bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer learning to detect COVID-19 automatically from X-ray images, using convolutional neural networks
Authors: Taresh Mundher , Zhu Ningbo , Ali Talal Ahmed Ali 
Published: August 2020

AbstractNovel coronavirus pneumonia (COVID-19) is a contagious disease that has already caused thousands of deaths and infected millions of people worldwide. Thus, all technological gadgets that allow the fast detection of COVID-19 infection with high accuracy can offer help to healthcare professionals. This study is purposed to explore the effectiveness of artificial intelligence (AI) in the rapid and reliable detection of COVID-19 based on chest X-ray imaging. In this study, reliable pre-trained deep learning algorithms were applied to achieve the automatic detection of COVID-19-induced pneumonia from digital chest X-ray images.Moreover, the study aims to evaluate the performance of advanced neural architectures proposed for the classification of medical images over recent years. The data set used in the experiments involves 274 COVID-19 cases, 380 viral pneumonia, and 380 healthy cases, which was derived from several open sources of X-Rays, and the data available online. The confusion matrix provided a basis for testing the post-classification model. Furthermore, an open-source library PYCM was used to support the statistical parameters. The study revealed the superiority of Model vgg16 over other models applied to conduct this research where the model performed best in terms of overall scores and based-class scores. According to the research results, deep Learning with X-ray imaging is useful in the collection of critical biological markers associated with COVID-19 infection. The technique is conducive for the physicians to make a diagnosis of COVID-19 infection. Meanwhile, the high accuracy of this computer-aided diagnostic tool can significantly improve the speed and accuracy of COVID-19 diagnosis.
Noc corrals migration of FtsZ protofilaments during cytokinesis inBacillus subtilis
Authors: Yu Yuanchen , Zhou Jinsheng , Gueiros-Filho Fredy , Kearns Daniel B. , Jacobson Stephen C. 
Published: August 2020

ABSTRACTBacteria that divide by binary fission form FtsZ rings at the geometric midpoint of the cell between the bulk of the replicated nucleoids. InB. subtilis, the DNA- and membrane-binding Noc protein is thought to mediate nucleoid occlusion to prevent FtsZ rings from forming over the chromosome. To explore the role of Noc, we used time-lapse fluorescence microscopy to monitor FtsZ and the nucleoid of cells growing in microfluidic channels. Our data show that Noc does not prevent FtsZ formation over the chromosome or control cell division site selection. Instead, Noc inhibits migration of FtsZ protofilaments from one FtsZ structure to the next. Moreover, we show that FtsZ protofilaments travel due to a local reduction in ZapA association, and the Noc mutant phenotype can be suppressed by ZapA overexpression. Thus, Noc maintains a high local concentration of FtsZ to stabilize FtsZ rings during cytokinesis.IMPORTANCEIn bacteria, a condensed structure of FtsZ (Z-ring) recruits cell division machinery, and Z-ring formation is inhibited over the chromosome by a poorly understood phenomenon called nucleoid occlusion. InB. subtilis, nucleoid occlusion has been reported to be mediated by the DNA-membrane bridging protein, Noc. Using time-lapse fluorescence microscopy of cells growing in microchannels, we show that Noc neither protects the chromosome from proximal Z-ring formation nor determines the future site of cell division. Rather, Noc plays a corralling role by preventing protofilaments from leaving a Z-ring undergoing cytokinesis and traveling over the nucleoid.
dagLogo: an R/Bioconductor Package for Identifying and Visualizing Differential Amino Acid Group Usage in Proteomics data
Authors: Ou Jianhong , Liu Haibo , Nirala Niraj K. , Stukalov Alexey , Acharya Usha , Green Michael R. , Zhu Lihua Julie 
Published: August 2020

