bluuebunny/crossref_metadata_2025_split huggingface dataset:
ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities
Authors: Li Douyue , Min Zhuochao , Guo Jia , Chen Yubin , Zhang Wenliang 
Published: April 2024

AbstractMotivationHigh-throughput technologies have yielded a broad spectrum of multi-omics datasets, offering unparalleled insights into complex biological systems. However, effectively analyzing this diverse array of data presents challenges, given factors such as species diversity, data types, costs, and limitations of available tools.ResultsWe propose ExpOmics, a comprehensive web platform featuring seven applications and four toolkits with 28 customizable analysis functions, spanning various aspects of differential expression, co-expression, WGCNA analysis, feature selection, and functional enrichment analysis. ExpOmics empowers users to effortlessly upload and explore multi-omics data without organism restriction, supporting a wide array of data types including gene, mRNA, lncRNA, miRNA, circRNA, piRNA, and protein expression data. It is compatible with diverse gene nomenclatures and expression value types. Moreover, ExpOmics enables users to comprehensive analysis of 22,427 transcriptomic datasets sourced from 63 projects and 196 cancer subtypes in TCGA, discovering cancer biomarkers and targets. The analysis results from ExpOmics are visually presented in high-quality graphical formats suitable for publication, available for free download. In summary, ExpOmics can serves as a robust platform for global researchers to delve into diverse expression datasets, gain biological insights, and formulate testable hypotheses.Availability and implementationExpOmics is available athttp://www.biomedical-web.com/expomics.
SARS-CoV-2 Omicron Envelope T9I adaptation confers resistance to autophagy
Authors: Klute Susanne , Nchioua Rayhane , Cordsmeier Arne , Vishwakarma Jyoti , Koepke Lennart , Alshammary Hala , Jung Christoph , Hirschenberger Maximilian , Hoenigsperger Helene , Fischer Jana-Romana , Zech Fabian , Stenger Steffen , Serra-Moreno Ruth , Gonzalez-Reiche Ana S. , Sordillo Emilia Mia , van Bakel Harm , Simon Viviana , Kirchhoff Frank , Jacob Timo , Kmiec Dorota , Pichlmair Andreas , Ensser Armin , Sparrer Konstantin MJ 
Published: April 2024

ABSTRACTTo date, five variants of concern (VOCs) of SARS-CoV-2 have emerged that show increased fitness and/or immune evasion. While the continuously evolving escape from humoral immune responses has been analyzed in detail, adaptation of SARS-CoV-2 to human innate immune defenses such as autophagy is less understood. Here, we demonstrate that mutation T9I in the structural envelope (E) protein confers autophagy resistance of Omicron VOCs (BA.1, BA.5 and XBB.1.5) compared to 2020 SARS-CoV-2 or the Delta VOC. Mechanistic analyses revealed that Omicron-associated E T9I shows increased inhibition of autophagic flux and colocalization/interaction with autophagosomes, thus shielding incoming SARS-CoV-2 S pseudotyped virions from autophagy. Rare Omicron isolates carrying ancestral E T9 remain sensitive towards autophagy whereas recombinant early 2020 SARS-CoV-2 expressing E T9I shows increases resistance against autophagy. Our data indicate that the E T9I mutation drives autophagy resistance of the Omicron variants and thus may have contributed to their effective spread.
Reproducible, data-driven characterization of sleep based on brain dynamics and transitions from whole-night fMRI
Authors: Yang Fan Nils , Picchioni Dante , de Zwart Jacco A. , Wang Yicun , van Gelderen Peter , Duyn Jeff H. 
Published: April 2024

