bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical and mental health of long-term users of HIV preexposure prophylaxis in Australia
Authors: Cornelisse Vincent J. , Murphy Dean , Lee Sue J. , Stoove Mark , Traeger Michael W. , Wright Edwina J. ,   for the X-PLORE Study Team
Published: October 2023

Introduction:
HIV preexposure prophylaxis (PrEP) is highly effective at preventing HIV. We aimed to assess mental and physical health among long-term PrEP users in Australia's X-PLORE cohort.

Methods:
In early 2021, 1485 X-PLORE participants were emailed a survey covering demographics, sexual practices, ongoing PrEP use, physical and psychological diagnoses received since commencing PrEP, substance use, and impacts of the COVID-19 pandemic. Current anxiety and depression were assessed using GAD-7 and PHQ-9 questionnaires.

Results:
Of 476 participants (completion rate 32.1%), 99.8% were cis-gender men. Median PrEP use duration was 48 months (2002 person-years), with 81.7% currently using PrEP. PrEP-related toxicity was uncommon: 2.9% reported bone fractures, 1.3% low bone density, and 4.0% reported kidney problems, largely not necessitating PrEP cessation. Most (92.0%) rated their health as ‘good’ to ‘excellent’, and 22.6% reported improved health since starting PrEP, often because of improved mental health. Only 6.2% reported deterioration in health since starting PrEP, largely unrelated to PrEP. The most common diagnoses were hypertension (9.9%), depression (13.2%) and anxiety (14.9%); 17% had PHQ-9 scores indicating current moderate-to-severe depression, which was associated with unemployment [adjusted odds ratio (aOR) 3.90], regular cannabis use (aOR 2.49), and having ceased PrEP (aOR 2.13).

Conclusion:
Among long-term PrEP users, of which over 80% were currently using PrEP, self-reported PrEP toxicity was uncommon. With almost one in five PrEP users categorized as having depression, and with higher risk among those having ceased PrEP, we recommend routine screening for depression and anxiety in PrEP users and corresponding follow-up of patients no longer attending for PrEP.
MULTIPLE MACHINE LEARNING METHODS AND COMPARATIVE TRANSCRIPTOMICS IDENTIFY PIVOTAL GENES FOR ISCHEMIA-REPERFUSION INJURY IN HUMAN DONOR TISSUE UNDERGOING ORTHOTOPIC LIVER TRANSPLANTATION
Authors: Chen Chengxin , Wang Qiang , Yang Zhe , Zuo Shi , Cao Kun , Li Haiyang 
Published: October 2023

ABSTRACT

Background: Hepatic ischemia-reperfusion injury (HIRI) is a major complication affecting patient prognosis during the period after orthotopic liver transplantation (OLT). Although an increasing number of scientists have investigated the molecular biology of ischemia-reperfusion injury (IRI) during OLT in animal and cellular models in recent years, studies using comprehensive and high-quality sequencing results from human specimens to screen for key molecules are still lacking. Aims: The objective of this study is to explore the molecular biological pathways and key molecules associated with HIRI during OLT through RNA sequencing and related bioinformatics analysis techniques. Methods: The study was done by performing mRNA sequencing on liver tissue samples obtained from 15 cases of in situ liver transplantation patients who experienced ischemia and reperfusion injury within 1 year at Guizhou Medical University, and combined with bioinformatics analysis and machine learning methods, we identified the genes and transcription factors that are closely associated with IRI during in situ liver transplantation surgery. Results: There were 877 differentially expressed genes (DEGs) identified in the included liver samples, of which 817 DEGs were upregulated and 60 were downregulated. Functional enrichment analysis revealed significant enrichment of immune-related terms, such as inflammation, defense responses, responses to cytokines, immune system processes, and cellular activation. In addition, core gene enrichment analysis after cytoHubba screening suggested that liver reperfusion injury might be associated with translation-related elements as a pathway together with protein translation processes. Machine learning with the weighted correlation network analysis screening method identified PTGS2, IRF1, and CDKN1A as key genes in the reperfusion injury process. Conclusions: This study demonstrated that the pathways and genomes whose expression is altered throughout the reperfusion process might be critical for the progression of HIRI during OLT.
BACTERIAL EXTRACELLULAR VESICLES IN THE REGULATION OF INFLAMMATORY RESPONSE AND HOST-MICROBE INTERACTIONS
Authors: Liu Benjamin D. , Akbar Rubab , Oliverio Anna , Thapa Kajol , Wang Xiaohong , Fan Guo-Chang 
Published: October 2023

