bluuebunny/crossref_metadata_2025_split huggingface dataset:
Joint effect of sleep patterns and secondhand smoke exposure with mortality among non-smoking adults
Authors: Chen Chen , Jin Hongyu , Jiang Zhiping , Wei Wang , Li Wen-Yang 
Published: February 2025

Abstract

Introduction
Unhealthy sleep and secondhand smoke (SHS) exposure are independent risk factors for death. Their joint association with all-cause and cardiovascular disease (CVD) mortality (ACDM) deserves to be investigated in a nationally representative population.

Methods
Data from 15175 adults from the National Health and Nutrition Examination Survey database (2005–2014) were analyzed. The study endpoints were all-cause and CVD mortality. Sleep patterns (healthy, intermediate, and poor) were classified based on self-reported questionnaires, including sleep duration, self-reported trouble sleeping and doctor-diagnosed sleep disorders. SHS exposure among nonsmokers was defined according to cotinine levels in serum. Multivariate Cox hazards regression models were conducted to assess the association between sleep patterns and SHS exposure, alone and in combination, with ACDM.

Results
During 15 years of follow-up, 2016 all-cause deaths and 678 CVD deaths were recorded. In multivariable models, poor sleep was independently associated with higher risk of all-cause (hazard ratio [HR] 1.32; 95% confidence interval [CI] 1.15-1.51) and CVD mortality (HR= 1.31; 95% CI: 1.02-1.68). Exposure to SHS was associated with higher risk of all-cause (HR, 1.21; 95% CI, 1.08-1.36) and CVD mortality (HR, 1.25; 95% CI, 1.04-1.50). In the joint analyses, participants with both unhealthy sleep patterns (intermediate and poor) and SHS exposure had a significantly higher risk of all-cause (HR, 1.48; 95% CI: 1.26–1.74) and CVD mortality (HR, 1.51; 95% CI, 1.15–1.97) than those with neither risk factor.

Conclusions
The coexistence of SHS exposure and unhealthy sleep patterns was associated with an increased risk of death from all causes and CVD.

Implications
The findings of this study indicate that both poor sleep patterns and exposure to SHS are independently associated with a higher risk of all-cause and CVD mortality. Furthermore, the coexistence of SHS exposure and unhealthy sleep patterns further increases the risk of mortality from all causes and CVD. Since both sleep patterns and SHS exposure are modifiable factors, interventions aimed at reducing SHS exposure and improving sleep quality could have significant implications in reducing these adverse effects and lowering mortality risk.
Abnormal Arteriolar Blood Volume Measured by 3D Inflow-Based Vascular-Space-Occupancy (iVASO) MRI and resting-state BOLD fluctuations at 7T in Individuals with Recent-Onset Schizophrenia
Authors: Bodnár Andor L , Stevens Daniel A , Paez Adrian G , Ultz Kia , Ross Christopher A , Hua Jun , Margolis Russell L 
Published: February 2025

Abstract

Background
Using ultra-high field (7T) magnetic resonance imaging (MRI) and 3D Inflow-Based Vascular-Space-Occupancy (iVASO) MRI, we previously reported lower baseline arteriolar cerebral blood volumes (CBVa) in almost all grey matter regions in a cohort of patients with schizophrenia with varying ages and disease duration. The extent to which decreased CBVa is also present in early-stage schizophrenia, and how this impacts neurovascular coupling, remains to be determined.

Objective
We sought to determine the extent of CBVa deficits in recent-onset schizophrenia and the relationship of CBVa to region-specific resting-state neural activity.

Methods
Using ultra-high field (7T) MRI, CBVa was measured in 90 regions using 3D iVASO imaging in 16 individuals with recent-onset schizophrenia (disease duration: x̄ = 1.18 ± 1.4 yrs) and 12 age-matched controls. Resting-state functional MRI (rs-fMRI) was used to determine fractional amplitudes of low-frequency fluctuations (fALFF) and intrinsic connectivity (ICC) in spontaneous blood oxygen level-dependent (BOLD) signal, and the region-specific relationship between CBVa and fALFF was determined as an index of neurovascular coupling.

