bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly specific assay for the detection of SARS-CoV-2-reactive CD4+ and CD8+ T cells in COVID-19 patients
Authors: Zelba Henning , Worbs David , Harter Johannes , Pieper Natalia , Kyzirakos-Feger Christina , Kayser Simone , Seibold Marcel , Bartsch Oliver , Ködding Jiri , Biskup Saskia 
Published: August 2020

AbstractGaining detailed insights into the role of host immune responses in viral clearance is critical for understanding COVID-19 pathogenesis and future treatment strategies. While studies analyzing humoral immune responses against SARS-CoV-2 were available rather early during the pandemic, cellular immunity came into focus of investigations just recently.For the present work, we have adapted a protocol, designed for the detection of rare neoantigen-specific Memory T cells in cancer patients for studying cellular immune responses against SARS-CoV-2. Both, CD4+ and CD8+ T cells were detected after 6 days of in vitro expansion using overlapping peptide libraries representing the whole viral protein. The assay readout was an Intracellular cytokine staining and flow cytometric analysis detecting four functional markers simultaneously (CD154, TNF, IL-2, IFN-γ).We were able to detect SARS-CoV-2-specific T cells in 9 of 9 COVID-19 patients with mild symptoms. All patients had reactive T cells against at least one of 12 analyzed viral antigens and all patients had Spike-specific T cells. While some antigens were detected by CD4+ and CD8+ T cells, Membrane protein was mainly recognized by CD4+ T cells. Strikingly, we were not able to detect SARS-CoV-2-specific T cells in 9 unexposed healthy individuals.We are presenting a highly specific protocol for the detection of SARS-CoV-2-reactive T cells. Our data confirmed the important role of cellular immune responses in understanding SARS-CoV-2 clearance. We showed that Spike is the most immunogenic antigen. We have introduced Membrane protein as interesting target for studying humoral immune responses in convalescent COVID-19 patients.
Decontamination of SARS-CoV-2 and other RNA viruses from N95 level meltblown polypropylene fabric using heat under different humidities
Authors: Campos Rafael K. , Jin Jing , Rafael Grace H. , Zhao Mervin , Liao Lei , Simmons Graham , Chu Steven , Weaver Scott C , Chiu Wah , Cui Yi 
Published: August 2020

ABSTRACTIn March of 2020, the World Health Organization declared a pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The pandemic led to a shortage of N95-grade filtering facepiece respirators (FFRs), especially for protection of healthcare professionals against airborne transmission of SARS-CoV-2. We and others have previously reported promising decontamination methods that may be applied to the recycling and reuse of FFRs. In this study we tested disinfection of three viruses including SARS-CoV-2, dried on a piece of meltblown fabric, the principal component responsible for filtering of fine particles in N95-level FFRs, under a range of temperatures (60-95°C) at ambient or 100% relative humidity (RH) in conjunction with filtration efficiency testing. We found that heat treatments of 75°C for 30 min or 85°C for 20 min at 100% RH resulted in efficient decontamination from the fabric of SARS-CoV-2, human coronavirus NL63 (HCoV-NL63), and another enveloped RNA virus, chikungunya virus vaccine strain 181 (CHIKV-181), without lowering the meltblown fabric’s filtration efficiency.
Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies
Authors: Du Xiao , Li Lili , Liang Fan , Liu Sanyang , Zhang Wenxin , Sun Shuai , Sun Yuhui , Fan Fei , Wang Linying , Liang Xinming , Qiu Weijin , Fan Guangyi , Wang Ou , Yang Weifei , Zhang Jiezhong , Xiao Yuhui , Wang Yang , Wang Depeng , Qu Shoufang , Chen Fang , Huang Jie 
Published: August 2020