ABSTRACT
Extracellular vesicles (EVs) are a new revelation in cross-kingdom communication, with increasing evidence showing the diverse roles of bacterial EVs (BEVs) in mammalian cells and host-microbe interactions. Bacterial EVs include outer membrane vesicles released by gram-negative bacteria and membrane vesicles generated from gram-positive bacteria. Recently, BEVs have drawn attention for their potential as biomarkers and therapeutic tools because they are nano-sized and can deliver bacterial cargo into host cells. Importantly, exposure to BEVs significantly affects various physiological and pathological responses in mammalian cells. Herein, we provide a comprehensive overview of the various effects of BEVs on host cells (i.e., immune cells, endothelial cells, and epithelial cells) and inflammatory/infectious diseases. First, the biogenesis and purification methods of BEVs are summarized. Next, the mechanisms and pathways identified by BEVs that stimulate either proinflammatory or anti-inflammatory responses are highlighted. In addition, we discuss the mechanisms by which BEVs regulate host-microbe interactions and their effects on the immune system. Finally, this review focuses on the contribution of BEVs to the pathogenesis of sepsis/septic shock and their therapeutic potential for the treatment of sepsis.
Clinical Value of Syndecan-1 Levels in Trauma Brain Injury: A Meta-Analysis
Authors: Xie Wei-Wei , Ding Ya-Jun , Bhandari Suwas , Li Hui , Chen Hua-Sen , Jin Sheng-Wei , Weng Hai-Xu , Hao Yu 
Published: October 2023

Abstract

Background
Traumatic brain injury (TBI) is a head trauma, usually associated with death and endothelial glycocalyx damage. Syndecan-1 (SDC-1)—a biomarker of glycocalyx degradation—has rarely been reported in meta-analyses to determine the clinical prognostic value in TBI patients.

Methods
We looked into PubMed, EMBASE, Cochrane Library, and Web of Science databases from January 01, 1990, to May 1, 2023, to identify eligible studies. A meta-analysis was conducted using RevMan 5.4 and Stata 16.0 with the search terms “SDC-1” and “traumatic brain injury”.

Results
The present study included five studies with a total of 640 enrolled patients were included. SDC-1 concentrations were higher in the Iso-trauma TBI group than in the non-TBI group [standardized mean difference (SMD) = 0.52; 95% CI: 0.03 – 1.00; P = 0.04]. Subgroup analysis revealed statistical significance when comparing the SDC-1 level of multi-trauma TBI (TBI + other injuries) group with the Iso-trauma TBI group (SMD = 0.74; 95% CI: 0.42–1.05; P < 0.001), and the SDC-1 level of the TBI coagulopathy (+) group (TBI with early coagulopathy) with the TBI coagulopathy (-) group (SMD =1.75; 95% CI:0.41–3.10; P = 0.01). Iso-trauma TBI patients with higher SDC-1 level were at a higher risk of 30-day in-hospital mortality [odds ratio (OR) =3.32; 95% CI: 1.67–6.60; P = 0.0006].

Conclusion
This meta-analysis suggests that SDC-1 could be a biomarker of endotheliopathy and coagulopathy in TBI, as it was increased in iso-trauma TBI patients and was higher in multi-trauma TBI patients. There is a need for additional research into the use of syndecan-1 as a prognostic biomarker in TBI, especially in iso-trauma TBI patients.
Primary central nervous system vasculitis and headache: Ten themes
Authors: Younger David S. 
Published: October 2023

Purpose of review
The primary central nervous system (CNS) vasculitides refers to clinicopathologic disorders that share the histopathology of inflammation of cerebral or spinal blood vessels. Unrecognized and therefore untreated, vasculitis of the CNS results in irreversible injury and disability making these disorders of paramount importance to clinicians.

