bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Learning Model for Improving the Characterization of Coronavirus on Chest X-ray Images Using CNN
Authors: Oyelade Olaide N. , Ezugwu Absalom E. 
Published: November 2020

AbstractThe novel Coronavirus, also known as Covid19, is a pandemic that has weighed heavily on the socio-economic affairs of the world. Although researches into the production of relevant vaccine are being advanced, there is, however, a need for a computational solution to mediate the process of aiding quick detection of the disease. Different computational solutions comprised of natural language processing, knowledge engineering and deep learning have been adopted for this task. However, deep learning solutions have shown interesting performance compared to other methods. This paper therefore aims to advance the application deep learning technique to the problem of characterization and detection of novel coronavirus. The approach adopted in this study proposes a convolutional neural network (CNN) model which is further enhanced using the technique of data augmentation. The motive for the enhancement of the CNN model through the latter technique is to investigate the possibility of further improving the performances of deep learning models in detection of coronavirus. The proposed model is then applied to the COVID-19 X-ray dataset in this study which is the National Institutes of Health (NIH) Chest X-Ray dataset obtained from Kaggle for the purpose of promoting early detection and screening of coronavirus disease. Results obtained showed that our approach achieved a performance of 100% accuracy, recall/precision of 0.85, F-measure of 0.9, and specificity of 1.0. The proposed CNN model and data augmentation solution may be adopted in pre-screening suspected cases of Covid19 to provide support to the use of the well-known RT-PCR testing.
Modeling COVID-19 Transmissions and Evaluation of Large Scale Social Restriction in Jakarta, Indonesia
Authors: Hasan A. , Nasution Y. , Susanto H. , Putri E.R.M. , Tjahjono V.R. , Puspita D. , Sukandar K. , Nuraini N. , Widyastuti W. 
Published: November 2020

AbstractThis paper presents mathematical modeling and quantitative evaluation of Large Scale Social Restriction (LSSR) in Jakarta between 10 April and 4 June 2020. The special capital region of Jakarta is the only province among 34 provinces in Indonesia with an average Testing Positivity Rate (TPR) below 5% recommended by the World Health Organization (WHO). The transmission model is based on a discrete-time compartmental epidemiological model incorporating suspected cases. The quantitative evaluation is measured based on the estimation of the time-varying effective reproduction number (ℛt). Our results show the LSSR has been successfully suppressed the spread of COVID-19 in Jakarta, which was indicated by ℛt < 1. However, once the LSSR was relaxed, the effective reproduction number increased significantly. The model is further used for short-term forecasting to mitigate the course of the pandemic.
Availability of personal protective equipment and satisfaction of healthcare professionals during COVID-19 pandemic in Ethiopia
Authors: Deressa Wakgari , Worku Alemayehu , Abebe Workeabeba , Gizaw Muluken , Amogne Wondwosson 
Published: November 2020

