bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candidate genes associated with fatty acid compositions in north American Atlantic salmon (Salmo salar)
Authors: Langille Barbara L. , Juárez Manuel , Prieto Nuria , Boison Solomon , Lim Panya Sae , Swift Bruce D. , Garber Amber F. 
Published: December 2024

AbstractFatty acids are a requirement for normal development, however, since humans are unable to de novo produce essential fatty acids, they must be obtained from diet. Atlantic salmon is a major dietary source of nutritious and digestible fatty acids. Here, we set out to uncover the genomic basis of individual fatty acids and indices (saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, n-3, and n-6) in 208 North American Atlantic salmon, to understand selection potential toward increasing relative quantities of essential fatty acids and to identify candidate genes for future research. Total n-6 (pro-inflammatory) was higher than total n-3 (anti-inflammatory) fatty acids with a ratio of 1 : 1.31 (n-3 : n-6). Heritability of fatty acids ranged from 0 to 0.99, however, most fatty acids and indices had moderate to high heritabilities (ranged from 0.20 to 0.88), implying that selection for improvement of traits could be possible. We found the same significant markers on chromosome 23 (based on false discovery rate thresholds of 2.0e-6 and suggestive significant thresholds of 2.0e-5 in Manhattan plots) in four fatty acids (γ-linoleic acid, stearidonic acid, dihimo-γ-linolenic acid, and eicosatrienoic acid), where three genes (sin3b, acbd6, and fads2) are known to be involved in lipid metabolism. These genes, fads2 in particular, would all make ideal candidates for future functional studies. In addition, there were four fatty acids with loci over the suggestive significant threshold with a variety of markers on different chromosomes (lauric acid, stearic acid, eicosatetraenoic acid (ETA), and docosadienoic acid), with associated genes that had relevant functions to fatty acids or adipose cells in general.
CGRclust: Chaos Game Representation for twin contrastive clustering of unlabelled DNA sequences
Authors: Alipour Fatemeh , Hill Kathleen A. , Kari Lila 
Published: December 2024

Abstract
Background
Traditional supervised learning methods applied to DNA sequence taxonomic classification rely on the labor-intensive and time-consuming step of labelling the primary DNA sequences. Additionally, standard DNA classification/clustering methods involve time-intensive multiple sequence alignments, which impacts their applicability to large genomic datasets or distantly related organisms. These limitations indicate a need for robust, efficient, and scalable unsupervised DNA sequence clustering methods that do not depend on sequence labels or alignment.

Results
This study proposes CGRclust, a novel combination of unsupervised twin contrastive clustering of Chaos Game Representations (CGR) of DNA sequences, with convolutional neural networks (CNNs). To the best of our knowledge, CGRclust is the first method to use unsupervised learning for image classification (herein applied to two-dimensional CGR images) for clustering datasets of DNA sequences. CGRclust overcomes the limitations of traditional sequence classification methods by leveraging unsupervised twin contrastive learning to detect distinctive sequence patterns, without requiring DNA sequence alignment or biological/taxonomic labels. CGRclust accurately clustered twenty-five diverse datasets, with sequence lengths ranging from 664 bp to 100 kbp, including mitochondrial genomes of fish, fungi, and protists, as well as viral whole genome assemblies and synthetic DNA sequences. Compared with three recent clustering methods for DNA sequences (DeLUCS, iDeLUCS, and MeShClust v3.0.), CGRclust is the only method that surpasses 81.70% accuracy across all four taxonomic levels tested for mitochondrial DNA genomes of fish. Moreover, CGRclust also consistently demonstrates superior performance across all the viral genomic datasets. The high clustering accuracy of CGRclust on these twenty-five datasets, which vary significantly in terms of sequence length, number of genomes, number of clusters, and level of taxonomy, demonstrates its robustness, scalability, and versatility.

Conclusion
CGRclust is a novel, scalable, alignment-free DNA sequence clustering method that uses CGR images of DNA sequences and CNNs for twin contrastive clustering of unlabelled primary DNA sequences, achieving superior or comparable accuracy and performance over current approaches. CGRclust demonstrated enhanced reliability, by consistently achieving over 80% accuracy in more than 90% of the datasets analyzed. In particular, CGRclust performed especially well in clustering viral DNA datasets, where it consistently outperformed all competing methods.
A PubMed search filter for efficiently retrieving exercise training studies
Authors: Yin Dawei , Engracia Mikaela V. , Edema Matthew K. , Clarke David C. 
Published: December 2024

Abstract
Background
A barrier to evidence-informed exercise programming is locating studies of exercise training programs. The purpose of this study was to create a search filter for studies of exercise training programs for the PubMed electronic bibliographic database.

