bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severity, criticality, and fatality of the SARS-CoV-2 Beta variant
Authors: Abu-Raddad Laith J. , Chemaitelly Hiam , Ayoub Houssein H. , Yassine Hadi M. , Benslimane Fatiha M. , Al Khatib Hebah A. , Tang Patrick , Hasan Mohammad R. , Coyle Peter , AlMukdad Sawsan , Al Kanaani Zaina , Al Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Nasrallah Gheyath K. , Al Kuwari Mohamed Ghaith , Butt Adeel A. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Al Khal Abdullatif , Bertollini Roberto 
Published: August 2021

AbstractSeverity (acute-care hospitalization), criticality (ICU hospitalization), and fatality of SARS-CoV-2 Beta (B.1.351) variant was investigated through case-control studies applied to complete national cohorts of infection, disease, and death cases in Qatar. Compared to Alpha (B.1.1.7) variant, odds of progressing to severe disease were 1.24-fold (95% CI: 1.11-1.39) higher for Beta. Odds of progressing to critical disease were 1.49-fold (95% CI: 1.13-1.97) higher. Odds of COVID-19 death were 1.57-fold (95% CI: 1.03-2.43) higher. Findings highlight risks to healthcare systems, particularly to intensive care facilities and resources, with increased circulation of Beta.
Estimating infection-related human mobility networks based on time series data of COVID-19 infection in Japan
Authors: Yamada Tetsuya , Shi Shoi 
Published: August 2021

AbstractComprehensive and evidence-based countermeasures against emerging infectious diseases have become increas-ingly important in recent years. COVID-19 and many other infectious diseases are spread by human movement and contact, but complex transportation networks in 21 century make it difficult to predict disease spread in rapidly changing situations. It is especially challenging to estimate the network of infection transmission in the countries that the traffic and human movement data infrastructure is not yet developed. In this study, we devised a method to estimate the network of transmission of COVID-19 from the time series data of its infection and applied it to determine its spread across areas in Japan. We incorporated the effects of soft lockdowns, such as the declaration of a state of emergency, and changes in the infection network due to government-sponsored travel promotion, and predicted the spread of infection using the Tokyo Olympics as a model. The models used in this study are available online, and our data-driven infection network models are scalable, whether it be at the level of a city, town, country, or continent, and applicable anywhere in the world, as long as the time-series data of infections per region is available. These estimations of effective distance and the depiction of infectious disease networks based on actual infection data are expected to be useful in devising data-driven countermeasures against emerging infectious diseases worldwide.
Lymphocyte count is a universal predictor to the health status and outcomes of patients with coronavirus disease 2019 (COVID-19): A systematic review and meta-regression analysis
Authors: Lai Kuan-Lang , Hu Fu-Chang , Wen Fang-Yu , Chen Ju-Ju 
Published: August 2021

SummaryBackgroundThis study aimed to evaluate the prediction capabilities of clinical laboratory biomarkers to the prognosis of COVID-19 patients.MethodsObservational studies reporting at least 30 cases of COVID-19 describing disease severity or mortality were included. Meta-data of demographics, clinical symptoms, vital signs, comorbidities, and 14 clinical laboratory biomarkers on initial hospital presentation were extracted. Taking the outcome group as the analysis unit, meta-regression analysis with the generalized estimating equations (GEE) method for clustered data was performed sequentially. The unadjusted effect of each potential predictor of the three binary outcome variables (i.e., severe vs. non-severe, critically severe vs. non-critically severe, and dead vs. alive) was examined one by one by fitting three series of simple GEE logistic regression models due to missing data. The worst one was dropped one at a time. Then, a final multiple GEE logistic regression model for each of the three outcome variables was obtained.FindingsMeta-data was extracted from 76 articles, reporting a total of 26,627 cases of COVID-19. Patients were recruited across 16 countries. The number of studies (patients) included in the final models of the analysis for severity, critical severity, and mortality was 38 studies (9,764 patients), 21 studies (4,792 patients), and 24 studies (14,825 patients), respectively. After adjusting for the effect of age, lymphocyte count mean or median ≤ 1.03 (estimated hazard ratio [HR] = 46.2594, p < 0.0001), smaller lymphocyte count mean or median (HR < 0.0001, p = 0.0028), and lymphocyte count mean or median ≤ 0.8714 (HR = 17.3756, p = 0.0079) were the strongest predictor of severity, critical severity, and mortality, respectively.InterpretationLymphocyte count should be closely watched for COVID-19 patients in clinical practice.
COVID19 vaccine type and humoral immune response in patients receiving dialysis
Authors: Garcia Pablo , Anand Shuchi , Han Jialin , Montez-Rath Maria , Sun Sumi , Shang Tiffany , Parsonnet Julie , Chertow Glenn M , Schiller Brigitte , Abra Graham 
Published: August 2021

