bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations Among Experiences With Racial Discrimination, Religion/Spirituality, and Cigarette Smoking Among African American Adults: The Jackson Heart Study
Authors: Cottrell-Daniels Cherell , Aycock Dawn M , Pecháček Terry F , Sims Mario , Spears Claire A 
Published: October 2024

Abstract

Background
African American adults exhibit disproportionately high rates of tobacco-related diseases and associated death. Experiences with racial discrimination contribute to health disparities among African Americans, but more research is needed to understand associations between perceived discrimination and tobacco use as well as potential protective factors.

Purpose
This study examined associations between perceived racial discrimination and cigarette smoking, as well as religion and spirituality as moderators of any associations.

Methods
Cross-sectional data were drawn from the Jackson Heart Study, a study of cardiovascular disease risk factors among African American adults in Jackson, MS. Measures included perceived everyday discrimination and major life events discrimination that was attributed to race. Participants also reported religious attendance, prayer, spirituality, and whether they prayed in response to discriminatory experiences. Logistic regression models tested associations between perceived racial discrimination and cigarette smoking status, and interactions between religiosity/spirituality and discrimination in predicting smoking status.

Results
A total of 2,972 participants were included in the analysis (62.7% female, mean age 55.1 years). Thirteen percent reported currently smoking cigarettes. Everyday racial discrimination was associated with a higher likelihood of current smoking (p = .01). The association between lifetime racial discrimination and current smoking status was weaker for those who reported prayer as a reaction compared to those who did not report prayer as a reaction (adjusted odds ratio = 0.32, 95% confidence interval: 0.11 to 0.91) while adjusting for demographics and covariates.

Conclusions
Stressful experiences with racial discrimination may create risks for health behaviors like smoking. However, prayer may act as a coping strategy to help buffer the effects of racial discrimination on smoking behavior.
The case of the kid sister: adapting Enola Holmes for a new generation
Authors: West Nancy 
Published: October 2024

Abstract
In adapting the Enola Holmes book series, the Netflix films rework the figure of the girl sleuth to suit a new generation of feminist viewers. They also provide a deeper exploration of power and the risks of trying to improve a world resistant to change. Netflix also amplifies the stories’ feminism by rehabilitating the ‘toxic’ male figure of Holmes himself.
Methodological challenges and actionable recommendations in studying the health effects of high-concentration THC products
Authors: Li Tianjing , Wang George Sam , Brooks-Russell Ashley , Tung Gregory , Leslie Louis , Rittiphairoj Thanitsara , Oberste Jean-Pierre , Yim Tsz Wing , Bero Lisa , Samet Jonathan M 
Published: October 2024

Abstract
In conducting a scoping review on the health effects of high-concentration cannabis products, we have uncovered pervasive methodological shortcomings within the cannabis literature. This paper begins by defining the ‘causal effect’ of interest for public health and delineating the desirable features of study design that can address crucial questions pertaining to public health and policy. We further delve into the methodological complexities inherent in studying the health effects of high-concentration cannabis products, describing challenges associated with the measurement of exposures and outcomes, confounding, selection bias, and the generalizability of findings. We introduce causal inference methods to mitigate potential biases in observational cannabis use studies. We identify specific areas that necessitate further development and investigation to deepen our understanding of this topic. Finally, this paper extends actionable recommendations, serving as a roadmap for upcoming research initiatives in this domain.
Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity
Authors: Verma Paras , Thakur Deeksha , Pandit Shashi B 
Published: October 2024

Abstract

Motivation
Gene transcripts are distinguished by the composition of their exons, and this different exon composition may contribute to advancing proteome complexity. Despite the availability of alternative splicing information documented in various databases, a ready association of exonic variations to the protein sequence remains a mammoth task.

Results
To associate exonic variation(s) with the protein systematically, we designed the Exon Nomenclature and Classification of Transcripts (ENACT) framework for uniquely annotating exons that tracks their loci in gene architecture context with encapsulating variations in splice site(s) and amino acid coding status. After ENACT annotation, predicted protein features (secondary structure/disorder/Pfam domains) are mapped to exon attributes. Thus, ENACTdb provides trackable exonic variation(s) association to isoform(s) and protein features, enabling the assessment of functional variation due to changes in exon composition. Such analyses can be readily performed through multiple views supported by the server. The exon-centric visualizations of ENACT annotated isoforms could provide insights on the functional repertoire of genes due to alternative splicing and its related processes and can serve as an important resource for the research community.