AbstractSequence logos have been widely used as graphical representations of conserved nucleic acid and protein motifs. Due to the complexity of the amino acid (AA) alphabet, rich post-translational modification, and diverse subcellular localization of proteins, few versatile tools are available for effective identification and visualization of protein motifs. In addition, various reduced AA alphabets based on physicochemical, structural, or functional properties have been valuable in the study of protein alignment, folding, structure prediction, and evolution. However, there is lack of tools for applying reduced AA alphabets to the identification and visualization of statistically significant motifs. To fill this gap, we developed an R/Bioconductor package dagLogo, which has several advantages over existing tools. First, dagLogo allows various formats for input sets and provides comprehensive options to build optimal background models. It implements different reduced AA alphabets to group AAs of similar properties. Furthermore, dagLogo provides statistical and visual solutions for differential AA (or AA group) usage analysis of both large and small data sets. Case studies showed that dagLogo can better identify and visualize conserved protein sequence patterns from different types of inputs and can potentially reveal the biological patterns that could be missed by other logo generators.
Preconditioning ofCaenorhabditis elegansto Anoxic Insult by Inactivation of Cholinergic, GABAergic, and Muscle Activity
Authors: Bennett Heather L. , McClanahan Patrick D. , Fang-Yen Christopher , Kalb Robert G. 
Published: August 2020

AbstractFor most metazoans, oxygen deprivation leads to cell dysfunction and if severe, death. Sublethal stress prior to a hypoxic or anoxic insult (“preconditioning”) can protect cells from subsequent oxygen deprivation. The molecular mechanisms by which sublethal stress can buffer against a subsequent toxic insult and the role of the nervous system in the response are not well understood. We studied the role of neuronal activity preconditioning to oxygen deprivation inC. elegans. Animals expressing the histamine gated chloride channels (HisCl1) in select cell populations were used to temporally and spatially inactivate the nervous system or tissue prior to an anoxic insult. We find that inactivation of the nervous system for 3 hours prior to the insult confers resistance to a 48-hour anoxic insult in 4th-stage larval animals. Experiments show that this resistance can be attributed to loss of activity in cholinergic and GABAergic neurons as well as in body wall muscles. These observations indicate that the nervous system activity can mediate the organism’s response to anoxia.
Performance Evaluation and Selection of ImprovedTef(Eragrostis tefL)varieties at Main Campus Site Hadiya Zone, Southern Ethiopia
Authors: Dutamo Dargicho , Assefa Ermias , Menamo Muluneh 
Published: August 2020

ABSTRACTTef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. It is, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gareth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. The experiment was conducted to identify, select and recommend adaptable, high yielding, Insect pest and disease resistant twelve released and one local variety at Main Campus Site Hadiya zone of SNNPR. Twelve tef varieties were evaluated in RCBD with three replications on station of Main Campus Site during main cropping season of 2019/2020. Analysis of variance revealed that there were significant differences among tef varieties, Culm length, panicle length, plant height, days to heading, days to maturity, grain filling period, primary panicle brunch, grain yield, biomass yield and harvest index at Main Campus site. Based on the obtained result, the improved tef varieties namely; DZ-Cr-438 DZ-Cr-974 (Dukem), DZ-01-899 (Gimbechu) and DZ-01-196 (Magna) at Main Campus site. Therefore, these varieties showed better performance for most of the studied characters including grain yield. Therefore, these varieties were selected and recommended for the study area and similar ecologies of Hadiya Zone. This finding, being the result of one year with single location, it is recommended that the experiment should be repeated at multi locations for several years to confirm the obtained results.
Cold Exposure Protects from Neuroinflammation Through Immunologic Reprogramming
Authors: Spiljar Martina , Steinbach Karin , Rigo Dorothée , Suárez-Zamorano Nicolas , Wagner Ingrid , Hadadi Noushin , Vincenti Ilena , Page Nicolas , Klimek Bogna , Rochat Mary-Aude , Kreutzfeldt Mario , Chevalier Claire , Stojanović Ozren , Mack Matthias , Cansever Dilay , Greter Melanie , Merkler Doron , Trajkovski Mirko 
Published: August 2020