Recent findings
Headache is an important clue to vasculitic involvement of CNS vessels. CNS vasculitis can be primary, in which only intracranial or spinal vessels are involved in the inflammatory process, or secondary to another known disorder with overlapping systemic involvement. The suspicion of vasculitis based on the history, clinical examination, and laboratory studies warrants prompt evaluation and treatment to prevent cerebral ischemia or infarction.

Summary
Primary CNS vasculitides can be diagnosed with certainty after intensive evaluation that includes tissue confirmation whenever possible. As in its systemic counterparts, clinicians must choose from among the available immune modulating, suppressive, and targeted immunotherapies to induce and maintain remission status and prevent relapse, tempered by anticipated medication adverse effects.
Federated Learning-Driven Collaborative Diagnostic System for Metastatic Breast Cancer
Authors: Gao William , Wang Dayong , Huang Yi 
Published: October 2023

AbstractMetastatic breast cancer is one of the leading causes of cancer mortality. While there has been progress in developing deep learning-driven diagnostic system for metastatic breast cancer based on histopathological images, it faces a major challenge in real-world application, i.e., how to improve generalizability of the diagnostic models for diverse patient populations and variations in sample and image processing across different geographic regions. Multi-institutional collaborative learning, which trains a single model using data from multiple institutions, can address the challenges of data inadequacy, lack of data diversity, and data quality. However, the current practice of direct medical data transfer among institutions faces increasing restrictions including patient privacy, intellectual property, data ownership and legal obligations. To enable multi-institutional collaborative learning for cancer diagnosis, we developed a federated learning-driven collaborative diagnostic system for metastatic breast cancer. This system preserves patient privacy by decoupling model training from the need for direct medical data transfer between institutions. Further, this study has demonstrated that the federate learning-driven system can improve diagnostic model accuracy and generalizability by leveraging information derived from diverse data sources across multiple institutions. This study has also shown that this collaborative diagnostic system has a strong potential of improving local diagnosis performance on lower quality images at a resource constrained institution. Our research indicated that federated learning-driven diagnostic system is a feasible and robust framework for multi-institutional collaborative development of diagnostic models for metastatic breast cancer. In addition to the benefits of improving diagnostic model generalizability for diverse patient populations, the collaborative diagnostic system presents a new opportunity to enable under-resourced healthcare institutions to leverage external data resources to improve local diagnosis performance while preserving patient privacy.
Hypertension control and its relationship with cognitive impairment among adults aged 45 to 80 in China
Authors: Li Xin , wu Qian , Chen Xing , Tang Yanmin , Fei Beini , zhao Qi , Ding Jing , Wang Xin 
Published: October 2023

AbstractThis cross-sectional study aimed to investigate the control of hypertension and its association with cognitive impairment in Chinese adults aged 45-80 years. Using cross-sectional surveys conducted in Shanghai and Guizhou from 2019-2021, 9,688 eligible subjects were eventually included. After analyzing the data using statistical methods such as unconditional logistic regression and restricted cubic splines (RCS), we found that severe blood pressure was positively associated with the risk of cognitive impairment. There was no significant association between mild/moderate BP and the risk of cognitive impairment. Moreover, diastolic blood pressure was significantly positively correlated with cognitive impairment. The restricted cubic spline modelresults showed that the associations with cognitive impairment seem to be U-shaped for SBP and linear for DBP. In conclusion, this study shows that uncontrolled hypertension is an independent risk factor for cognitive impairment and that the risk of cognitive impairment increases as diastolic blood pressures continues to rise.
In vitrophenotypic susceptibility of HIV-1 non-group M to CCR5 inhibitor (Maraviroc): TROPI-CO study
Authors: Gracias Ségolène , El Yaalaoui Ikrame , Visseaux Benoît , Charpentier Charlotte , Descamps Diane , Martin Charlène , Lermechain Fanny , Plantier Jean-Christophe , Alessandri-Gradt Elodie 
Published: October 2023