AbstractUnderstanding the function of sleep requires studying the dynamics of brain activity across whole-night sleep and their transitions. However, current gold standard polysomnography (PSG) has limited spatial resolution to track brain activity. Additionally, previous fMRI studies were too short to capture full sleep stages and their cycling. To study whole-brain dynamics and transitions across whole-night sleep, we used an unsupervised learning approach, the Hidden Markov model (HMM), on two-night, 16-hour fMRI recordings of 12 non-sleep-deprived participants who reached all PSG-based sleep stages. This method identified 21 recurring brain states and their transition probabilities, beyond PSG-defined sleep stages. The HMM trained on one night accurately predicted the other, demonstrating unprecedented reproducibility. We also found functionally relevant subdivisions within rapid eye movement (REM) and within non-REM 2 stages. This study provides new insights into brain dynamics and transitions during sleep, aiding our understanding of sleep disorders that impact sleep transitions.TeaserAn unsupervised learning model provides new insights into brain activity during human nocturnal sleep
Severe Maternal Morbidity Disparities Before and During the COVID Pandemic in a Medicaid Population
Authors: Meghea Cristian I. , Johnson Jennifer E. , Roman Lee Anne , Bolder Hannah , Key Kent , McCoy White Jonne , Yu Xiao 
Published: April 2024

AbstractThis study assessed racial and ethnic disparities in severe maternal mortality during delivery through 6 weeks postpartum, before and during the COVID pandemic, in a statewide Medicaid population. This retrospective, population-based, cohort study used Medicaid claims data linked to birth certificates from the Michigan Department of Health and Human Services Health Services Data Warehouse that included all individuals giving birth between January 1, 2017, and October 31, 2021, in Michigan who had Medicaid insurance during the month of childbirth. The SMM rate increased more during the COVID pandemic for Black (1.36 [1.26-1.46]) compared to White individuals (1.17 [1.09-1.26], p-value<0.01 Black vs White). The Black-White and Hispanic-White disparities in severe maternal morbidity, already high in the Medicaid population, widened during the COVID pandemic. Multilevel interventions are needed to reduce disparities in maternal morbidity and mortality.Conflict of interest disclosureNo conflicts to disclose.
Validity of self-screening with the KOJI AWARENES™ test for range of motion and strength in healthy subjects
Authors: Hirohata Kenji , Furuya Hidetaka , Mitomo Sho , Osaka Yuki , Murofushi Koji , Yagishita Kazuyoshi 
Published: April 2024

AbstractObjectiveThis study aimed to establish the validity of the KOJI AWARENESSTM sub-components by determining whether there is a connection between the sub-component scores and joint range of motion, muscle strength, and balance.MethodsFifty healthy adults (17 females and 33 males) participated in the study, completing both the KOJI AWARENESSTMand measurements of joint range of motion, muscle strength, and balance. The range of motion of the upper and lower extremities and trunk was measured using either a goniometer or an inclinometer. A handheld dynamometer was used to measure muscle strength. Balance ability was assessed using a modified balance error scoring system. Using the Mann–Whitney U test or Jonckheere–Terpstra test, we compared the KOJI AWARENESS™ score and the corresponding body segments, with a significance level of P ≤ 0.05.ResultsOur results indicated that there were associations between external references and many items, but no associations were found for flexion, extension, and rotation of the "neck mobility," extension and external rotation of the "hip mobility," and strength of the "mid-section stability strength" in the KOJI AWARENESSTM.ConclusionOverall, the KOJI AWARENESSTMsub-component scores showed good validity, with the exception of the items related to neck and hip flexibility and trunk muscle strength. Future analyses should include a wider range of age groups, such as middle-aged and elderly individuals.
Multi-ancestry genome-wide association meta-analysis of mosaic loss of chromosome Y in the Million Veteran Program identifies 167 novel loci
Authors: Francis Michael , Gorman Bryan R. , Bigdeli Tim B. , Genovese Giulio , Voloudakis Georgios , Bendl Jaroslav , Zeng Biao , Venkatesh Sanan , Chatzinakos Chris , McAuley Erin , Ji Sun-Gou , Markianos Kyriacos , Schreiner Patrick A. , Partan Elizabeth , Shi Yunling , Devineni Poornima ,   VA Million Veteran Program, Moser Jennifer , Muralidhar Sumitra , Ramoni Rachel , Bick Alexander G. , Natarajan Pradeep , Assimes Themistocles L. , Tsao Philip S. , Klarin Derek , Tcheandjieu Catherine , Peachey Neal S. , Iyengar Sudha K. , Roussos Panos , Pyarajan Saiju 
Published: April 2024