AbstractThe importance of structural variants (SVs) on phenotypes and human diseases is now recognized. Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed, few benchmarking procedures are available to confidently assess their performances in biological and clinical research. To facilitate the validation and application of those approaches, our work established an Asian reference material comprising identified benchmark regions and high-confidence SV calls. We established a high-confidence SV callset with 8,938 SVs in an EBV immortalized B lymphocyte line, by integrating four alignment-based SV callers [from 109× PacBio continuous long read (CLR), 22× PacBio circular consensus sequencing (CCS) reads, 104× Oxford Nanopore long reads, and 114× optical mapping platform (Bionano)] and onede novoassembly-based SV caller using CCS reads. A total of 544 randomly selected SVs were validated by PCR and Sanger sequencing, proofing the robustness of our SV calls. Combining trio-binning based haplotype assemblies, we established an SV benchmark for identification of false negatives and false positives by constructing the continuous high confident regions (CHCRs), which cover 1.46Gb and 6,882 SVs supported by at least one diploid haplotype assembly. Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology, disease, and clinical diagnosis.
Conformational changes and channel gating induced by CO2binding to Connexin26
Authors: Brotherton Deborah H. , Savva Christos G. , Ragan Timothy J. , Linthwaite Victoria L. , Cann Martin J. , Dale Nicholas , Cameron Alexander D. 
Published: August 2020

AbstractCO2is the inevitable by-product of oxidative metabolism. Many physiological processes such as breathing1and cerebral blood flow2are sensitive to CO2. Historically, the physiological actions of CO2have been regarded as being mediated exclusivelyviachanges in pH. Here, we change this consensus by showing that the gap junction protein Connexin26 (Cx26) acts as a receptor for CO2showing sensitivity to modest changes in PCO2around the physiological norm3-6. Mass spectrometry analysis7shows that CO2carbamylates specific lysines on a regulatory loop of Cx26 at high, but not at low levels of PCO2. By means of high resolution cryo-EM, we have solved structures of Cx26 gap junctions at 1.9, 2.2 and 2.1 Å for PCO2of 90, 55 and 20 mmHg respectively, all at pH 7.4. Classification of the particles at each level of PCO2, shows the transmembrane helices and N-terminal helix flexing at the dynamic cytoplasmic side of the protein. Gating of Cx26 gap junctions by CO2involves movements of the N-terminus to plug the channel at high PCO2. We therefore provide mechanistic detail for a new paradigm by which CO2can directly control breathing8and other key physiological functions9.
Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Authors: Müller Maik , Gräbnitz Fabienne , Barandun Niculò , Shen Yang , Vetterli Stefan U. , Mondal Milon , Prudent James R. , Severin Yannik , van Oostrum Marc , Hofmann Raphael , Sarott Roman , Nesvizhskii Alexey I. , Carreira Erick M. , Bode Jeffrey , Snijder Berend , Robinson John A. , Loessner Martin J. , Oxenius Annette , Wollscheid Bernd 
Published: August 2020

AbstractDelineating the molecular nanoscale organization of the surfaceome is pre-requisite for understanding cellular signaling. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would open up theranostic opportunities and the possibility to engineer extracellular signaling. Here, we developed an optoproteomic technology termed LUX-MS that exploits singlet oxygen generators (SOG) for the light-triggered identification of acute protein interactions on living cells. Using SOG-coupled antibodies, small molecule-drugs, biologics and intact viral particles, we show that not only ligand-receptor interactions can be decoded across organisms, but also the surfaceome receptor nanoscale organization ligands engage in with direct implications for drug action. Furthermore, investigation of functional immunosynapses revealed that intercellular signaling inbetween APCs and CD8+T cells can be mapped now providing insights into T cell activation with spatiotemporal resolution. LUX-MS based decoding of surfaceome signaling architectures provides unprecedented molecular insights for the rational development of theranostic strategies.
Analysis of fungal genomes reveals commonalities of intron loss/gain and functions in intron-poor species
Authors: Lim Chun Shen , Weinstein Brooke N. , Roy Scott W. , Brown Chris M. 
Published: August 2020