ABSTRACTBackgroundPatients on dialysis vaccinated with the attenuated adenovirus SARS-CoV-2 vaccine might mount an impaired response to vaccination.MethodsWe evaluated the humoral vaccination response among 2,099 fully vaccinated patients receiving dialysis. We used commercially available assays (Siemens) to assess prevalence of no response or diminished response to COVID-19 vaccination by vaccine type. We defined “no seroconversion” as lack of change from negative to positive in total RBD Ig antibody, no detectable response on semiquantitative RBD IgG antibody (index value <1) as “no RBD IgG response”, and a semiquantitative RBD IgG index value <10 as “diminished RBD IgG response”ResultsOf the 2,099 fully vaccinated patients on dialysis, the proportion receiving the mRNA1273, BNT162b2, and Ad26.COV2.S were 62% (n=1316), 20% (n=416) and 18% (n=367), respectively. A third (33.3%) of patients receiving the attenuated adenovirus Ad26.COV2.S vaccine failed to seroconvert and an additional 36% had no detectable or diminished IgG response even 28-60 days post vaccination.ConclusionOne in three fully vaccinated patients receiving dialysis had evidence of an impaired immune response to the attenuated adenovirus Ad26.COV2.S vaccine.
BWA-mem is not the best aligner for ancient DNA short reads
Authors: Oliva Adrien , Tobler Raymond , Llamas Bastien , Souilmi Yassine 
Published: August 2021

AbstractXu and colleagues (Xu et al., 2021) recently suggested a new parameterisation of BWA-mem (Li, 2013) as an alternative to the current standard BWA-aln (Li and Durbin, 2009) to process ancient DNA sequencing data. The authors tested several combinations of the -k and -r parameters to optimise BWA-mem’s performance with degraded and contaminated ancient DNA samples. They report that using BWA-mem with −k 19 −r 2.5 parameters results in a mapping efficiency comparable to BWA-aln with −I 1024 −n 0.03 (i.e. a derivation of the standard parameters used in ancient DNA studies; (Schubert et al., 2012)), while achieving significantly faster run times.We recently performed a systematic benchmark of four mapping software (i.e. BWA-aln, BWA-mem, NovoAlign (http://www.novocraft.com/products/novoalign), and Bowtie2 (Langmead and Salzberg, 2012) for ancient DNA sequencing data and quantified their precision, accuracy, specificity, and impact on reference bias (Oliva et al., 2021). Notably, while multiple parameterisations were tested for BWA-aln, NovoAlign, and Bowtie2, we only tested BWA-mem with default parameters.Here, we use the alignment performance metrics from Oliva et al. to directly compare the recommended BWA-mem parameterisation reported in Xu et al. with the best performing alignment methods determined in the Oliva et al. benchmarks, and we make recommendations based on the results.
SigTools: Exploratory Visualization for Genomic Signals
Authors: Masoumi Shohre , Libbrecht Maxwell W. , Wiese Kay C. 
Published: August 2021

AbstractMotivationWith the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. An example of genomic signals is Epigenomic marks which are utilized to locate functional and nonfunctional elements in genome annotation studies. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data.ResultsSigTools is an R-based genomic signals visualization package developed with two objectives: 1) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement, and development by including distribution and autocorrelation plots. 2) to enable genomic signals interpretation by including correlation, and aggregation plots. Moreover, Sigtools also provides text-based descriptive statistics of the given signals which can be practical when developing and evaluating learning models. We also include results from 2 case studies. The first examines several previously studied genomic signals called histone modifications. This use case demonstrates how SigTools can be beneficial for satisfying scientists’ curiosity in exploring and establishing recognized datasets. The second use case examines a dataset of novel chromatin state features which are novel genomic signals generated by a learning model. This use case demonstrates how SigTools can assist in exploring the characteristics and behavior of novel signals towards their interpretation. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools.AvailabilitySigTools source code, installation guide, and manual is available on http://github.com/shohre73.Contactshohre_masoumi@sfu.ca
Black Dots: Microcontact-Printed, Reference-Free Traction Force Microscopy
Authors: Beussman Kevin M. , Mollica Molly Y. , Leonard Andrea , Miles Jeffrey , Hocter John , Song Zizhen , Stolla Moritz , Han Sangyoon J. , Emery Ashley , Thomas Wendy E. , Sniadecki Nathan J. 
Published: August 2021

