bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of the European SCORE2 models in a Canadian primary care cohort
Authors: Sud Maneesh , Sivaswamy Atul , Austin Peter C , Abdel-Qadir Husam , Anderson Todd J , Khera Rohan , Naimark David M J , Lee Douglas S , Roifman Idan , Thanassoulis George , Tu Karen , Wijeysundera Harindra C , Ko Dennis T 
Published: November 2023

Abstract

Aims
Systematic Coronary Risk Evaluation Model 2 (SCORE2) was recently developed to predict atherosclerotic cardiovascular disease (ASCVD) in Europe. Whether these models could be used outside of Europe is not known. The objective of this study was to test the validity of SCORE2 in a large Canadian cohort.

Methods and results
A primary care cohort of persons with routinely collected electronic medical record data from 1 January 2010 to 31 December 2014, in Ontario, Canada, was used for validation. The SCORE2 models for younger persons (YP) were applied to 57 409 individuals aged 40–69 while the models for older persons (OPs) were applied to 9885 individuals 70–89 years of age. Five-year ASCVD predictions from both the uncalibrated and low-risk region recalibrated SCORE2 models were evaluated. The C-statistic for SCORE2-YP was 0.74 in women and 0.69 in men. The uncalibrated SCORE2-YP overestimated risk by 17% in women and underestimated by 2% in men. In contrast, the low-risk region recalibrated model demonstrated worse calibration, overestimating risk by 100% in women and 36% in men. The C-statistic for SCORE2-OP was 0.64 and 0.62 in older women and men, respectively. The uncalibrated SCORE2-OP overestimated risk by more than 100% in both sexes. The low-risk region recalibrated model demonstrated improved calibration but still overestimated risk by 60% in women and 13% in men.

Conclusion
The performance of SCORE2 to predict ASCVD risk in Canada varied by age group and depended on whether regional calibration was applied. This underscores the necessity for validation assessment of SCORE2 prior to implementation in new jurisdictions.
A nematode model to evaluate microdeletion phenotype expression
Authors: Antkowiak Katianna R , Coskun Peren , Noronha Sharon T , Tavella Davide , Massi Francesca , Ryder Sean P 
Published: November 2023

Abstract
Microdeletion syndromes are genetic diseases caused by multilocus chromosomal deletions too small to be detected by karyotyping. They are typified by complex pleiotropic developmental phenotypes that depend both on the extent of the deletion and variations in genetic background. Microdeletion alleles cause a wide array of consequences involving multiple pathways. How simultaneous haploinsufficiency of numerous adjacent genes leads to complex and variable pleiotropic phenotypes is not well understood. CRISPR/Cas9 genome editing has been shown to induce microdeletion-like alleles at a meaningful rate. Here, we describe a microdeletion allele in Caenorhabditis elegans recovered during a CRISPR/Cas9 genome editing experiment. We mapped the allele to chromosome V, balanced it with a reciprocal translocation crossover suppressor, and precisely defined the breakpoint junction. The allele simultaneously removes 32 protein-coding genes, yet animals homozygous for this mutation are viable as adults. Homozygous animals display a complex phenotype including maternal effect lethality, producing polynucleated embryos that grow into uterine tumors, vulva morphogenesis defects, body wall distensions, uncoordinated movement, and a shortened life span typified by death by bursting. Our work provides an opportunity to explore the complexity and penetrance of microdeletion phenotypes in a simple genetic model system.
Blood donation practices, processing and utilisation of blood components in government tertiary hospitals in Nigeria: a multicentre cooperative study
Authors: Umar Garba , Abdulqadir Ibrahim , Ugwu Ngozi , Adeyemo Titilope , Yau Nabila , Hassan Abdulazziz , Olaniyi John , Musa Abubakar , Abubakar Sharafa , Ndakotsu Muhammad , James Jasini , Uche Chika , Musa Awwal , Ukoma Chikadibia , Nwogoh Benedict , David Ekaete , Ugwu Angela , Nwankwo Chizoba , Omokanye Olaitan , Abba Aisha , Owojuyigbe Temilola , Isyaku Mujtabba , Obi Esther , Jatau Ezra , Ekwere Timothy , Oladosu-Olayiwola Rashidat , Isah Hezekiah , Diggi Sirajo , Nwannadi Alexander , Yuguda Saleh , Iheanacho Obinna , Tikau Hadiza , Adeleke Ibijola , Ekanem Mabel , Madu Anazoeze , Ikusemoro Augustina , Chukwu Celestine , Galadanci Amal , Bassey Okon , Otu Theresa , Agwu Obineche , Osho Patrick , Gwarzo Aisha , Hassan Sadiya , Majeed Adepoju , Umar Anas , Abubakar Habib , Gimba Mohamed , Ugbor Michael , Ali Abdulmalik , Ajuba Clara 
Published: November 2023

Abstract

Background
Timely access to safe blood and blood components is still a challenge in Nigeria. This study aimed to determine blood donation practices, processing and utilization of blood components across government tertiary hospitals (THs) in Nigeria.