AbstractMosaic loss of chromosome Y (mLOY) is a common somatic mutation in leukocytes of older males. mLOY was detected in 126,108 participants of the Million Veteran Program: 106,054 European (EUR), 13,927 admixed African (AFR), and 6,127 Hispanic. In multi-ancestry genome-wide association analysis, we identified 323 genome-wide significant loci, 167 of which were novel–more than doubling the number of known mLOY loci. Tract-based ancestry deconvolution resolved local inflation at AFR lead SNPs. Transcriptome-wide associations yielded 2,297 significant genes, including seven additional novel genes; integrative eQTL analyses highlighted 51 genes that causally influence mLOY via differential expression. Thirty-two significant traits found in a phenome-wide polygenic score scan were used in Mendelian randomization (MR). MR implicated six traits as causal influences on mLOY: triglycerides, high-density lipoprotein, smoking, body mass index, testosterone, and sex hormone-binding globulin; and found influence of mLOY on plateletcrit, prostate cancer, lymphocyte percentage, and neutrophil percentage. These results mark a major step forward in our understanding of the genetic architecture of mLOY and its associated risks.
Transcriptional Remodeling of the Stromal and Endothelial Microenvironment in MGUS to Multiple Myeloma Progression
Authors: Cenzano Itziar , Cócera Miguel , Bantan Azari , Larrayoz Marta , Vilas-Zornoza Amaia , San-Martin Patxi , Aguirre-Ruiz Paula , Alignani Diego , Lopez Aitziber , Barrios Marta Miñana , Agreda Delia Quilez , González Ignacio Sancho , Ruiz Javier , Lagani Vincenzo , Tegner Jesper , Martín-Subero Ignacio , Agirre Xabier , Paiva Bruno , Rodriguez-Otero Paula , Tamariz-Amador Luis-Esteban , San-Miguel Jesús , Martinez-Climent Jose A. , Saez Borja , Hernáez Mikel , Calvo Isabel A. , Gomez-Cabrero David , Prosper Felipe 
Published: April 2024

ABSTRACTThe role of the bone marrow microenvironment (BME) in the transition from monoclonal gammopathy of undetermined significance (MGUS) into clinically active multiple myeloma (MM) is not completely determined. To address this issue, we performed single-cell RNA sequencing (scRNA-seq) of non-hematopoietic BME cells as well as plasma cells (PC) from two genetically engineered mouse models of MM termed BIcγ1and MIcγ1that recapitulate the progression of MGUS into MM. Our results identify distinct transcriptional dynamics between endothelial cells (EC) and mesenchymal stem cells (MSC). While EC acquire a stress state during MGUS, a proliferating and angiogenic profile characterizes MM. On the other hand, MSC compromised their differentiation potential, exhibiting a more inflammatory profile that initiates from the MGUS stage. Interestingly, we identified an interferon (IFN)-related myeloma signature in malignant EC of the BIcγ1model, which is also expressed in MSC but not observed in the more aggressive MIcγ1model and can be identified in MSC from a subgroup of MM patients. The analysis of the EC and MSC interactions with malignant PC revealed stage-specific interactions that contribute to angiogenesis, immunomodulation, and MM extravasation. Finally, the translational relevance of our results in humans was confirmed on MSC from newly diagnosed patients with monoclonal gammopathies at different stages of the disease. In summary, these results show a remodeling of the non-hematopoietic BME in MM progression, providing potential targets at the tumor-niche interface that may hold clinical significance and complement existing immunotherapies.Abstract FigureKEY POINTSEC stress pre-vascular state in MGUS, shifts to angiogenic in MM, while MSC early transcriptional changes in MGUS persist in overt MM.Identification of a myeloma-specific IFN signature in the non-hematopoietic BME that could define a subgroup of MM patients.
Carbonic anhydrase plays multiple roles in acetotrophic growth of a model marine methanogen from the domainArchaea
Authors: Santiago-Martínez Michel Geovanni , Zimmerman Sabrina , Apolinario Ethel E. , Sowers Kevin R. , Ferry James G. 
Published: April 2024