ABSTRACTThe susceptibility of genetically divergent HIV-1 strains (HIV-1 non-M) from group O, N and P to the CCR5 co-receptor antagonist, Maraviroc (MVC) was investigated among a large panel of 45 clinical strains, representative of the genetic diversity. The results were compared to reference strains of HIV-1 group M (HIV-1/M) with known tropism. Among the non-M strains, a wide range of phenotypic susceptibilities to MVC was observed. The large majority of HIV-1/O strains (40/42) displayed a high susceptibility to MVC with median and mean IC50values at 1.23 and 1.33 nM respectively, similar to the HIV-1/M R5 strain (1.89 nM). However, the 2 remaining HIV-1/O strains exhibited a lower susceptibility (IC50at 482 and 496 nM), in accordance with their dual/mixed (DM) tropism. Interestingly, the 2 HIV-1/N strains demonstrated varying susceptibility patterns, despite always having relatively low IC50values (2.87 and 47.5 nM). This emphasized the complexity of determining susceptibility solely based on IC50values.Our study examined the susceptibility of all HIV-1 non-M groups to MVC and correlated these findings with virus tropism (X4, R5 or DM). The results confirm the critical significance of tropism determination before initiating MVC treatment in patients infected with HIV-1 non-M. Furthermore, we advocate for the consideration of additional parameters, such as the slope of inhibition curves, to provide a more thorough characterization of phenotypic susceptibility profiles.
Cryptic diversity and signatures of domestication in the Black Soldier Fly (Hermetia illucens)
Authors: Generalovic Tomas N. , Sandrock Christoph , Roberts Benjamin J. , Meier Joana I. , Hauser Martin , Warren Ian A. , Pipan Miha , Durbin Richard , Jiggins Chris D. 
Published: October 2023

AbstractThe black soldier fly (Hermetia illucens) is the prime species in the developing global industry of insects as food and feed, but the genetic basis of its domestication has not been studied. We obtained whole genome sequences for 54 individuals from both wild and captive populations. We identified two genetic lineages at least 3 million years divergent, revealing cryptic diversity within the species complex. Our study indicates that the most common populations used for commercial and academic applications are primarily derived from just one of these divergent lineages, originating from a wild North American progenitor. Despite insect farming practices only reaching mass production scale over the past two decades, we find that captive populations show strong genome-wide signatures of domestication. Selective sweeps are found in multiple independently domesticated populations but are not seen in wild populations and suggest five major domestication loci located on chromosomes two, four and five. These regions contain development, behaviour, reproduction, metabolism and immunity genes. Populations experiencing independent domestication events, in the early stages of domestication, also show evidence of convergent genome evolution with repeated signatures of domestication in these same regions. Some limited evidence of gene flow between divergent lineages was observed, as well as evidence of hybridisation from domesticated populations into the wild. Our study reveals the genetic basis of ongoing domestication and provides a genomic platform for breeding and genetic surveillance in this novel agricultural species.
Air pollution from biomass burning disrupts early adolescent cortical microarchitecture development
Authors: Bottenhorn Katherine L. , Sukumaran Kirthana , Cardenas-Iniguez Carlos , Habre Rima , Schwartz Joel , Chen Jiu-Chiuan , Herting Megan M. 
Published: October 2023

AbstractExposure to outdoor particulate matter (PM2.5) represents a ubiquitous threat to human health, and particularly the neurotoxic effects of PM2.5from multiple sources may disrupt neurodevelopment. Studies addressing neurodevelopmental implications of PM exposure have been limited by small, geographically limited samples and largely focus either on macroscale cortical morphology or postmortem histological staining and total PM mass. Here, we leverage residentially assigned exposure to six, data-driven sources of PM2.5and neuroimaging data from the longitudinal Adolescent Brain Cognitive Development Study (ABCD Study®), collected from 21 different recruitment sites across the United States. To contribute an interpretable and actionable assessment of the role of air pollution in the developing brain, we identified alterations in cortical microstructure development associated with exposure to specific sources of PM2.5using multivariate, partial least squares analyses. Specifically, average annual exposure (i.e., at ages 8-10 years) to PM2.5from biomass burning was related to differences in neurite development across the cortex between 9 and 13 years of age.Graphical Abstract
Unraveling the Impact of Therapeutic Drug Monitoring via Machine Learning
Authors: Ates H. Ceren , Alshanawani Abdallah , Hagel Stefan , Cotta Menino O , Roberts Jason A , Dincer Can , Ates Cihan 
Published: October 2023

