bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses
Authors: Campelo Felipe , de Oliveira Ana Laura Grossi , Reis-Cunha João , Fraga Vanessa Gomes , Bastos Pedro Henrique , Ashford Jodie , Ekárt Anikó , Adelino Talita Emile Ribeiro , Silva Marcos Vinicius Ferreira , de Melo Iani Felipe Campos , de Jesus Augusto César Parreiras , Bartholomeu Daniella Castanheira , de Souza Trindade Giliane , Fujiwara Ricardo Toshio , Bueno Lilian Lacerda , Lobo Francisco Pereira 
Published: November 2024

Abstract
We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.
IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction
Authors: Kushwaha Anjana , Duroux Patrice , Giudicelli Véronique , Todorov Konstantin , Kossida Sofia 
Published: November 2024

Abstract
The accurate prediction of peptide-major histocompatibility complex (MHC) class I binding probabilities is a critical endeavor in immunoinformatics, with broad implications for vaccine development and immunotherapies. While recent deep neural network based approaches have showcased promise in peptide-MHC (pMHC) prediction, they have two shortcomings: (i) they rely on hand-crafted pseudo-sequence extraction, (ii) they do not generalize well to different datasets, which limits the practicality of these approaches. While existing methods rely on a 34 amino acid pseudo-sequence, our findings uncover the involvement of 147 positions in direct interactions between MHC and peptide. We further show that neural architectures can learn the intricacies of pMHC binding using even full sequences. To this end, we present PerceiverpMHC that is able to learn accurate representations on full-sequences by leveraging efficient transformer based architectures. Additionally, we propose IMGT/RobustpMHC that harnesses the potential of unlabeled data in improving the robustness of pMHC binding predictions through a self-supervised learning strategy. We extensively evaluate RobustpMHC on eight different datasets and showcase an overall improvement of over 6% in binding prediction accuracy compared to state-of-the-art approaches. We compile CrystalIMGT, a crystallography-verified dataset presenting a challenge to existing approaches due to significantly different pMHC distributions. Finally, to mitigate this distribution gap, we further develop a transfer learning pipeline.
STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data
Authors: Ran Peng , Wang Yunzhi , Li Kai , He Shiman , Tan Subei , Lv Jiacheng , Zhu Jiajun , Tang Shaoshuai , Feng Jinwen , Qin Zhaoyu , Li Yan , Huang Lin , Yin Yanan , Zhu Lingli , Yang Wenjun , Ding Chen 
Published: November 2024

Abstract
Mass spectrometry (MS)-based proteomics has become instrumental in comprehensively investigating complex biological systems. Data-independent acquisition (DIA)-MS, utilizing hybrid spectral library search strategies, allows for the simultaneous quantification of thousands of proteins, showing promise in enhancing protein identification and quantification precision. However, low-quality profiles can considerably undermine quantitative precision, resulting in inaccurate protein quantification. To tackle this challenge, we introduced STAVER, a novel algorithm that leverages standardized benchmark datasets to reduce non-biological variation in large-scale DIA-MS analyses. By eliminating unwanted noise in MS signals, STAVER significantly improved protein quantification precision, especially in hybrid spectral library searches. Moreover, we validated STAVER’s robustness and applicability across multiple large-scale DIA datasets, demonstrating significantly enhanced precision and reproducibility of protein quantification. STAVER offers an innovative and effective approach for enhancing the quality of large-scale DIA proteomic data, facilitating cross-platform and cross-laboratory comparative analyses. This advancement significantly enhances the consistency and reliability of findings in clinical research. The complete package is available at https://github.com/Ran485/STAVER.
Zygotic activin A is dispensable for the mouse preimplantation embryo development and for the derivation and pluripotency of embryonic stem cells
Authors: Winek Eliza , Wolińska-Nizioł Lidia , Szczepańska Katarzyna , Szpakowska Anna , Gewartowska Olga , Wysocka Izabela , Grzesiak Magdalena , Suwińska Aneta 
Published: November 2024

Abstract
In this work, we aimed to determine the role of activin A during crucial events of mouse embryogenesis and distinguish the function of the protein of zygotic origin and the one secreted by the maternal reproductive tract. To this end, we recorded the progression of development and phenotype of Inhba knockout embryos and compared them with the heterozygotes and wild-type embryos using time-lapse imaging and detection of lineage-specific markers. We revealed that the zygotic activin A deficiency does not impair the course and rate of development of embryos to the blastocyst stage. Inhba knockout embryos form functional epiblast, as evidenced by their ability to give rise to embryonic stem cells. Our study is the first to show that derivation, maintenance in culture, and pluripotency of embryo-derived embryonic stem cells are exogenous and endogenous activin A independent. However, the implantation competence of activin A–deficient embryos may be compromised as indicated in the outgrowth assay.
Outcomes of elective open surgical repair or fenestrated endovascular aneurysm repair for juxtarenal abdominal aortic aneurysms in Sweden
Authors: Yu Harry H Y , Asciutto Giuseppe , Dias Nuno , Wanhainen Anders , Karelis Angelos , Sonesson Björn , Mani Kevin 
Published: November 2024

