bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a Telehealth Smoking Cessation Program in Primarily Socioeconomically Disadvantaged Black Patients: Courage to Quit Rolling-Virtual (CTQ-RV)
Authors: Brett Emma I , Fridberg Daniel J , Lee Zoe , Feather Abigayle R , King Andrea C 
Published: October 2024

Abstract

Background
Preliminary data indicate that smoking cessation offered in a rolling group format is feasible and effective.

Purpose
The current study evaluated the implementation and outcomes of the remote Courage to Quit-Rolling Virtual (CTQ-RV) smoking group treatment compared to its precursor in-person format (Courage to Quit-Rolling, CTQ-R).

Methods
Virtual materials for CTQ-RV were adapted from in-person evidence-based programming, thus content in both groups was similar but delivered via videoconference or in-person. We used an interrupted time series design to examine feasibility by comparing attendance, monthly enrollment, and program completion between those who attended CTQ-R (July 2018-March 2020) versus CTQ-RV (April 2020—December 2022).

Results
There were 611 patients enrolled in tobacco cessation (N = 221 CTQ-R, N = 390 CTQ-RV). The average age was 59.4 years and most patients reported Black/African American race (81%) and female sex (69.5%). CTQ-RV proved feasible relative to CTQ-R, with higher rates of attendance (5.5 vs. 2.7 sessions, respectively), program completion (39.4% vs. 19%) and increased enrollment across each year (from 44.6 sessions per month in CTQ-R vs. 72.3 in CTQ-RV). CTQ-RV patients requested nicotine replacement therapy (NRT) at substantially higher rates (81.4%) than CTQ-R members (42.1%). Self-reported smoking abstinence at final session was higher in CTQ-RV compared with CTQ-R (33.3% vs. 15.7%). Within CTQ-RV, more than half (57%) of patients attended by video format, with outreach improving rates of video attendance each year.

Conclusions
Results show that a transition to virtual rolling enrollment smoking group treatment is feasible and can augment treatment outcomes, such as engagement, NRT use, and self-reported cessation.
Genomic analyses of the southern and eastern yellowjacket wasps (Hymenoptera: Vespidae) reveal evolutionary signatures of social life
Authors: Catto Michael A , Caine Paige B , Orr Sarah E , Hunt Brendan G , Goodisman Michael A D 
Published: October 2024

Abstract
Insects have evolved remarkably complex social systems. Social wasps are particularly noteworthy because they display gradations in social behaviors. Here, we sequence the genomes of two highly diverged Vespula wasps, V. squamosa and V. maculifrons Buysson (Hymenoptera: Vespidae), to gain greater insight into the evolution of sociality. Both V. squamosa and V. maculifrons are social wasps that live in large colonies characterized by distinct queen and worker castes. However, V. squamosa is a facultative social parasite, and V. maculifrons is its frequent host. We found that the genomes of both species were ~200 Mbp in size, similar to the genome sizes of congeneric species. Analyses of gene expression from members of different castes and developmental stages revealed similarities in expression patterns among immature life stages. We also found evidence of DNA methylation within the genome of both species by directly analyzing DNA sequence reads. Moreover, genes that were highly and uniformly expressed were also relatively highly methylated. We further uncovered evidence of differences in patterns of molecular evolution in the two taxa, consistent with V. squamosa exhibiting alterations in evolutionary pressures associated with its facultatively parasitic or polygyne life history. Finally, rates of gene evolution were correlated with variation in gene expression between castes and developmental stages, as expected if more highly expressed genes were subject to stronger levels of selection. Overall, this study expands our understanding of how social behavior relates to genome evolution in insects.
Risk of SARS-CoV-2 infection in healthcare workers with insufficient use of personal protective equipment in Denmark
Authors: Bungum Ane Berger , Tøttenborg Sandra Søgaard , Begtrup Luise Mølenberg , Petersen Kajsa Ugelvig , Worm Maja Søndergård , Bonde Jens Peter , Dalbøge Annett , Kinnerup Martin Byskov , Würtz Else Toft , Kolstad Henrik Albert , Schlünssen Vivi , Cramer Christine , Biering Karin , Nielsen Kent Jacob , Meulengracht Flachs Esben 
Published: October 2024

Abstract

Aim
The aim was to evaluate the role of insufficient use of personal protective equipment (PPE) in SARS-CoV-2 transmission risk for healthcare workers (HCW) during the COVID-19 pandemic.

