bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient evaluation of lattice Green’s functions
Authors: Zhugayevych Andriy 
Published: December 2024

Abstract
We develop and implement efficient algorithms for calculating lattice Green’s functions (LGFs) at any point and argument. This includes several approaches: recurrence relations in lattice coordinates, series at zero and infinity, and finite-precision uniform approximations. The methodology can be applied to any simple lattice, whereas program code is provided for triangular and hypercubic lattices. In particular, the obtained generic recurrence relations are applicable to any lattice with a root-free band dispersion. Except for lattices with a high coordination number, these relations allow LGF to be presented as a linear combination of d non-polynomial functions with polynomial coefficients, where d is the lattice dimension. The non-polynomial functions are solutions of d-order differential equation with polynomial coefficients which allows their series expansion at singularities to be performed. For series at infinity, we estimate the remainder, thus extending its use to the zero value of the argument. The remainder itself provides a good finite-precision estimate for the LGF. Finally, we derive a large-scale approximation that smoothly connects the lattice and the continuum Green’s functions. The provided open-source code allows for arbitrary-precision and symbolic computations of LGF.
A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity
Authors: Lu Tong , Guo Wei , Guo Wei , Meng Wangyang , Han Tianyi , Guo Zizhen , Li Chengqiang , Gao Shugeng , Ye Youqiong , Li Hecheng 
Published: December 2024

Abstract
Intratumor heterogeneity significantly challenges the accuracy of existing prognostic models for esophageal squamous cell carcinoma (ESCC) by introducing biases related to the varied genetic and molecular landscapes within tumors. Traditional models, relying on single-sample, single-region bulk RNA sequencing, fall short of capturing the complexity of intratumor heterogeneity. To fill this gap, we developed a computational model for intratumor heterogeneity corrected signature (ITHCS) by employing both multiregion bulk and single-cell RNA sequencing to pinpoint genes that exhibit consistent expression patterns across different tumor regions but vary significantly among patients. Utilizing these genes, we applied multiple machine-learning algorithms for sophisticated feature selection and model construction. The ITHCS model significantly outperforms existing prognostic indicators in accuracy and generalizability, markedly reducing sampling biases caused by intratumor heterogeneity. This improvement is especially notable in the prognostic assessment of early-stage ESCC patients, where the model exhibits exceptional predictive power. Additionally, we found that the risk score based on ITHCS may be associated with epithelial-mesenchymal transition characteristics, indicating that high-risk patients may exhibit a diminished efficacy to immunotherapy.
Queer voices in computational biology: the first ISCB LGBTQI+ Symposium
Authors: Parra R Gonzalo , Wass Mark N , Munholland Seth , Wiper Mallory L , Kovats Diane , Pantano Lorena , Dunbrack Roland L 
Published: December 2024

Abstract
The first ISCB LGBTQI+ Symposium, held during Pride Month in 2024, marked a significant milestone for the International Society for Computational Biology (ISCB) community to promote diversity. This event aimed to provide a safe and supportive space for LGBTQI+ members of the society to share their experiences, address unique challenges in Bioinformatics and Computational Biology, and foster strategies for creating an equitable environment within ISCB. Through keynote presentations, short talks, and a roundtable discussion, participants explored topics such as minority stress, visibility, and the impact of role models. The symposium was rooted in a recognition of the historical and ongoing marginalization faced by LGBTQI+ individuals and sought to challenge systemic barriers while emphasizing the importance of community and representation. This article details the journey behind organizing the symposium, including overcoming the challenges of ensuring inclusivity and privacy, and highlights the profound impact of role models and collective action in advancing LGBTQI+ equity in science.
Genetic signature of demographic history explains the current sympatric distribution of sibling species of Craseomys (Rodentia: Arvicolinae)
Authors: Saitoh Takashi , Murakami Shota , de Guia Anna Pauline O , Ohnishi Naoki , Kawai Kuniko 
Published: December 2024