ABSTRACTCurrent evolutionary reconstructions predict that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. However, some extant eukaryotes have few introns, raising the question as to why these few introns are retained. Here we have used recently available fungal genomes to address this question. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species support the idea that massive intron loss has occurred in multiple clades. The intron densities estimated in the fungal ancestral states differ from zero to 8.28 introns per one kbp of protein-coding gene. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts (0.01 and 0.05 introns/kbp on average, respectively), but also in diverse smuts and allies (e.g.Ustilago maydis, Meira miltonrushiiandMalassezia globosahave 0.06, 0.10 and 0.20 introns/kbp, respectively). To investigate the roles of introns, we searched for their special characteristics using 1302 orthologous genes from eight intron-poor fungi. Notably, most of these introns are found close to the translation initiation codons. Our transcriptome and translatome data analyses showed that these introns are from genes with both higher mRNA expression and translation efficiency. Furthermore, these introns are common in specific classes of genes (e.g. genes involved in translation and Golgi vesicle transport), and rare in others (e.g. base-excision repair genes). Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
Obesity promotes glucocorticoid-dependent muscle atrophy in male C57BL/6J mice
Authors: Gunder Laura C. , Harvey Innocence , Redd JeAnna R. , Davis Carol S. , AL-Tamimi Ayat , Brooks Susan V. , Bridges Dave 
Published: August 2020

AbstractGlucocorticoids promote muscle atrophy by inducing a class of proteins called atrogenes, resulting in reductions in muscle size and strength. In this work, we evaluated whether a mouse model with pre-existing diet-induced obesity had altered glucocorticoid responsiveness. We observed that all animals treated with the synthetic glucocorticoid dexamethasone had reduced strength, but that obesity exacerbated this effect. These changes were concordant with more pronounced reductions in muscle size, particularly in Type II muscle fibers, and potentiated induction of atrogene expression in the obese mice relative to lean mice. Furthermore, we show that the reductions in lean mass do not fully account for the dexamethasone-induced insulin resistance observed in these mice. Together these data suggest that obesity potentiates glucocorticoid-induced muscle atrophy.
Mechanically induced cytoskeletal remodeling in trabecular meshwork cells requires TRPV4 - Rho signaling interactions
Authors: Lakk Monika , Križaj David 
Published: August 2020

AbstractIntraocular pressure (IOP) is dynamically regulated by the trabecular meshwork (TM), a mechanosensitive tissue that protects the eye from injury through dynamic regulation of aqueous humor outflow from the anterior chamber of the eye. IOP-dependent increases in TM stiffness and contractility drive open angle glaucoma but the mechanotransduction mechanisms that regulate these processes remain poorly understood. We used fluorescence imaging and biochemical analyses to investigate cytoskeletal and focal adhesion remodeling in human TM cells stimulated with cyclic strain. The cells showed enhanced F-actin polymerization, increased number and size of focal adhesions, and activation of the Rho-associated protein kinase (ROCK). Stretch-induced activation of the small GTPase RhoA, and tyrosine phosphorylations of focal adhesion proteins paxillin, focal adhesion kinase (FAK), vinculin and zyxin were time-dependently inhibited by HC-067047, an antagonist of transient receptor potential vanilloid 4 (TRPV4) channels, and the ROCK inhibitor Y-27632. TRPV4 and ROCK activation were required for zyxin translocation and increase in the number/size of focal adhesions in stretched cells. Y-27632 blocked actin polymerization without affecting calcium influx induced by membrane stretch and the TRPV4 agonist GSK1016790A. These results reveal that mechanical tuning of TM cells requires parallel activation of TRPV4, integrins and ROCK, with chronic stress leading to sustained remodeling of the cytoskeleton and focal complexes.
Age-related alterations in prelimbic cortical neuronArcexpression vary by behavioral state and cortical layer
Authors: Hernandez Abbi R. , Truckenbrod Leah M. , Barrett Maya E. , Lubke Katelyn N. , Clark Benjamin J. , Burke Sara N. 
Published: August 2020

