bluuebunny/crossref_metadata_2025_split huggingface dataset:
TEINet: a deep learning framework for prediction of TCR–epitope binding specificity
Authors: Jiang Yuepeng , Huo Miaozhe , Cheng Li Shuai 
Published: March 2023

AbstractThe adaptive immune response to foreign antigens is initiated by T-cell receptor (TCR) recognition on the antigens. Recent experimental advances have enabled the generation of a large amount of TCR data and their cognate antigenic targets, allowing machine learning models to predict the binding specificity of TCRs. In this work, we present TEINet, a deep learning framework that utilizes transfer learning to address this prediction problem. TEINet employs two separately pretrained encoders to transform TCR and epitope sequences into numerical vectors, which are subsequently fed into a fully connected neural network to predict their binding specificities. A major challenge for binding specificity prediction is the lack of a unified approach to sampling negative data. Here, we first assess the current negative sampling approaches comprehensively and suggest that the Unified Epitope is the most suitable one. Subsequently, we compare TEINet with three baseline methods and observe that TEINet achieves an average AUROC of 0.760, which outperforms baseline methods by 6.4–26%. Furthermore, we investigate the impacts of the pretraining step and notice that excessive pretraining may lower its transferability to the final prediction task. Our results and analysis show that TEINet can make an accurate prediction using only the TCR sequence (CDR3$\beta $) and the epitope sequence, providing novel insights to understand the interactions between TCRs and epitopes.
scAnnotate: an automated cell-type annotation tool for single-cell RNA-sequencing data
Authors: Ji Xiangling , Tsao Danielle , Bai Kailun , Tsao Min , Xing Li , Zhang Xuekui 
Published: March 2023

AbstractMotivationSingle-cell RNA-sequencing (scRNA-seq) technology enables researchers to investigate a genome at the cellular level with unprecedented resolution. An organism consists of a heterogeneous collection of cell types, each of which plays a distinct role in various biological processes. Hence, the first step of scRNA-seq data analysis is often to distinguish cell types so they can be investigated separately. Researchers have recently developed several automated cell-type annotation tools, requiring neither biological knowledge nor subjective human decisions. Dropout is a crucial characteristic of scRNA-seq data widely used in differential expression analysis. However, no current cell annotation method explicitly utilizes dropout information. Fully utilizing dropout information motivated this work.ResultsWe present scAnnotate, a cell annotation tool that fully utilizes dropout information. We model every gene’s marginal distribution using a mixture model, which describes both the dropout proportion and the distribution of the non-dropout expression levels. Then, using an ensemble machine learning approach, we combine the mixture models of all genes into a single model for cell-type annotation. This combining approach can avoid estimating numerous parameters in the high-dimensional joint distribution of all genes. Using 14 real scRNA-seq datasets, we demonstrate that scAnnotate is competitive against nine existing annotation methods. Furthermore, because of its distinct modelling strategy, scAnnotate’s misclassified cells differ greatly from competitor methods. This suggests using scAnnotate together with other methods could further improve annotation accuracy.Availability and implementationWe implemented scAnnotate as an R package and made it publicly available from CRAN: https://cran.r-project.org/package=scAnnotate.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
Decreasing incidence of dialysis in older patients in The Netherlands as compared with other European countries: an international perspective
Authors: van Oevelen Mathijs , Abrahams Alferso C , Hoekstra Tiny , ten Dam Marc A G J , Kramer Anneke , Jager Kitty J , Ocak Gurbey , van Buren Marjolijn , Bos Willem Jan W 
Published: March 2023

ABSTRACT

Introduction
After decades of increasing dialysis incidence, we observed a decreasing trend in the Netherlands in the last decade. We compared this trend with trends in other European countries.

Materials and Methods
Aggregated data for calendar years 2001–2019 from the Dutch registries of kidney replacement therapy patients and the European Renal Association Registry were used. Dialysis incidence in the Netherlands was compared with that in 11 other European countries/regions using three age groups: 20–64, 65–74, and ≥75 years, taking into account pre-emptive kidney transplantation (PKT) incidence. Time trends were assessed as annual percentage change (APC) with 95% confidence intervals (CI) using joinpoint regression analysis.