Methods
Prospective study within the COBRA cohort, including 15,127 HCW. Daily assessment of insufficient use of PPE, defined as self-reported PPE failure or noncompliance, in relation to SARS-CoV-2 infection ascertained by polymerase chain reaction (PCR) test. Statistical analysis involved calculating incidence rate ratios with 95% confidence intervals (CI).

Results
The included HCW contributed to 780,515 risk days including 67,723 d (8.7%) with insufficient PPE use and 133 events (positive PCR test). Self-reported insufficient use of PPE was slightly associated with infection with COVID-19 in HCW, but the data were statistically consistent with parameter values ranging from a protective effect to a to a doubling in risk (IRR 1.3, 95% CI 0.8; 2.3). Sensitivity analyses restricted to high-risk departments and to a period with a sufficient supply of PPE and a fully developed testing system, respectively, confirmed these findings.

Conclusion
Insufficient use of PPE among HCW during the pandemic in Denmark was uncommon but associated with a slightly increased risk of COVID-19 among HCW. However, the findings are uncertain due to the limited number of cases and the potential for misclassification bias stemming from the self-reported nature of the exposure.
A multi-omics study of brain tissue transcription and DNA methylation revealing the genetic pathogenesis of ADHD
Authors: Wang Jingkai , Zhu Qiu-Wen , Mai Jia-Hao , Zhang Shun , Wang Yuqing , Liang Jiatong , Zhou Ji-Yuan 
Published: October 2024

Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a chronic psychiatric disease that often affects a patient’s whole life. Research has found that genetics plays an important role in the development of ADHD. However, there is still a lack of knowledge about the tissue-specific causal effects of biological processes beyond gene expression, such as alternative splicing (AS) and DNA methylation (DNAm), on ADHD. In this paper, a multi-omics study was conducted to investigate the causal effects of the transcription and the DNAm on ADHD, by integrating ADHD genome-wide association data with quantitative trait loci data of gene expression, AS, and DNAm across 14 different brain tissues. The causal effects were estimated using four different two-sample Mendelian randomization methods. Finally, we also prioritized the expression of 866 genes showing significant causal effects, including COMMD5, ENSG00000271904, HYAL3, etc., within at least one brain tissue. We prioritized 966 unique genes that have statistically significant causal AS events, within at least one of the 14 different brain tissues. These genes include PPP1R16A, GGT7, TREM2, etc. Furthermore, through mediation analysis, 106 regulatory pathways were inferred where DNAm influences ADHD through gene expression or AS processes. Our research findings provide guidance for future experimental studies on the molecular mechanisms of ADHD development, and also put forward valuable knowledge for the prevention, diagnosis, and treatment of ADHD.
MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides
Authors: Yan Chaorui , Geng Aoyun , Pan Zhuoyu , Zhang Zilong , Cui Feifei 
Published: October 2024

Abstract
Inflammatory responses may lead to tissue or organ damage, and proinflammatory peptides (PIPs) are signaling peptides that can induce such responses. Many diseases have been redefined as inflammatory diseases. To identify PIPs more efficiently, we expanded the dataset and designed an ensemble learning model with manually encoded features. Specifically, we adopted a more comprehensive feature encoding method and considered the actual impact of certain features to filter them. Identification and prediction of PIPs were performed using an ensemble learning model based on five different classifiers. The results show that the model's sensitivity, specificity, accuracy, and Matthews correlation coefficient are all higher than those of the state-of-the-art models. We named this model MultiFeatVotPIP, and both the model and the data can be accessed publicly at https://github.com/ChaoruiYan019/MultiFeatVotPIP. Additionally, we have developed a user-friendly web interface for users, which can be accessed at http://www.bioai-lab.com/MultiFeatVotPIP.
HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights
Authors: Su Xinwan , Shi Chengyu , Liu Fangzhou , Tan Manman , Wang Ying , Zhu Linyu , Chen Yu , Yu Meng , Wang Xinyi , Liu Jian , Liu Yang , Lin Weiqiang , Fang Zhaoyuan , Sun Qiang , Zhou Tianhua , Lin Aifu 
Published: October 2024