Abstract

Background
A juxtarenal abdominal aortic aneurysm is defined as a short (less than 4 mm) or no-neck aneurysm, which is often treated with open or complex endovascular repair. The evidence to support the best treatment strategy is scarce. The aim of this study was to assess the short- and mid-term outcomes of elective open surgical repair or fenestrated endovascular aneurysm repair for juxtarenal abdominal aortic aneurysms in Sweden.

Methods
Patients who underwent elective open surgical repair or fenestrated endovascular aneurysm repair for juxtarenal abdominal aortic aneurysms between 2018 and 2021 were identified in the Swedish Vascular Registry. Demographics, practice patterns, and operative details were assessed. The primary outcome was 30-day mortality. Secondary outcomes included perioperative complications and mid-term survival.

Results
Among 3777 aortic aneurysm repairs performed, 418 involved juxtarenal abdominal aortic aneurysms (open surgical repair 228 (54.5%), fenestrated endovascular aneurysm repair 176 (42.1%), chimney endovascular aneurysm repair 6 (1.4%), and branched endovascular aneurysm repair 8 (1.9%)). Some 25 centres performed juxtarenal abdominal aortic aneurysm repairs with open surgical repair and fenestrated endovascular aneurysm repair. The caseload varied from 2 to 54 repairs per centre. The mean aneurysm diameter was 61 mm. Endovascularly treated patients were older and had more pulmonary co-morbidities. The 30-day mortality rate was 2.2% (open surgical repair 2.6% and fenestrated endovascular aneurysm repair 1.7%; P = 0.397). Perioperative major complications occurred in 14.1% of patients (open surgical repair 19.3% and fenestrated endovascular aneurysm repair 7.4%; P &lt; 0.001) and perioperative vascular complications occurred in 12.1% of patients (open surgical repair 8.8% and fenestrated endovascular aneurysm repair 11.9%; P = 0.190). The survival rate (estimated using Kaplan–Meier analysis) at 1 year and 3 years was 93.1% and 85.9% respectively for open surgical repair and 95.2% and 80.9% respectively for fenestrated endovascular aneurysm repair (P = 0.477).

Conclusion
This nationwide study reveals considerable variations in volume and treatment strategy between Swedish centres performing juxtarenal abdominal aortic aneurysm repairs. Survival is comparable for open surgical repair and fenestrated endovascular aneurysm repair, although there are significant baseline demographic differences between patients selected for the two treatment modalities.
Tau, synapse loss and gliosis progress in an Alzheimer’s mouse model after amyloid-β immunotherapy
Authors: Welikovitch Lindsay A , Mate de Gerando Anastasie , Khasnavis Anita , Bhavsar Harshil , Meltzer Jonah C , Buée Luc , Chibnik Lori B , Bussiere Thierry , Hyman Bradley T 
Published: November 2024

Abstract
Preclinical studies assessing drugs for Alzheimer’s disease (AD) are conducted in animal models that usually display only one neuropathological feature of AD, whereas patients present with a complex combination of comorbidities and neuropathologies. Importantly, it is well established that amyloid-β (Aβ) plaque and tau tangle accumulation interact in a phase-dependent manner, making it difficult to predict how targeting one might influence the other, as well as downstream degeneration.
We developed a transgenic mouse model, APP/PS1xTau22, with progressive cortical Aβ deposition and hippocampal tau neurofibrillary inclusions, to investigate how both neuropathologies act jointly to bring about neural degeneration, synapse loss and glial phenotypes. We then assessed whether applying murine chimeric aducanumab, an anti-amyloid immunotherapy, could impact the synergistic relationship between amyloid and tau.
Drug treatment resulted in a ∼70% reduction in Aβ deposition in hippocampal and cortical areas and produced a robust peri-plaque microglial and astrocytic response. Removing amyloid from the brain did not reverse or slow tau pathology or alter synapse loss.
Our findings suggest that, once the interaction between amyloid and tau is set in motion, reducing plaque burden by Aβ immunotherapy may stimulate glial responses, but is insufficient to curb degenerative phenotypes in this model.
Luminescent anthracene-based elastic mixed molecular crystals for flexible and FRET-assisted optical waveguides
Authors: Ikeda Koki , Matsuo Takumi , Yano Keigo , Hayashi Shotaro 
Published: November 2024

