bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motivations for a large self-interacting dark matter cross-section from Milky Way satellites
Authors: Silverman Maya , Bullock James S , Kaplinghat Manoj , Robles Victor H , Valli Mauro 
Published: November 2022

ABSTRACT
We explore the properties of Milky Way (MW) subhaloes in self-interacting dark matter models for moderate cross-sections of 1–5 cm2 g−1 using high-resolution zoom-in N-body simulations. We include the gravitational potential of a baryonic disc and bulge matched to the MW, which is critical for getting accurate predictions. The predicted number and distribution of subhaloes within the host halo are similar for 1 and 5 cm2 g−1 models, and they agree with observations of MW satellite galaxies only if subhaloes with peak circular velocity over all time &gt;7 km s−1 are able to form galaxies. We do not find distinctive signatures in the pericentre distribution of the subhaloes that could help distinguish the models. Using an analytical model to extend the simulation results, we are able to show that subhaloes in models with cross-sections between 1 and 5 cm2 g−1 are not dense enough to match the densest ultrafaint and classical dwarf spheroidal galaxies in the MW. This motivates exploring velocity-dependent cross-sections with values larger than 5 cm2 g−1 at the velocities relevant for the satellites such that core collapse would occur in some of the ultrafaint and classical dwarf spheroidals.
Using peculiar velocity surveys to constrain the growth rate of structure with the wide-angle effect
Authors: Lai Yan , Howlett Cullan , Davis Tamara M 
Published: November 2022

ABSTRACT
Amongst the most popular explanations for dark energy are modified theories of gravity. The galaxy overdensity and peculiar velocity fields help us to constrain the growth rate of structure and distinguish different models of gravity. We introduce an improved method for constraining the growth rate of structure with the galaxy overdensity and peculiar velocity fields. This method reduces the modelling systematic error by accounting for the wide-angle effect and the zero-point calibration uncertainty during the modelling process. We also speed up the posterior sampling by around 30 times by first calculating the likelihood at a small number of fiducial points and then interpolating the likelihood values during MCMC sampling. We test the new method on mocks and we find it is able to recover the fiducial growth rate of structure. We applied our new method to the SDSS PV catalogue, which is the largest single peculiar velocity catalogue to date. Our constraint on the growth rate of structure is $f\sigma _8 = 0.405_{-0.071}^{+0.076}$ (stat) ±0.009 (sys) at the effective redshift of 0.073. Our constraint is consistent with a Planck 2018 cosmological model, fσ8 = 0.448, within one standard deviation. Our improved methodology will enable similar analysis on future data, with even larger sample sizes and covering larger angular areas on the sky.
LitCovid in 2022: an information resource for the COVID-19 literature
Authors: Chen Qingyu , Allot Alexis , Leaman Robert , Wei Chih-Hsuan , Aghaarabi Elaheh , Guerrerio John J , Xu Lilly , Lu Zhiyong 
Published: November 2022

Abstract
LitCovid (https://www.ncbi.nlm.nih.gov/research/coronavirus/)—first launched in February 2020—is a first-of-its-kind literature hub for tracking up-to-date published research on COVID-19. The number of articles in LitCovid has increased from 55 000 to ∼300 000 over the past 2.5 years, with a consistent growth rate of ∼10 000 articles per month. In addition to the rapid literature growth, the COVID-19 pandemic has evolved dramatically. For instance, the Omicron variant has now accounted for over 98% of new infections in the United States. In response to the continuing evolution of the COVID-19 pandemic, this article describes significant updates to LitCovid over the last 2 years. First, we introduced the long Covid collection consisting of the articles on COVID-19 survivors experiencing ongoing multisystemic symptoms, including respiratory issues, cardiovascular disease, cognitive impairment, and profound fatigue. Second, we provided new annotations on the latest COVID-19 strains and vaccines mentioned in the literature. Third, we improved several existing features with more accurate machine learning algorithms for annotating topics and classifying articles relevant to COVID-19. LitCovid has been widely used with millions of accesses by users worldwide on various information needs and continues to play a critical role in collecting, curating and standardizing the latest knowledge on the COVID-19 literature.
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource
Authors: Sollis Elliot , Mosaku Abayomi , Abid Ala , Buniello Annalisa , Cerezo Maria , Gil Laurent , Groza Tudor , Güneş Osman , Hall Peggy , Hayhurst James , Ibrahim Arwa , Ji Yue , John Sajo , Lewis Elizabeth , MacArthur Jacqueline A L , McMahon Aoife , Osumi-Sutherland David , Panoutsopoulou Kalliope , Pendlington Zoë , Ramachandran Santhi , Stefancsik Ray , Stewart Jonathan , Whetzel Patricia , Wilson Robert , Hindorff Lucia , Cunningham Fiona , Lambert Samuel A , Inouye Michael , Parkinson Helen , Harris Laura W 
Published: November 2022