Results
Compared with healthy control participants, CBVa was lower in individuals with schizophrenia in almost all brain regions with a global effect size of 0.23 and regional effect sizes reaching up to 0.41. Individuals with schizophrenia also exhibited lower fALFF in spontaneous BOLD signals diffusely across cortical and subcortical grey matter regions. Ratios of mean regional CBVa to fALFF and ICC were significantly lower in patients in numerous brain regions, suggesting disease-related disruptions of neurovascular coupling.

Conclusion
Taken together these observations indicate that early-stage schizophrenia is associated with widespread microvascular abnormalities and associated resting-state deficits in neural activity. These results suggest that abnormalities in neurovascular coupling may contribute to the pathophysiology of schizophrenia.
DNA adducts form in mouse lung and liver after oral naphthalene exposure
Authors: Domanico Morgan C , Collette Nicole M , Ubick Esther , Ding Xinxin , Buchholz Bruce A , Van Winkle Laura S 
Published: February 2025

Abstract
Naphthalene is a ubiquitous combustion product and environmental contaminant with known human exposure. Chronic exposure to naphthalene vapor leads to respiratory tumor formation in rodents. Naphthalene forms DNA adducts (precursors to genotoxicity) in tissue explants but it is unclear if this occurs in vivo. Wild-type C57BL/6 mice were orally exposed to 50 mg/kg 14C-naphthalene. Naphthalene-DNA adducts were detected by accelerator mass spectrometry at 2- to 72-h post-exposure in both lung and liver, with decreasing abundance over time. Adducts persisted even at 72-h after exposure, which indicates possible evasion of DNA repair and potential to contribute to mutagenesis.
Role of Funiculitis in Sonographic Diagnosis of Acute Epididymitis
Authors: Gupta Akshya , Schartz Emily , Schartz Derrek , Baran Timothy , Dogra Vikram S. 
Published: February 2025

Abstract
Ultrasonography is the gold standard for diagnosing acute epididymitis. However, it is not well understood if the simultaneous inflammation of the spermatic cord (funiculitis) is a helpful imaging finding in diagnosing acute epididymitis. This study aimed to investigate the frequency of funiculitis in cases of epididymitis and determine its sensitivity and specificity. This retrospective study included 50 consecutive patients with acute epididymitis. Funiculitis was defined as increased echogenicity of the spermatic cord fat with mass-like cord thickening. All scrotal ultrasound examinations were reviewed for the size of the spermatic cord and surrounding fat, indistinct margins between the spermatic cord and epididymis, similar findings on the contralateral side, and scrotal wall thickening. Spermatic cord inflammation was present in 96% (48/50) of patients with acute epididymitis, significantly higher than in the asymptomatic side (18%, n = 9/50, P < 0.0001). The presence of funiculitis had a sensitivity of 95.9% (confidence interval [CI] 86–99.5%), a specificity of 81.6% (CI 68–91.2%), a positive predictive value of 83.9% (CI 71.7–93%), and a negative predictive value of 95.2% (CI 84–99%) for diagnosing acute epididymitis. The sonographic presence of funiculitis in the setting of acute scrotal pain is a sensitive marker for concomitant acute epididymitis.
High-throughput chemical toxicity testing for beneficial insects: The value of coated vials
Authors: Thia Joshua A. , Digard Julie , Dorai Ashritha P.S. , Brown Courtney , Hoffmann Ary A. 
Published: February 2025

ABSTRACTNon-target effects of insecticides used in agriculture can impact the ecosystem services provided by beneficial insects. Understanding the broader effects of chemical usage requires multi-species investigations on the impact of different insecticide active ingredients. In this work, we tested the utility of coated vials as a quick, cheap, and efficient dried residue chemical toxicity assay. This method was compared against dishes sprayed with a Potter tower, which is an industry standard instrument used to apply precise insecticide doses. Our study focused on 2 natural enemies of aphids, larval and adultHippodamia variegataladybird beetle, and the parasitoid wasp,Diaeretiella rapae. These natural enemies were exposed to multiple doses of 3 insecticides that are registered for aphid control in Australian agriculture: alpha-cypermethrin (pyrethroid), dimethoate (organophosphate), and sulfoxaflor (sulfoximine). Modelled dose-response relationships showed evidence of general differences in the intercepts between methods, but not in slope (rate of mortality with concentration). However, these subtle statistically significant effects did not translate into marked differences in LC50-values, which were comparable across assay methods for all natural enemies and insecticides tested. Coated vials therefore produced estimates of chemical toxicity that were consistent with those derived from Potter tower sprays. This underscores the validity of coated vials as a method for performing high-throughput chemical toxicity experiments, as required when examining different populations of multiple taxa across a range of insecticide active ingredients.
Peritoneal cavity-derived GATA6+macrophages inhibit fibrosis through IL33 in endometrium
Authors: Yin Lijie , Li Jingman , Dong Yue , Wang Jiali , Wang Xiuzhu , Li Yajun , Hu Yali , Hou Yayi , Zhao Guangfeng 
Published: February 2025