Methods
Candidate search terms were identified from three sources: exercise-relevant MeSH terms and their corresponding Entry terms, word frequency analysis of articles in a gold-standard reference set curated from systematic reviews focused on exercise training, and retrospective searching of articles retrieved in the search filter development and testing steps. These terms were assembled into an exercise training search filter, and its performance was assessed against a basic search string applied to six case studies. Search string performance was measured as sensitivity (relative recall), precision, and number needed to read (NNR). We aimed to achieve relative recall ≥ 85%, and a NNR ≥ 2.

Results
The reference set consisted of 71 articles drawn from six systematic reviews. Sixty-one candidate search terms were evaluated for inclusion, 21 of which were included in the finalized exercise-training search filter. The relative recall of the search filter was 96% for the reference set and the precision mean ± SD was 54 ± 16% across the case studies, with the corresponding NNR = ~ 2. The exercise training search filter consistently outperformed the basic search string.

Conclusion
The exercise training search filter fosters more efficient searches for studies of exercise training programs in the PubMed electronic bibliographic database. This search string may therefore support evidence-informed practice in exercise programming.
TB treatment delays and associated risk factors in Dushanbe, Tajikistan, 2019–2021
Authors: Sharifov Radzhabali , Nabirova Dilyara , Tilloeva Zulfiya , Zikriyarova Sanam , Kishore Nishant , Jafarov Navruz , Yusufi Salomuddin , Horth Roberta 
Published: December 2024

Abstract
Background
In Tajikistan, where there are about 8,000 cases annually, many new cases are being diagnosed with severe disease, indicating a delay in receiving care. We aimed to estimate the proportion with delayed care and the main factors contributing to delayed care.

Methods
Using a retrospective cohort design, we conducted a study that included all people aged over 15 years who were newly diagnosed with pulmonary TB in Dushanbe from 2019 to 2021. We defined ‘patient delay’ as > 14 days from TB symptom onset to the first provider visit and ‘provider delay’ as > 3 days from the first visit to treatment initiation. Data was abstracted from medical records and participants were interviewed in-person. Multivariable negative binomial regression was used to estimate adjusted risk ratios (aRR) and 95% confidence intervals (CI).

Results
Of 472 participants, 49% were male, 65% had lung tissue cavitation, 33% had drug resistant TB, 11% had diabetes, 4% had HIV, and. Reported cases dropped from 196 in 2019 to 109 in 2020 and increased to 167 in 2021. The proportion of people experiencing patient delays was 82%, 72%, and 90% per year, respectively. The proportion of provider delays was 44%, 41% and 29% per year. Patient delay was associated with year (aRR: 1.09 [CI:1.02–1.18] in 2021 vs. 2019), age (aRR:0.91 [0.82–0.99] for 40–59-year-olds vs. 15–39-year-olds), having HIV (aRR:1.22 [1.08–1.38]), having blood in sputum (aRR:1.19 [1.10–1.28]), chest pain (aRR:1.32 [1.14–1.54]), having at least two structural barriers vs. none (aRR:1.52 [1.28–1.80]), having one of the following barriers: long wait lines (aRR:1.36 [1.03–1.80]), feeling that healthcare services were expensive (aRR:1.54 [1.28–1.85]), or having no time or too much work (aRR:1.54 [1.29–1.84]). Provider delay was associated with year (aRR: 0.67 [0.51–0.89] in 2021 vs. 2019), patients having to pay for X-ray services (aRR: 1.59 [1.22–2.07]) and lacking direct-observed-therapy (DOTS) in facility (aRR: 1.61 [1.03–2.52]).

Conclusions
Patient delay was high before the COVID-19 pandemic and increased in 2021, while provider delay decreased during this time. Addressing structural barriers to healthcare services, such as increased DOTS facilities, expanded hours, and zero fees, may decrease delays.
A spheroid whole mount drug testing pipeline with machine-learning based image analysis identifies cell-type specific differences in drug efficacy on a single-cell level
Authors: Vitacolonna Mario , Bruch Roman , Schneider Richard , Jabs Julia , Hafner Mathias , Reischl Markus , Rudolf Rüdiger 
Published: December 2024

Abstract
Background
The growth and drug response of tumors are influenced by their stromal composition, both in vivo and 3D-cell culture models. Cell-type inherent features as well as mutual relationships between the different cell types in a tumor might affect drug susceptibility of the tumor as a whole and/or of its cell populations. However, a lack of single-cell procedures with sufficient detail has hampered the automated observation of cell-type-specific effects in three-dimensional stroma-tumor cell co-cultures.

Methods
Here, we developed a high-content pipeline ranging from the setup of novel tumor-fibroblast spheroid co-cultures over optical tissue clearing, whole mount staining, and 3D confocal microscopy to optimized 3D-image segmentation and a 3D-deep-learning model to automate the analysis of a range of cell-type-specific processes, such as cell proliferation, apoptosis, necrosis, drug susceptibility, nuclear morphology, and cell density.