Abstract
The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to &gt;200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for &gt;45 000 published GWAS across &gt;5000 human traits, and &gt;40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.
GenBank 2023 update
Authors: Sayers Eric W , Cavanaugh Mark , Clark Karen , Pruitt Kim D , Sherry Stephen T , Yankie Linda , Karsch-Mizrachi Ilene 
Published: November 2022

Abstract
GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 19.6 trillion base pairs from over 2.9 billion nucleotide sequences for 504 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include resources for data from the SARS-CoV-2 virus, NCBI Datasets, BLAST ClusteredNR, the Submission Portal, table2asn, a Foreign Contamination Screening tool and BioSample.
Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis
Authors: Rietmeyer Lauriane , Li De La Sierra-Gallay Inès , Schepers Guy , Dorchêne Delphine , Iannazzo Laura , Patin Delphine , Touzé Thierry , van Tilbeurgh Herman , Herdewijn Piet , Ethève-Quelquejeu Mélanie , Fonvielle Matthieu 
Published: November 2022

Abstract
Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1′,5′-anhydrohexitol (HNA), 2′-fluoro ribose (2′F-RNA) and 2′-fluoro arabinose. L-Ala-tXNA containing HNA or 2′F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis
Authors: Teixeira Miguel Cacho , Viana Romeu , Palma Margarida , Oliveira Jorge , Galocha Mónica , Mota Marta Neves , Couceiro Diogo , Pereira Maria Galhardas , Antunes Miguel , Costa Inês V , Pais Pedro , Parada Carolina , Chaouiya Claudine , Sá-Correia Isabel , Monteiro Pedro Tiago 
Published: November 2022

Abstract
YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users’ choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.
scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes
Authors: Cha Junha , Yu Jiwon , Cho Jae-Won , Hemberg Martin , Lee Insuk 
Published: November 2022

Abstract
A major challenge in single-cell biology is identifying cell-type-specific gene functions, which may substantially improve precision medicine. Differential expression analysis of genes is a popular, yet insufficient approach, and complementary methods that associate function with cell type are required. Here, we describe scHumanNet (https://github.com/netbiolab/scHumanNet), a single-cell network analysis platform for resolving cellular heterogeneity across gene functions in humans. Based on cell-type-specific gene networks (CGNs) constructed under the guidance of the HumanNet reference interactome, scHumanNet displayed higher functional relevance to the cellular context than CGNs built by other methods on single-cell transcriptome data. Cellular deconvolution of gene signatures based on network compactness across cell types revealed breast cancer prognostic markers associated with T cells. scHumanNet could also prioritize genes associated with particular cell types using CGN centrality and identified the differential hubness of CGNs between disease and healthy conditions. We demonstrated the usefulness of scHumanNet by uncovering T-cell-specific functional effects of GITR, a prognostic gene for breast cancer, and functional defects in autism spectrum disorder genes specific for inhibitory neurons. These results suggest that scHumanNet will advance our understanding of cell-type specificity across human disease genes.
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome
Authors: Zhou Hufeng , Arapoglou Theodore , Li Xihao , Li Zilin , Zheng Xiuwen , Moore Jill , Asok Abhijith , Kumar Sushant , Blue Elizabeth E , Buyske Steven , Cox Nancy , Felsenfeld Adam , Gerstein Mark , Kenny Eimear , Li Bingshan , Matise Tara , Philippakis Anthony , Rehm Heidi L , Sofia Heidi J , Snyder Grace ,   NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Zhiping , Neale Benjamin , Sunyaev Shamil R , Lin Xihong 
Published: November 2022

Abstract
Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https://favor.genohub.org.
TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms
Authors: Zhou Ziheng , Tan Cong , Chau Matthew Hoi Kin , Jiang Xiaosen , Ke Ziyuan , Chen Xiaoyan , Cao Ye , Kwok Yvonne K , Bellgard Matthew , Leung Tak Yeung , Choy Kwong Wai , Dong Zirui 
Published: November 2022

Abstract
Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene−gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.
PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens
Authors: Novak Lance C , Chou Juihsuan , Colic Medina , Bristow Christopher A , Hart Traver 
Published: November 2022