Results
Between 2001 and 2019 the Dutch dialysis incidence decreased slightly among patients aged 20–64 years (APC −0.9, 95% CI −1.4; −0.5). For patients 65–74 and ≥75 years old, a peak was seen in 2004 and 2009, respectively. Afterwards, the decrease was most marked in patients aged ≥75 years: APC −3.2 (−4.1; −2.3) versus APC −1.8 (−2.2; −1.3) for patients 65–74 years old. PKT incidence increased significantly during the study period but remained limited compared to the observed decrease in dialysis incidence, especially among older patients. Large differences in dialysis incidence were observed among European countries/regions. A decreasing dialysis incidence among older patients was also seen in Austria, Denmark, England/Wales, Finland, Scotland, and Sweden.

Conclusions
The Dutch dialysis incidence decreased most profoundly among older patients. This was also observed in several other European countries/regions. Although PKT incidence increased, it can only explain a minor part of the decrease in dialysis incidence.
A New Fuzzy Smoothing Term Model For Stereo Matching
Authors: Hongjin Zhang , Hui Wei , Bo Wang 
Published: March 2023

Abstract
In this study, we construct a smoothing term structure, which is an essential part of the energy function in binocular matching. However, the existing energy models are mainly deterministic, which cannot adapt to processing low-quality images, especially when there exists a large proportion of vague areas. In order to perform better in processing these low-quality images, in this paper, we construct the smoothing term based on a fuzzy model, which includes fuzzy segmentation, the fuzzy network between the superpixels and the fuzzy relationship between the pixels. These can be compatible with the uncertainty in the image. In addition, to explain the rationality of the calculation of the degree of correlation between superpixels and further elaborate on the property of these degrees between each superpixel, we propose five corresponding theorems with proofs. After we solve the energy model combined with our proposed smoothing term, we compare our disparity results with the corresponding deterministic model and several state-of-the-art algorithms in the experiment. The results verify the effectiveness of the proposed algorithm.
Effectiveness and Safety of Vedolizumab in Inflammatory Bowel Disease: A Comprehensive Meta-analysis of Observational Studies
Authors: Macaluso Fabio Salvatore , Ventimiglia Marco , Orlando Ambrogio 
Published: March 2023

AbstractBackground and AimsMany observational studies on the use of vedolizumab [VDZ] in patients with Crohn’s disease [CD] and ulcerative colitis [UC] have been published in the past few years. We aimed to comprehensively summarise its effectiveness and safety by pooling data only from observational studies.MethodsPubMed/Medline and Embase were systematically searched for observational studies on patients with CD and UC treated with VDZ through December 2021. The rates of clinical remission and overall adverse events were the primary outcomes. The rates of steroid-free clinical remission, clinical response, mucosal healing, C-reactive protein normalisation, loss of response, VDZ dose escalation, colectomy, serious adverse events, infections, and malignancies were considered as secondary outcomes.ResultsIn all, 88 studies comprising 25 678 patients [13 663 with CD and 12 015 with UC] met the inclusion criteria. In patients with CD, the pooled estimate rates of clinical remission were 36% at induction and 39% at maintenance. In patients with UC, the pooled estimate rates of clinical remission were 40% at induction and 45% at maintenance. The pooled estimate of incidence rate of adverse events was 34.6 per 100 person-years. At multivariable meta-regression analysis, studies with increased male proportion were independently associated with higher rates of clinical remission and steroid-free clinical remission at both induction and maintenance, and clinical response at maintenance in patients with CD. Studies with increased disease duration were independently associated with higher mucosal healing rates at maintenance in patients with UC.ConclusionsObservational studies demonstrated extensively the effectiveness of VDZ, with a reassuring safety profile.
Isolation and molecular identification of nematode surface mutants with resistance to bacterial pathogens
Authors: O’Rourke Delia , Gravato-Nobre Maria J , Stroud Dave , Pritchett Emily , Barker Emily , Price Rebecca L , Robinson Sarah A , Spiro Simon , Kuwabara Patricia , Hodgkin Jonathan 
Published: March 2023