SUMMARYAutoimmunity is energetically costly, but the impact of a metabolically active state on immunity and immune-mediated diseases is unclear. Ly6Chimonocytes are key effectors in CNS autoimmunity with elusive role in priming naïve autoreactive T cells. Here we provide unbiased analysis of the immune changes in various compartments during cold exposure, and show that this energetically costly stimulus markedly ameliorates active experimental autoimmune encephalomyelitis (EAE). Cold exposure decreases MHCII on monocytes at steady-state and in various inflammatory mouse models, and suppresses T cell priming and pathogenicity through the modulation of monocytes. Genetic, or antibody-mediated monocyte depletion, or adoptive transfer of Th1- or Th17-polarized cells for EAE abolish the cold-induced effects on T cells or EAE, respectively. These findings provide a mechanistic link between environmental temperature and neuroinflammation, and suggest competition between cold-induced metabolic adaptations and autoimmunity as energetic trade-off beneficial for the immune-mediated diseases.
Cellxgene VIP unleashes full power of interactive visualization and integrative analysis of scRNA-seq, spatial transcriptomics, and multiome data
Authors: Li Kejie , Ouyang Zhengyu , Chen Yirui , Gagnon Jacob , Lin Dongdong , Mingueneau Michael , Chen Will , Sexton David , Zhang Baohong 
Published: August 2020

AbstractTo meet the growing demands from scientists to effectively extract deep insights from single cell RNA sequencing, spatial transcriptomics, and emerging multiome datasets, we developed cellxgene VIP (Visualization In Plugin), a frontend interactive visualization plugin of cellxgene framework, which greatly expanded capabilities of the base tool in the following aspects. First, it generates a comprehensive set of over eighteen commonly used quality control and analytical plots in high resolution with highly customizable settings in real time. Second, it provides more advanced analytical functions to gain insights on cellular compositions and deep biology, such as marker gene identification, differential gene expression analysis, and gene set enrichment analysis. Third, it empowers advanced users to perform analysis in a Jupyter Notebook like environment, dubbed Command Line Interface (CLI) by programming in Python and/or R directly without limiting themselves to functional modules available via graphical user interface (GUI). Finally, it pioneers methods to visualize multi-modal data, such as spatial transcriptomics embedding aligned with histological image on one slice or multiple slices in a grid format, and the latest 10x Genomic Multiome dataset where both DNA accessibility and gene expression in the same cells are measured, under the same framework in an integrative way to fully leverage the functionalities mentioned above. Taken together, the open-source tool makes large scale single cell data visualization and analysis more accessible to biologists in a user-friendly manner and fosters computational reproducibility by simplifying data and code reuse through the CLI. Going forward, it has the potential to become a crowdsourcing ecosystem for the scientific community to contribute even more modules to the Swiss Army knife of single cell data exploration tools.
Insect threats and conservation through the lens of global experts
Authors: Miličić Marija , Popov Snežana , Branco Vasco Veiga , Cardoso Pedro 
Published: August 2020

AbstractWhile many recent studies have focused on global insect population trends, all are limited either in space or taxonomic scope. Since global monitoring programs for insects are not implemented, biased data are therefore the norm. However, expert opinion is both valuable and widely available, and should be fully exploited when hard data are not available. Our aim is to use global expert opinion to provide insights on the root causes of potential insect declines worldwide, as well as on effective conservation strategies that could mitigate insect biodiversity loss. We obtained 753 responses from 413 respondents with a wide variety of expertise. The most relevant threats identified through the survey were agriculture and climate change, followed by pollution, while land management and land protection were recognized as the most significant conservation measures. Nevertheless, there were differences across regions and insect groups, reflecting the variability within the most diverse class of living organisms on our planet. Lack of answers for certain biogeographic regions or taxa also reflects the need for research, particularly in less investigated settings. Our results provide a first step towards understanding global threats and conservation measures for insects.
Spontaneous neurotransmission at evocable synapses predicts their responsiveness to action potentials
Authors: Grasskamp Andreas T. , Jusyte Meida , McCarthy Anthony W. , Götz Torsten W.B. , Ditlevsen Susanne , Walter Alexander M. 
Published: August 2020