AbstractMacrophages exhibit a high degree of plasticity and play pivotal roles both in the normal physiological cycle of the endometrium and in its regeneration following injury. Although some new subsets of endometrial macrophages have been identified, their origins and functions remain to be further explored. In this study, we employed single-cell sequencing to analyze the endometrium of patients with normal endometrium and intrauterine adhesion (IUA) caused by injury. We identified a unique subset of macrophages distinguished by the expression of GATA6, a marker indicative of cavity macrophages. We verified that these GATA6+macrophages were large peritoneal macrophages (LPMs) that migrated from the peritoneal cavity to the injured endometrium. Upon activation by injured endometrium, these LPMs demonstrated increased expression of Interleukin-33 (IL33), mediated by the Lars-Fos signaling axis, which interacts with the IL33 enhancer. Moreover, our studies revealed that IL33 derived from LPMs inhibited the differentiation of endometrial stromal cells (ESCs) into myofibroblasts, a critical step in the development of endometrial fibrosis. Furthermore, we confirmed the inhibitory effect occurred through the binding of IL33 to the ST2 receptor on ESCs, leading to the upregulation of JMJD3 and subsequent suppression of myofibroblast differentiation. Our findings highlight the essential role of LPMs in promoting endometrial repair and inhibiting fibrosis in IUA.Significance StatementThis study reveals the presence of a unique population of macrophages within the endometrium, originating from large peritoneal macrophages (LPMs), that are pivotal in endometrial repair. This finding offers new insights into the plasticity of macrophages and their potential therapeutic applications in treating endometrial fibrotic disorders.
What is expected of people who lead meetings where the goal is to reach consensus? A scoping review with implications for improving the quality of health research grant peer review and clinical guideline development
Authors: Ghannad Mona , Armond Anna Catharina V. , Ng Jeremy Y , Khan Hassan , Giustini Dean , Lasinsky Anne , Sims-Gould Joanie , Blazey Paul , Martino Nadia , Nag Sammy , Mota Adrian , Moher David , Khan Karim M , Ardern Clare L 
Published: February 2025

AbstractBackgroundThe specific roles and responsibilities expected of leaders of consensus-based decision committees, such as grant peer review panels and guideline development panels, are not well-defined, which makes it difficult to train people to lead well. We aimed to explore, describe and define the roles, responsibilities, and leadership characteristics of leaders of meetings where the goal was to reach a consensus decision.MethodsWe conducted a scoping review with thematic synthesis, guided by the Joanna Briggs Institute Scoping Review Methodology, and Arksey & O’Malley’s framework for scoping reviews as refined by Levac et al. We searched five bibliographic databases from January 2002-2023 in English: Medline (Ovid), Embase (Ovid), CINAHL (EBSCO) and PsycInfo (EBSCO); Proquest Digital Dissertations and ABI-Inform. We searched grey literature in the fields of health science, biomedicine, education, psychology, management, law, ethics and policy. Abstracts and full-text articles were screened in duplicate to identify eligible studies; data were extracted regarding the roles, responsibilities and characteristics of consensus decision committee leaders. Themes were constructed using reflexive thematic analysis.ResultsFrom 6732 electronic database records and 126 grey literature records, we included 24 articles and 16 websites. There were 166 unique statements extracted related to roles and responsibilities. We constructed 4 themes to describe the roles for leaders of consensus-based decision meetings: (1)organizer and/or resource manager, (2)facilitator, (3)adjudicatorand, (4)administrator.ConclusionLeaders of consensus committees assumed the roles of organiser and/or resource manager, facilitator, adjudicator and administrator. Better clarification of and training for the expected roles and responsibilities of leading consensus decisions are needed. Establishing the roles and responsibilities can inform a systematic process for evaluating the performance of leaders of consensus decision committees.
ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation’s Functional Effect
Authors: Glaser Moritz , Brägelmann Johannes 
Published: February 2025