Abstract
Numerous mutants of the nematode Caenorhabditis elegans with surface abnormalities have been isolated by utilizing their resistance to a variety of bacterial pathogens (Microbacterium nematophilum, Yersinia pseudotuberculosis, and 2 Leucobacter strains), all of which are able to cause disease or death when worms are grown on bacterial lawns containing these pathogens. Previous work led to the identification of 9 srf or bus genes; here, we report molecular identification and characterization of a further 10 surface-affecting genes. Three of these were found to encode factors implicated in glycosylation (srf-2, bus-5, and bus-22), like several of those previously reported; srf-2 belongs to the GT92 family of putative galactosyltransferases, and bus-5 is homologous to human dTDP-D-glucose 4,6-dehydratase, which is implicated in Catel–Manzke syndrome. Other genes encoded proteins with sequence similarity to phosphatidylinositol phosphatases (bus-6), Patched-related receptors (ptr-15/bus-13), steroid dehydrogenases (dhs-5/bus-21), or glypiation factors (bus-24). Three genes appeared to be nematode-specific (srf-5, bus-10, and bus-28). Many mutants exhibited cuticle fragility as revealed by bleach and detergent sensitivity; this fragility was correlated with increased drug sensitivity, as well as with abnormal skiddy locomotion. Most of the genes examined were found to be expressed in epidermal seam cells, which appear to be important for synthesizing nematode surface coat. The results reveal the genetic and biochemical complexity of this critical surface layer, and provide new tools for its analysis.
Seascape Genomics and Phylogeography of the Sailfish (Istiophorus platypterus)
Authors: Ferrette Bruno Lopes da Silva , Coimbra Raphael T F , Winter Sven , De Jong Menno J , Williams Samuel Mackey , Coelho Rui , Rosa Daniela , Rotundo Matheus Marcos , Arocha Freddy , Mourato Bruno Leite , Mendonça Fernando Fernandes , Janke Axel 
Published: March 2023

AbstractPermeable phylogeographic barriers characterize the vast open ocean, boosting gene flow and counteracting population differentiation and speciation of widely distributed and migratory species. However, many widely distributed species consists of distinct populations throughout their distribution, evidencing that our understanding of how the marine environment triggers population and species divergence are insufficient. The sailfish is a circumtropical and highly migratory billfish that inhabits warm and productive areas. Despite its ecological and socioeconomic importance as a predator and fishery resource, the species is threatened by overfishing, requiring innovative approaches to improve their management and conservation status. Thus, we presented a novel high-quality reference genome for the species and applied a seascape genomics approach to understand how marine environmental features may promote local adaptation and how it affects gene flow between populations. We delimit two populations between the Atlantic and Indo-Western Pacific oceans and detect outlier loci correlated with sea surface temperature, salinity, oxygen, and chlorophyll concentrations. However, the most significant explanatory factor that explains the differences between populations was isolation by distance. Despite recent population drops, the sailfish populations are not inbred. For billfishes in general, genome-wide heterozygosity was found to be relatively low compared to other marine fishes, evidencing the need to counteract overfishing effects. In addition, in a climate change scenario, management agencies must implement state-of-the-art sequencing methods, consider our findings in their management plans, and monitor genome-wide heterozygosity over time to improve sustainable fisheries and the long-term viability of its populations.
The Effect of Developmental Pleiotropy on the Evolution of Insect Immune Genes
Authors: Williams Alissa M , Ngo Thi Minh , Figueroa Veronica E , Tate Ann T 
Published: March 2023