AbstractCarbonic anhydrase (CA) catalyzes the reversible hydration of CO2to bicarbonate and a proton. The enzyme is universally distributed in all three domains of life and plays diverse physiological roles in the domainsEukaryaandBacteria. Remarkably, a physiological role has not been identified for any CA from the domainArchaea. Herein are described roles for a gamma class CA (Cam) from the methane-producing marine archaeonMethanosarcina acetivorans. Acetate-dependent growth of a Δcammutant showed an extended lag phase, lower final cell density, and metabolized acetate to a threshold of 20.0 mM compared to 1.0 mM for wild-type. Molar growth yields (Ymethane) were substantially greater for wild-type compared to the mutant. In contrast, growth parameters were identical for the methanol-grown wild-type and mutant. Rates of methane formation in resting cell suspensions containing 20.0 mM acetate were significantly less in the mutantversuswild-type and dependent on the presence of CO2. Rates for the wild-type decreased with increasing pH that was more pronounced for the mutant. CA activity was 100-fold greater in the membraneversussoluble fraction of acetate-grown cells. Addition of a surrogate CA stimulated acetate-dependent methanogenesis in resting cell suspensions of the mutant. The results support a role for Cam to supply protons for symport of acetate by the AceP symporter that also optimizes and facilitates growth at low acetate concentrations and high pH values encountered in the marine environment whereM. acetivoranswas isolated.Significance StatementAlthough CA plays major physiological roles in the domainsEukaryaandBacteria, a role has not been reported for the domainArchaeain which methanogens comprise the major group with abundant genomic annotations for CAs. Acetotrophic methanogens account for most of the methane produced in Earth’s biosphere where it is a major greenhouse gas. Although the biochemistry of the conversion of acetate to methane and carbon dioxide is well known, little is understood of acetate transport. The finding that CA has multiple roles facilitating thermodynamically constrained growth of a model marine acetotrophic methanogen has implications for advancing ecological understanding of the methane cycle that impacts global warming and climate change. Finally, the work is an introduction to anticipated physiological roles of CAs in the domainArchaeafor which genomic annotations are abundant.
Large circulation of a novel vesiculovirus in bats in the Mediterranean region
Authors: Luo Dong-Sheng , Harazim Markéta , Maufrais Corinne , Bonas Simon , Martinkova Natalia , Lalis Aude , Nakouné Emmanuel , Adjogoua Edgard Valéry , Douno Mory , Kadjo Blaise , López-Roig Marc , Pikula Jiri , Shi Zheng-Li , Bourhy Hervé , Serra-Cobo Jordi , Dacheux Laurent 
Published: April 2024

AbstractBats are the natural reservoirs of a variety of emerging or re-emerging viruses. Among them, rabies virus (genusLyssavirus, familyRhabdoviridae) is of the first and most iconic described in these animals. Since its first description, various new bat lyssaviruses have been regularly described. Apart from lyssaviruses, other bat rhabdoviruses have been also identified, including members of theVesiculovirus,Ledantevirusand more recentlyAlphanemrhavirusandTupavirusgenera. However, the familyRhabdoviridaeis one of the most abundant and diverse viral families, with 318 officially recognized species divided into 3 subfamilies and 46 different genera. Thus, the number of bat- associated rhabdoviruses is probably higher.In this study, we first developed and validated a combined nested RT-qPCR technique (pan-rhabdo RT-nqPCR) dedicated to the broad detection of animal rhabdovirus. After validation, this technique was used for a large retrospective screening of archival bat samples (n= 1962), including blood (n= 816), brain (n= 723) and saliva (n= 423). These samples were collected from various bat species over a period of 12 years (2007-2019) in 9 different countries in Europe and Africa. A total of 23 samples (1.2%) fromMiniopterus schreibersii,Rhinolophus euryaleandRhinolophus ferrumequinumbat species was found positive for rhabdovirus infection, including 17 (2.1%) blood and 6 (1.4%) saliva samples, all collected from bats originated from the Mediterranean region.The complete virus genome sequences were obtained by next-generation sequencing for most of the positive samples. Molecular and phylogenetic analysis of these sequences demonstrated that these virus isolates, named Mediterranean bat virus (MBV), were closely related, and represented a new speciesVesiculovirus mediterraneanwithin theVesiculovirusgenus. MBV was more specifically related to the other bat vesiculoviruses previously described in China and North America, together clustering into a distinct group of bat viruses within this genus. Interestingly, our results suggest that MBV is widely distributed, at least in the West part of the Mediterranean region, where it can act as an arbovirus infecting and circulating in multiple bat species. These findings expand the host range and the viral diversity of bat vesiculoviruses and pave the way for further investigations to determine the route of transmission and the dynamic of diffusion of these viruses into bat colonies, as well as to evaluate their potential hazard for public health.
Parallel-plate avalanche counters for heavy-ion beam tracking: History and mysteries
Authors: Di Carlo Salvatore , Cortesi Marco 
Published: April 2024