AbstractHealthcare professionals (HCPs) are at the frontline in the fight against COVID-19 and are at an increased risk of becoming infected with coronavirus. Risk of infection can be minimized by use of proper personal protective equipment (PPE). This study assessed the availability of PPE and satisfaction of HCPs in six public hospitals in Addis Ababa, Ethiopia. A cross-sectional study was conducted from 9th to 26th June 2020. The study hospitals included: Tikur Anbessa Specialized Hospital, Zewditu Memorial Hospital, Ghandi Memorial Hospital, Menelik II Hospital, Yekatit 12 Hospital Medical College and St. Paul Hospital Millennium Medical College. Data were collected using a self-administered questionnaire. Descriptive statistics were used to describe the data and Chi-square test was used to assess the association between the groups. Bivariate and multivariable logistic regression models were used to assess factors associated with the satisfaction level of healthcare workers with regard to the availability and use of proper PPE during the current COVID-19 pandemic. A total of 1,134 (92.3%) valid questionnaires from a possible 1,228 were included in the analysis. The mean (±SD) age of the participants was 30.26±6.43 year and 52.6% were females. Nurses constituted about 40% of the overall sample, followed by physicians (22.2%), interns (10.8%), midwives (10.3%) and others (16.7%). An overall shortage of PPE was reported in all study hospitals. The majority (77%) of the healthcare professionals reported that their hospital did not have adequate PPE. A critical shortage of N95 respirator was particularly reported, the self-reported availability of N95 increased from 13% to 24% before and during COVID-19, respectively. The self-reported use of N95 increased from 9% to 21% before and during COVID-19, respectively. Almost 72% of the respondents were dissatisfied with the availability of PPE in their hospital. The independent predictors of the respondents’ satisfaction level about PPE were male gender (adjusted OR=1.39, 95% CI:1.05-1.85), healthcare workers who reported that PPE was adequately available in the hospital (adjusted OR=7.53, 95% CI:5.08-11.16), and preparedness to provide care to COVID-19 cases (adjusted OR=1.65, 95% CI:1.22-2.12). A critical shortage of appropriate PPE both before and during COVID-19 was identified. The high level of dissatisfaction with the availability of PPE might potentially lead to a lower level of preparedness and readiness to fight against COVID-19. Therefore, urgent efforts are needed to adequately supply the healthcare facilities with appropriate PPE to alleviate the challenges.
Senotherapeutic peptide reduces skin biological age and improves skin health markers
Authors: Zonari Alessandra , Brace Lear E. , Al-Katib Kallie Z. , Porto William F. , Foyt Daniel , Guiang Mylieneth , Cruz Edgar Andres Ochoa , Marshall Bailey , Salgueiro Willian G. , Inan Mehmet Dinçer , Rahman Mizanur , Anupom Taslim , Vanapalli Siva , Mori Marcelo A. , Franco Octavio L. , Oliveira Carolina R. , Boroni Mariana , Carvalho Juliana L. 
Published: November 2020

AbstractSkin aging has been primarily related to aesthetics and beauty. Therefore, interventions have focused on reestablishing skin appearance, but not necessarily skin health, function, and resilience. Recently, cellular senescence was shown to play a role in age-related skin function deterioration and influence organismal health and, potentially, longevity. In the present study, a two-step screening was performed to identify peptides capable of reducing cellular senescence in human dermal fibroblasts (HDF) from Hutchinson-Gilford Progeria (HGPS) patients. From the top four peptides of the first round of screening, we built a 764-peptide library using amino acid scanning, of which the second screen led to the identification of peptide 14. Peptide 14 effectively decreased HDF senescence induced by HGPS, chronological aging, ultraviolet-B radiation, and etoposide treatment, without inducing significant cell death, and likely by modulating longevity and senescence pathways. We further validated the effectiveness of peptide 14 using human skin equivalents and skin biopsies, where peptide 14 promoted skin health and reduced senescent cell markers, as well as the biological age of samples, according to the Skin-Specific DNA methylation clock, MolClock. Topical application of peptide 14 outperformed Retinol treatment, the current gold-standard in “anti-aging” skin care. Finally, we determined that peptide 14 is safe for long-term applications and also significantly extends both the lifespan and healthspan ofC. elegansworms tested in two independent testings. This highlights the potential for geroprotective applications of the senotherapeutic compounds identified using our screening platform beyond the skin.
TMExplorer: A Tumour Microenvironment Single-cell RNAseq Database and Search Tool
Authors: Christensen Erik , Naidas Alaine , Husic Mia , Shooshtari Parisa 
Published: November 2020

ABSTRACTTumour microenvironments (TME) contain a variety of cells including but not limited to stromal fibroblasts, endothelial cells, immune cells, malignant cells, and cells of the tissues of origin, whose interactions likely influence tumour behaviour and response to cancer treatment. The specific composition of the TME can be elucidated using single-cell RNA sequencing (scRNA-seq) by measuring expression profiles of individual cells. Several scRNA-seq datasets from multiple cancer types have been published in recent years, yet we still lack a comprehensive database for the collection and presentation of TME data from these studies in an easily accessible format. We have thus built a database of TME scRNA-seq data, containing 21 TME scRNA-seq datasets from 12 different cancer types. We have also created an R package called TMExplorer, which provides an interface to easily search and access all available datasets and their metadata. Data and metadata are kept in a consistent format across all datasets, with multiple expression formats available depending on the use case. Users can view a table of metadata and select individual datasets or filter them by specific characteristics. Users may also select a specific type of cancer and view all published scRNA-seq data for that cancer type available in our database. Users are provided with an option to save the data in multiple formats in order to view or process it outside of R. Thus, the TMExplorer database and search tool allows for thorough examination of the TME using scRNA-seq in a way that is streamlined and allows for easy integration into already existing scRNA-seq analysis pipelines.
Characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein
Authors: Moreira Rodrigo A. , Guzman Horacio V. , Boopathi Subramanian , Baker Joseph L. , Poma Adolfo B. 
Published: November 2020