AbstractPredicting functional properties of mutations like the change in enzyme activity remains challenging and is not well captured by traditional pathogenicity prediction. Yet such functional predictions are crucial in areas like targeted cancer therapy where some drugs may only be administered if a mutation causes an increase in enzyme activity. Current approaches either leverage static Protein-Language Model (PLM) embeddings or complex multi-modal features (e.g., static PLM embeddings, structure, and evolutionary data) and either (1) fall short in accuracy or (2) involve complex data processing and pre-training. Standardized datasets and metrics for robust benchmarking would benefit model development but do not yet exist for functional effect prediction.To address these challenges we develop ESM-Effect, an optimized PLM-based functional effect prediction framework through extensive ablation studies. ESM-Effect fine-tunes ESM2 PLM with an inductive bias regression head to achieve state-of-the-art performance. It surpasses the multi-modal state-of-the-art method PreMode, indicating redundancy of structural and evolutionary features, while training 6.7-times faster.In addition, we develop a benchmarking framework with robust test datasets and strategies, and propose a novel metric for prediction accuracy termed relative Bin-Mean Error (rBME): rBME emphasizes prediction accuracy in challenging, non-clustered, and rare gain-of-function regions and correlates more intuitively with model performance than commonly used Spearman’s rho. Finally, we demonstrate partial generalization of ESM-Effect to unseen mutational regions within the same protein, illustrating its potential in precision medicine applications. Extending this generalization across different proteins remains a promising direction for future research. ESM-Effect is available at:https://github.com/moritzgls/ESM-Effect.
CD68+Follicular Macrophages Harbor HIV Reservoirs in Human Lymph Node Tissues During Suppressive ART
Authors: Moodley Merantha , Chasara Caroline , Khaba Trevor , Mahlobo Bongiwe , Reddy Nicole , Nxele Sifundo , Msipa Sibongiseni , Reddy Kavidha , Ngubane Thandekile , Jajbhay Ismail , Pansegrouw Johan , Ndung’u Thumbi , Ndhlovu Zaza M. 
Published: February 2025

AbstractUncertainty persists regarding the contribution of tissue macrophages to HIV reservoirs, largely due to insufficient characterization of these reservoirs within their native tissue microenvironments. This study aimed to characterize and quantify macrophage reservoirs in human lymph node (LN) tissues in terms of their phenotype, location, and their potential for sustained productive infection during suppressive antiretroviral therapy.We examined the topology, nature, and size of macrophage reservoirs in lymph nodes (LNs) from 45 PLWH subtype C on suppressive ART and 14 matched controls usingin situimaging and multiplexed immunofluorescence microscopy. Germinal center CD68+macrophages harbored HIVgag-polDNA, HIVgag-polRNA and Gagp24 protein. Digital droplet PCR confirmed the presence of proviral reservoirs in myeloid cells within LNs. High-resolution imaging techniques revealed that infected macrophages within GCs displayed distinct morphological characteristics, featuring larger and irregular shapes. In contrast, phagocytic macrophages exhibited intracellular staining for CD4+T cells, had regular shapes, and were predominantly found outside the GCs.Our findings provide detailed quantitative, spatial, and phenotypic characterization of macrophage reservoirs in LNs, offering a clear estimation of the extent to which macrophages contribute to persistent HIV reservoirs in these tissues. These findings establish a basis for developing targeted strategies aimed at the elimination of these reservoirs in LN tissues.Author summaryHIV hides in reservoirs within immune cells across the body in the blood and various tissues, making it a complex challenge to cure. Therefore, it is essential to identify and understand all sources of HIV reservoirs aid the development of an HIV cure. Macrophages are increasingly recognized as key contributors of viral reservoir persistence. However, the role of macrophages as latent HIV reservoirs remains unclear due to limited studies in human tissues. In this study we investigated macrophage reservoirs in human lymph nodes to answer key questions: where do they hide, how can we identify them, what is their contribution to the lymph node reservoir burden, and are they truly able to support productive viral replication? We found that macrophages residing within lymph node germinal centers, identified by CD68 expression, contained HIV DNA, RNA, and Gagp24 protein. Moreover, using high resolution microscopy, we were able to distinguish between productively infected macrophages from those that engulfed T cells. By unveiling these unique features of macrophage reservoirs, our research paves the way for the design of targeted therapy aimed at eliminating these reservoirs, towards an HIV cure.
The Winner Takes It All: a single genotype ofKalanchoe×houghtoniiis a global invader
Authors: Pascual-Díaz Joan Pere , Besolí Neus , López-Pujol Jordi , Nualart Neus , Pérez-Lorenzo Iván , Shtein Ronen , Valenzuela Laura , Garcia Sònia , Vitales Daniel 
Published: February 2025