AbstractPrefrontal cortical and medial temporal lobe connectivity is critical for higher cognitive functions that decline in older adults. Likewise, these cortical areas are among the first to show anatomical, functional, and biochemical alterations in advanced age. The prelimbic subregion of the prefrontal cortex and the perirhinal cortex of the medial temporal lobe are densely reciprocally connected and well-characterized as undergoing age-related neurobiological changes that correlate with behavioral impairment. Despite this fact, it remains to be determined how changes within these brain regions manifest as alterations in their functional connectivity. In our previous work, we observed an increased probability of age-related dysfunction for perirhinal cortical neurons that projected to the prefrontal cortex in old rats compared to neurons that were not identified as projection neurons. The current study was designed to investigate the extent to which aged prelimbic cortical neurons also had altered patterns ofArcexpression during behavior, and if this was more evident in those cells that had long-range projections to the perirhinal cortex. The expression patterns of the immediate-early geneArcwere quantified in behaviorally characterized rats that also received the retrograde tracer cholera toxin B (CTB) in the perirhinal cortex to identify projection neurons to this region. As in our previous work, the current study found that CTB+ cells were more active than those that did not have the tracer. Moreover, there were age-related reductions in prelimbic cortical neuronArcexpression that correlated with a reduced ability of aged rats to multitask. Unlike the perirhinal cortex, however, the age-related reduction inArcexpression was equally likely in CTB+ and CTB− negative cells. Thus, the selective vulnerability of neurons with long-range projections to dysfunction in old age may be a unique feature of the perirhinal cortex. Together, these observations identify a mechanism involving prelimbic-perirhinal cortical circuit disruption in cognitive aging.
Aggression is induced by resource limitation in the monarch caterpillar
Authors: Collie Joseph , Granela Odelvys , Brown Elizabeth , Keene Alex C. 
Published: August 2020

AbstractFood represents a limiting resource for the growth and developmental progression of many animal species. As a consequence, competition over food, space, or other resources can trigger territoriality and aggressive behavior. Throughout their early development stages, insect larvae eat voraciously and limited food availability can potently impact their viability through metamorphosis. In the monarch butterfly,Danaus plexippus,caterpillars feed predominantly on milkweed, raising the possibility that access to milkweed is critical for growth and survival. Here, we characterize the role of food availability on aggression in monarch caterpillars. We find that monarch caterpillars display stereotyped aggressive lunges that increase during development, peaking during the 4thand 5thinstar stages. Detailed behavioral analysis reveals that aggressive actions are most likely to occur when the target is feeding and increases the probability that the target will leave the food source. To determine the relationship between food availability and the initiation of an aggressive encounter, we provided groups of caterpillars differing amounts of food availability and measured aggressive behavior. The number of lunges toward a conspecific caterpillar was significantly increased under conditions of low food availability, suggesting resource defense may trigger aggression. We find that aggression occurs independently of light, suggesting the visual system is dispensable for the induction of aggression. These findings establish monarch caterpillars as a model for investigating interactions between resource availability and aggressive behavior under ecologically relevant conditions and set the stage for future investigations into the neuroethology of aggression in this system.
Chronic Exposure to Palmitic Acid Downregulates AKT in Beta-Cells through Activation of mTOR
Authors: Aggarwal Richa , Peng Zhechu , Zeng Ni , Silva Joshua , He Lina , Chen Jingyu , Debebe Anketse , Stiles Eileen X. , Chen Chien-Yu , Stiles Bangyan L. 
Published: August 2020

ABSTRACTHigh circulating lipids occurring in obese individuals and insulin resistant patients are considered a contributing factor to Type 2 Diabetes (T2D). Exposure to high lipids initially causes the beta-cells to expand in population. Long-term exposure to high lipids however is associated with failure of beta-cells and the development of T2D. To prevent the failure of beta-cells and development of Type 2 Diabetes, this study focuses on understanding the molecular mechanisms that underlie this biphasic response of beta-cells to lipid exposure. Using palmitic acid (PA) in cultured beta-cells and islets, we demonstrated that chronic exposure to lipids leads to reduced viability and inhibition of cell cycle progression concurrent with downregulation of a pro-growth/survival kinase AKT, independent of glucose. This AKT downregulation by PA treatment is correlated with a consistent induction of mTOR/S6K activity concurrent with AKT downregulation. Inhibiting mTOR activity restores AKT activity and allows beta-cells to gain proliferation capacity that are lost after high fat diet exposure. In summary, we elucidated a novel mechanism for which lipid exposure may cause the dipole effects on beta-cell growth, where mTOR acts as a lipid sensor. These mechanisms can be novel targets for future therapeutic developments.
Knowledge, attitudes and practices (KAP) towards COVID-19 among Palestinians during the COVID-19 outbreak: A cross-sectional survey
Authors: Qutob Nouar , Awartani Faisal 
Published: August 2020