AbstractThe novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome – novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein trimer. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested the participation of more than one RBD as a possible mechanism to enhance cell entry. Here we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson-Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.
Silencing of E-cadherin in induced human pluripotent stem cells promotes extraembryonic fates accompanying multilineage differentiation
Authors: Libby Ashley RG , Vasic Ivana , Joy David A , Krakora Martina Z , Mendoza-Camacho Fredrico N , Conklin Bruce R , McDevitt Todd C 
Published: November 2020

Summary/AbstractIn embryonic development, symmetry breaking events and the mechanical milieus in which they occur coordinate the specification of separate cell lineages. Here, we use 3D aggregates of human pluripotent stem cells (hPSCs) encapsulated in alginate microbeads to model the early blastocyst prior to zona pellucida hatching. We demonstrate that 3D confinement combined with modulation of cell-cell adhesions is sufficient to drive differentiation and collective migration reminiscent of the pre-implantation embryo. Knockdown of the cell adhesion protein CDH1 in encapsulated hPSC aggregates resulted in protrusion morphologies and emergence of extra-embryonic lineages, whereas unencapsulated CDH1(-) aggregates displayed organized radial delamination and mesendoderm specification bias. Transcriptomic similarities between single-cell RNA-sequencing data of early human embryos and encapsulated CDH1(-) aggregates establishes thisin vitrosystem as a competent surrogate for studying early embryonic fate decisions and highlights the relationship between cell-cell adhesions and the mechanical microenvironment in directing cell fate and behavior.HighlightsGeneration of embryonic scale 3D morphogenesis using hydrogel encapsulationManipulating adhesion triggers emergence of specific morphologies and cell fatesAcquisition of germ layer cell fates mimics early human embryonic diversity
Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic
Authors: Lou Jingzhi , Zhao Shi , Cao Lirong , Chen Zigui , Chan Renee WY , Chong Marc KC , Zee Benny CY , Chan Paul KS , Wang Maggie H 
Published: November 2020

AbstractBackgroundDuring the pandemic of coronavirus disease 2019 (COVID-19), the genetic mutations occurred in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cumulatively or sporadically. In this study, we employed a computational approach to identify and trace the emerging patterns of the SARS-CoV-2 mutations, and quantify accumulative genetic distance across different periods and proteins.MethodsFull-length human SARS-CoV-2 strains in United Kingdom were collected. We investigated the temporal variation in the evolutionary genetic distance defined by the Hamming distance since the start of COVID-19 pandemic.FindingsOur results showed that the SARS-CoV-2 was in the process of continuous evolution, mainly involved in spike protein (S protein), the RNA-dependent RNA polymerase (RdRp) region of open reading frame 1 (ORF1) and nucleocapsid protein (N protein). By contrast, mutations in other proteins were sporadic and genetic distance to the initial sequenced strain did not show an increasing trend.
Glucose and NAADP trigger elementary intracellular β-cell Ca2+signals
Authors: Heister Paula Maria , Powell Trevor , Galione Antony 
Published: November 2020