Availability and implementation
The database is publicly available at https://www.iscbglab.in/enactdb/. It contains protein-coding genes and isoforms for Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens.
AAclust: k-optimized clustering for selecting redundancy-reduced sets of amino acid scales
Authors: Breimann Stephan , Frishman Dmitrij 
Published: October 2024

Abstract

Summary
Amino acid scales are crucial for sequence-based protein prediction tasks, yet no gold standard scale set or simple scale selection methods exist. We developed AAclust, a wrapper for clustering models that require a pre-defined number of clusters k, such as k-means. AAclust obtains redundancy-reduced scale sets by clustering and selecting one representative scale per cluster, where k can either be optimized by AAclust or defined by the user. The utility of AAclust scale selections was assessed by applying machine learning models to 24 protein benchmark datasets. We found that top-performing scale sets were different for each benchmark dataset and significantly outperformed scale sets used in previous studies. Noteworthy is the strong dependence of the model performance on the scale set size. AAclust enables a systematic optimization of scale-based feature engineering in machine learning applications.

Availability and implementation
The AAclust algorithm is part of AAanalysis, a Python-based framework for interpretable sequence-based protein prediction, which is documented and accessible at https://aaanalysis.readthedocs.io/en/latest and https://github.com/breimanntools/aaanalysis.
findGSEP: estimating genome size of polyploid species usingk-mer frequencies
Authors: Fu Laiyi , Xie Yanxin , Ling Shunkang , Wang Ying , Wang Binzhong , Du Hejun , Peng Qinke , Sun Hequan 
Published: October 2024

AbstractSummaryEstimating genome size using k-mer frequencies, which plays a fundamental role in designing genome sequencing and analysis projects, has remained challenging for polyploid species, i.e., ploidy p &gt; 2. To address this, we introduce “findGSEP,” which is designed based on iterative curve fitting of k-mer frequencies. Precisely, it first disentangles up to p normal distributions by analyzing k-mer frequencies in whole genome sequencing of the focal species. Second, it computes the sizes of genomic regions related to 1∼p (homologous) chromosome(s) using each respective curve fitting, from which it infers the full polyploid and average haploid genome size. “findGSEP” can handle any level of ploidy p, and infer more accurate genome size than other well-known tools, as shown by tests using simulated and real genomic sequencing data of various species including octoploids.Availability and implementation“findGSEP” was implemented as a web server, which is freely available at http://146.56.237.198:3838/findGSEP/. Also, “findGSEP” was implemented as an R package for parallel processing of multiple samples. Source code and tutorial on its installation and usage is available at https://github.com/sperfu/findGSEP.
Semi-supervised distribution learning
Authors: Wen Mengtao , Jia Yinxu , Ren Haojie , Wang Zhaojun , Zou Changliang 
Published: October 2024

Abstract
This study addresses the challenge of distribution estimation and inference in a semi-supervised setting. In contrast to prior research focusing on parameter inference, this work explores the complexities of semi-supervised distribution estimation, particularly the uniformity problem inherent in functional processes. To tackle this issue, we introduce a versatile framework designed to extract valuable information from unlabelled data by approximating a conditional distribution on covariates. The proposed estimator is derived using K-fold cross-fitting, and exhibits both consistency and asymptotic Gaussian process properties. Under mild conditions, the proposed estimator outperforms the empirical cumulative distribution function in terms of asymptotic efficiency. Several applications of the methodology are given, including parameter inference and goodness-of-fit tests.
Clustering computer mouse tracking data with informed hierarchical shrinkage partition priors
Authors: Song Ziyi , Shen Weining , Vannucci Marina , Baldizon Alexandria , Cinciripini Paul M , Versace Francesco , Guindani Michele 
Published: October 2024

ABSTRACT
Mouse-tracking data, which record computer mouse trajectories while participants perform an experimental task, provide valuable insights into subjects’ underlying cognitive processes. Neuroscientists are interested in clustering the subjects’ responses during computer mouse-tracking tasks to reveal patterns of individual decision-making behaviors and identify population subgroups with similar neurobehavioral responses. These data can be combined with neuroimaging data to provide additional information for personalized interventions. In this article, we develop a novel hierarchical shrinkage partition (HSP) prior for clustering summary statistics derived from the trajectories of mouse-tracking data. The HSP model defines a subjects’ cluster as a set of subjects that gives rise to more similar (rather than identical) nested partitions of the conditions. The proposed model can incorporate prior information about the partitioning of either subjects or conditions to facilitate clustering, and it allows for deviations of the nested partitions within each subject group. These features distinguish the HSP model from other bi-clustering methods that typically create identical nested partitions of conditions within a subject group. Furthermore, it differs from existing nested clustering methods, which define clusters based on common parameters in the sampling model and identify subject groups by different distributions. We illustrate the unique features of the HSP model on a mouse tracking dataset from a pilot study and in simulation studies. Our results show the ability and effectiveness of the proposed exploratory framework in clustering and revealing possible different behavioral patterns across subject groups.
Coproducing recovery with people affected by substance use and criminalization
Authors: Buck Gillian , Pratt Emma , Yarwood Peter , Arnold Victoria , O’Mara Sarah 
Published: October 2024

