bluuebunny/crossref_metadata_2025_split huggingface dataset:
The global burden of HIV among Long-distance truck drivers: A systematic review and meta-analysis
Authors: Mutie Cyrus , Otieno Berrick , Mwangi Elijah , Kawira Rosemary , Mutisya Albanus , Gachohi John , Mbuthia Grace 
Published: December 2023

AbstractLong-distance truck drivers (LDTDs) endure a disproportionately high burden of HIV in various global settings. However, unlike other most at-risk populations, the global burden of HIV among LDTDs has not been documented so far. The result has been poor allocation and distribution of the limited HIV preventive resources for LDTDs in most parts of the world. Thus, a systematic review and meta-analysis were conducted to assess the global burden of HIV among LDTDs. A comprehensive electronic search was conducted in PubMed, ProQuest Central, PubMed Central, CINAHL, and Global Index Medicus to identify relevant information published in English on HIV prevalence among LDTDs from 1989 to the 16thof May 2023. A random-effects meta-analysis was conducted to establish the burden of HIV at global and regional levels. The Joanna Briggs Institute (JBI) and Newcastle-Ottawa Scale (NOS) tools were used to assess the quality of the included studies.Of the 1787 articles identified, 43 were included. Most of the included studies were conducted in sub-Saharan Africa (44.19%, n=19), and Asia and the Pacific (37.21%, n=16). The pooled prevalence of HIV was 3.82%. The burden of HIV was highest in sub-Saharan Africa at 14.34%, followed by Asia and the Pacific at 2.14%, and lastly Western, Central Europe and North America at 0.17%. The overall heterogeneity score was (I2= 98.2%, p < 0.001).The global burden of HIV among LDTDs is 3.82%, six times higher than that of the general population globally. Compared to other regions, the burden of HIV is highest in sub-Saharan Africa at 14.34%, where it’s estimated to be 3% in the general population. Thus, LDTDs endure a disproportionately high burden of HIV compared to other populations. Consequently, more LDTD-centred HIV research and surveillance is needed at national and regional levels to institute tailored preventive policies and interventions.PROSPERO NumberCRD42023429390
Chromosome-level genome assembly of the European Green woodpeckerPicus viridis
Authors: Forest Thomas , Achaz Guillaume , Marbouty Martial , Bignaud Amaury , Thierry Agnès , Koszul Romain , Milhes Marine , Lledo Joanna , Pons Jean-Marc , Fuchs Jérôme 
Published: December 2023

AbstractThe European Green Woodpecker,Picus viridis, is a widely distributed species found in the Western Palearctic region. Here we assembled a highly contiguous genome assembly for this species using a combination of short and long reads sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of thePicus viridisgenome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics ofP. viridisand the comparative evolution of woodpeckers.
SGLT2 inhibitors attenuate endothelial to mesenchymal transition and cardiac fibroblast activation
Authors: Schmidt Kevin , Schmidt Arne , Groß Sonja , Just Annette , Pfanne Angelika , Fuchs Maximilian , Jordan Maria , Mohr Elisa , Pich Andreas , Fiedler Jan , Thum Thomas 
Published: December 2023

