bluuebunny/crossref_metadata_2025_split huggingface dataset:
PGS-Depot: a comprehensive resource for polygenic scores constructed by summary statistics based methods
Authors: Cao Chen , Zhang Shuting , Wang Jianhua , Tian Min , Ji Xiaolong , Huang Dandan , Yang Sheng , Gu Ning 
Published: November 2023

Abstract
Polygenic score (PGS) is an important tool for the genetic prediction of complex traits. However, there are currently no resources providing comprehensive PGSs computed from published summary statistics, and it is difficult to implement and run different PGS methods due to the complexity of their pipelines and parameter settings. To address these issues, we introduce a new resource called PGS-Depot containing the most comprehensive set of publicly available disease-related GWAS summary statistics. PGS-Depot includes 5585 high quality summary statistics (1933 quantitative and 3652 binary trait statistics) curated from 1564 traits in European and East Asian populations. A standardized best-practice pipeline is used to implement 11 summary statistics-based PGS methods, each with different model assumptions and estimation procedures. The prediction performance of each method can be compared for both in- and cross-ancestry populations, and users can also submit their own summary statistics to obtain custom PGS with the available methods. Other features include searching for PGSs by trait name, publication, cohort information, population, or the MeSH ontology tree and searching for trait descriptions with the experimental factor ontology (EFO). All scores, SNP effect sizes and summary statistics can be downloaded via FTP. PGS-Depot is freely available at http://www.pgsdepot.net.
Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions
Authors: Martini Leonardo , Baek Seung Han , Lo Ian , Raby Benjamin A , Silverman Edwin K , Weiss Scott T , Glass Kimberly , Halu Arda 
Published: November 2023

Abstract
The versatility of cellular response arises from the communication, or crosstalk, of signaling pathways in a complex network of signaling and transcriptional regulatory interactions. Understanding the various mechanisms underlying crosstalk on a global scale requires untargeted computational approaches. We present a network-based statistical approach, MuXTalk, that uses high-dimensional edges called multilinks to model the unique ways in which signaling and regulatory interactions can interface. We demonstrate that the signaling-regulatory interface is located primarily in the intermediary region between signaling pathways where crosstalk occurs, and that multilinks can differentiate between distinct signaling-transcriptional mechanisms. Using statistically over-represented multilinks as proxies of crosstalk, we infer crosstalk among 60 signaling pathways, expanding currently available crosstalk databases by more than five-fold. MuXTalk surpasses existing methods in terms of model performance metrics, identifies additions to manual curation efforts, and pinpoints potential mediators of crosstalk. Moreover, it accommodates the inherent context-dependence of crosstalk, allowing future applications to cell type- and disease-specific crosstalk.
Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts
Authors: Crisalli Alicia M , Chen Yi-Tzai , Cai Ang , Li Deyu , Cho Bongsup P 
Published: November 2023

Abstract
Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5′-CTTCTC#G*NCCTCATTC-3′], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3′ flanking pyrimidine were better bypassed when the 5′ base was 5mC, whereas sequences with a 3′ purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer
Authors: Quesnel-Vallières Mathieu , Jewell San , Lynch Kristen W , Thomas-Tikhonenko Andrei , Barash Yoseph 
Published: November 2023

Abstract
Quantification of RNA splicing variations based on RNA-Sequencing can reveal tissue- and disease-specific splicing patterns. To study such splicing variations, we introduce MAJIQlopedia, an encyclopedia of splicing variations that encompasses 86 human tissues and 41 cancer datasets. MAJIQlopedia reports annotated and unannotated splicing events for a total of 486 175 alternative splice junctions in normal tissues and 338 317 alternative splice junctions in cancer. This database, available at https://majiq.biociphers.org/majiqlopedia/, includes a user-friendly interface that provides graphical representations of junction usage quantification for each junction across all tissue or cancer types. To demonstrate case usage of MAJIQlopedia, we review splicing variations in genes WT1, MAPT and BIN1, which all have known tissue or cancer-specific splicing variations. We also use MAJIQlopedia to highlight novel splicing variations in FDX1 and MEGF9 in normal tissues, and we uncover a novel exon inclusion event in RPS6KA6 that only occurs in two cancer types. Users can download the database, request the addition of data to the webtool, or install a MAJIQlopedia server to integrate proprietary data. MAJIQlopedia can serve as a reference database for researchers seeking to understand what splicing variations exist in genes of interest, and those looking to understand tissue- or cancer-specific splice isoform usage.
OpenProt 2.0 builds a path to the functional characterization of alternative proteins
Authors: Leblanc Sébastien , Yala Feriel , Provencher Nicolas , Lucier Jean-François , Levesque Maxime , Lapointe Xavier , Jacques Jean-Francois , Fournier Isabelle , Salzet Michel , Ouangraoua Aïda , Scott Michelle S , Boisvert François-Michel , Brunet Marie A , Roucou Xavier 
Published: November 2023