AbstractThe pressure to survive ever-changing pathogen exposure explains the frequent observation that immune genes are among the fastest evolving in the genomes of many taxa, but an intriguing proportion of immune genes also appear to be under purifying selection. Though variance in evolutionary signatures of immune genes is often attributed to differences in gene-specific interactions with microbes, this explanation neglects the possibility that immune genes participate in other biological processes that could pleiotropically constrain adaptive selection. In this study, we analyzed available transcriptomic and genomic data from Drosophila melanogaster and related species to test the hypothesis that there is substantial pleiotropic overlap in the developmental and immunological functions of genes involved in immune signaling and that pleiotropy would be associated with stronger signatures of evolutionary constraint. Our results suggest that pleiotropic immune genes do evolve more slowly than those having no known developmental functions and that signatures of constraint are particularly strong for pleiotropic immune genes that are broadly expressed across life stages. These results support the general yet untested hypothesis that pleiotropy can constrain immune system evolution, raising new fundamental questions about the benefits of maintaining pleiotropy in systems that need to rapidly adapt to changing pathogen pressures.
Distinct Wolbachia localization patterns in oocytes of diverse host species reveal multiple strategies of maternal transmission
Authors: Radousky Yonah A , Hague Michael T J , Fowler Sommer , Paneru Eliza , Codina Adan , Rugamas Cecilia , Hartzog Grant , Cooper Brandon S , Sullivan William 
Published: March 2023

Abstract
A broad array of endosymbionts radiate through host populations via vertical transmission, yet much remains unknown concerning the cellular basis, diversity, and routes underlying this transmission strategy. Here, we address these issues, by examining the cellular distributions of Wolbachia strains that diverged up to 50 million years ago in the oocytes of 18 divergent Drosophila species. This analysis revealed 3 Wolbachia distribution patterns: (1) a tight clustering at the posterior pole plasm (the site of germline formation); (2) a concentration at the posterior pole plasm, but with a significant bacteria population distributed throughout the oocyte; and (3) a distribution throughout the oocyte, with none or very few located at the posterior pole plasm. Examination of this latter class indicates Wolbachia accesses the posterior pole plasm during the interval between late oogenesis and the blastoderm formation. We also find that 1 Wolbachia strain in this class concentrates in the posterior somatic follicle cells that encompass the pole plasm of the developing oocyte. In contrast, strains in which Wolbachia concentrate at the posterior pole plasm generally exhibit no or few Wolbachia in the follicle cells associated with the pole plasm. Taken together, these studies suggest that for some Drosophila species, Wolbachia invade the germline from neighboring somatic follicle cells. Phylogenomic analysis indicates that closely related Wolbachia strains tend to exhibit similar patterns of posterior localization, suggesting that specific localization strategies are a function of Wolbachia-associated factors. Previous studies revealed that endosymbionts rely on 1 of 2 distinct routes of vertical transmission: continuous maintenance in the germline (germline-to-germline) or a more circuitous route via the soma (germline-to-soma-to-germline). Here, we provide compelling evidence that Wolbachia strains infecting Drosophila species maintain the diverse arrays of cellular mechanisms necessary for both of these distinct transmission routes. This characteristic may account for its ability to infect and spread globally through a vast range of host insect species.
The proposed role of MSL-lncRNAs in causing sex lability of female poplars
Authors: Mao Jinyan , Wei Suyun , Chen Yingnan , Yang Yonghua , Yin Tongming 
Published: March 2023

Abstract
Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity is also observed in many Populus species. Here we carried out a systematic study on a maleness-promoting gene, MSL, detected in the Populus deltoides genome. Our results showed that both strands of MSL contained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. deltoides did not have the male-specific MSL gene, a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome. Based on sequence alignment, the MSL sequence could be divided into three partial sequences, and heterologous expression of these partial sequences in Arabidopsis confirmed that they could promote maleness. Since activation of the MSL sequences can only result in female sex lability, we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.
AGO2a but not AGO2b mediates antiviral defense against infection of wild-type cucumber mosaic virus in tomato
Authors: Zhao Liling , Chen Yingfang , Xiao Xingming , Gao Haiying , Cao Jiamin , Zhang Zhongkai , Guo Zhongxin 
Published: March 2023