AbstractBeneficial effects of sodium glucose co-transporter 2 inhibitors (SGLT2is) in cardiovascular diseases have been extensively reported leading to the inclusion of these drugs in the treatment guidelines for heart failure. However, molecular actions especially on non-myocyte cells remain uncertain. We observed dose-dependent inhibitory effects of two SGLT2is, dapagliflozin (DAPA) and empagliflozin (EMPA), on inflammatory signaling in human umbilical vein endothelial cells (HUVECs). Proteomics analyses and subsequent enrichment analyses discovered profound effects of these SGLT2is on proteins involved in mitochondrial respiration and actin cytoskeleton. Validation in functional oxygen consumption measurements as well as tube formation and migration assays revealed strong impacts of DAPA. Considering that most influenced parameters played central roles in endothelial to mesenchymal transition (EndMT), we performedin vitroEndMT assays and identified substantial reduction of mesenchymal and fibrosis marker expression as well as changes in cellular morphology upon treatment with SGLT2is. In line, human cardiac fibroblasts (HCFs) exposed to DAPA showed less proliferation, reduced ATP production, and decelerated migration capacity while less extensive impacts were observed upon EMPA. Mechanistically, sodium proton exchanger 1 (NHE1) as well as sodium-myoinositol cotransporter (SMIT) and sodium-multivitamin cotransporter (SMVT) could be identified as relevant targets of SGLT2is in non-myocyte cardiovascular cells as validated by individual siRNA-knockdown experiments. In summary, we found comprehensive beneficial effects of SGLT2is on human endothelial cells and cardiac fibroblasts. The results of this study therefore support a distinct effect of selected SGLT2i on non-myocyte cardiovascular cells and grant further insights into potential molecular mode of action of these drugs.
Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy
Authors: Bodansky Aaron , Yu David JL , Rallistan Alysa , Kalaycioglu Muge , Boonyaratanakornkit Jim , Green Damian J. , Gauthier Jordan , Turtle Cameron J. , Zorn Kelsey , O’Donovan Brian , Mandel-Brehm Caleigh , Asaki James , Kortbawi Hannah , Kung Andrew F. , Rackaityte Elze , Wang Chung-Yu , Saxena Aditi , de Dios Kimberly , Masi Gianvito , Nowak Richard J. , O’Connor Kevin C. , Li Hao , Diaz Valentina E. , Casaletto Kaitlin B. , Gontrum Eva Q. , Chan Brandon , Kramer Joel H. , Wilson Michael R. , Utz Paul J. , Hill Joshua A. , Jackson Shaun W. , Anderson Mark S. , DeRisi Joseph L. 
Published: December 2023

AbstractThe prevalence and burden of autoimmune and autoantibody mediated disease is increasing worldwide, yet most disease etiologies remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in programmable-phage immunoprecipitation (PhIP-Seq) methodology to explore the modulation, or lack thereof, of proteome-wide autoantibody profiles in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or “autoreactome”, that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual’s autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.
ChatGPT for tinnitus information and support: response accuracy and retest after three months
Authors: Jedrzejczak W. Wiktor , Skarzynski Piotr H. , Raj-Koziak Danuta , Sanfins Milaine Dominici , Hatzopoulos Stavros , Kochanek Krzysztof 
Published: December 2023

AbstractBackgroundChatGPT – a conversational tool based on artificial intelligence – has recently been tested on a range of topics. However most of the testing has involved broad domains of knowledge. Here we test ChatGPT’s knowledge of tinnitus, an important but specialized aspect of audiology and otolaryngology. Testing involved evaluating ChatGPT’s answers to a defined set of 10 questions on tinnitus. Furthermore, given the technology is advancing quickly, we re-evaluated the responses to the same 10 questions 3 months later.Material and methodChatGPT (free version 3.5) was asked 10 questions on tinnitus at two points of time – August 2023 and November 2023. The accuracy of the responses was rated by 6 experts using a Likert scale ranging from 1 to 5. The number of words in each response was also counted, and responses were specifically examined for whether references were provided or whether consultation with a specialist was suggested.ResultsMost of ChatGPT’s responses were rated as satisfactory or better. However, we did detect a few instances where the responses were not accurate and might be considered somewhat misleading. The responses from ChatGPT were quite long (averaging over 400 words) and they occasionally tended to stray off-topic. No solid references to sources of information were ever supplied, and when references were specifically asked for the sources were artificial. For most responses consultation with a specialist was suggested. It is worth noting that after 3 months the responses generally improved.ConclusionsChatGPT provided surprisingly good responses, given that the questions were quite specific. Although no potentially harmful errors were identified, some mistakes could be seen as somewhat misleading. No solid references were ever supplied. ChatGPT shows great potential if further developed by experts in specific areas, but for now it is not yet ready for serious application.
Genomic analysis identifies risk factors in restless legs syndrome
Authors: Akçimen Fulya , Chia Ruth , Saez-Atienzar Sara , Ruffo Paola , Rasheed Memoona , Ross Jay P. , Liao Calwing , Ray Anindita , Dion Patrick A. , Scholz Sonja W. , Rouleau Guy A. , Traynor Bryan J. 
Published: December 2023