AbstractPancreatic β-cells release insulin upon a rise in blood glucose. The precise mechanisms of stimulus-secretion coupling, and its failure in Diabetes Mellitus Type 2, remain to be elucidated. The consensus model, as well as a class of currently prescribed anti-diabetic drugs, are based around the observation that glucose-evoked ATP production in β-cells leads to closure of cell membrane ATP-gated potassium (KATP) channels, plasma membrane depolarisation, Ca2+influx, and finally the exocytosis of insulin granules (Ashcroft et al., 1984; Cook and Hales, 1984). However, it has been demonstrated by the inactivation of this pathway using genetic and pharmacological means that closure of the KATPchannel alone may not be sufficient to explain all β-cell responses to glucose elevation (Henquin, 1998; Seghers et al., 2000). Here we show using total internal reflection fluorescence (TIRF) microscopy (Axelrod, 1981) that glucose as well as the Ca2+mobilising messenger nicotinic acid adenine dinucleotide phosphate (NAADP), known to operate in β-cells (Johnson and Misler, 2002; Masgrau et al., 2003), lead to highly localised elementary intracellular Ca2+signals. These were found to be obscured by measurements of global Ca2+signals and the action of powerful SERCA-based sequestration mechanisms at the endoplasmic reticulum (ER). This is the first demonstration of elemental Ca2+signals in response to NAADP, although they have been suspected (Davis et al., 2020). Optical quantal analysis of these events reveals a unitary event amplitude equivalent to that of known elementary Ca2+signalling events, inositol trisphosphate (IP3) receptor mediated blips (Parker et al., 1996; Parker and Ivorra, 1990), and ryanodine receptor mediated sparks (Cheng et al., 1993). We propose that a mechanism based on these highly localised intracellular Ca2+signalling events mediated by NAADP may initially operate in β-cells when they respond to elevations in blood glucose.
MetaPop: A pipeline formacro- andmicro-diversity analyses and visualization of microbial and viral metagenome-derived populations
Authors: Gregory Ann C. , Gerhardt Kenji , Zhong Zhi-Ping , Bolduc Benjamin , Temperton Ben , Konstantinidis Konstantinos T. , Sullivan Matthew B. 
Published: November 2020

AbstractBackgroundMicrobes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter- (macrodiversity) and intra- (microdiversity) population variation, analytical tools to do so remain scattered or under-developed.ResultsHere we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both themacro- andmicro-diversity levels.Macrodiversity estimates include population abundances and α- and β-diversity.Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ) and selective pressures (pN/pS and Tajima’s D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. Themacrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available), that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifyingmicrodiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better ‘bet hedge’ in changing environments. Further, comparisons ofmicrodiversity pre- and post-FMT in the autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment ofmicrodiverseviral populations, with children who received their FMT rectally having highermicrodiversitypost-FMT. Overall, these results show that analyses at themacro-levelalone can miss important biological differences.ConclusionsThese findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tools package to explore the dual impact ofmacro- andmicro-diversity across microbial communities.
Population differentiation and structural variation in theManduca sextagenome across the United States
Authors: Mongue Andrew J. , Kawahara Akito Y. 
Published: November 2020

AbstractMany species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species’ genome. Here we investigate genomic variation in three natural North American populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other two populations using Illumina whole-genome resequencing. Peaks of differentiation exist across the genome, but here we focus in on the most striking regions. In particular, we identify two likely segregating inversions found in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome. The larger, autosomal inversion contains a pseudogene may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to support this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for both pest management and evolutionary genetics of this insect species.
A biophysical limit for quorum sensing in biofilms
Authors: Narla Avaneesh V. , Borenstein David , Wingreen Ned S. 
Published: November 2020

Bacteria grow on surfaces in complex immobile communities known as biofilms, which are composed of cells embedded in an extracellular matrix. Within biofilms, bacteria often interact with members of their own species, and cooperate or compete with members of other species via quorum sensing (QS). QS is a process by which microbes produce, secrete, and subsequently detect small molecules called autoinducers (AIs) to assess their local population density. We explore the competitive advantage of QS through agent-based simulations of a spatial model in which colony expansion via extracellular matrix production provides greater access to a limiting diffusible nutrient. We note a significant difference in results based on whether AI production is constitutive or limited by nutrient availability: If AI production is constitutive, simple QS-based matrix-production strategies can be far superior to any fixed strategy. However, if AI production is limited by nutrient availability, QS-based strategies fail to provide a significant advantage over fixed strategies. To explain this dichotomy, we derive a novel biophysical limit for the dynamic range of nutrient-limited AI concentrations in biofilms. This range is remarkably small (less than 10-fold) for the realistic case in which a growth-limiting diffusible nutrient is taken up within a narrow active growth layer. This biophysical limit implies that for QS to be most effective in biofilms, AI production should be a protected function not directly tied to metabolism.Significance StatementBiofilms are a ubiquitous form of bacterial community. Within biofilms, bacteria communicate via chemical signals in a process called quorum sensing (QS). However, if signal production is nutrient-limited, then the nutrient-deficient interior of a biofilm cannot contribute to QS, which limits the ability of bacteria to assess their own population and behave accordingly. Numerical simulations of competitions among biofilm bacteria led us to discover a novel biophysical limit on the efficacy of nutrient-limited QS. In view of this limit, we conclude that to be most effective, QS signal production should be a prized function that is not metabolically slaved.