Abstract
Advancements in peptidomics have revealed numerous small open reading frames with coding potential and revealed that some of these micropeptides are closely related to human cancer. However, the systematic analysis and integration from sequence to structure and function remains largely undeveloped. Here, as a solution, we built a workflow for the collection and analysis of proteomic data, transcriptomic data, and clinical outcomes for cancer-associated micropeptides using publicly available datasets from large cohorts. We initially identified 19 586 novel micropeptides by reanalyzing proteomic profile data from 3753 samples across 8 cancer types. Further quantitative analysis of these micropeptides, along with associated clinical data, identified 3065 that were dysregulated in cancer, with 370 of them showing a strong association with prognosis. Moreover, we employed a deep learning framework to construct a micropeptide-protein interaction network for further bioinformatics analysis, revealing that micropeptides are involved in multiple biological processes as bioactive molecules. Taken together, our atlas provides a benchmark for high-throughput prediction and functional exploration of micropeptides, providing new insights into their biological mechanisms in cancer. The HMPA is freely available at http://hmpa.zju.edu.cn.
Mut-Map: Comprehensive Computational Pipeline for Structural Mapping and Analysis of Cancer-Associated Mutations
Authors: Alsulami Ali F 
Published: October 2024

Abstract
Understanding the functional impact of genetic mutations on protein structures is essential for advancing cancer research and developing targeted therapies. The main challenge lies in accurately mapping these mutations to protein structures and analysing their effects on protein function. To address this, Mut-Map (https://genemutation.org/) is a comprehensive computational pipeline designed to integrate mutation data from the Catalogue Of Somatic Mutations In Cancer database with protein structural data from the Protein Data Bank and AlphaFold models. The pipeline begins by taking a UniProt ID and proceeds through mapping corresponding Protein Data Bank structures, renumbering residues, and assessing disorder percentages. It then overlays mutation data, categorizes mutations based on structural context, and visualizes them using advanced tools like MolStar. This approach allows for a detailed analysis of how mutations may disrupt protein function by affecting key regions such as DNA interfaces, ligand-binding sites, and dimer interactions. To validate the pipeline, a case study on the TP53 gene, a critical tumour suppressor often mutated in cancers, was conducted. The analysis highlighted the most frequent mutations occurring at the DNA-binding interface, providing insights into their potential role in cancer progression. Mut-Map offers a powerful resource for elucidating the structural implications of cancer-associated mutations, paving the way for more targeted therapeutic strategies and advancing our understanding of protein structure–function relationships.
Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data
Authors: Wang Zhen , Fang Yanhua , Wang Ruoyu , Kong Liwen , Liang Shanshan , Tao Shuai 
Published: October 2024

Abstract
The heterogeneity of tumor clones drives the selection and evolution of distinct tumor cell populations, resulting in an intricate and dynamic tumor evolution process. While tumor bulk DNA sequencing helps elucidate intratumor heterogeneity, challenges such as the misidentification of mutation multiplicity due to copy number variations and uncertainties in the reconstruction process hinder the accurate inference of tumor evolution. In this study, we introduce a novel approach, REconstructing Tumor Clonal Heterogeneity and Evolutionary Relationships (RETCHER), which characterizes more realistic cancer cell fractions by accurately identifying mutation multiplicity while considering uncertainty during the reconstruction process and the credibility and reasonableness of subclone clustering. This method comprehensively and accurately infers multiple forms of tumor clonal heterogeneity and phylogenetic relationships. RETCHER outperforms existing methods on simulated data and infers clearer subclone structures and evolutionary relationships in real multisample sequencing data from five tumor types. By precisely analysing the complex clonal heterogeneity within tumors, RETCHER provides a new approach to tumor evolution research and offers scientific evidence for developing precise and personalized treatment strategies. This approach is expected to play a significant role in tumor evolution research, clinical diagnosis, and treatment. RETCHER is available for free at https://github.com/zlsys3/RETCHER.
Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis
Authors: Mongardi Sofia , Cascianelli Silvia , Masseroli Marco 
Published: October 2024