AbstractBackground and AimsInvasive alien plant species pose a global challenge, and their impact is amplified by globalisation and the accelerating pace of climate change. In mild-climate regions, drought-tolerant invasive plants showing broad environmental tolerance have a competitive advantage. One example isKalanchoe×houghtonii(Crassulaceae), popularly known as “mother of millions”. It is a hybrid resulting from the interploid cross betweenK. daigremontianaandK. delagoensis, both native to Madagascar.Kalanchoe×houghtonii, propagated as an ornamental plant, has emerged as a global invader in less than a century. Four morphotypes of this hybrid have been identified, with different ploidy levels and varying invasive capacities. Here we aim to investigate the genomic variability behind the invasion success ofKalanchoe×houghtonii.MethodsWe sampled 57 accessions ofKalanchoe×houghtonii, K. daigremontiana, K. delagoensisand closely related taxa, including old herbarium materials, from all over the world. We analysed genome size, chromosome numbers, sequenced the whole genome, analysed the complete plastome sequence of each accession, and studied the diversity of the ribosomal RNA genes. We also performed a detailed phylogenomic study using nuclear BUSCO genes.Key ResultsOur study reveals the genetic and cytogenetic variability between morphotypes, and shows that a single tetraploid genotype (morphotype A) dominates all populations, emerging as the first reported clonal hybrid capable of worldwide colonisation. Morphotype A shows a striking genetic uniformity, high phenotypic plasticity, and extremely high rates of vegetative reproduction, representing an example of a “general-purpose genotype”.ConclusionsThe astonishing reproductive capacity, broad adaptability and the speed at whichK.×houghtoniiis colonising new regions by clonal spread highlight the importance of understanding hybridisation and polyploidy in the invasion of ecosystems. Our findings call for the need for risk assessments before developing new hybrids for ornamental plant breeding that may exhibit invasive characteristics.
Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues
Authors: Heery Richard , Schaefer Martin H 
Published: February 2025

AbstractDNA methylation at gene promoters is generally considered to be associated with transcriptional repression. However, lack of a clear picture of where promoter methylation is most important for transcriptional regulation has hindered our understanding of this relationship and resulted in the use of a wide variety of arbitrary promoter definitions. We demonstrate here that the use of different promoter definitions can lead to contradictory results between studies of promoter methylation. In response, we have developed Methodical, a computational method that combines RNA-seq and whole genome bisulfite sequencing (WGBS) data to identify genomic regions where DNA methylation is highly correlated with transcriptional activity. We refer to these regions as transcript-proximal methylation-associated regulatory sites (TMRs). We applied Methodical to one normal prostate tissue data set, one prostate tumour dataset and one prostate metastases dataset and characterized the identified TMRs. We show that the region just downstream of the TSS, particularly within the first exon and intron, is the most common location for TMRs and that TMRs are enriched for particular genomic features, chromatin states and transcription factor binding sites. Finally, we demonstrate that the methylation of TMRs is generally strongly correlated with transcription in diverse cancer types and that TMRs are highly subject to altered DNA methylation in cancer.