AbstractRestless legs syndrome (RLS) is a neurological condition that causes uncomfortable sensations in the legs and an irresistible urge to move them, typically during periods of rest. The genetic basis and pathophysiology of RLS are incompletely understood. Here, we present a whole-genome sequencing and genome-wide association meta-analysis of RLS cases (n = 9,851) and controls (n = 38,957) in three population-based biobanks (All of Us, Canadian Longitudinal Study on Aging, and CARTaGENE). Genome-wide association analysis identified nine independent risk loci, of which eight had been previously reported, and one was a novel risk locus (LMX1B, rs35196838, OR = 1.14, 95% CI = 1.09-1.19,p-value = 2.2 × 10-9). A genome-wide, gene-based common variant analysis identifiedGLO1as an additional risk gene (p-value = 8.45 × 10-7). Furthermore, a transcriptome-wide association study also identifiedGLO1and a previously unreported gene,ELFN1. A genetic correlation analysis revealed significant common variant overlaps between RLS and neuroticism (rg= 0.40, se = 0.08,p-value = 5.4 × 10-7), depression (rg= 0.35, se = 0.06,p-value = 2.17 × 10-8), and intelligence (rg= -0.20, se = 0.06,p-value = 4.0 × 10-4). Our study expands the understanding of the genetic architecture of RLS and highlights the contributions of common variants to this prevalent neurological disorder.
Sub-Optimal Oral Health, Multimorbidity and Access to Dental Care
Authors: Limo L , Nicholson K , Stranges S , Gomaa N 
Published: December 2023

ABSTRACTINTRODUCTIONEmerging research on the links between sub-optimal oral health and multimorbidity (MM), or the co-existence of multiple chronic conditions, has raised queries on whether enhancing access to dental care may mitigate the MM burden, especially in older age. Here, we aim to assess the association between sub-optimal oral health and MM and whether access to dental care can mitigate the risk of MM in individuals with sub-optimal oral health.METHODSWe conducted a cross-sectional analysis using data from the Canadian Longitudinal Study on Aging (CLSA) (n=44,815, 45-84 years old). Edentulism, self-reported oral health (SROH), and other oral health problems (e.g., toothache, bleeding gums), were each used as indicators of sub-optimal oral health. MM was defined according to the Public Health Agency of Canada as having 2 or more chronic conditions out of cancer, cardiovascular diseases, chronic respiratory diseases, diabetes, and mental illnesses. Variables for access to dental care included the number of dental visits within the last year, dental insurance status, and cost barriers to dental care. We constructed multivariable step-wise logistic regression models and interaction terms with 95% confidence intervals and estimated prevalence ratio (PR) to assess the associations of interest, adjusting fora prioridetermined sociodemographic and behavioural factors.RESULTSEach of the sub-optimal oral health indicators were significantly associated with MM (edentulism PR=1.48, 95%CI 1.31, 1.68; poor SROH PR=1.81, 95%CI 1.62, 2.01; other oral health problems PR = 1.91, 95%CI 1.78, 2.06). The magnitude of this association was exacerbated in individuals who lacked dental insurance, could not afford dental care, and those who reported fewer dental visits within the last year.CONCLUSIONThe association between sub-optimal oral health and MM may be exacerbated by the lack of access to dental care. Policies aiming to enhance access to dental care may help mitigate the risk of MM.
Large Language Models Facilitate the Generation of Electronic Health Record Phenotyping Algorithms
Authors: Yan Chao , Ong Henry H. , Grabowska Monika E. , Krantz Matthew S. , Su Wu-Chen , Dickson Alyson L. , Peterson Josh F. , Feng QiPing , Roden Dan M. , Stein C. Michael , Kerchberger V. Eric , Malin Bradley A. , Wei Wei-Qi 
Published: December 2023