AbstractEvolutionarily conserved antiviral RNA interference (RNAi) mediates a primary antiviral innate immunity preventing infection of broad-spectrum viruses in plants. However, the detailed mechanism in plants is still largely unknown, especially in important agricultural crops, including tomato. Varieties of pathogenic viruses evolve to possess viral suppressors of RNA silencing (VSRs) to suppress antiviral RNAi in the host. Due to the prevalence of VSRs, it is still unknown whether antiviral RNAi truly functions to prevent invasion by natural wild-type viruses in plants and animals. In this research, for the first time we applied CRISPR-Cas9 to generate ago2a, ago2b, or ago2ab mutants for two differentiated Solanum lycopersicum AGO2s, key effectors in antiviral RNAi. We found that AGO2a but not AGO2b was significantly induced to inhibit the propagation of not only VSR-deficient Cucumber mosaic virus (CMV) but also wild-type CMV-Fny in tomato; however, neither AGO2a nor AGO2b regulated disease induction after infection with either virus. Our findings firstly reveal a prominent role of AGO2a in antiviral RNAi innate immunity in tomato and demonstrate that antiviral RNAi evolves to defend against infection of natural wild-type CMV-Fny in tomato. However, AGO2a-mediated antiviral RNAi does not play major roles in promoting tolerance of tomato plants to CMV infection for maintaining health.
Post-traumatic stress disorder among COVID-19-affected high-risk cardiac patients
Authors: Wesemann Ulrich , Sahebi Ali , Vogel Julia , Köhler Kai , Kupusovic Jana , Rassaf Tienush , Siebermair Johannes 
Published: March 2023

Abstract

Background
During the first coronavirus disease 2019 (COVID-19) wave there was a high prevalence of mental health impairments and post-traumatic stress disorder (PTSD), particularly in patients with comorbid cardiac diseases.

Methods
During waves 2–5, all hospitalized patients with cardiac problems and suspected COVID-19 were eligible to participate in this study.

Results
The prevalence of PTSD was 31.4% (n=48) in 153 participants. No age- and gender-related differences for PTSD were found.

Conclusions
The prevalence is lower than during the first wave but higher than in patients reported in other studies who were isolated at home. Routine mental health assessments are strongly recommended for patients at risk.
Adverse birth outcomes of adolescent and young adult women diagnosed with cancer during pregnancy
Authors: Betts Andrea C , Shay L Aubree , Lupo Philip J , Pruitt Sandi L , Roth Michael E , Allicock Marlyn A , Cohn Barbara A , Murphy Caitlin C 
Published: March 2023

Abstract

Background
We examined adverse birth outcomes among adolescent and young adult women diagnosed with cancer (AYA women, ages 15-39 years) during pregnancy.

Methods
We linked data from the Texas Cancer Registry, vital records, and Texas Birth Defects Registry to identify all singleton births to AYA women diagnosed during pregnancy from January 1999 to December 2016. We compared prevalence of adverse live birth outcomes between AYA women and women without cancer (matched 1:4 on age, race and ethnicity, and year). Among AYA women, we used log-binomial regression to identify factors associated with these outcomes. Statistical tests were 2-sided.

Results
AYA women had 1271 singleton live births and 20 stillbirths. AYA women (n = 1291) were 33.3% Hispanic and 9.8% non-Hispanic Black and most commonly had breast (22.5%), thyroid (19.8%), and gynecologic (13.3%) cancers. Among live births, AYA women had a higher prevalence of low birth weight offspring (30.1% vs 9.0%), very preterm (5.7% vs 1.2%), and preterm birth (25.1% vs 7.2%); cesarean delivery (44.3% vs 35.2%); and low Apgar score (2.7% vs 1.5%), compared with women without cancer (n = 5084) (all P &lt; .05). Prevalence of any birth defect by age 12 months did not statistically differ (5.2% vs 4.7%; P = .48), but live births to AYA women more often had heart and circulatory system defects (2.2% vs 1.3%; P = .01). In adjusted models, cancer type and chemotherapy were associated with adverse live birth outcomes.

Conclusions
AYA women diagnosed during pregnancy have higher prevalence of adverse birth outcomes and face difficult decisions in balancing treatment risks and benefits.
Phosphoglucomutase comes into the spotlight
Authors: Doello Sofía , Forchhammer Karl 
Published: March 2023

This article comments on:Ortega-Martínez P, Roldán M, Díaz-Troya S, Florencio FJ. 2023. Stress response requires an efficient glycogen and central carbon metabolism connection by phosphoglucomutases in cyanobacteria. Journal of Experimental Botany 74, 1532–1550