Results
This demonstrated that co-cultures of KP-4 tumor cells with CCD-1137Sk fibroblasts exhibited a growth advantage compared to tumor cell mono-cultures, resulting in higher cell counts following cytostatic treatments with paclitaxel and doxorubicin. However, cell-type-specific single-cell analysis revealed that this apparent benefit of co-cultures was due to a higher resilience of fibroblasts against the drugs and did not indicate a higher drug resistance of the KP-4 cancer cells during co-culture. Conversely, cancer cells were partially even more susceptible in the presence of fibroblasts than in mono-cultures.

Conclusion
In summary, this underlines that a novel cell-type-specific single-cell analysis method can reveal critical insights regarding the mechanism of action of drug substances in three-dimensional cell culture models.
Exploring autism spectrum disorder and co-occurring trait associations to elucidate multivariate genetic mechanisms and insights
Authors: Salenius Karoliina , Väljä Niina , Thusberg Sini , Iris Francois , Ladd-Acosta Christine , Roos Christophe , Nykter Matti , Fasano Alessio , Autio Reija , Lin Jake ,   the GEMMA study
Published: December 2024

Abstract
Background
Autism spectrum disorder (ASD) is a partially heritable neurodevelopmental trait, and people with ASD may also have other co-occurring trait such as ADHD, anxiety disorders, depression, mental health issues, learning difficulty, physical health traits and communication challenges. The concomitant development of ASD and other neurological traits is assumed to result from a complex interplay between genetics and the environment. However, only a limited number of studies have performed multivariate genome-wide association studies (GWAS) for ASD.

Methods
We conducted to-date the largest multivariate GWAS on ASD and 8 ASD co-occurring traits (ADHD, ADHD childhood, anxiety stress (ASDR), bipolar (BIP), disruptive behaviour (DBD), educational attainment (EA), major depression, and schizophrenia (SCZ)) using summary statistics from leading studies. Multivariate associations and central traits were further identified. Subsequently, colocalization and Mendelian randomization (MR) analysis were performed on the associations identified with the central traits containing ASD. To further validate our findings, pathway and quantified trait loci (QTL) resources as well as independent datasets consisting of 112 (45 probands) whole genome sequence data from the GEMMA project were utilized.

Results
Multivariate GWAS resulted in 637 significant associations (p < 5e-8), among which 322 are reported for the first time for any trait. 37 SNPs were identified to contain ASD and one or more traits in their central trait set, including variants mapped to known SFARI ASD genes MAPT, CADPS and NEGR1 as well as novel ASD genes KANSL1, NSF and NTM, associated with immune response, synaptic transmission, and neurite growth respectively. Mendelian randomization analyses found that genetic liability for ADHD childhood, ASRD and DBT has causal effects on the risk of ASD while genetic liability for ASD has causal effects on the risk of ADHD, ADHD childhood, BIP, WA, MDD and SCZ. Frequency differences of SNPs found in NTM and CADPS genes, respectively associated with neurite growth and neural/endocrine calcium regulation, were found between GEMMA ASD probands and controls. Pathway, QTL and cell type enrichment implicated microbiome, enteric inflammation, and central nervous system enrichments.

Conclusions
Our study, combining multivariate GWAS with systematic decomposition, identified novel genetic associations related to ASD and ASD co-occurring driver traits. Statistical tests were applied to discern evidence for shared and interpretable liability between ASD and co-occurring traits. These findings expand upon the current understanding of the complex genetics regulating ASD and reveal insights of neuronal brain disruptions potentially driving development and manifestation.
Differential late-stage face processing in autism: a magnetoencephalographic study of fusiform gyrus activation
Authors: Sarovic Darko , Schneiderman Justin , Lundström Sebastian , Riaz Bushra , Orekhova Elena , Khan Sheraz , Gillberg Christopher 
Published: December 2024

Abstract
Background
Autism is associated with alterations of social communication, such as during face-to-face interactions. This study aimed to probe face processing in autistics with normal IQ utilizing magnetoencephalography to examine event-related fields within the fusiform gyrus during face perception.

Methods
A case–control cohort of 22 individuals diagnosed with autism and 20 age-matched controls (all male, age 29.3 ± 6.9 years) underwent magnetoencephalographic scanning during an active task while observing neutral faces, face-like pareidolic objects, and non-face objects. The fusiform face area was identified using a face localizer for each participant, and the cortical activation pattern was normalized onto an average brain for subsequent analysis.

Results
Early post-stimulus activation amplitudes (before 100–200 ms) indicated differentiation between stimuli containing fundamental facial features and non-face objects in both groups. In contrast, later activation (400–550 ms) differentiated real faces from both pareidolic and non-face objects across both groups and faces from objects in controls but not in autistics. There was no effect of autistic-like traits.