Abstract
Optical waveguides based on elastic molecular crystals are of interest as flexible and compact optical communication materials. Low emission efficiency is often a problem in terms of communication signal strength, and an increase in the loss factor α due to fluorescence reabsorption in the crystal reduces the photon transport efficiency. Here, we report the development and improvement of Förster resonance energy transfer (FRET)-assisted optical waveguides using anthracene-based elastic mixed molecular crystals. 9,10-Dicyanoanthracene was selected as the dopant for solution-grown crystallization of 9,10-dibromoanthracene. 1H NMR measurements of the obtained crystals showed that the acceptor doping to be 1% to 5%. Elastic behavior was observed even when doped with a few percent of the acceptor. The quantum efficiency was 0.016, a dramatic improvement over the previous luminescent elastic mixed molecular crystals (0.004). The α value (92 dB/cm) of this crystal containing 1%-doped 9,10-dicyanoanthracene is much lower than that of the crystal consisting of only 9,10-dibromoanthracene (1258 dB/cm) due to the reduced reabsorption in the FRET system. We have demonstrated a practical approach toward developing improved fluorescent, highly efficient, and flexible optical waveguides by constructing the mixed crystal structure by selecting appropriate acceptor molecules and their low doping ratios.
Preliminary assessment of the accuracy of cutaneous T-cell lymphoma diagnosis through deep sequencing of the TRG gene
Authors: Hong Jin-Bon , Hsieh Tyng-Shiuan , Tsai Tsen-Fang , Liau Jau-Yu , Chiu Hsien-Ching , Lee Tung-Lung , Huang Tai-Chung 
Published: November 2024

Abstract

Background
The diagnostic challenges in early mycosis fungoides (MF) and other cutaneous T-cell lymphomas (CTCLs) persist despite advancements in molecular methods.

Objectives
To provide a preliminary assessment of next-generation sequencing (NGS) in analysing TRG (T-cell receptor gamma locus) sequences for distinguishing CTCLs from benign inflammatory skin disorders.

Methods
NGS was used to assess TRG sequences in skin samples from clinicopathologically proven CTCLs and benign inflammatory skin disorders.

Results
Our study analysed skin samples from a total of 36 participants, comprising 22 cases of CTCL, including 14 MF and 8 other CTCLs, alongside 14 cases of benign inflammatory skin disorders. According to LymphoTrack® criteria, monoclonality was detected in 16 (73%) of the 22 patients with CTCL. Specifically, in cases of MF, 10 of 14 (71%) were identified as monoclonal, with all 4 non-monoclonal cases being in the patch stage. For the other cases of CTCL, six of eight displayed monoclonality. Among the 22 patients with CTCL, 10 (45%) had multiple biopsies, with 8 (36%) displaying the same dominant clone across different sites. Among the 14 benign cases, only the case of erythrodermic psoriasis exhibited monoclonality. Our decision tree analysis suggests that a high frequency of the most abundant clone, its ratio to the third most abundant clone and TRG VγI segment usage are effective markers that can help in the diagnosis of CTCL.

Conclusions
A combination of the clone frequencies and TRG V segment usage may enhance diagnosis of MF and other CTCLs, helping to differentiate them from benign conditions. However, molecular diagnosis for patch-stage MF remains challenging.
Clinical mechanism of muscle mass loss during neoadjuvant chemotherapy in older patients with esophageal cancer: a prospective cohort study
Authors: Harada Tsuyoshi , Tsuji Tetsuya , Ueno Junya , Konishi Nobuko , Yanagisawa Takumi , HIjikata Nanako , Ishikawa Aiko , Hashimoto Kakeru , Kagaya Hitoshi , Tatematsu Noriatsu , Zenda Sadamoto , Kotani Daisuke , Kojima Takashi , Fujita Takeo 
Published: November 2024