AbstractSynaptic transmission relies on presynaptic neurotransmitter (NT) release from synaptic vesicles (SVs) and on NT detection by postsynaptic receptors. Transmission exists in two principal modes: action-potential (AP) evoked and AP-independent, “spontaneous” transmission. AP-evoked neurotransmission is considered the primary mode of inter-neural communication, whereas spontaneous transmission is required for neuronal development, homeostasis, and plasticity. While some synapses appear dedicated to spontaneous transmission only, all AP-responsive synapses also engage spontaneously, but whether this encodes functional information regarding their excitability is unknown. Here we report on functional interdependence of both transmission modes at individual synaptic contacts ofDrosophilalarval neuromuscular junctions (NMJs) which were identified by the presynaptic scaffolding protein Bruchpilot (BRP). Consistent with its role in organizing the AP-dependent release machinery (voltage-dependent Ca2+channels and SV fusion machinery), most active BRP-positive synapses (>85%) responded to APs. At these synapses, the level of spontaneous activity was a precise predictor for their responsiveness to AP-stimulation. Both transmission modes engaged an overlapping pool of SVs and NT-receptors, and both were affected by the non-specific Ca2+channel blocker cadmium. Thus, by using overlapping machinery, spontaneous transmission is a continuous, stimulus independent predictor for the AP-responsiveness of individual synapses.
A Micro-engineered Human Colon Intestine-Chip Platform to Study Leaky Barrier
Authors: Apostolou Athanasia , Panchakshari Rohit A. , Banerjee Antara , Manatakis Dimitris V. , Paraskevopoulou Maria D. , Luc Raymond , AbuAli Galeb , Dimitriou Alexandra , Lucchesi Carolina , Kulkarni Gauri , Maulana Tengku Ibrahim , Bleck Bertram , Manolakos Elias S. , Hamilton Geraldine A. , Giallourakis Cosmas , Karalis Katia 
Published: August 2020

ABSTRACTThe intestinal epithelial barrier supports the symbiotic relationship between the microbiota colonizing the intestinal epithelium and the host immune system to maintain homeostasis. Leaky barrier is increasingly recognized as part of the pathogenesis of a number of chronic conditions in addition to inflammatory and infectious diseases. As our understanding on the regulation of the barrier remains limited, effective therapeutic targeting for the compromised barrier is still an unmet need. Here we combined advancements on the organoids and Organ-on-Chip technologies to establish a micro-engineered Colon Intestine-Chip for studying development and regulation of the human intestinal barrier. Our data demonstrate the significance of the endothelium in co-culture with the epithelial cells within a tissue-relevant microenvironment for the establishment of a tight epithelial barrier of polarized cells. Pathway analysis of the RNA sequencing (RNA-Seq), revealed significant upregulation of mechanisms relevant to the maturation of the intestinal epithelium in organoid-derived epithelial cells in co-culture with endothelium as compared to organoids maintained in suspension. We provide evidence that the Colon Intestine-Chip platform responds to interferon gamma (IFNγ), a prototype cytokine utilized to model inflammation-induced barrier disruption, by induction of apoptosis and reorganization of the apical junctional complexes as shown with other systems. We also describe the mechanism of action of interleukin 22 (IL-22) on mature, organoid-derived intestinal epithelial cells that is consistent with barrier disruption. Overall we propose the Colon Intestine-Chip as a promising human organoid-derived platform to decipher mechanisms driving the development of leaky gut in patients and enable their translation for this unmet medical need.
A simple and dynamic thermal gradient device for measuring thermal performance in small ectotherms
Authors: Ritchie Marshall W. , Dawson Jeff W. , MacMillan Heath A. 
Published: August 2020