Conclusions
The absence of group differences in early activation suggest intact face detection in autistics possessing a normal IQ. Later activation captures a greater degree of the complexity and social information from actual faces. Although both groups distinguished faces from pareidolic and non-face objects, the control group exhibited a slightly heightened differentiation at this latency, indicating a potential disadvantage for autistics in real face processing. The subtle difference in late-stage face processing observed in autistic individuals may reflect specific cognitive mechanisms related to face perception in autism.
A cross-sectional study applying the PRECEDE model to explore factors influencing epidemic prevention behaviors among preschool educators
Authors: He Yi-Ying , Huang Wei-Hsiang , Tung Chen-Yin 
Published: December 2024

Abstract
Background
This study investigates the epidemic prevention behaviors of preschool educators and the factors influencing these behaviors, applying the PRECEDE model as a framework for analysis.

Methods
A cross-sectional survey was conducted among 190 preschool educators from public and private institutions in Taipei City and New Taipei City. A 64-item self-developed questionnaire was used to assess epidemic prevention behaviors and their determinants. The instrument’s reliability was supported by internal consistency (Cronbach’s α ranging from 0.85 to 0.92), while its validity was confirmed through expert review, item analysis, and confirmatory factor analysis (CFA). Statistical analyses included hierarchical regression to examine the influence of predisposing, reinforcing, and enabling factors on behavior.

Results
The model explained 54% of the variance in epidemic prevention behaviors. Enabling factors had the strongest influence (β = 0.46, p < 0.001), followed by reinforcing factors (β = 0.15, p < 0.05) and predisposing attitudes (β = 0.14, p < 0.05). Background variables, such as age (β = 0.23, p < 0.001) and years of service, collectively explained 14% of the variance.

Conclusion
The findings underscore the critical role of institutional support and professional training in enhancing epidemic prevention practices among preschool educators. Recommendations include integrating disease prevention training into professional development initiatives.
Occupational groups and risk of suicidal behavior in men: a Swedish national cohort study during 2002–2019
Authors: Nyberg Jenny , Wessman Catrin , Söderberg Mia , LaMontagne Anthony D. , Toren Kjell , Waern Margda , Åberg Maria 
Published: December 2024

Abstract
Introduction
The risk of suicide has been shown to vary by occupation. We aim to identify contemporary occupational groups at greatest risk for suicidal behaviour (fatal and non-fatal), in Swedish men of working-age.

Methods
A population-based cohort study of male conscripts without history of self-harm who enlisted during 1968–2001 and were followed-up during 2002–2019 (n = 1 542 665). Occupational groups and suicidal behaviours were identified using national registers. Incidence rate ratios (IRR) for suicidal behaviour at ages 25–65 were calculated among occupational groups, and compared to the incidence rate of the whole cohort.

Results
Major occupational groups with increased risk for suicidal behavior included elementary occupations, building and manufacturing, service, care and shop sale and mechanical manufacturing and transport. Subgroup analyses revealed particularly high risks for assistant nurses, other service workers not elsewhere classified, building frame and related trades workers and cleaners and helpers.

Conclusions
Men with elementary occupations as well as personal care and building and manufacturing workers were at greatest risk. This study provides a comprehensive description of risks for suicidal behaviour among occupational groups in men of working-age. These results suggest occupational groups that should be targeted for general suicide prevention intervention.
A multi-stage approach to support timely health policy decisions during crisis: the fast-track Delphi
Authors: Velarde Crézé Camille , Duperrex Olivier , Lebon Luc , Faivre Vincent , Pasche Myriam , Cornuz Jacques 
Published: December 2024

Abstract
Background
Scientists can play an important role in policymaking by providing evidence and consensual expert opinion on the state of scientific knowledge. Delphi surveys have been widely used to develop consensus on a topical issue, yet not compatible with public health crisis situations requiring rapid decisions. We developed a fast-track Delphi process, providing experts with a structured approach to rapidly develop and quantify consensus in support of informed policy decisions.

Methods
We identified key elements of consensus-building techniques through a literature review and derived methodological procedures that served as the basis for the elaboration of the new process. Selected methodological experts provided advice on necessary adjustments. The process was pilot tested using a real-world public health issue.

Results
The fast-track Delphi process is a hybrid approach between a conventional Delphi and the nominal group technique: one group session followed by two rounds of e-questionnaire, with predefined steps. We developed an ad hoc toolkit (REDCap templates, R code for analysis and production of reports, user guide) to overcome time constraints, which we pilot tested with experts. The feasibility test conducted in 18 days in the field of tobacco control demonstrated the applicability and usefulness of the process in real-world conditions.

Conclusions
We strongly believe that this fast-track Delphi process has the potential to help inform policy decisions in various types of crises, including emerging diseases or novel potentially harmful products.