Abstract
This study details the coproduction approach taken by Red Rose Recovery (RRR), a non-profit organization that coproduces recovery systems with people affected by substance use and criminalization. RRR is ‘lived-experience-led’ in that those who manage and work for the organization use their own experiences of recovery or desistance from crime to provide inspiration and hope to others. We explored people’s experiences of working with RRR using a ‘photovoice’ research design, where people use cameras to document their realities. Data were analysed collaboratively, offering a depth of insight into the perspectives of people involved. The images and words produced by photographers illustrate this article and indicate that, in contexts of pain, shame, exclusion, and disconnection, coproduced services can offer valued relationships, community, and a sense of belonging within built and natural environments.
Investigating the role of auditory cues in modulating motor timing: insights from EEG and deep learning
Authors: Jounghani Ali Rahimpour , Backer Kristina C , Vahid Amirali , Comstock Daniel C , Zamani Jafar , Hosseini Hadi , Balasubramaniam Ramesh , Bortfeld Heather 
Published: October 2024

Abstract
Research on action-based timing has shed light on the temporal dynamics of sensorimotor coordination. This study investigates the neural mechanisms underlying action-based timing, particularly during finger-tapping tasks involving synchronized and syncopated patterns. Twelve healthy participants completed a continuation task, alternating between tapping in time with an auditory metronome (pacing) and continuing without it (continuation). Electroencephalography data were collected to explore how neural activity changes across these coordination modes and phases. We applied deep learning methods to classify single-trial electroencephalography data and predict behavioral timing conditions. Results showed significant classification accuracy for distinguishing between pacing and continuation phases, particularly during the presence of auditory cues, emphasizing the role of auditory input in motor timing. However, when auditory components were removed from the electroencephalography data, the differentiation between phases became inconclusive. Mean accuracy asynchrony, a measure of timing error, emerged as a superior predictor of performance variability compared to inter-response interval. These findings highlight the importance of auditory cues in modulating motor timing behaviors and present the challenges of isolating motor activation in the absence of auditory stimuli. Our study offers new insights into the neural dynamics of motor timing and demonstrates the utility of deep learning in analyzing single-trial electroencephalography data.
Mortality associated with the COVID-19 pandemic in the Swiss dialysis population beyond SARS-CoV-2 infection
Authors: Jaques David A , Hoessly Linard , Guidotti Rebecca , Koller Michael , Ponte Belen , Ambühl Patrice 
Published: October 2024

ABSTRACT

Background
While SARS-CoV-2 infection has direct obvious consequences on patients undergoing dialysis, the COVID-19 pandemic also had an indirect impact on health systems. Therefore, we aimed to determine whether the COVID-19 era itself was associated with adverse consequences in the Swiss dialysis population as compared to the pre-COVID-19 era, while accounting for direct impact of SARS-CoV-2 infection.

Methods
We retrospectively included all patients recorded in the Swiss dialysis registry from January 2014 to December 2022. The pre-COVID-19 era and the COVID-19 era were defined based on the cut-off date of January 2020. Cox proportional hazard model was used with all-cause mortality as the primary outcome.

Results
The cohort consisted of 7837 patients from 97 dialysis centres. Median age was 68.6 years with 66.1% men. Crude mortality rates were 11.6% (11.0% to 12.2%) and 14.2% (13.4% to 14.9%) person-years for the pre-COVID-19 era and the COVID-19 era, respectively. In multivariable analysis, SARS-CoV-2 infection was associated with an increased risk of mortality (HR 4.26, 95% CI 3.65 to 4.97, P &lt; .001) while the COVID-19 era itself was not (HR 0.98, 95% CI 0.88 to 1.08, P = .687).

Conclusions
The COVID-19 era was not associated with an excess of mortality in the Swiss dialysis population as compared to the pre-COVID-19 era when accounting for the direct effect of SARS-CoV-2 infection. This suggests that control measures established during the pandemic did not have a negative impact on dialysis patients at the national level. These results could inform health policy makers in the eventuality of future pandemics.
Navigating Reproductive Care in Patients With Inflammatory Bowel Disease: A Comprehensive Review
Authors: Sousa Paula , Gisbert Javier P , Julsgaard Mette , Selinger Christian Philipp , Chaparro María 
Published: October 2024