ABSTRACTMeasuring the traction forces produced by cells provides insight into their behavior and physiological function. Here, we developed a technique (dubbed ‘black dots’) that microcontact prints a fluorescent micropattern onto a flexible substrate to measure cellular traction forces without constraining cell shape or needing to detach the cells. To demonstrate our technique, we assessed human platelets, which can generate a large range of forces within a population. We find platelets that exert more force have more spread area, are more circular, and have more uniformly distributed F-actin filaments. As a result of the high yield of data obtainable by this technique, we were able to evaluate multivariate mixed effects models with interaction terms and conduct a clustering analysis to identify clusters within our data. These statistical techniques demonstrated a complex relationship between spread area, circularity, F-actin dispersion, and platelet force, including cooperative effects that significantly associate with platelet traction forces.GRAPHICAL ABSTRACT
Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging
Authors: Freitag Kiara , Eede Pascale , Ivanov Andranik , Schneeberger Shirin , Borodina Tatiana , Sauer Sascha , Beule Dieter , Heppner Frank L. 
Published: August 2021

SummaryAstrocytes are resident glia cells of the central nervous system (CNS) that play complex and heterogeneous roles in brain development, homeostasis and disease. Since their vast involvement in health and disease is becoming increasingly recognized, suitable and reliable tools for studying these cells in vivo and in vitro are of utmost importance. One of the key challenges hereby is to adequately mimic their context-dependent in vivo phenotypes and functions in vitro. To better understand the spectrum of astrocytic variations in defined settings we performed a side-by-side-comparison of embryonic stem cell (ESC)-derived astrocytes as well as primary neonatal and adult astrocytes, revealing major differences on a functional and transcriptomic level, specifically on proliferation, migration, calcium signaling and cilium activity. Our results highlight the need to carefully consider the choice of astrocyte origin and phenotype with respect to age, isolation and culture protocols based on the respective biological question.
A Chromosome-level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
Authors: Sætre Camilla Lo Cascio , Eroukhmanoff Fabrice , Rönkä Katja , Kluen Edward , Thorogood Rose , Torrance James , Tracey Alan , Chow William , Pelan Sarah , Howe Kerstin , Jakobsen Kjetill S. , Tørresen Ole K. 
Published: August 2021

AbstractThe reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behaviour in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here we present a high-quality reference genome for the reed warbler, based on PacBio, 10X and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of genes in the assembly were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, of which 97.5% were complete BUSCO orthologs. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.Significance statementThe reed warbler (Acrocephalus scirpaceus) has been lacking a genomic resource, despite having been broadly researched in studies of coevolution, ecology and adaptations to climate change. Here, we generated a chromosome-length genome assembly of the reed warbler, and found evidence of macrochromosomal fusions in its genome, which are likely of recent origin. This genome will provide the opportunity for a deeper understanding of the evolution of genomes in birds, as well as the evolutionary path and possible future of the reed warbler.
A vibrissa pathway that activates the limbic system
Authors: Elbaz Michaël , Callado-Pérez Amalia , Demers Maxime , Zhao Shengli , Foo Conrad , Kleinfeld David , Deschênes Martin 
Published: August 2021

ABSTRACTVibrissa sensory inputs play a central role in driving rodent behavior. These inputs transit through the sensory trigeminal nuclei, which give rise to the ascending lemniscal and paralemniscal pathways. While lemniscal projections are somatotopically mapped from brain stem to cortex, those of the paralemniscal pathway are more widely distributed. Yet the extent and topography of paralemniscal projections are unknown, along with the potential role of these projections in controlling behavior. Here we used viral tracers to map paralemniscal projections. We find that this pathway broadcasts vibrissa-based sensory signals to brain stem regions that are involved in the regulation of autonomic functions and to forebrain regions that are involved in the expression of emotional reactions. We further provide evidence that GABAergic cells of the Kölliker-Fuse nucleus gate trigeminal sensory input in the paralemniscal pathway via a mechanism of presynaptic or extrasynaptic inhibition.
Integrative Gene Expression and Metabolic Analysis tool IgemRNA
Authors: Grausa Kristina , Mozga Ivars , Pleiko Karlis , Pentjuss Agris 
Published: August 2021

ABSTRACTGenome scale metabolic modelling is widely used technique to research metabolism impacts on organism’s properties. Additional omics data integration enables a more precise genotype-phenotype analysis for biotechnology, medicine and life sciences. Transcriptome data amounts rapidly increase each year. Many transcriptome analysis tools with integrated genome scale metabolic modelling are proposed. But these tools have own restrictions, compatibility issues and the necessity of previous experience and advanced user skills. We have analysed and classified published tools, summarized possible transcriptome pre-processing, and analysis methods and implemented them in the new transcriptome analysis tool IgemRNA. Tool novelty is the possibility of transcriptomics data pre-processing approach, analysis of transcriptome with or without genome scale metabolic models and different thresholding and gene mapping approach availability. In comparison with usual Gene set enrichment analysis methods, IgemRNA options provide additional transcriptome data validation, where minimal metabolic network connectivity and flux requirements are met. IgemRNA allows to process transcriptome datasets, compare data between different phenotypes, execute multiple analysis and data filtering functions. All this is done via graphical user interface. IgemRNA is compatible with Cobra Toolbox 3.0 and uses some of its functions for genome scale metabolic model optimization tasks. IgemRNA is open access software available at https://github.com/BigDataInSilicoBiologyGroup/IgemRNA.
Reduced expression of the psychiatric risk gene DLG2 (PSD93) impairs hippocampal synaptic integration and plasticity
Authors: Griesius Simonas , O’Donnell Cian , Waldron Sophie , Thomas Kerrie L. , Dwyer Dominic M. , Wilkinson Lawrence S. , Hall Jeremy , Robinson Emma S. J. , Mellor Jack R. 
Published: August 2021