Methods
This was a descriptive cross-sectional study done in Nigeria in June–July 2020. Data were analysed with SPSS version 21.0.

Results
Data were collected from 50 THs. The majority (68%) of the THs lack facilities for blood component preparation and only 18% and 32% provide cryoprecipitate and platelet concentrate, respectively. Whole blood was most commonly requested (57.04%). All facilities tested blood for HIV, HBV and HCV, but the majority (23 [46%]) employed rapid screening tests alone and nucleic acid testing was not available in any hospitals. The manual method was the most common method of compatibility testing in 90% (45/50) and none of the THs routinely perform extended red cell typing. The average time to process routine, emergency and uncross-matched requests were a mean of 109.58±79.76 min (range 45.00–360.00), 41.62±25.23 (10.00–240.00) and 11.09±4.92 (2.00–20.00), respectively.

Conclusion
Facilities for blood component preparation were not widely available. Concerned government authorities should provide facilities for blood component preparation.
Energy justice in times of crisis: protection of consumers and market-based renewable energy investments
Authors: Boute Anatole 
Published: November 2023

ABSTRACT
In response to the 2022 energy crisis, caused by the disruption of Russian gas supplies to Europe, the European Union (EU) emphasized the importance of accelerating the deployment of renewable energy to ensure supply security and lower energy prices. Paradoxically, renewable energy investments were also one of the main targets of the EU efforts to contain the hardship of the crisis. Based on the reasoning that investors in wind and solar energy received profits that by far exceeded pre-crisis levels, the EU capped their ‘surplus revenues’ and initially proposed to decouple electricity from gas prices. These initiatives were justified based on considerations of distributive energy justice. Yet, by interfering with revenues and the electricity market structure, the EU signalled to renewable energy investors the risk of regulatory intervention with the market basis governing their investments. Building on the arbitral practice on renewable energy and electricity regulation, this article examines the international protection of market-based renewable energy investments and critically reflects on how investment protection affects states’ right to ensure energy justice in times of crisis.
Combined Ravitch and Nuss procedure for pectus excavatum with dyspnea following scoliosis repair
Authors: Oka Naoyuki , Masai Kyohei , Okubo Yu , Kaseda Kaoru , Hishida Tomoyuki , Asakura Keisuke 
Published: November 2023

Abstract
Pectus excavatum (PE) is often associated with scoliosis and can elicit cardiovascular disturbances under rare conditions. Here we report a patient who was treated with a combined Ravitch and Nuss procedure for PE with dyspnea following scoliosis repair to improve her symptoms. The patient was a 49-year-old woman with a history of PE and scoliosis. Right inferior pulmonary vein stenosis was caused by posterior spinal fusion for scoliosis prior to the PE repair. We could safely correct the chest wall deformity and treat dyspnea by performing a modified Ravitch repair in combination with the Nuss procedure.
The Question of Logic
Authors: Kripke Saul A 
Published: November 2023

Abstract
Under the influence of Quine’s famous manifesto, many philosophers have thought that logical theories are scientific theories that can be ‘adopted’ and tested as scientific theories. Here we argue that this idea is untenable. We discuss it with special reference to Putnam’s proposal to ‘adopt’ a particular non-classical logic to solve the foundational problems of quantum mechanics in his famous paper ‘Is Logic Empirical?’ (1968), which we argue was not really coherent.
The characteristic shape of damping wings during reionization
Authors: Chen Huanqing 
Published: November 2023

