bluuebunny/crossref_metadata_2025_split huggingface dataset:
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events
Authors: Richardson Mary O. , Eddy Sean R. 
Published: December 2023

Abstract
Background
In canonical protein translation, ribosomes initiate translation at a specific start codon, maintain a single reading frame throughout elongation, and terminate at the first in-frame stop codon. However, ribosomal behavior can deviate at each of these steps, sometimes in a programmed manner. Certain mRNAs contain sequence and structural elements that cause ribosomes to begin translation at alternative start codons, shift reading frame, read through stop codons, or reinitiate on the same mRNA. These processes represent important translational control mechanisms that can allow an mRNA to encode multiple functional protein products or regulate protein expression. The prevalence of these events remains uncertain, due to the difficulty of systematic detection.

Results
We have developed a computational model to infer non-canonical translation events from ribosome profiling data.

Conclusion
ORFeus identifies known examples of alternative open reading frames and recoding events across different organisms and enables transcriptome-wide searches for novel events.
Investigating the impact of non-additive genetic effects in the estimation of variance components and genomic predictions for heat tolerance and performance traits in crossbred and purebred pig populations
Authors: de Oliveira Letícia Fernanda , Brito Luiz F. , Marques Daniele Botelho Diniz , da Silva Delvan Alves , Lopes Paulo Sávio , dos Santos Cassiane Gomes , Johnson Jay S. , Veroneze Renata 
Published: December 2023

Abstract
Background
Non-additive genetic effects are often ignored in livestock genetic evaluations. However, fitting them in the models could improve the accuracy of genomic breeding values. Furthermore, non-additive genetic effects contribute to heterosis, which could be optimized through mating designs. Traits related to fitness and adaptation, such as heat tolerance, tend to be more influenced by non-additive genetic effects. In this context, the primary objectives of this study were to estimate variance components and assess the predictive performance of genomic prediction of breeding values based on alternative models and two independent datasets, including performance records from a purebred pig population and heat tolerance indicators recorded in crossbred lactating sows.

Results
Including non-additive genetic effects when modelling performance traits in purebred pigs had no effect on the residual variance estimates for most of the traits, but lower additive genetic variances were observed, especially when additive-by-additive epistasis was included in the models. Furthermore, including non-additive genetic effects did not improve the prediction accuracy of genomic breeding values, but there was animal re-ranking across the models. For the heat tolerance indicators recorded in a crossbred population, most traits had small non-additive genetic variance with large standard error estimates. Nevertheless, panting score and hair density presented substantial additive-by-additive epistatic variance. Panting score had an epistatic variance estimate of 0.1379, which accounted for 82.22% of the total genetic variance. For hair density, the epistatic variance estimates ranged from 0.1745 to 0.1845, which represent 64.95–69.59% of the total genetic variance.

Conclusions
Including non-additive genetic effects in the models did not improve the accuracy of genomic breeding values for performance traits in purebred pigs, but there was substantial re-ranking of selection candidates depending on the model fitted. Except for panting score and hair density, low non-additive genetic variance estimates were observed for heat tolerance indicators in crossbred pigs.
Chromosome-scale genome assembly of the ‘Munstead’ cultivar of Lavandula angustifolia
Authors: Hamilton John P. , Vaillancourt Brieanne , Wood Joshua C. , Wang Haiyan , Jiang Jiming , Soltis Douglas E. , Buell C. Robin , Soltis Pamela S. 
Published: December 2023

Abstract
Objectives
Lavandula angustifolia (English lavender) is commercially important not only as an ornamental species but also as a major source of fragrances. To better understand the genomic basis of chemical diversity in lavender, we sequenced, assembled, and annotated the ‘Munstead’ cultivar of L. angustifolia.

Data description
A total of 80 Gb of Oxford Nanopore Technologies reads was used to assemble the ‘Munstead’ genome using the Canu genome assembler software. Following multiple rounds of error correction and scaffolding using Hi-C data, the final chromosome-scale assembly represents 795,075,733 bp across 25 chromosomes with an N50 scaffold length of 31,371,815 bp. Benchmarking Universal Single Copy Orthologs analysis revealed 98.0% complete orthologs, indicative of a high-quality assembly representative of genic space. Annotation of protein-coding sequences revealed 58,702 high-confidence genes encoding 88,528 gene models. Access to the ‘Munstead’ genome will permit comparative analyses within and among lavender accessions and provides a pivotal species for comparative analyses within Lamiaceae.
Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships
Authors: Hamza Hammadi , Villa Sara , Torre Sara , Marchesini Alexis , Benabderrahim Mohamed Ali , Rejili Mokhtar , Sebastiani Federico 
Published: December 2023

Abstract
Background
Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail.