Abstract
In older patients with locally advanced esophageal cancer (LAEC), loss of skeletal muscle mass during neoadjuvant chemotherapy (NAC) is associated with poor clinical outcomes. This study aimed to investigate factors associated with loss of skeletal muscle mass during NAC in older patients with LAEC. This was a single-center exploratory prospective cohort study. Consecutive patients aged ≥65 years with LAEC scheduled for curative esophagectomy after NAC were enrolled between October 2021 and December 2023. As a primary endpoint, loss of skeletal muscle mass index (ΔSMI: pre-NAC minus post-NAC value) was calculated from computed tomography images before and after NAC. Significant pre-NAC and during-NAC factors with ΔSMI were detected with a multivariate regression model. Statistical significance was considered as two-tailed P &lt;0.05. A total of 69 patients were analyzed. The mean age was 72.9 years, and 53 (77%) were male. Mean SMI before and after NAC was 43.1 and 40.9 cm2/m2, and mean ΔSMI was 2.2 cm2/m2. In multivariate analysis, ΔSMI was associated with increased sitting time during NAC (per 1 min/day, adjusted coefficient 0.007, 95% confidence interval [CI] 0.001 to 0.013, P = 0.016), decreased Geriatric Nutritional Risk Index during NAC (per 1 score, adjusted coefficient −0.146, 95% CI −0.213 to −0.013, P = 0.002), and worsening decreased appetite during NAC (vs. no worsening, adjusted coefficient 1.571, 95% CI 0.279 to 2.862, P = 0.018). It was hypothesized that the inactivity-related mechanism and malnutrition-related mechanism are important for skeletal muscle mass loss during NAC in older patients with LAEC.
Employer Screening and Optimal Unemployment Insurance
Authors: Meier Mario , Obermeier Tim 
Published: November 2024

Abstract
Field experiments show that employers are less likely to consider long-term unemployed job seekers for interviews. We study the implications for optimal unemployment insurance. Based on a structural model of job search and recruitment, estimated with German data, we analyse the optimal two-tier unemployment system. We find that screening makes the optimal initial benefit level 4 percentage points higher and the potential benefit duration seven months longer. Using an extended Baily–Chetty formula, we study the mechanisms through which screening affects the consumption smoothing gain and moral hazard cost of providing unemployment insurance and highlight the role of the externality from endogenous firm behaviour.
Can survey design reduce anchoring bias in recall data? Evidence from smallholder farmers in Malawi
Authors: Godlonton Susan , Hernandez Manuel A , Paz Cynthia 
Published: November 2024

Abstract
Recall biases in retrospective self-reported survey data have important implications for empirical research. We leverage the survey design literature and test three strategies to attenuate mental anchoring in retrospective data collection: question ordering, retrieval cues and aggregate (community) anchoring. We focus on maize production and happiness reports among smallholder farmers in Malawi. Asking for retrospective before concurrent data on average reduces recall bias (i.e. the deviation of the recalled versus the concurrent outcome reported in the previous period) by 34 per cent for maize production, a meaningful improvement with no increase in data collection costs. Retrieval cues are less successful and community anchors can exacerbate the bias. None of the strategies help to ease the recall bias for happiness reports.
Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China
Authors: Hu Xueqian , Bi Jie , Yu Qiaoling , Li Huan 
Published: November 2024

Abstract
Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.
Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim
Authors: Markowitz Lindsey M , Nearman Anthony , Zhao Zexuan , Boncristiani Dawn , Butenko Anzhelika , de Pablos Luis Miguel , Marin Arturo , Xu Guang , Machado Carlos A , Schwarz Ryan S , Palmer-Young Evan C , Evans Jay D 
Published: November 2024

Abstract
Lotmaria passim is a ubiquitous trypanosomatid parasite of honey bees nestled within the medically important subfamily Leishmaniinae. Although this parasite is associated with honey bee colony losses, the original draft genome—which was completed before its differentiation from the closely related Crithidia mellificae—has remained the reference for this species despite lacking improvements from newer methodologies. Here, we report the updated sequencing, assembly, and annotation of the BRL-type (Bee Research Laboratory) strain (ATCC PRA-422) of Lotmaria passim. The nuclear genome assembly has been resolved into 31 complete chromosomes and is paired with an assembled kinetoplast genome consisting of a maxicircle and 30 minicircle sequences. The assembly spans 33.7 Mb and contains very little repetitive content, from which our annotation of both the nuclear assembly and kinetoplast predicted 10,288 protein-coding genes. Analyses of the assembly revealed evidence of a recent chromosomal duplication event within chromosomes 5 and 6 and provided evidence for a high level of aneuploidy in this species, mirroring the genomic flexibility employed by other trypanosomatids as a means of adaptation to different environments. This high-quality reference can therefore provide insights into adaptations of trypanosomatids to the thermally regulated, acidic, and phytochemically rich honey bee hindgut niche, which offers parallels to the challenges faced by other Leishmaniinae during the challenges they undergo within insect vectors, during infection of mammals, and exposure to antiparasitic drugs throughout their multi-host life cycles. This reference will also facilitate investigations of strain-specific genomic polymorphisms, their role in pathogenicity, and the development of treatments for pollinator infection.