Abstract

Motivation
Feature selection approaches are widely used in gene expression data analysis to identify the most relevant features and boost performance in regression and classification tasks. However, such algorithms solely consider each feature’s quantitative contribution to the task, possibly limiting the biological interpretability of the results. Feature-related prior knowledge, such as functional annotations and pathways information, can be incorporated into feature selection algorithms to potentially improve model performance and interpretability.

Results
We propose an embedded integrative approach to feature selection that combines weighted LASSO feature selection and prior biological knowledge in a single step, by means of a novel score of biological relevance that summarizes information extracted from popular biological knowledge bases. Findings from the performed experiments indicate that our proposed approach is able to identify the most predictive genes while simultaneously enhancing the biological interpretability of the results compared to the standard LASSO regularized model.

Availability and implementation
Code is available at https://github.com/DEIB-GECO/GIS-weigthed_LASSO.
Application of new genre public art in community empowerment: a case study of Chongqing Tie Lu San Cun Village, China
Authors: Chen Guanxi , Lee Min 
Published: October 2024

Abstract

Purpose
This paper aims to explore the necessity of using new genre public art (NGPA) to enhance community empowerment based on the characteristics of this art form and in conjunction with community empowerment theory. The study analyzes representative cases of NGPA to investigate its potential for strengthening community empowerment.

Methodology
The research primarily employs a case study approach, which selects samples based on their influence and project sustainability to examine the characteristics of NGPA.

Content
The study first analyzes the theories and characteristics of community empowerment and NGPA. Then, it selects the community practice activities of NGPA in Chongqing’s Tie Lu San Cun Village (Railway Third Village) as a case for empowerment analysis. Finally, it discusses the achievements of the project and the areas that need improvement.

Conclusion and recommendations
The findings show that NGPA can enhance community empowerment. They propose methods for improving areas that need enhancement and provide academic insights for policymakers to support artistic practices due to their benefits for community empowerment.
Antiphospholipid antibody positivity is associated with maturation failure and thrombosis of native arteriovenous fistula: a retrospective study in HD patients
Authors: Taghavi Maxime , Jacobs Lucas , Demulder Anne , Jabrane Abla , Mesquita Maria Do Carmo Filomena , Defawe Catherine , Laureys Marc , Dernier Yves , Pozdzik Agnieszka , Collart Frédéric , Nortier Joëlle 
Published: October 2024

ABSTRACT

Background and hypothesis
The prevalence of antiphospholipid antibody (aPL) is high among hemodialysis (HD) patients compared to the general population and is inconsistently associated with arteriovenous fistula (AVF) thrombosis or stenosis. The association with maturation failure has never been investigated. This study aims to evaluate native AVF complications (thrombosis, stenosis, and maturation failure) and primary patency in aPL positive HD patients.

Methods
We retrospectively identified 116 HD patients with native AVF. We collected the aPL profiles, the clinical and biological data potentially involved in AVF maturation failure, thrombosis, and stenosis, and investigated the association of these complications and aPL positivity. Kaplan–Meier survival analysis was performed.

Results
In our cohort, the prevalence of aPL persistent positivity was 32.7% and this was strongly associated with AVF maturation failure defined by ultrasound. aPL persistent positivity was a strong predictor in multivariate analysis and this association was independent of AVF stenosis or thrombosis during maturation process. There was no association with primary and functional primary patency, and stenosis. However, aPL persistent positivity according to ACR/EULAR classification criteria was associated with thrombosis when compared to strictly negative aPL patients.