Results
Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico.

Conclusions
The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.
Where the joy comes from: a qualitative exploration of deep GP-patient relationships
Authors: Thomas Hayley , Lynch Johanna , Burch Emily , Best Megan , Ball Lauren , Sturgiss Elizabeth , Sturman Nancy 
Published: December 2023

Abstract
Background
Relationship-based, whole person care is foundational to quality general practice. Previous research has identified several characteristics of deep General Practitioner (GP)-patient relationships and their association with improved patient concordance, satisfaction and perceived health outcomes. Psychological attachment theory has been used to understand therapeutic relationships, but has only been explored to a limited extent in the general practice context. Additionally, evolving changes in sociocultural and commercial practice contexts may threaten relationship-based care. In view of this, we aimed to explore the nature and experience of deep GP-patient relationships, as identified by patients, from GP and patient perspectives.

Methods
Semi-structured interview design. An initial survey assessed patients’ perceived depth of their relationship with their GP, using the Health Care Provider Attachment Figure Survey and Patient-Doctor Depth of Relationship Scale. Patients who reported a deep relationship, and their GPs, were purposively selected for individual interviews exploring their experience of these relationships. A post-interview survey assessed interviewees’ attachment styles, using the Modified and Brief Experiences in Close Relationships Scale. Patient interviewees also rated the patient-centredness of their GP’s clinic using the Person-Centred Primary Care Measure. Transcripts were analysed using thematic analysis.

Results
Thirteen patients and five GPs were interviewed. Four themes characterised deep relationships: the ‘professional’; human connection; trust; and ‘above and beyond’. Patient, GP and practice team all contributed to their cultivation.

Conclusions
We present a revised conceptual framework of deep GP-patient relationships. Deep relationships come to the fore in times of patient trouble. Like attachment relationships, they provide a sense of safety, caring and support for patients experiencing vulnerability. They can stretch GP boundaries and capacity for self-care, but also provide joy and vocational satisfaction. Patients may not always desire or need deep relationships with their GP. However, findings highlight the importance of enabling and cultivating these for times of patient hardship, and challenges of doing so within current healthcare climates.
Challenges of Implementing an Effective Primary Health Care Accreditation Program: a qualitative study in Iran
Authors: Gharibi Farid , Moshiri Esmaeil , Tavani Masoumeh Ebrahimi , Dalal Koustuv 
Published: December 2023

Abstract
Background
Accreditation is a prerequisite for scientific management of the health system, owing to its numerous benefits on health centres’ performance. The current study examined Iran’s primary healthcare accreditation program to ascertain the challenges to its successful implementation.

Methods
This qualitative study examined the perspectives of 32 managers and staff members in the pilot accreditation program (from the Ministry of Health and Medical Education, Semnan University of Medical Sciences, and Aradan District Health Network). Three in-depth group interviews were conducted using a semi-structured questionnaire, and the data obtained were assessed using thematic analysis. As a result of this investigation identified six themes, 29 sub-themes, and 218 codes as challenges to the successful accreditation of primary health care in Iran.

Results
Six main themes, including “organisational culture”, “motivational mechanisms”, “staff workload”, “training system”, “information systems”, and “macro-executive infrastructure”, were identified as the main domain of challenges, with seven, five, two, four, three, and eight sub-themes respectively.

Conclusion
Accreditation of PHC in Iran faces significant challenges and obstacles that, if ignored, can jeopardise the program’s success and effectiveness. By identifying challenges and obstacles and making practical suggestions for overcoming them, the findings of this study can aid in the program’s successful implementation and achievement of desired outcomes.
Predictors for quality of life in older adults: network analysis on cognitive and neuropsychiatric symptoms
Authors: He Chaoqun , Kong Xiangyi , Li Jinhui , Wang Xingyi , Chen Xinqiao , Wang Yuanyi , Zhao Qing , Tao Qian 
Published: December 2023