ABSTRACT
Spectroscopic analysis of Ly α damping wings of bright sources at z &gt; 6 is a promising way to measure the reionization history of the universe. However, the theoretical interpretation of the damping wings is challenging due to the inhomogeneous nature of the reionization process and the proximity effect of bright sources. In this Letter, we analyse the damping wings arising from the neutral patches in the radiative transfer cosmological simulation suite cosmic reionization on computers. We find that the damping wing profile remains a tight function of volume-weighted neutral fraction &lt;xH i&gt;v, especially when &lt;xH i&gt;v &gt; 0.5, despite the patchy nature of reionization and the proximity effect. This small scatter indicates that with a well-measured damping wing profile, we could constrain the volume-weighted neutral fraction as precise as Δ &lt;xH i&gt;v ≲ 0.1 in the first half of reionization. Due to resonant Ly α absorption from the residual neutral hydrogen inside the ionized bubble, it may be challenging to find the starting point of the damping wing for faint sources like normal galaxies or gamma-ray bursts. However, for bright sources like quasars, it is hopeful to measure the entire damping wing and use them to measure the neutral fraction accurately.
Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency
Authors: Chanou Anna , Weiβ Matthias , Holler Karoline , Sajid Atiqa , Straub Tobias , Krietsch Jana , Sanchi Andrea , Ummethum Henning , Lee Clare S K , Kruse Elisabeth , Trauner Manuel , Werner Marcel , Lalonde Maxime , Lopes Massimo , Scialdone Antonio , Hamperl Stephan 
Published: November 2023

Abstract
Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned +1 and +2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.
The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
Authors: Abarenkov Kessy , Nilsson R Henrik , Larsson Karl-Henrik , Taylor Andy F S , May Tom W , Frøslev Tobias Guldberg , Pawlowska Julia , Lindahl Björn , Põldmaa Kadri , Truong Camille , Vu Duong , Hosoya Tsuyoshi , Niskanen Tuula , Piirmann Timo , Ivanov Filipp , Zirk Allan , Peterson Marko , Cheeke Tanya E , Ishigami Yui , Jansson Arnold Tobias , Jeppesen Thomas Stjernegaard , Kristiansson Erik , Mikryukov Vladimir , Miller Joseph T , Oono Ryoko , Ossandon Francisco J , Paupério Joana , Saar Irja , Schigel Dmitry , Suija Ave , Tedersoo Leho , Kõljalg Urmas 
Published: November 2023

Abstract
UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.
DGIdb 5.0: rebuilding the drug–gene interaction database for precision medicine and drug discovery platforms
Authors: Cannon Matthew , Stevenson James , Stahl Kathryn , Basu Rohit , Coffman Adam , Kiwala Susanna , McMichael Joshua F , Kuzma Kori , Morrissey Dorian , Cotto Kelsy , Mardis Elaine R , Griffith Obi L , Griffith Malachi , Wagner Alex H 
Published: November 2023

Abstract
The Drug–Gene Interaction Database (DGIdb, https://dgidb.org) is a publicly accessible resource that aggregates genes or gene products, drugs and drug–gene interaction records to drive hypothesis generation and discovery for clinicians and researchers. DGIdb 5.0 is the latest release and includes substantial architectural and functional updates to support integration into clinical and drug discovery pipelines. The DGIdb service architecture has been split into separate client and server applications, enabling consistent data access for users of both the application programming interface (API) and web interface. The new interface was developed in ReactJS, and includes dynamic visualizations and consistency in the display of user interface elements. A GraphQL API has been added to support customizable queries for all drugs, genes, annotations and associated data. Updated documentation provides users with example queries and detailed usage instructions for these new features. In addition, six sources have been added and many existing sources have been updated. Newly added sources include ChemIDplus, HemOnc, NCIt (National Cancer Institute Thesaurus), Drugs@FDA, HGNC (HUGO Gene Nomenclature Committee) and RxNorm. These new sources have been incorporated into DGIdb to provide additional records and enhance annotations of regulatory approval status for therapeutics. Methods for grouping drugs and genes have been expanded upon and developed as independent modular normalizers during import. The updates to these sources and grouping methods have resulted in an improvement in FAIR (findability, accessibility, interoperability and reusability) data representation in DGIdb.
ncRNADrug: a database for validated and predicted ncRNAs associated with drug resistance and targeted by drugs
Authors: Cao Xinyu , Zhou Xu , Hou Fei , Huang Yu-e , Yuan Mengqin , Long Min , Chen Sina , Lei Wanyue , Zhu Jicun , Chen Jiahao , Zhang Tao , Guo An-Yuan , Jiang Wei 
Published: November 2023