ABSTRACTObjectivesPhenotyping is a core task in observational health research utilizing electronic health records (EHRs). Developing an accurate algorithm demands substantial input from domain experts, involving extensive literature review and evidence synthesis. This burdensome process limits scalability and delays knowledge discovery. We investigate the potential for leveraging large language models (LLMs) to enhance the efficiency of EHR phenotyping by generating high-quality algorithm drafts.Materials and MethodsWe prompted four LLMs—GPT-4 and GPT-3.5 of ChatGPT, Claude 2, and Bard—in October 2023, asking them to generate executable phenotyping algorithms in the form of SQL queries adhering to a common data model (CDM) for three phenotypes (i.e., type 2 diabetes mellitus, dementia, and hypothyroidism). Three phenotyping experts evaluated the returned algorithms across several critical metrics. We further implemented the top-rated algorithms and compared them against clinician-validated phenotyping algorithms from the Electronic Medical Records and Genomics (eMERGE) network.ResultsGPT-4 and GPT-3.5 exhibited significantly higher overall expert evaluation scores in instruction following, algorithmic logic, and SQL executability, when compared to Claude 2 and Bard. Although GPT-4 and GPT-3.5 effectively identified relevant clinical concepts, they exhibited immature capability in organizing phenotyping criteria with the proper logic, leading to phenotyping algorithms that were either excessively restrictive (with low recall) or overly broad (with low positive predictive values).ConclusionGPT versions 3.5 and 4 are capable of drafting phenotyping algorithms by identifying relevant clinical criteria aligned with a CDM. However, expertise in informatics and clinical experience is still required to assess and further refine generated algorithms.
Potential Utility of C-reactive Protein for Tuberculosis Risk Stratification among Patients with Non-Meningitic Symptoms at HIV Diagnosis in Low- and Middle-Income Countries
Authors: Dupnik Kathryn , Rivera Vanessa R. , Dorvil Nancy , Akbarnejad Hanane , Gao Yipeng , Liu Jingyi , Apollon Alexandra , Dumond Emelyne , Riviere Cynthia , Severe Patrice , Lavoile Kerlyne , Duran Mendicuti Maria Alejandra , Pierre Samuel , Rouzier Vanessa , Walsh Kathleen F. , Byrne Anthony L. , Joseph Patrice , Cremieux Pierre-Yves , Pape Jean William , Koenig Serena P. 
Published: December 2023

ABSTRACTArticle SummaryWe assessed the association between C-reactive protein (CRP) andMycobacterium tuberculosis(TB) diagnosis in symptomatic patients at HIV diagnosis. We found that CRP concentrations can improve tuberculosis risk stratification, facilitating decision making about whether (specific) tuberculosis testing is indicated before antiretroviral therapy initiation.BackgroundThe World Health Organization recommends initiating same-day ART while tuberculosis testing is underway for patients with non-meningitic symptoms at HIV diagnosis, though safety data are limited. C-reactive protein (CRP) testing may improve tuberculosis risk stratification in this population.MethodsIn this baseline analysis of 498 adults (>18 years) with tuberculosis symptoms at HIV diagnosis who were enrolled in a trial of rapid ART initiation in Haiti, we describe test characteristics of varying CRP thresholds in the diagnosis of TB. We also assessed predictors of high CRP (≥3 mg/dL) using generalized linear models.ResultsEighty-seven (17.5%) patients were diagnosed with baseline TB. The median CRP was 33.0 mg/L (IQR: 5.1, 85.5) in those with TB, and 2.6 mg/L (IQR: 0.8, 11.7) in those without TB. As the CRP threshold increased from ≥1 mg/L to ≥10 mg/L, the positive predictive value for TB increased from 22.4% to 35.4%, and negative predictive value decreased from 96.9% to 92.3%. With CRP thresholds varying from <1 to <10 mg/L, a range from 25.5% to 64.9% of the cohort would have been eligible for same-day ART, and 0.8% to 5.0% would have untreated TB at ART initiation.ConclusionsCRP concentrations can be used to improve TB risk stratification, facilitating same-day decisions about ART initiation. Depending on the CRP threshold, one-quarter to two-thirds of patients could be eligible for same-day ART, with a reduction of 3-fold to 20-fold in the proportion with untreated TB, compared with a strategy of same-day ART while awaiting TB test results.
c-fosinduction in the choroid plexus, tanycytes and pars tuberalis is an early indicator of spontaneous arousal from torpor in a deep hibernator
Authors: Markussen Fredrik A.F , Cázarez-Marquez Fernando , Melum Vebjørn J. , Hazlerigg David , Wood Shona 
Published: December 2023