AbstractCoronavirus disease 2019 (COVID-19) is a highly contagious illness that spreads rapidly through human-to-human transmission. On March 5, the government of Palestine declared a state of emergency in order to curb the spread of the virus, a declaration that it extended for a fifth time on July 5th. The degree to which a population complies with corresponding safety measures is surely affected by the people’s knowledge, attitudes and practices (KAP) towards the disease. To explore this hypothesis, we gathered data from 1,731 Palestinians between April 19thand May 1st, 2020 through a KAP questionnaire. The participant pool represented a stratified sample of Palestinians living across a number of governorates in the Gaza Strip and the West Bank, with 36.5% from Gaza and (63.5%) from the West Bank. Gender was almost equally distributed within the sample with (51%) male respondents and (49%) female respondent. The questionnaire included 17 questions about participants’ knowledge and awareness of COVID- 19, 17 questions regarding the safety measures they had taken in the wake of the outbreak and 3 questions asking them to assess the efficacy of the government’s response to the pandemic. The overall correct mean of the knowledge was 79.26+-0.35. Most participants expressed confidence that Covid-19 would be successfully controlled and that Palestine could win the battle against Covid-19, though 62% believed that stricter measurements must be applied. Based on the results of this study, we conclude that health education programs aimed at improving the public’s understanding of COVID-19 are important in helping the population maintain appropriate practices, and that findings such as those discussed in this report may provide valuable feedback to lawmakers working to stop the spread of the virus.
FITs: Forest of imputation trees for recovering true signals in single-cell open chromatin profiles
Authors: Sharma Rachesh , Pandey Neetesh , Mongia Anchal , Mishra Shreya , Majumdar Angshul , Kumar Vibhor 
Published: August 2020

AbstractThe advent of single-cell open-chromatin profiling technology has facilitated the analysis of heterogeneity of activity of regulatory regions at single-cell resolution. However, stochasticity and availability of low amount of relevant DNA cause high drop-out rate and noise in single-cell open-chromatin profiles. We introduce here a robust method called as Forest of Imputation Trees (FITs) to recover original signals from highly sparse and noisy single-cell open-chromatin profiles. FITs makes a forest of imputation trees to avoid bias during the restoration of read-count matrices. It resolves the challenging issue of recovering open chromatin signals without blurring out information at genomic sites with cell-type-specific activity. FITs is generalized for wider applicability, especially for highly sparse read-count matrices. The superiority of FITs in recovering signals of minority cells also makes it highly useful for single-cell open-chromatin profile fromin vivosamples.First made online as thesis work athttps://repository.iiitd.edu.in/xmlui/handle/123456789/807
Investigation of white spot syndrome virus (WSSV) infection in wild crustaceans in the Bohai Sea
Authors: Xu Tingting , Shan Xiujuan , Li Yingxia , Yang Tao , Teng Guangliang , Wu Qiang , Wang Chong , Tang Kathy F.J. , Zhang Qingli , Jin Xianshi 
Published: August 2020

AbstractThe ecological risks of white spot syndrome virus (WSSV), an important aquatic pathogen, has been causing increasing concern recently. A continuous survey on the prevalence of WSSV in the wild crustaceans of the Bohai Sea was conducted in present study. The result of loop-mediated isothermal amplification detection showed that WSSV positivity rates of sampling sites were determined to be 76.73%, 55.0% and 43.75% in 2016, 2017 and 2018, respectively. And the WSSV positivity rates of samples were 17.43%, 12.24% and 7.875% in 2016, 2017 and 2018, respectively. Meanwhile, the investigation revealed that 11 wild species from the sea were identified to be WSSV positive. The WSSV infection in wild crustacean species was confirmed by transmission electron microscopy analysis. The results of this study suggest that WSSV had been colonized in wild species offshore and the impact caused by WSSV to the wild marine ecosystem cannot be ignored.