Abstract
PICKLES (https://pickles.hart-lab.org) is an updated web interface to a freely available database of genome-scale CRISPR knockout fitness screens in human cell lines. Using a completely rewritten interface, researchers can explore gene knockout fitness phenotypes across cell lines and tissue types and compare fitness profiles with fitness, expression, or mutation profiles of other genes. The database has been updated to include data from three CRISPR libraries (Avana, Score, and TKOv3), and includes information from 1162 whole-genome screens probing the knockout fitness phenotype of 18 959 genes. Source code for the interface and the integrated database are available for download.
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes
Authors: Marakulina Daria , Vorontsov Ilya E , Kulakovskiy Ivan V , Lennartsson Andreas , Drabløs Finn , Medvedeva Yulia A 
Published: November 2022

Abstract
We present an update of EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets, and products which is openly accessible at http://epifactors.autosome.org. An updated version of the EpiFactors contains information on 902 proteins, including 101 histones and protamines, and, as a main update, a newly curated collection of 124 lncRNAs involved in epigenetic regulation. The amount of publications concerning the role of lncRNA in epigenetics is rapidly growing. Yet, the resource that compiles, integrates, organizes, and presents curated information on lncRNAs in epigenetics is missing. EpiFactors fills this gap and provides data on epigenetic regulators in an accessible and user-friendly form. For 820 of the genes in EpiFactors, we include expression estimates across multiple cell types assessed by CAGE-Seq in the FANTOM5 project. In addition, the updated EpiFactors contains information on 73 protein complexes involved in epigenetic regulation. Our resource is practical for a wide range of users, including biologists, bioinformaticians and molecular/systems biologists.
InterPro in 2022
Authors: Paysan-Lafosse Typhaine , Blum Matthias , Chuguransky Sara , Grego Tiago , Pinto Beatriz Lázaro , Salazar Gustavo A , Bileschi Maxwell L , Bork Peer , Bridge Alan , Colwell Lucy , Gough Julian , Haft Daniel H , Letunić Ivica , Marchler-Bauer Aron , Mi Huaiyu , Natale Darren A , Orengo Christine A , Pandurangan Arun P , Rivoire Catherine , Sigrist Christian J A , Sillitoe Ian , Thanki Narmada , Thomas Paul D , Tosatto Silvio C E , Wu Cathy H , Bateman Alex 
Published: November 2022

Abstract
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.
Digital Diasporas and the Religious Reproduction of “Home”
Authors: Woods Orlando 
Published: November 2022

Abstract
The proliferation of the Internet, social media, and smartphones has ushered in a new era of social reproduction that is global in scope and rapid in its effects. This has brought about an epistemological reimagination of how “communities” are formed and maintained, of what it means to “belong,” and of what “home” is and where it might be located. Similarly, constructs like “religion” and “diaspora” have evolved and expanded in response to the mediatory role of the digital throughout people’s everyday lives. This chapter tracks these expansions and seeks to bring the idea of digital diasporas into conversation with the religious reproduction of home. It argues that whilst digital technologies provide displaced people with the tools needed to connect to, to claim and to contest the idea of “home,” religion can provide the motivation to do so. It offers both an overview of existing research that explores the nexus of the digital, the diaspora, and religion, and it identifies promising areas for future research.
Muslims Enacting Identity
Authors: Nisa Eva F. 
Published: November 2022

Abstract
This chapter discusses the intersections between gender issues, religious identity, and cyber-activism. The main discussion focuses on women, particularly due to the pervasive unequal offline and online power dynamics between men and women. It focuses on how Muslim women enact their identities through the Internet and various social media platforms. What does it mean for them to be active in these various forms of advanced communication technology? The chapter argues that although the Internet and social media has enabled Muslim women from varied Islamic currents—liberal, progressive, and ultra-conservative—to self-present themselves and enable them to speak from a position of religious authority, their online presence is not a direct sign of weakened Muslim patriarchy. Despite development in the gender digital divide, alternative and social media, offered through the Internet’s presence and affordability, remain gendered.
Digital Judaism
Authors: Golan Oren 
Published: November 2022

Abstract
The rise of digital media and its rapid integration into everyday life has transformed the Jewish world on communal and individual levels. Despite objections from rabbis and educators in various communities, most notably the ultra-Orthodox, digital media is increasingly supplementing, and occasionally replacing, traditional ways of practice, ritual, and learning. Thus, the question begs: how is digital media negotiated within the Jewish world? Scouring through the myriad uses of the Internet, mobile phones, digital games, and virtual reality programs, the author reviews three key facets of transformation that correspond with the primary properties of Jews’ “lived religion,” namely knowledge dissemination, consumption, and scripturalism; Jewish practice; communal authority; and identity. Exploring the accumulated scholarship on these themes enables a macroscopic perspective on the ways contemporary Jews respond to modernity by adopting or adapting to technologies to fit their rhythm of life. Ultimately, these understandings bear on the ways Jews incrementally enable changes in their religious experience, sources of learning, and manifestations of the rich variants of their Jewish identity.