglas , Ravanelli Nicholas 
Published: May 2022

BACKGROUNDDuring heat stress, sweating is initiated to mitigate the rise in core temperature. Relative to warm water, previous evidence has demonstrated that cold water ingestion prior to exercise‐induced heat stress in compensable conditions delays the onset of sweating, and produces a reduction in local sweat rate immediately following ingestion. However, it remains unknown whether ingestion of cold water will elicit a similar delay in the onset of sweating and reduction in local sweating during more extreme thermal challenges. It is hypothesized that cold water ingestion prior to and during passive heat stress will result in a delayed onset of sweating and a reduction in local sweat rate in comparison to warm water.METHODSTo date, three male participants (25±4 years, 82±8 kg, 1.9±0.1 m) have completed two passive heating sessions using a water perfused blanket system to increase rectal temperature by 1˚C above baseline. Participants ingested 3.2 ml‧kg‐1 (263±27 mL) of either cold (1.5˚C, CW) or warm (37˚C, WW) water five minutes before passive heating, and following a 0.5˚C and 1.0˚C increase in rectal temperature. Local sweat rate of the forearm and mean skin temperature were measured throughout baseline and passive heating.RESULTSBaseline rectal temperature was not different between CW (37.0±0.2˚C) and WW (36.9±0.1˚C, p=0.17) trials. Mean skin temperature was not different at baseline (CW: 33.5±0.2˚C, WW: 33.1±0.4˚C, p=0.60), and following a 0.5˚C (CW: 38.9±0.5˚C, WW: 38.9±0.6˚C, p = 0.99) and 1.0˚C (CW: 39.3±0.5˚C, WW: 39.2±0.4˚C, p=0.58) increase in rectal temperature. Mean body temperature at the onset of sweating on the forearm was not affected by the water temperature (CW: 37.1±0.2˚C, WW: 37.1±0.3˚C, p=0.79). When compared to the 5‐minutes before 37˚C water ingestion (PRE), mean local sweat rate of the forearm was not different during the 10‐minutes after (POST) at 0.5˚C (PRE: 0.98±0.23 mg‧cm‐2‧min‐1, POST: 1.05±0.36 mg‧cm‐2‧min‐1, p=0.48) and 1.0˚C (PRE: 1.11±0.37 mg‧cm‐2‧min‐1, POST: 1.15±0.49 mg‧cm‐2‧min‐1, p=0.74) increase in rectal temperature. Similarly, mean local sweat rate of the forearm was not different POST compared to PRE ingestion of 1.5˚C water following a 0.5˚C (PRE: 0.89±0.28 mg‧cm‐2‧min‐1, POST: 0.88±0.27 mg‧cm‐2‧min‐1, p=0.74) and 1.0˚C (PRE: 0.93±0.42 mg‧cm‐2‧min‐1, POST: 0.92±0.41 mg‧cm‐2‧min‐1, p=0.71) increase in rectal temperature. However, CW ingestion following a 0.5˚C increase in rectal temperature resulted in a lower local sweat rate of the forearm in comparison to WW for the remainder of heating (p<0.03).CONCLUSIONPreliminary data suggest cold water ingestion may alter the local sweating response in young healthy males during passive heating.
Resistance Breathing and Sympathetic Nerve Activity During Simulated Hemorrhage in Humans
Authors: Davis Kenneth A. , Sprick Justin , Kay Victoria , Rickards Caroline A. 
Published: May 2022

BackgroundResistance breathing amplifies the respiratory pump during inspiration, so may be an effective intervention for treatment of hemorrhagic injuries. In animal studies of actual hemorrhage, and human studies of simulated hemorrhage, resistance breathing protects arterial pressure, and improves tolerance to this stress. Anecdotally, resistance breathing also increases the coupling between sympathetic nerve activity and arterial pressure. The impact of resistance breathing on overall sympathetic nerve activity, however, has not been examined. We tested the hypothesis that resistance breathing increases sympathetic nerve activity during simulated hemorrhage in healthy humans.MethodsLower body negative pressure (LBNP) was used to simulate hemorrhage in five human subjects (3M, 2F; 29.2 ± 6.8 y). Two experiments were conducted (randomized order): 1) a control condition in which LBNP was applied at 3 mmHg/min until the onset of presyncope, and 2) a resistance breathing condition in which the same LBNP protocol was used, but subjects breathed through a resistance device (set at ‐7 cm.H2O) during the final stages of the protocol. Arterial pressure and muscle sympathetic nerve activity (MSNA) of the radial nerve were monitored continuously. Bursts frequency (bursts/min) and burst incidence (burst/ 100 heart beats) were used to quantify MSNA. Coupling between diastolic arterial pressure (DAP) and MSNA was assessed by transfer function analysis coherence within the low frequency range (0.04‐0.15 Hz). Two‐way repeated measures ANOVAs were conducted for assessment of responses in the control and resistance breathing conditions, between baseline and at matched time points late in the LBNP protocol.ResultsWhile LBNP induced increases in both MSNA burst frequency (P=0.003) and burst incidence (P=0.06), there was no effect of resistance breathing on MSNA for either index during LBNP (control, 57.9 ± 25.9 bursts/min vs. resistance breathing, 50.6 ± 21.7 bursts/min, P=0.99; control, 55.6 ± 25.6 b/100 heart beats vs. resistance breathing, 42.3 ± 18.3 b/100 heart beats, P=0.42). Additionally, there was no effect of resistance breathing on DAP (control, 73.2 ± 9.9 mmHg vs. resistance breathing, 72.8 ± 4.4 mmHg; P=0.99), or coherence between MSNA and DAP during LBNP (control, 0.53 ± 0.21 vs. resistance breathing, 0.69 ± 0.17; P=0.46).ConclusionContrary to our hypothesis, resistance breathing had no effect on sympathetic nerve activity during LBNP. A limitation of this study is the low sample size (N=5), and high variability of MSNA. Future investigations with a larger sample size are needed to determine if respiratory dynamics can influence the coupling between MSNA and arterial pressure.
Ciprofloxacin Permanently Accelerates Gastrointestinal Transit in a Rodent Model of Fluoroquinolones Associated Disability
Authors: Kerler Jacqueline , Getaneh Bitseat , Bove Cecilia 
Published: May 2022