Despite being an old detector concept, position-sensitive parallel-plate avalanche counters (PPACs) remain widely used today for heavy-ion position and timing measurements. In modern rare isotope beam facilities and large-acceptance fragment separators, PPACs are used to characterize beam properties (diagnostics), facilitate beam delivery (tuning), and provide event-by-event beam tracking for particle identification (PID). Most popular particle localization methods in PPAC detectors are based on strip electrodes electrically connected to resistive-chain circuits or delay lines. More exotic systems include optical readouts based on recording electroluminescence light with high-granularity photodetector arrays or high-resolution resistive anode electrodes. PPACs with conventional resistive-chain or delay-line readouts achieve typical position and time resolutions of below 1 mm (σ) and around 150 ps (σ), respectively. In addition, delay-line systems are capable of counting rates above several hundred kHz for beam areas of a few millimeters square, and around 1 MHz for larger beam sizes. Resistive-chain readouts have limited rates of a few tens of kHz. A review of the operation principles and performance of PPAC detectors is presented in this paper. We will discuss decades-long experience building and operating PPACs developed at the National Superconducting Cyclotron Laboratory, and then refined at the Facility for Rare Isotope Beams (FRIB), mostly focusing on the delay-line readout technique (DLPPAC). We will also discuss problems that arise due to electric discharges at high rates and briefly describe ongoing developments at FRIB.

Published by the American Physical Society
2024
An information flow field model for human–machine interaction
Authors: Wu Qiuqi , Sun Youchao , Xu Man 
Published: April 2024

Purpose
About 70% of all aircraft accidents are caused by human–machine interaction, thus identifying and quantifying performance shaping factors is a significant challenge in the study of human reliability. An information flow field model of human–machine interaction is put forward to help better pinpoint the factors influencing performance and to make up for the lack of a model of information flow and feedback processes in the aircraft cockpit. To enhance the efficacy of the human–machine interaction, this paper aims to examine the important coupling factors in the system using the findings of the simulation.

Design/methodology/approach
The performance-shaping factors were retrieved from the model, which was created to thoroughly describe the information flow. The coupling degree between the performance shaping factors was calculated, and simulation and sensitivity analysis are based on system dynamics.

Findings
The results show that the efficacy of human–computer interaction is significantly influenced by individual important factors and coupling factors. To decrease the frequency of accidents after seven hours, attention should be paid to these factors.

Originality/value
The novelty of this work lies in proposing a theoretical model of cockpit information flow and using system dynamics to analyse the effect of the factors in the human–machine loop on human–machine efficacy.
Exploring insect-based food consumption experiences and their consequences in a mature entomophagous community
Authors: Liu Yunyao , Kim Seongseop (Sam) 
Published: April 2024

PurposeTo generate the measurement instrument seven steps were implemented. A total of 819 questionnaires were collected in Yunnan Province, China, where it has long tradition of eating insects.Design/methodology/approachThis study aims to explore the influences of the multidimensional benefits of consuming insect-based food on its consequences. Food neophilia and hedonic motivation are used as moderating variables.FindingsHealth, nutritional value, taste and cultural domains effectively explained consumers’ attitudes toward insect-based food, food consumption value, satisfaction, subjective well-being, loyalty to the restaurant and community attachment. Food neophilia and hedonic motivation partially moderated the relationships between the proposed constructs.Research limitations/implicationsThis study provides a conceptual model for exploring insect-based food consumption experiences and offers a useful guideline for developing and designing marketing strategies for stakeholders in the food and restaurant industry.Originality/valueThis is one of the few studies examining the benefits of consuming insect-based food from the perspective of consumers.