AbstractThe body temperature of ectothermic animals is heavily dependent on environmental temperature, impacting fitness. Laboratory exposure to favorable and unfavorable temperatures is used to understand these effects, as well as the physiological, biochemical, and molecular underpinnings of variation in thermal performance. Although small ectotherms, like insects, can often be easily reared in large numbers, it can be challenging and expensive to simultaneously create and manipulate several thermal environments in a laboratory setting. Here, we describe the creation and use of a thermal gradient device that can produce a wide range of constant or varying temperatures concurrently. This device is composed of a solid aluminum plate and copper piping, combined with a pair of programmable refrigerated circulators. As a simple proof-of-concept, we completed single experimental runs to produce a low-temperature survival curve for flies (Drosophila melanogaster) and explore the effects of daily thermal cycles of varying amplitude on growth rates of crickets (Gryllodes sigillatus). This approach avoids the use of multiple heating/cooling water or glycol baths or incubators for large-scale assessments of organismal thermal performance. It makes static or dynamic thermal experiments (e.g., creating a thermal performance or survival curves, quantifying responses to fluctuating thermal environments, or monitoring animal behaviour across a range of temperatures) easier, faster, and less costly.
The life-history fitness of F1hybrids of the microcrustaceanDaphnia pulexandD. pulicaria(Crustacea, Anomopoda)
Authors: Moy Irene , Green Makayla , Pham Thinh Phu , Luu Dustin , Xu Sen 
Published: August 2020

AbstractNegative interaction between alleles that arise independently in diverging populations (i.e., Dobzhansky-Muller incompatibilities) can cause reduction of fitness in their hybrids. However, heterosis in hybrids can emerge if hybridization breaks down detrimental epistatic interaction within parental lineages. In this study, we examined the life-history fitness of the inter-specific F1hybrids of two recently diverged microcrustacean speciesDaphnia pulexandD. pulicariaas well as intra-specific F1hybrids ofD. pulex. We identified heterosis in four out of five life-history traits in the inter-specific F1 hybrids. The observation of heterosis in these life-history traits suggests that there are no major genetic incompatibilities between these two species affecting these traits. This also suggests thatD. pulexandD. pulicariaare at the early stage of speciation where heterosis can still occur.
Single extracellular vesicles protein profiling classifies renal fibrosis stages in mice model
Authors: Cai Yanling , Cao Rong , Liu Yuefei , Xiang Jinsheng , Li Zesong , Wan Qijun , Wu Di 
Published: August 2020

AbstractRenal fibrosis is a common consequence of various chronic kidney diseases (CKD), leading to the loss of renal function and even end-stage renal failure. Extracellular vesicles (EVs) were shown to be involved in development of CKD and renal fibrosis. In this study, we induced renal fibrosis in mice model through unilateral ureteral obstruction (UUO) and extracted EVs from the kidney with induced fibrosis. Proximity barcoding assay (PBA) was performed to detect the expression of 112 proteins at individual EVs level for renal fibrosis of Grade I to IV and sham control group as well. The single EVs are classified into subpopulations according to the surface proteomic characteristics. We discovered several EV subpopulations, with presence of ITGAM, ITGA6, CD73, CD13 and ALDH1, increase significantly with development of renal fibrosis. These findings indicate that besides protein expression, proteomic fingerprints of single EVs can be potential biomarkers for surveillance of CKD and renal fibrosis.
gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration
Authors: Orvis Joshua , Gottfried Brian , Kancherla Jayaram , Adkins Ricky S. , Song Yang , Dror Amiel A. , Olley Dustin , Rose Kevin , Chrysostomou Elena , Kelly Michael C. , Milon Beatrice , Matern Maggie S. , Azaiez Hela , Herb Brian , Colantuoni Carlo , Carter Robert L. , Ament Seth A. , Kelley Matthew W. , White Owen , Bravo Hector Corrada , Mahurkar Anup , Hertzano Ronna 
Published: August 2020

ABSTRACTThe gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data types (bulk, sorted, single cell/nucleus) and epigenomics data, from multiple species, time points and tissues in a single-page, user-friendly browsable format. An integrated scRNA-seq workbench provides access to raw data of scRNA-seq datasets forde novoanalysis, as well as marker-gene and cluster comparisons of pre-assigned clusters. Users can upload, view, analyze and privately share their own data in the context of previously published datasets. Short, permanent URLs can be generated for dissemination of individual or collections of datasets in published manuscripts. While the gEAR is currently curated for auditory research with over 90 high-value datasets organized in thematic profiles, the gEAR also supports the BRAIN initiative (via nemoanalytics.org) and is easily adaptable for other research domains.