AbstractHibernation is an extreme state of seasonal energy conservation, reducing metabolic rate to as little as 1% of the active state. During the hibernation season, many species of hibernating mammals cycle repeatedly between the active (aroused) and hibernating (torpid) states (T-A cycling), using brown adipose tissue (BAT) to drive cyclical rewarming. The regulatory mechanisms controlling this process remain undefined but are presumed to involve thermoregulatory centres in the hypothalamus. Here, we use the golden hamster (Mesocricetus auratus), and high-resolution monitoring of BAT, core body temperature (Tb), and ventilation rate, to sample at precisely defined phases of the T-A cycle. Usingc-fosas a marker of cellular activity we show that although the dorso-medial hypothalamus (DMH) is active during torpor entry, neither it nor the pre-optic area (POA) show any significant changes during the earliest stages of spontaneous arousal. Contrastingly, in 3 non-neuronal sites previously linked to control of metabolic physiology over seasonal and daily timescales, the choroid plexus (CP), pars tuberalis (PT) and third ventricle tanycytes, peakc-fosexpression is seen at arousal initiation. We suggest that through their sensitivity to factors in the blood or cerebrospinal fluid (CSF), these sites may mediate metabolic feedback-based initiation of the spontaneous arousal process.
Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance and resetting in winter wheat
Authors: Liu Xuemei , Lin Xuelei , Deng Min , Shi Bingxin , Chen Jinchao , Li Haoran , Xu Shujuan , Bie Xiaomin , Zhang Xiansheng , Chong Kang , Xiao Jun 
Published: December 2023

AbstractWinter plants rely on vernalization, a vital process for adapting to cold and ensuring successful reproduction. However, understanding the role of histone modifications in guiding the vernalization process in winter wheat is limited. In this study, we investigate the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the field. Two core histone modifications, H3K27me3 and H3K36me3, exhibit opposite pattern on the key vernalization geneVERNALIZATION1(VRN1), correlated with its induction during cold exposure. Additionally, H3K36me3 remains high atVRN1after cold exposure, maintaining its active state. Mutations in FERTILIZATION-INDEPENDENT ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8 (TaSDG8), writer complex components of H3K27me3 and H3K36me3, respectively, affect flowering time. Interestingly,VRN1loses its high expression after cold exposure memory in the absence of H3K36me3. During embryo development,VRN1is silenced with the removal of H3K36me3 in both winter and spring alleles. H3K27me3 is selectively added to the winter allele, influencing the cold exposure requirement for the next generation. Integrating gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of flowering. This study reveals distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and resetting in winter wheat.Significance StatementVernalization, initially observed in cereals, lacks a comprehensive understanding of its underlying mechanism, particularly regarding chromatin-mediated transcriptional regulation in winter wheat. By delving into the transcriptome and chromatin dynamics in the shoot apex throughout winter wheat’s life cycle, we pinpointed two crucial histone modifications, H3K27me3 and H3K36me3, each playing distinct roles at different vernalization stages. H3K27me3 is implicated in establishing and resetting the extended cold exposure requirement for winter wheat, gradually diminishing during vernalization. On the other hand, H3K36me3 is crucial for maintainingVRN1’s active state post-cold exposure, contributing to the memory of the vernalization treatment. Additionally, the integration of transcriptome and histone modification profiles unveiled potential novel regulators of flowering in winter wheat.
Zelda is dispensable forDrosophila melanogasterhistone gene regulation
Authors: O’Haren Tommy , Aoki Tsutomu , Rieder Leila E. 
Published: December 2023

AbstractTo ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The pioneer factors Zelda and CLAMP collaborate at a subset of genes to regulate zygotic genome activation in Drosophila melanogaster and target early activated genes to induce transcription. CLAMP also regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis. The relationship between Zelda and CLAMP led us to hypothesize that Zelda helps identify histone genes for early embryonic expression. We found that Zelda targets the histone locus early during embryogenesis, prior to histone gene expression. However, depletion ofzeldain the early embryo does not affect histone mRNA levels or histone locus body formation. While surprising, these results concur with other investigations into Zelda’s role in the early embryo, suggesting the earliest factors responsible for specifying the zygotic histone genes remain undiscovered.