Abstract
Sequences of mitochondrial DNA were analysed in two vole species (Craseomys rex and Craseomys rufocanus), which are closely related based on phylogeny, morphology, and ecology. In Hokkaido, Japan, they occur sympatrically in forests, but Craseomys rufocanus also inhabits open fields. Capture records of 2532 specimens from 114 localities confirmed the widespread and fragmented distribution of Craseomys rufocanus and Craseomys rex and indicated that abundance of Craseomys rufocanus was 9.2–19.8 times higher than that of Craseomys rex. The phylogenetic tree illustrated four regional clades for Craseomys rex, but no distinct clades for Craseomys rufocanus. The observed mismatch distribution of Craseomys rufocanus matched with a spatial expansion model, indicating population expansion through range extension with frequent migration. Using 47 haplotypes from 151 Craseomys rex and 302 haplotypes from 1037 Craseomys rufocanus, a skyline plot revealed that Craseomys rufocanus increased during the Last Glacial Cycle (LGC) when grassy vegetation dominated forests. Craseomys rex expanded following forest recovery following LGC survival. The current effective population size (Ne) of Craseomys rufocanus was 15.9–33.8 times higher than that of Craseomys rex, in good agreement with capture records. Population expansion of Craseomys rufocanus during the LGC resulted in range extension and its current distribution, whereas the current range of Craseomys rex was derived from glacial refugia.
Morbidity and Mortality Risk Among People With Human Immunodeficiency Virus and Central or Visceral Adiposity: A Targeted Literature Review
Authors: Bjornson Alison M , Bedimo Roger J , Szabo Shelagh M , Rochon Hannah , Lee Daniel 
Published: December 2024

Abstract

Background
Given the known relationship between human immunodeficiency virus (HIV), antiretroviral therapies, and excess visceral adipose tissue (VAT), this review sought to characterize risk of negative health outcomes associated with excess VAT and increased waist circumference (WC) in people with HIV (PWH).

Methods
Comprehensive targeted literature searches were conducted in Medline/Embase (27 June 2022), identifying peer-reviewed articles and conference abstracts reporting on cohorts of PWH. Screening was guided by PECOS (Population, Exposure, Comparator, Outcomes, Study design) criteria. From the included studies, outcomes of interest including mortality and morbidity risk by VAT area and WC were extracted, overall, and by sex, race/ethnicity, and duration of HIV. Relationships between outcome and exposure variables were summarized.

Results
Thirty-five studies were included (sample size range: 31–1748 PWH). Twenty-five studies characterized the relationship between increased WC and negative health outcomes—cardiovascular disease (CVD), arteriosclerosis, hypertension, diabetes, hepatic fat and fibrosis, and cognitive impairment—among PWH. Fifteen studies reported on increased VAT and negative health outcomes: all-cause mortality, CVD, atherosclerosis, hepatic fat, and fibrosis. Importantly, there was a 2.1-times higher odds of 5-year all-cause mortality among PWH with the highest amount of VAT in the only study identified reporting on mortality. Among the studies characterizing the relationship between morbidity and VAT, for example, 1 found that, for each 10-cm2 increase in VAT, the risk of prevalent CVD increased by 1.05 (95% CI: 1.0–1.1) times.

Conclusions
WC may be a useful and cost-effective surrogate for visceral adiposity, which is an important marker of morbidity and mortality among PWH.
Admiring the Greeks with Roman eyes: F. A. Wolf, Quintilian, and the Latin roots of German philhellenism
Authors: Loporcaro Laura 
Published: December 2024

Abstract
This paper argues for the underlying importance of Latin learning in a key text of German philhellenism, Friedrich August Wolf’s ‘Darstellung der Alterthums-Wissenschaft’ (1807). It contends that Wolf supported his educational authority by modelling himself on the Roman rhetorical writer Quintilian, and that he drew on him to formulate the notion of a philological encyclopaedia. First, this paper uncovers how Wolf’s self-staging at the start of the ‘Darstellung’ channels Quintilian’s Institutio oratoria. Then, it shows that Wolf argued that Altertumswissenschaft was ‘scientific’ because it was ‘encyclopaedic’, and that he drew on Quintilian not necessarily to conceptualize, but to formulate, this conception. Uncovering the presence of Quintilian in Wolf’s ‘Darstellung’, an influential programmatic text that asserted the superiority of Greece over Rome, this paper argues for the persistence of Latin learning, just as it was dismissed, as a key irony underlying this foundational work of modern classical philology.
The Migrant Mother’s Silence in Her Mother Tongue as a Mothering Strategy
Authors: Kačkutė Eglė 
Published: December 2024