Abstract
The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases. Enhancements in this update are largely the result of user feedback and include the prediction of structure, subcellular localization, and intrinsic disorder, using cutting-edge algorithms based on machine learning techniques. The mass spectrometry pipeline now integrates a machine learning-based peptide rescoring method to improve peptide identification. We continue to help users explore this cryptic proteome by providing OpenCustomDB, a tool that enables users to build their own customized protein databases, and OpenVar, a genomic annotator including genetic variants within AltORFs and protein sequences. A new interface improves the visualization of all functional annotations, including a spectral viewer and the prediction of multicoding genes. All data on OpenProt are freely available and downloadable. Overall, OpenProt continues to establish itself as an important resource for the exploration and study of new proteins.
The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem
Authors: Baron J Allen , Johnson Claudia Sanchez-Beato , Schor Michael A , Olley Dustin , Nickel Lance , Felix Victor , Munro James B , Bello Susan M , Bearer Cynthia , Lichenstein Richard , Bisordi Katharine , Koka Rima , Greene Carol , Schriml Lynn M 
Published: November 2023

Abstract
In 2003, the Human Disease Ontology (DO, https://disease-ontology.org/) was established at Northwestern University. In the intervening 20 years, the DO has expanded to become a highly-utilized disease knowledge resource. Serving as the nomenclature and classification standard for human diseases, the DO provides a stable, etiology-based structure integrating mechanistic drivers of human disease. Over the past two decades the DO has grown from a collection of clinical vocabularies, into an expertly curated semantic resource of over 11300 common and rare diseases linking disease concepts through more than 37000 vocabulary cross mappings (v2023-08-08). Here, we introduce the recently launched DO Knowledgebase (DO-KB), which expands the DO’s representation of the diseaseome and enhances the findability, accessibility, interoperability and reusability (FAIR) of disease data through a new SPARQL service and new Faceted Search Interface. The DO-KB is an integrated data system, built upon the DO’s semantic disease knowledge backbone, with resources that expose and connect the DO’s semantic knowledge with disease-related data across Open Linked Data resources. This update includes descriptions of efforts to assess the DO’s global impact and improvements to data quality and content, with emphasis on changes in the last two years.
EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments
Authors: Zhou Bailing , Ji Baohua , Shen Congcong , Zhang Xia , Yu Xue , Huang Pingping , Yu Ru , Zhang Hongmei , Dou Xianghua , Chen Qingshuai , Zeng Qiangcheng , Wang Xiaoxin , Cao Zanxia , Hu Guodong , Xu Shicai , Zhao Huiying , Yang Yuedong , Zhou Yaoqi , Wang Jihua 
Published: November 2023

Abstract
Long noncoding RNAs (lncRNAs) have emerged as crucial regulators across diverse biological processes and diseases. While high-throughput sequencing has enabled lncRNA discovery, functional characterization remains limited. The EVLncRNAs database is the first and exclusive repository for all experimentally validated functional lncRNAs from various species. After previous releases in 2018 and 2021, this update marks a major expansion through exhaustive manual curation of nearly 25 000 publications from 15 May 2020, to 15 May 2023. It incorporates substantial growth across all categories: a 154% increase in functional lncRNAs, 160% in associated diseases, 186% in lncRNA-disease associations, 235% in interactions, 138% in structures, 234% in circular RNAs, 235% in resistant lncRNAs and 4724% in exosomal lncRNAs. More importantly, it incorporated additional information include functional classifications, detailed interaction pathways, homologous lncRNAs, lncRNA locations, COVID-19, phase-separation and organoid-related lncRNAs. The web interface was substantially improved for browsing, visualization, and searching. ChatGPT was tested for information extraction and functional overview with its limitation noted. EVLncRNAs 3.0 represents the most extensive curated resource of experimentally validated functional lncRNAs and will serve as an indispensable platform for unravelling emerging lncRNA functions. The updated database is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/.
The European Nucleotide Archive in 2023
Authors: Yuan David , Ahamed Alisha , Burgin Josephine , Cummins Carla , Devraj Rajkumar , Gueye Khadim , Gupta Dipayan , Gupta Vikas , Haseeb Muhammad , Ihsan Maira , Ivanov Eugene , Jayathilaka Suran , Kadhirvelu Vishnukumar Balavenkataraman , Kumar Manish , Lathi Ankur , Leinonen Rasko , McKinnon Jasmine , Meszaros Lili , O’Cathail Colman , Ouma Dennis , Paupério Joana , Pesant Stephane , Rahman Nadim , Rinck Gabriele , Selvakumar Sandeep , Suman Swati , Sunthornyotin Yanisa , Ventouratou Marianna , Vijayaraja Senthilnathan , Waheed Zahra , Woollard Peter , Zyoud Ahmad , Burdett Tony , Cochrane Guy 
Published: November 2023