Abstract
Inflammatory bowel disease [IBD] is often diagnosed in patients during their reproductive years. It is crucial that both healthcare providers and patients are adequately informed to avoid misguided decisions regarding family planning.
One of the most important aspects during conception and pregnancy is to maintain disease remission, as disease activity is associated with adverse pregnancy outcomes. Apart from methotrexate, most conventional drugs used in IBD are considered low risk during conception and pregnancy. For newer agents, evidence is still limited. If needed, surgery must not be postponed and should ideally be performed in specialized centres.
In most patients, delivery should be vaginal except for patients with complex perianal disease, with an ileoanal pouch anastomosis, or if there is an obstetric contraindication.
In children exposed to biological treatments during pregnancy, the risk of infections appears to be low, and psychomotor development is probably not affected. Regarding immunizations, the standard vaccination schedule for inactivated vaccines should be followed for children exposed to biologics in utero. In the case of live vaccines, such as rotavirus, decisions should be individualized and take into consideration the risk–benefit ratio, particularly in developing countries.
In this review, we provide a comprehensive and updated overview of aspects related to fertility, pregnancy, breastfeeding, and the impact on the care of children born to mothers with IBD. Both the available evidence and areas of uncertainty are discussed, with the goal of assisting healthcare professionals caring for IBD patients during this important stage of their lives.
Epidemiology of Inflammatory Bowel Disease across the Ages in the Era of Advanced Therapies
Authors: Caron Bénédicte , Honap Sailish , Peyrin-Biroulet Laurent 
Published: October 2024

Abstract

Background and Aims
The incidence of inflammatory bowel diseases [IBD] has risen over the past decade to become a global issue. The objectives of this review were to describe the incidence and/or prevalence of IBD in the era of advanced therapies, and to describe the association between environmental risk factors and both pathogenesis and disease course across the ages.

Methods
We performed a search of English language publications listed in PubMed regarding the epidemiology of IBD and key environmental factors implicated in IBD from January 2000 to December 2023.

Results
Annual incidence rates varied by geographical region with IBD estimates ranging from 10.5 to 46.14 per 100 000 in Europe, 1.37 to 1.5 per 100 000 in Asia and the Middle East, 23.67 to 39.8 per 100 000 in Oceania, 0.21 to 3.67 per 100 000 in South America, and 7.3 to 30.2 per 100 000 in North America. The burden of IBD among children and adolescents, and older people is rising globally. Key environmental factors implicated in IBD pathogenesis include exposure to tobacco smoking, antibiotics, non-steroidal anti-inflammatory drugs, oral contraceptives, infections, and ultra-high processed foods. Breastfeeding and a high-quality diet rich in fruit, vegetables, fish, and other fibre sources are important protective factors. Smoking has consistently been shown to negatively impact disease outcomes for Crohn’s disease.

Conclusion
The epidemiology of IBD has undergone considerable change in recent decades, with an increase in the burden of disease worldwide. Optimally studying and targeting environmental triggers in IBD may offer future opportunities for disease modification.
Considerations in Paediatric and Adolescent Inflammatory Bowel Disease
Authors: Vuijk Stephanie A , Camman Anouk E , de Ridder Lissy 
Published: October 2024

AbstractThe incidence of inflammatory bowel disease [IBD] is rising most rapidly among children and adolescents. Paediatric-onset IBD is associated with a more extensive and severe disease course compared to adult-onset IBD. At a young age, screening for underlying genetic and immunological disorders is important and may impact treatment management. Early and effective treatment is crucial to reach disease remission and prevent complications of ongoing active disease. In children with Crohn’s disease, exclusive enteral nutrition is an effective induction therapy. Other promising dietary therapies, such as the Crohn’s disease exclusion diet, are emerging. Within paediatric IBD, anti-tumour necrosis factor therapy is the only approved biological thus far and additional treatment options are crucially needed. Other biological therapies, such as vedolizumab and ustekinumab, are currently prescribed off-label in this population. A specific challenge in paediatric IBD is the unacceptable and major delay in approval of drugs for children with IBD. A guided transfer period of paediatric patients to adult care is associated with improved disease outcomes and is required. Major knowledge gaps and challenges within paediatric IBD include the aetiology, diagnostics, and monitoring of disease, tailoring of treatment, and both understanding and coping with the physical and psychological consequences of living with IBD. Challenges and research gaps in paediatrics should be addressed without any delay in comparison with the adult field, in order to ensure a high quality of care for all patients with IBD, irrespective of the age of onset.
Framework of IBD Care Delivery Across Ages
Authors: Delen Stefan , Jaghult Susanna , Blumenstein Irina , Pouillon Lieven , Bossuyt Peter 
Published: October 2024

Abstract
IBD care has gone through a real transformation over the last century, moving from the mere unidirectional interaction between the physician and the patient to a stronger framework with multiple stakeholders who interconnect and strengthen each other. The patient has evolved from a passive subject to the central pole in the care pathway. Key elements of the future framework include patient self-care and empowerment, and remote monitoring [eHealth]. This care will be delivered by a multidisciplinary team acknowledging the pivotal role of the IBD nurse, and emphasising and measuring the quality of its work. The big challenge for the future is to establish a financially viable model to make this evolution durable in the long term, and this by using the principles of value-based health care.