Abstract
Drug resistance is a major barrier in cancer treatment and anticancer drug development. Growing evidence indicates that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play pivotal roles in cancer progression, therapy, and drug resistance. Furthermore, ncRNAs have been proven to be promising novel therapeutic targets for cancer treatment. Reversing dysregulated ncRNAs by drugs holds significant potential as an effective therapeutic strategy for overcoming drug resistance. Therefore, we developed ncRNADrug, an integrated and comprehensive resource that records manually curated and computationally predicted ncRNAs associated with drug resistance, ncRNAs targeted by drugs, as well as potential drug combinations for the treatment of resistant cancer. Currently, ncRNADrug collects 29 551 experimentally validated entries involving 9195 ncRNAs (2248 miRNAs, 4145 lncRNAs and 2802 circRNAs) associated with the drug resistance of 266 drugs, and 32 969 entries involving 10 480 ncRNAs (4338 miRNAs, 6087 lncRNAs and 55 circRNAs) targeted by 965 drugs. In addition, ncRNADrug also contains associations between ncRNAs and drugs predicted from ncRNA expression profiles by differential expression analysis. Altogether, ncRNADrug surpasses the existing related databases in both data volume and functionality. It will be a useful resource for drug development and cancer treatment. ncRNADrug is available at http://www.jianglab.cn/ncRNADrug.
VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome
Authors: Wang Zheng , Zhao Guihu , Zhu Zhaopo , Wang Yijing , Xiang Xudong , Zhang Shiyu , Luo Tengfei , Zhou Qiao , Qiu Jian , Tang Beisha , Xia Kun , Li Bin , Li Jinchen 
Published: November 2023

Abstract
VarCards, an online database, combines comprehensive variant- and gene-level annotation data to streamline genetic counselling for coding variants. Recognising the increasing clinical relevance of non-coding variations, there has been an accelerated development of bioinformatics tools dedicated to interpreting non-coding variations, including single-nucleotide variants and copy number variations. Regrettably, most tools remain as either locally installed databases or command-line tools dispersed across diverse online platforms. Such a landscape poses inconveniences and challenges for genetic counsellors seeking to utilise these resources without advanced bioinformatics expertise. Consequently, we developed VarCards2, which incorporates nearly nine billion artificially generated single-nucleotide variants (including those from mitochondrial DNA) and compiles vital annotation information for genetic counselling based on ACMG-AMP variant-interpretation guidelines. These annotations include (I) functional effects; (II) minor allele frequencies; (III) comprehensive function and pathogenicity predictions covering all potential variants, such as non-synonymous substitutions, non-canonical splicing variants, and non-coding variations and (IV) gene-level information. Furthermore, VarCards2 incorporates 368 820 266 documented short insertions and deletions and 2 773 555 documented copy number variations, complemented by their corresponding annotation and prediction tools. In conclusion, VarCards2, by integrating over 150 variant- and gene-level annotation sources, significantly enhances the efficiency of genetic counselling and can be freely accessed at http://www.genemed.tech/varcards2/.
Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery
Authors: Vega Montserrat , Barrios Rubén , Fraile Rodrigo , de Castro Cogle Kevin , Castillo David , Anglada Roger , Casals Ferran , Ayté José , Lowy-Gallego Ernesto , Hidalgo Elena 
Published: November 2023

Abstract
Chromatin remodeling is essential to allow full development of alternative gene expression programs in response to environmental changes. In fission yeast, oxidative stress triggers massive transcriptional changes including the activation of hundreds of genes, with the participation of histone modifying complexes and chromatin remodelers. DNA transcription is associated to alterations in DNA topology, and DNA topoisomerases facilitate elongation along gene bodies. Here, we test whether the DNA topoisomerase Top1 participates in the RNA polymerase II-dependent activation of the cellular response to oxidative stress. Cells lacking Top1 are resistant to H2O2 stress. The transcriptome of Δtop1 strain was not greatly affected in the absence of stress, but activation of the anti-stress gene expression program was more sustained than in wild-type cells. Top1 associated to stress open reading frames. While the nucleosomes of stress genes are partially and transiently evicted during stress, the chromatin configuration remains open for longer times in cells lacking Top1, facilitating RNA polymerase II progression. We propose that, by removing DNA tension arising from transcription, Top1 facilitates nucleosome reassembly and works in synergy with the chromatin remodeler Hrp1 as opposing forces to transcription and to Snf22 / Hrp3 opening remodelers.
The UCSC Genome Browser database: 2024 update
Authors: Raney Brian J , Barber Galt P , Benet-Pagès Anna , Casper Jonathan , Clawson Hiram , Cline Melissa S , Diekhans Mark , Fischer Clayton , Navarro Gonzalez Jairo , Hickey Glenn , Hinrichs Angie S , Kuhn Robert M , Lee Brian T , Lee Christopher M , Le Mercier Phillipe , Miga Karen H , Nassar Luis R , Nejad Parisa , Paten Benedict , Perez Gerardo , Schmelter Daniel , Speir Matthew L , Wick Brittney D , Zweig Ann S , Haussler David , Kent W James , Haeussler Maximilian 
Published: November 2023

Abstract
The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.