AbstractBackground:Genetic variations indicating loss of function in theDLG2gene have been associated with markedly increased risk for schizophrenia, autism spectrum disorder, and intellectual disability.DLG2encodes the postsynaptic scaffolding protein DLG2 (PSD93) that interacts with NMDA receptors, potassium channels, and cytoskeletal regulators but the net impact of these interactions on synaptic plasticity, likely underpinning cognitive impairments associated with these conditions, remains unclear.Methods:Hippocampal CA1 neuronal excitability and synaptic function were investigated in a novel clinically relevant heterozygousDlg2+/−rat model usingex vivopatch-clamp electrophysiology, pharmacology, and computational modelling.Results:Dlg2+/−rats had increased NMDA receptor-mediated synaptic currents and, conversely, impaired associative long-term potentiation. This impairment resulted from an increase in potassium channel function leading to a decrease in input resistance and reduced supra-linear dendritic integration during induction of associative long-term potentiation. Enhancement of dendritic excitability by blockade of potassium channels or activation of muscarinic M1 receptors with selective allosteric agonist 77-LH-28-1 reduced the threshold for dendritic integration and 77-LH-28-1 rescued the associative long-term potentiation impairment in theDlg2+/−rats.Conclusions:Despite increasing synaptic NMDA receptor currents, the combined impact of reduced DLG2 impairs synaptic integration in dendrites resulting in disrupted associative synaptic plasticity. This biological phenotype can be reversed by compound classes used clinically such as muscarinic M1 receptor agonists and is therefore a potential target for therapeutic intervention.
Genome sequencing and assembly ofTinospora cordifolia(Giloy) plant
Authors: Mahajan Shruti , Chakraborty Abhisek , Sil Titas , Sharma Vineet K 
Published: August 2021

ABSTRACTDuring the ongoing COVID-19 pandemicTinospora cordifoliaalso known as Giloy gained immense popularity and use due to its immunity-boosting function and anti-viral properties.T. cordifoliais among the most important medicinal plants that has numerous therapeutic applications in health due to the production of a diverse array of secondary metabolites. Therefore, to gain genomic insights into the medicinal properties ofT. cordifolia, the first genome sequencing was carried out using 10x Genomics linked read technology and the draft genome assembly comprised of 1.01 Gbp. This is also the first genome sequenced from the plant family Menispermaceae. We also performed the first genome size estimation forT. cordifoliaand was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed followed by transcriptomic analysis to gain insights into the gene expression and functions. The genome and transcriptome assemblies were used to construct the gene set inT. cordifoliathat resulted in 19,474 coding gene sequences. Further, the phylogenetic position ofT. cordifoliawas also determined through the construction of a genome-wide phylogenetic tree using 35 other dicot species and one monocot species as an outgroup species.
IntroSpect: motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification
Authors: Zhang Le , Liu Geng , Hou Guixue , Xiang Haitao , Zhang Xi , Huang Ying , Zhang Xiuqing , Li Bo , Lee Leo J 
Published: August 2021

ABSTRACTAlthough database search tools originally developed for shotgun proteome have been widely used in immunopeptidomic mass spectrometry identifications, they have been reported to achieve undesirably low sensitivities and/or high false positive rates as a result of the hugely inflated search space caused by the lack of specific enzymic digestions in immunopeptidome. To overcome such a problem, we have developed a motif-guided immunopeptidome database building tool named IntroSpect, which is designed to first learn the peptide motifs from high confidence hits in the initial search and then build a targeted database for refined search. Evaluated on three representative HLA class I datasets, IntroSpect can improve the sensitivity by an average of 80% comparing to conventional searches with unspecific digestions while maintaining a very high accuracy (∼96%) as confirmed by synthetic validation experiments. A distinct advantage of IntroSpect is that it does not depend on any external HLA data so that it performs equally well on both well-studied and poorly-studied HLA types, unlike a previously developed method SpectMHC. We have also designed IntroSpect to keep a global FDR that can be conveniently controlled, similar to conventional database search engines. Finally, we demonstrate the practical value of IntroSpect by discovering neoantigens from MS data directly. IntroSpect is freely available at https://github.com/BGI2016/IntroSpect.