Fluoroquinolones (FQs) are a class of antibiotics intended to be prescribed for life‐threatening infections. However, they are often administered for less severe infections, which they are not meant to treat. In addition, studies suggest that FQs can lead to severe long‐lasting complications described as Fluoroquinolone Associated Disability (FQAD). Some of these permanent issues affect the central nervous system, cardiac, and musculoskeletal systems among others. Gastrointestinal issues have also been considered a possible side effect due to how FQs may negatively modulate the vagus nerve, which plays a major role in digestion and regulation of satiety. Indeed, the inhibitory neurotransmitter GABA regulates the motor portion of the vagus nerve, and FQs act as a selective inhibitor of GABAA receptors. This blockade of GABAA receptors is believed to contribute to the GI issues that seem to arise after taking FQs.To measure possible changes in digestion, Sprague Dawley rats were treated daily for 14 consecutive days with either 0.3ml of 0.9% saline (CTL n=6) or 20mg/kg of ciprofloxacin (CPX) via oral gavage. On experiment day (day 14 or 28; n=6 for both), rats were administered phenol red dye, sacrificed, and the stomach, proximal, middle, and distal small intestine were harvested to measure dye recovery via spectrophotometry as a measure of gastrointestinal transit. Results showed that both male and female rats in the 28 day group had significantly less dye recovered from their stomach compared to the 14 day and CTL group, with female rats being disproportionately affected compared to males (P<0.05). This data provides strong evidence that FQs lead to permanent acceleration in digestive patterns. Further experiments will analyze how the phenotype of enteric motor neurons, as well as the phenotype of neurons within the Dorsal Motor Nucleus of the vagus in the medulla oblongata, is affected by this drug. This will contribute to determining the mechanism underlying the observed digestion change in rats treated with ciprofloxacin.
Effects of passive heat exposure on myocardial blood flow in healthy young and older adults
Authors: Barry Hadiatou , Chaseling Georgia K. , D’Oliviera‐Sousa Caroline , Harel François , Pelletier‐Galarneau Matthieu , Gagnon Daniel 
Published: May 2022

INTRODUCTIONExtreme heat is associated with a greater risk of cardiovascular mortality in older adults (≥60 years). However, the pathophysiology that links extreme heat and cardiovascular mortality remains unknown. One possibility is that myocardial oxygen requirements during heat exposure cannot be met by sufficient increased in myocardial blood flow (MBF) thereby predisposing to ischemia. However, the extent to which MBF increases during heat exposure, and whether age alters this increase, is unknown. The objective of this study was to test the hypothesis that passive heat exposure increases MBF and that this increase is attenuated in healthy older adults.METHODSMBF was measured during passive heat exposure (water‐perfused suit) in 15 young (27 years, range: 24‐30) and 14 older (68 years, range: 64‐72) healthy adults with 82‐Rubidium positron emission tomography. Four MBF measurements were performed: prior to heat exposure (baseline) and at an increase in rectal temperature of 0.5°C, 1.0°C, and 1.5°C. Heart rate (ECG) and blood pressure (automated auscultation) were also measured to calculate rate pressure product (RPP; heart rate x systolic blood pressure). MBF reserve (MFR) was calculated by dividing the MBF at 1.5°C by baseline MBF.RESULTSBaseline MBF was 0.76 ± 0.19 mL/min/g in young adults and 0.88 ± 0.21 mL/min/g in older adults (p=0.14). MBF increased similarly in both groups during heat exposure (interaction, p=0.31). Nonetheless, older adults displayed a lower MFR at an increase in rectal temperature of 1.5°C (young: 2.3 ± 0.7 vs. older: 1.8 ± 0.4, p=0.03). The lower MFR in older adults was paralleled by an attenuated increase in RPP during passive heating (at + 1.5°C, young: 6.8 ± 1.7vs. older: 3.6 ± 2.2 bpm·mmHg·103, p<0.01), due to a blunted increase in heart rate (young: 50 ± 12vs. older: 34 ± 14 bpm, p<0.01). When the change in MBF was plotted against the change in RPP, the slope of the regression lines did not differ between young (0.11 [95% CI; 0.07, 0.15]) and older (0.08 [95% CI; 0.04, 0.11] mL/g/min/ bpm·mmHg·103,p=0.24) adults.CONCLUSIONThese results show that passive heat exposure roughly doubles MBF in healthy young and older adults. Furthermore, the results demonstrate that the increase in MBF during passive heat exposure is not altered by age and is proportional to the increase in RPP.