Conclusions
In our cohort, aPL persistent positivity was significantly associated with AVF maturation failure and thrombosis but not with AVF stenosis. To our knowledge, we report for the first time, a statistically significant association between aPL positivity and delay or absence of native AVF maturation.
Lingual artery thrombosis as a presentation of infective endocarditis in a pregnant patient: a case report
Authors: Castillo Martín , Hanuch Francisca , Rauch Geraldine , Avendaño Patricio , Cuevas Oscar 
Published: October 2024

Abstract

Background
Infective endocarditis during pregnancy is a rare condition that compromises the health of both the mother and the foetus, presenting high rates of morbidity and mortality. The clinical manifestations of this disease are varied, with embolic phenomena being a frequent presentation.

Case summary
We report the case of a Hispanic 37-year-old patient, at 29 weeks of pregnancy, with no known cardiovascular history, who presented with 48 h of sudden mandibular and lingual pain. The study showed acute thrombosis of the right lingual artery and the rest of the right external carotid artery. In this context, searching for the origin of the embolism, acute mitral valve endocarditis was diagnosed, which was effectively treated with antibiotic therapy and biological mitral valve replacement, as well as early delivery.

Discussion
We report the first case where lingual artery thrombosis was the key diagnostic feature of infective endocarditis.
Word of caution: clinically apparent coronary spasm following pulsed field cavotricuspid isthmus ablation despite nitroglycerin prophylaxis - a case report
Authors: Gunawardene Melanie A , Hartmann Jens , Tigges Eike , Jezuit Johanna , Willems Stephan 
Published: October 2024

Abstract

Background
Pulsed field ablation (PFA) is a novel ablation technology. A rare side-effect is the occurrence of mostly subclinical coronary spasms when PF energy is applied in proximity to coronary arteries. However, it has been described that prior application of nitroglycerin attenuates these effects.

Case summary
A 75-year-old female underwent catheter ablation with a penta-spline PFA catheter. After pulmonary vein isolation, the PFA catheter was positioned on the cavotricuspid isthmus (CTI). Before ablation, 2 mg of nitroglycerin was administered intravenously. After 10 PFA applications, the CTI was successfully blocked. After a timely delay of 95 s, a clinically apparent vasospasm with ST elevations in leads II, III, and aVF on the electrocardiogram was noticed. Shortly thereafter, the clinical course was aggravated by haemodynamically relevant non-sustained ventricular tachycardias (nsVTs) followed by asystole, requiring pacing and additional 4 mg of nitroglycerin. Twelve minutes later, a stable sinus rhythm with normalized ST segments was restored. The spasm resolved without any sequelae. Post-procedural coronary angiogram showed right dominant coronary circulation.

Discussion
This is the first report of a timely delayed, clinically apparent coronary spasm with a presentation of haemodynamically relevant nsVT and asystole despite the prophylactic application of high-dose intravenous nitroglycerin prior to PFA along the CTI. Subclinical vasospasm during PFA at the CTI has been described before. Severe spasms could be prevented by nitroglycerin. A word of caution needs to be raised as prophylactic nitroglycerin did not prevent the haemodynamically relevant coronary spasm in the here reported patient. Until now, it remains unclear how much later such effects may occur; therefore, patients should be monitored closely.
Use, limitations, and future directions of mixtures approaches to understand the health impacts of weather- and climate change-related exposures, an under-studied aspect of the exposome
Authors: Do Vivian , Parks Robbie M , Casey Joan A , Goin Dana E , Kioumourtzoglou Marianthi-Anna 
Published: October 2024

Abstract
The exposome concept aims to account for the comprehensive and cumulative effects of physical, chemical, biological, and psychosocial influences on biological systems. To date, limited exposome research has explicitly included climate change-related exposures. We define these exposures as those that will intensify with climate change, including direct effects like extreme heat, tropical cyclones, wildfires, downstream effects like air pollution, power outages, and limited or contaminated food and water supplies. These climate change-related exposures can occur individually or simultaneously. Here, we discuss the concept of a climate mixture, defined as three or more simultaneous climate change-related exposures, in the context of the exposome. In a motivating climate mixture example, we consider the impact of a co-occurring tropical cyclone, power outage, and flooding on respiratory hospitalizations. We identify current gaps and future directions for assessing the effect of climate mixtures on health. Mixtures methods allow us to incorporate climate mixtures into exposomics.