Abstract
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide Sequence Database Collaboration (INSDC). It serves the bioinformatics community worldwide via the submission, processing, archiving and dissemination of sequence data. The ENA supports data types ranging from raw reads, through alignments and assemblies to functional annotation. The data is enriched with contextual information relating to samples and experimental configurations. In this article, we describe recent progress and improvements to ENA services. In particular, we focus upon three areas of work in 2023: FAIRness of ENA data, pandemic preparedness and foundational technology. For FAIRness, we have introduced minimal requirements for spatiotemporal annotation, created a metadata-based classification system, incorporated third party metadata curations with archived records, and developed a new rapid visualisation platform, the ENA Notebooks. For foundational enhancements, we have improved the INSDC data exchange and synchronisation pipelines, and invested in site reliability engineering for ENA infrastructure. In order to support genomic surveillance efforts, we have continued to provide ENA services in support of SARS-CoV-2 data mobilisation and have adapted these for broader pathogen surveillance efforts.
STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization
Authors: Xu Zhicheng , Wang Weiwen , Yang Tao , Li Ling , Ma Xizheng , Chen Jing , Wang Jieyu , Huang Yan , Gould Joshua , Lu Huifang , Du Wensi , Sahu Sunil Kumar , Yang Fan , Li Zhiyong , Hu Qingjiang , Hua Cong , Hu Shoujie , Liu Yiqun , Cai Jia , You Lijin , Zhang Yong , Li YuXiang , Zeng Wenjun , Chen Ao , Wang Bo , Liu Longqi , Chen Fengzhen , Ma Kailong , Xu Xun , Wei Xiaofeng 
Published: November 2023

Abstract
Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.
The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids
Authors: Lawson Catherine L , Berman Helen M , Chen Li , Vallat Brinda , Zirbel Craig L 
Published: November 2023

Abstract
The Nucleic Acid Knowledgebase (nakb.org) is a new data resource, updated weekly, for experimentally determined 3D structures containing DNA and/or RNA nucleic acid polymers and their biological assemblies. NAKB indexes nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR and EM), including all held by the Protein Data Bank (PDB). As the planned successor to the Nucleic Acid Database (NDB), NAKB’s design preserves all functionality of the NDB and provides novel nucleic acid-centric content, including structural and functional annotations, as well as annotations from and links to external resources. A variety of custom interactive tools have been developed to enable rapid exploration and drill-down of NAKB’s content.
DrugBank 6.0: the DrugBank Knowledgebase for 2024
Authors: Knox Craig , Wilson Mike , Klinger Christen M , Franklin Mark , Oler Eponine , Wilson Alex , Pon Allison , Cox Jordan , Chin Na Eun (Lucy) , Strawbridge Seth A , Garcia-Patino Marysol , Kruger Ray , Sivakumaran Aadhavya , Sanford Selena , Doshi Rahil , Khetarpal Nitya , Fatokun Omolola , Doucet Daphnee , Zubkowski Ashley , Rayat Dorsa Yahya , Jackson Hayley , Harford Karxena , Anjum Afia , Zakir Mahi , Wang Fei , Tian Siyang , Lee Brian , Liigand Jaanus , Peters Harrison , Wang Ruo Qi (Rachel) , Nguyen Tue , So Denise , Sharp Matthew , da Silva Rodolfo , Gabriel Cyrella , Scantlebury Joshua , Jasinski Marissa , Ackerman David , Jewison Timothy , Sajed Tanvir , Gautam Vasuk , Wishart David S 
Published: November 2023