AbstractClinical studies investigating the benefits of beta-lactam therapeutic drug monitoring (TDM) among critically ill patients have been hindered by small patient group, variability between studies, patient heterogeneity and inadequate use of TDM. Accordingly, definitive conclusions regarding the efficacy of TDM have remained elusive. To address these challenges, we propose an innovative approach that leverages data-driven methods to unveil the concealed connections between therapy effectiveness and patient data. Our findings reveal that machine learning algorithms can identify informative features that distinguish between healthy and sick states. These hold promise as potential markers for disease classification and severity stratification, as well as offering a continuous and data-driven “multidimensional” SOFA score. The implementation of TDM-guided therapy was associated with improved recovery rates particularly during the critical 72 hours after sepsis onset. Providing the first-ever quantification of the impact of TDM, our approach has the potential to revolutionize the way TDM applied in critical care.
Increased Risks of Large-Artery Atherosclerosis and Brainstem Stroke in Patients With Nasopharyngeal Carcinoma
Authors: Lin Chin-Yang , Lin Cheng-Li , Liang Ji-An , Wang Yao-Ching , Lin Ying-Chun , Liao Chih-Ying , Lin Ting-Chun 
Published: October 2023

AbstractBackgroundInformation about the characteristics of stroke is crucial for improved screening, prevention, and treatment. The pattern of ischemic stroke in patients with nasopharyngeal carcinoma (NPC) is not well understood. The objective of this study is to investigate the etiology of ischemic stroke and the affected vascular territories in patients with NPC.MethodsThe Taiwan National Health Insurance Research Database and the Taiwan Stroke Registry were combined to identify the following 2 cohorts: patients with NPC having a subsequent stroke (NPC cohort) and patients without NPC having a stroke (non-NPC cohort). Data pertaining to the period from 2006 to 2018 were analyzed. The TOAST (Trial of ORG 10 172 in Acute Stroke Treatment) subtype of ischemic stroke and the affected vascular territories were analyzed and compared between the 2 cohorts.ResultsThe NPC cohort comprised 277 patients, whereas the non-NPC cohort comprised 125 024 patients. The most common TOAST subtype of ischemic stroke was large-artery atherosclerosis (LAA) in the NPC cohort and small-vessel occlusion in the non-NPC cohort. The prevalence of LAA was considerably higher in the NPC cohort (41.9%) than in the non-NPC cohort (28.3%). The analysis of the affected vascular territories revealed that the incidence of brainstem stroke was significantly higher in the NPC cohort (25.4%) than in the non-NPC cohort (14.5%).ConclusionsPatients with NPC tend to have increased risks of LAA and brainstem ischemic stroke. Physicians should consider sparing the vertebral and basilar arteries during definitive radiotherapy for NPC. Long-term follow-up for patients with NPC may include brain magnetic resonance imaging. This study may guide radiation oncologists in clinical decision-making.
Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry
Authors: Engelbrecht Eric , Rodriguez Oscar L. , Shields Kaitlyn , Schultze Steven , Tieri David , Jana Uddalok , Yaari Gur , Lees William , Smith Melissa L. , Watson Corey T. 
Published: October 2023

AbstractImmunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of IG loci has hindered effective use of standard high- throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we leverage long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n=36), representing the first comprehensive description of IGK haplotype variation at population-scale. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and a common novel ∼24.7 Kbp structural variant harboring a functional IGKV gene. Among 47 functional IGKV genes, we identify 141 alleles, 64 (45.4%) of which were not previously curated. We report inter-population differences in allele frequencies for 14 of the IGKV genes, including alleles unique to specific populations within this dataset. Finally, we identify haplotypes carrying signatures of gene conversion that associate with enrichment of SNVs in the IGK distal region. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.