AbstractBackgroundQuality of life (QoL) of older adults has become a pivotal concern of the public and health system. Previous studies found that both cognitive decline and neuropsychiatric symptoms (NPS) can affect QoL in older adults. However, it remains unclear how these symptoms are related to each other and impact on QoL. Our aim is to investigate the complex network relationship between cognitive and NPS symptoms in older adults, and to further explore their association with QoL.MethodsA cross-sectional study was conducted in a sample of 389 older individuals with complaints of memory decline. The instruments included the Neuropsychiatric Inventory, the Mini Mental State Examination, and the 36-item Short Form Health Survey. Data was analyzed using network analysis and mediation analysis.ResultsWe found that attention and agitation were the variables with the highest centrality in cognitive and NPS symptoms, respectively. In an exploratory mediation analysis, agitation was significantly associated with poor attention (β= -0.214,P < 0.001) and reduced QoL (β= -0.137,P = 0.005). The indirect effect of agitation on the QoL through attention was significant (95% confidence interval (CI) [-0.119, -0.035]). Furthermore, attention served as a mediator between agitation and QoL, accounting for 35.09% of the total effect.ConclusionsBy elucidating the NPS-cognition-QoL relationship, the current study provides insights for developing rehabilitation programs among older adults to ensure their QoL.
Preexisting depression and COVID-19: a cohort study on the risk of susceptibility and hospitalization
Authors: Nasirpour Nastaran , Esmailzadehha Neda , Hajebi Ahmad , Savari Ebtesam , Ghanbari Behrooz , Motevalian Abbas 
Published: December 2023

Abstract
Background
Depression can have negative effects on a person’s physical health. However, the available evidence on the risk of susceptibility to COVID-19 and its adverse outcomes in people with mental disorders, including depression, is limited and inconsistent. Therefore, we investigated the relationship between major depressive disorder (MDD) and the risk of susceptibility to COVID-19 infection and hospitalization. The data used in the study were obtained from the Employees’ Health Cohort Study of Iran (EHCSIR).

Methods
We conducted a cohort study that included 3355 participants who had complete data on major depressive disorder at baseline assessment and two annual telephone follow-ups between January 2020 and March 2022. Trained psychologists used the Persian version of the Composite International Diagnostic Interview (CIDI-2.1) to identify major depressive disorders during the baseline assessment. We applied log binomial regression models to adjust for sociodemographic factors and background health conditions.

Results
We found that 11.4% of participants had lifetime MDD and 7.3% had MDD in the past 12 months. During the pandemic, 26.1% of participants were infected with COVID-19, and 14.4% of those who were infected were hospitalized. The risk of susceptibility to COVID-19 infection was significantly higher among participants with lifetime MDD than among those without MDD (adjusted risk ratio (ARR) = 1.24, 95% CI: 1.06–1.47). However, lifetime MDD or 12-month MDD was not independently associated with hospitalization among COVID-19 cases.

Conclusions
Preexisting major depressive disorder may increase the risk of susceptibility to COVID-19.
The mental health of officials who regularly examine child sexual abuse material: strategies for harm mitigation
Authors: Mitchell Kimberly J. , Gewirtz-Meydan Ateret , Finkelhor David , O’Brien Jennifer E. , Jones Lisa M. 
Published: December 2023

Abstract
Background
The current study aims to better understand the mental health and subjective well-being of investigators and forensic examiners exposed to child sexual abuse material (CSAM) by examining which components of this work are associated with elevated mental health conditions and decreased well-being, as well as the intra-personal and organizational variables that may mitigate harm and improve well-being.

Methods
Police investigators, forensic examiners, and others connected with the criminal justice system from across the United States who were exposed to CSAM as part of their professions (N = 500) completed an anonymous online survey. Participants were recruited through connections with the National Criminal Justice Training Center.

Results
Duration, frequency, amount, and content of CSAM exposure was not related to poorer mental health with the exception of exposure to violent CSAM which was related to elevated post-traumatic stress symptoms. Several agency-level practices and policies, such as the availability of an Officer Wellness Program and more frequently knowing the final case resolution, were related to better mental health and well-being. Harm mitigation strategies, such as talking to other officers investigating the case and taking breaks from the material being viewed, were also related to better mental health.