Abstract
Historically silenced, literary mothers’ voices are finally now being given their due, but it is noteworthy that migrant mothers’ literary voices are yet to be fully heard. This essay focuses on literary representations of migrant mothers who refuse to speak their own mother tongue to their children. It looks at two texts by women writers originating directly or indirectly from two post-Soviet Baltic states, Estonia and Lithuania. The texts in question are the novel Stalinin lehmät (Stalin’s Cows) (2003) by Sofi Oksanen and the essay “Motinų tylėjimas” (“The Silence of the Mothers”) (2004) by Dalia Staponkutė. Drawing on postcolonial theory, memory studies, and transnational feminist theory, I suggest that the migrant mother’s silence in her own mother tongue connotes several unarticulated realities: the trauma of colonization, the negotiation of post-Soviet migrant femininity, and patriarchal gender regimes. I argue that the migrant mothers represented in both texts withhold their mother tongue as a mothering strategy designed to socialize their children to successfully negotiate the transnational, multilingual spaces they will navigate as adults.
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse
Authors: Wang Wenqing , Zhao Xinyu , Ma Tianyu , Zhong Tengwei , Zheng Junnuo , Guo Zhiyun 
Published: December 2024

Abstract
Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Investigating eccDNA at the single-cell level is crucial for understanding cellular heterogeneity, evolution, development, and specific cellular functions. However, high-throughput identification methods for single-cell eccDNA are complex, and the lack of mature, widely applicable technologies has resulted in limited resources. To address this gap, we built scEccDNAdb, a database based on single-cell whole-genome sequencing data. It contains 3 195 464 single-cell eccDNA entries from human and mouse samples, with annotations including oncogenes, typical enhancers, super-enhancers, CCCTC-binding factor-binding sites, single nucleotide polymorphisms, chromatin accessibility, expression quantitative trait loci, transcription factor binding sites, motifs, and structural variants. Additionally, it provides nine online analysis and visualization tools, which enable the creation of publication-quality figures through user-uploaded files. Overall, scEccDNAdb is a comprehensive database for analyzing single-cell eccDNA data across diverse cell types, tissues, and species.
Database URL: https://lcbb.swjtu.edu.cn/scEccDNAdb/
Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum)
Authors: Sato Mitsuhiko P , Arafa Ramadan A , Rakha Mohamed T , Emeran Amero A , Isobe Sachiko , Shirasawa Kenta 
Published: December 2024

Abstract
Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt in 5,5000 BCE and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for 2 Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging 2 contigs. The total length of the resultant chromosome-level assemblies was 547.7 Mb for Helaly and 536.3 Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between 2 cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.
The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani
Authors: Nomosatryo Sulung , Lipus Daniel , Bartholomäus Alexander , Henny Cynthia , Ridwansyah Iwan , Sujarta Puguh , Yang Sizhong , Wagner Dirk , Kallmeyer Jens 
Published: December 2024

Abstract
Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here, we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes, and Cyanobacteria, which could be attributed to pollution and eutrophication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia, and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.
Focusing on Caregiver Neglect: A Novel Strategy for Mistreatment of Older Adults Screening and Intervention
Authors: Rosen Tony , Shaw Amy , Elman Alyssa , Baek Daniel , Gottesman Elaine , Park Sophie , Costantini Helena , Cury Hincapie Mariana , Chang E-Shien , Hancock David , Jaret Adrienne D , Lees Haggerty Kristin , Burnes David , Lachs Mark S , Pillemer Karl , Czaja Sara J 
Published: December 2024

Abstract
Mistreatment of older adults is common and has serious health consequences but is underrecognized and underreported. Screening for mistreatment of older adults and initiation of intervention in primary care clinics may be helpful, but the value of existing tools is not supported by evidence. We argue that shifting the focus to individual subtypes of mistreatment of older adults can provide improved approaches to screening and ultimately to intervention. We focus on the example of caregiver neglect, the subtype associated with highest mortality. To develop caregiver neglect screening and intervention programs and to measure their effectiveness and impact, we assert that it is critical to: (1) define the phenomenon, (2) develop a conceptual model to explain why it occurs, (3) develop measurement strategies, and (4) systematically examine existing literature. We describe here the initial components of this development process.
Thou Shalt Not Conduct Research on Software? Text and Data Mining of Computer Programs in the Current EU Copyright Framework
Authors: Widła Bohdan 
Published: December 2024