Abstract
First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the ‘gold standard’ knowledge resource for drug, drug–target and related pharmaceutical information. DrugBank is widely used across many diverse biomedical research and clinical applications, and averages more than 30 million views/year. Since its last update in 2018, we have been actively enhancing the quantity and quality of the drug data in this knowledgebase. In this latest release (DrugBank 6.0), the number of FDA approved drugs has grown from 2646 to 4563 (a 72% increase), the number of investigational drugs has grown from 3394 to 6231 (a 38% increase), the number of drug–drug interactions increased from 365 984 to 1 413 413 (a 300% increase), and the number of drug–food interactions expanded from 1195 to 2475 (a 200% increase). In addition to this notable expansion in database size, we have added thousands of new, colorful, richly annotated pathways depicting drug mechanisms and drug metabolism. Likewise, existing datasets have been significantly improved and expanded, by adding more information on drug indications, drug–drug interactions, drug–food interactions and many other relevant data types for 11 891 drugs. We have also added experimental and predicted MS/MS spectra, 1D/2D-NMR spectra, CCS (collision cross section), RT (retention time) and RI (retention index) data for 9464 of DrugBank's 11 710 small molecule drugs. These and other improvements should make DrugBank 6.0 even more useful to a much wider research audience ranging from medicinal chemists to metabolomics specialists to pharmacologists.
Folic Acid Ameliorates Anxiety- and Depressive-Like Behavior Induced by Nicotine Withdrawal Through Restoration of Behavioral and Biochemical Alterations in Adolescent Male Rats
Authors: Rezaei Moghadam Mikael , Khoshrou Alireza , Kakhki Samaneh , Hosseini Seyed Hossein , Shirinzadeh Feizabadi Atefeh , Beheshti Farimah 
Published: November 2023

Abstract

Background
The present study aimed to assess the efficacy of folic acid (FA) on withdrawal following nicotine (Nic) administration in adolescent male rats.

Aims and Methods
Adolescent male rats were divided into two groups: (1) vehicle and (2) Nic (Nic-2 mg/kg), and were under treatment from 21 to 42 days of age. After that, they continued the experiment without treatment and returned to a regular diet, except for one of those who received Nic. The rats were divided into four groups where they were treated with different doses of FA (5, 10, and 15 mg/kg) and bupropion (Bup) by oral gavage, and the final group included normal rats that received only FA (15 mg/kg) from 42 days of age for three weeks during which withdrawal occurred.

Results
Results showed that adolescent Nic exposure exacerbated the behavioral indices of anxiety- and depression-like behaviors, while FA attenuated the effects of Nic withdrawal on anxiety and depression as well as Bup. In support, the biochemical results demonstrated a balance between oxidant and antioxidant mediators in addition to the increase and decrease of serotonin and monoamine oxidase (MAO) activity in cortical tissue. TNF-α as an inflammatory agent was decreased, whereas IL-10 as an anti-inflammatory parameter was increased.

Conclusions
The present findings suggest anxiety and depression caused by Nic withdrawal were attenuated by FA more likely through the reduction activity of MAO, the important enzyme responsible for serotonin metabolism along with balance between oxidant/antioxidant and pro-inflammatory/anti-inflammatory mediators. However, various mechanisms might be involved, which requires further investigation.

Implications
Nic withdrawal-induced depression and anxiety like behavior in rats followed by neuro-oxidative damage and neuro-inflammation. FA supplementation as well as Bup improved cognitive disorders induced by Nic withdrawal by increasing neuro-inflammation and neuro-oxidative damage.
Evaluation of Dolutegravir- and Bictegravir-Based Antiretroviral Regimen Utilization in Patients who Cannot Take Medications by Mouth
Authors: LoFaso Megan , Marchionda Olivia , Bass Stephanie , Torbic Heather , Blackewicz Caitlin , Pallotta Andrea 
Published: November 2023

Abstract
A retrospective review of patients unable to take medications by mouth showed short interruptions of therapy for most patients. In a secondary analysis, our data showed maintenance and/or achievement of viral suppression for most patients. A retrospective review of intensive care patients unable to take antiretrovirals by mouth showed 56.6% of patients experiencing a transient interruption in therapy. Additionally, our case series further supports previous literature on crushing dolutegravir and bictegravir regimens to maintain and achieve viral suppression.