Abstract
The proliferation of generative AI has steered the discussion about text and data mining (TDM) in copyright law towards the problem of generative models. However, generative AI is not the only case for TDM. Mining data from computer programs can improve defect detection, discover design patterns, facilitate maintenance, summarize code in natural language or identify security vulnerabilities. The potential of such research, and the risk of skewing its results due to inadequate data justifies a venture into the scope of permitted TDM activities in relation to software.
This article explores the intersection of TDM and the protection of computer programs in EU copyright law, focusing on the reproduction and alteration rights under the Software Directive. It argues that although among the new TDM exceptions and limitations in the Directive on Copyright in the Digital Single Market only the general one explicitly mentions computer programs, the research exception can also be applied if implemented carefully. This article also shows that computer programs can be reproduced in a way relevant to copyright law during TDM activities aimed at extracting data from traditional literary or artistic works. It offers an interpretation of Art. 5(1) of the Software Directive that prevents the misusing of copyright to thwart TDM in such scenarios. Finally, it analyses the diverging implementation strategies of TDM provisions adopted by EU Member States in the context of computer programs. By examining these issues, this article aims to clarify the scope of permissible TDM activities and advocate for policies that support research.
Integrated multi-omics analysis revealed the molecular networks and potential targets of cellular senescence in Alzheimer’s disease
Authors: Xu Yudi , Liu Shutong , Zhou Zhaokai , Qin Hongzhuo , Zhang Yuyuan , Zhang Ge , Ma Hongxuan , Han Xinwei , Liu Huimin , Liu Zaoqu 
Published: December 2024

Abstract
Cellular senescence (CS) is a hallmark of Alzheimer’s disease (AD). However, the mechanisms through which CS contributes to AD pathogenesis remain poorly understood. We found that CS level in AD was higher compared with the healthy control group. Transcriptome-based differential expression analysis identified 113 CS-related genes in blood and 410 in brain tissue as potential candidate genes involved in AD. To further explore the causal role of these genes, an integrative mendelian randomization analysis was conducted, combining AD genome-wide association study summary statistics with expression quantitative trait loci (eQTL) and DNA methylation quantitative trait loci (mQTL) data from blood samples, which identified five putative AD-causal genes (CENPW, EXOSC9, HSPB11, SLC44A2, and SLFN12) and 18 corresponding DNA methylation probes. Additionally, integrative analysis between eQTLs and mQTLs from blood uncovered two genes and 12 corresponding regulatory elements involved in AD. Furthermore, two genes (CDKN2B and ITGAV) were prioritized as putative causal genes in brain tissue and were validated through in vitro experiments. The multi-omics integration study revealed the potential role and underlying biological mechanisms of CS driven by genetic predisposition in AD. This study contributed to fundamental understanding of CS in AD pathogenesis and facilitated the identification of potential therapeutic targets for AD prevention and treatment.
Increased risk of subsequent antiphospholipid syndrome in patients with endometriosis
Authors: Chen Zhiyong , Cui Ran , Wang Shiow-Ing , Zhang Hua , Chen Miao , Wang Qian , Tong Qiang , Wei James Cheng-Chung , Dai Sheng-Ming 
Published: December 2024

Abstract

Background
Although autoimmune abnormalities are common in patients with endometriosis, it is unknown whether patients with endometriosis have a higher risk of developing antiphospholipid syndrome (APS).

Methods
We conducted a retrospective cohort study by using the multi-institutional research network TriNetX from 1 January 2012 to 31 December 2021. A total of 13 131 782 women aged 20–60 years from networks within the USA were included. The risks of APS were compared between an endometriosis cohort and a non-endometriosis cohort in subgroup analyses by age, obesity and systemic lupus erythematosus (SLE), and the sensitivity analysis was stratified by the presence or absence of a history of surgery of the uterus.

Results
After 1:1 propensity score matching, the endometriosis and non-endometriosis cohorts each included 50 078 participants. Compared to individuals without endometriosis, patients with endometriosis had a higher risk of incident APS (log-rank test, P &lt; 0.001). The hazard ratios (HRs) ranged from 1.82 [APS within 30 days to 1 year after the index date, 95% confidence intervals (CIs) 1.40–2.53] to 2.44 (APS within 30 days to any time after the index date, 95% CI 1.65–3.61). In the subgroup analyses, an increased risk of APS was observed in all ages, White race, and subgroups without smoking, obesity, asthma, inflammatory bowel disease and SLE (HR range 1.85–2.84). Sensitivity analyses revealed that the risk of APS increased in patients without surgery history of the uterus.

Conclusions
Patients with endometriosis had a higher risk (2.84-fold) of developing APS. Future large-scale prospective studies are warranted to confirm our results.