Conclusions
Findings indicate that police agencies have options for implementing agency-level procedures and practices that have the potential to reduce the negative impact of CSAM investigations. Additionally, many investigators use strategies that are correlated with greater well-being, suggesting opportunities for improving training programs.
The psychosexual and psychosocial impacts of polygamous marriages: a cross-sectional study among Somali women
Authors: Barut Adil , Mohamud Samira Ahmed 
Published: December 2023

Abstract
Background
Polygamous marriages are common in many Africa countries. This study aimed to document psychosexual and psychosocial problems of Somali women engaged in monogamous or polygamous marriages.

Methods
This cross-sectional study included 607 consecutive women who had presented between June 7 and October 1, 2022, to the Department of Gynaecology of Mogadishu Somali Turkey Training and Research Hospital in Mogadishu, the capital city of Somalia. Data included maternal age, type of marriage (polygamy, monogamy, and arranged marriage), wives’ education, husbands’ education, husband income, residence area (rural or urban), number of marriages, living in houses (same or different), number of co-wives, and age of marriage. The participants were asked to complete three questionnaires: The Female Sexual Function Index (FSFI), the Rosenberg Self-Esteem Scale (RSE), and the Brief Symptom Inventory-18 (BSI-18).

Results
Of 607 women, 435 (71.7%) had monogamous marriages and 172 (28.3%) had polygamous marriages. The mean age was 29.0 ± 7.2 years (range 16–46). In polygamous marriages, the mean number of wives a husband had was 2.4 ± 0.7 women (range 2– 4). The overall incidences of sexual dysfunction, low self-esteem and arranged marriage were 59.8%, 79.4% and 64.4%, respectively. Wives in polygamous marriages differed from those in monogamous marriages with significantly higher rate of illiterateness (41.9% vs. 27.4%, p = 0.004). Increases in husband income corresponded to higher rates of polygamous marriage. Women in polygamous marriages had significantly lower scores in the desire, arousal, orgasm, and satisfaction sub-domains. Sexual dysfunction, with a significantly increased rate among women in polygamous marriages. Polygamous marriages were associated with significantly higher levels of anxiety, and depression, and a significantly higher total BSI score (p = 0.010, p = 0.004, and p = 0.020, respectively). Women in both groups had similar levels of low self-esteem (p > 0.05). In univariate analysis, polygamous marriage was in significant inverse associations with the total FSFI score and subdomain scores of desire, arousal, orgasm, satisfaction, and sexual dysfunction and in significant associations with the BSI total score and subdomain scores of anxiety and depression (p < 0.05).

Conclusion
Our findings suggest that women in polygamous marriages experience considerably higher psychosexual and psychosocial adverse effects as compared with their monogamous counterparts.
Multi-staged development and pilot testing of a self-assessment tool for organizational health literacy
Authors: Klockmann Izumi , Jaß Leonie , Härter Martin , von dem Knesebeck Olaf , Lüdecke Daniel , Heeg Johanna 
Published: December 2023

Abstract
Background
Until now a comprehensive, consensus-based tool that can be used by a variety of health care organizations for assessing their organizational health literacy (OHL) is not available. Therefore, we aimed to develop and test a literature- and consensus-based self-assessment tool.

Methods
The study is based on a scoping review that was previously published by the authors. For the development of the self-assessment tool, the criteria identified in the literature were synthesized with criteria gained through group discussions with representatives of different types of health care organizations (N = 27) all based in Hamburg (Germany). Consensus on the criteria was reached by conducting a Delphi process (N = 22). A review by the project’s patient advisory council was included in the process. The self-assessment tool was converted into an online tool and refined by a pretest. Finally, the online survey was piloted (N = 53) and the reliability and item loadings for each scale were analyzed.

Results
In total, 77 criteria (items) characterizing a health literate health care organization were developed and grouped into five main categories (scales): (1) “easy access and navigation”, (2) “integration, prioritization, and dissemination of OHL”, (3) “qualification, quality management, evaluation, and needs assessment”, (4) “communication with target groups”, and (5) “involvement and support of target groups”. The results of the online survey showed that the tool is suitable for assessing an organization’s status quo on OHL. The psychometric analysis showed good to excellent internal consistency. Item analyses of the developed self-assessment tool was satisfactory.

Conclusions
We were able to define a set of 77 items to characterize OHL, which were integrated into a new, comprehensive, and consensus-based self-assessment tool to identify areas for improvement. We found evidence that the self-assessment tool, based on the identified criteria, consists of the assumed five scales. Further research should analyze the validity of the self-assessment tool on a higher detail level.
Deep learning prediction of hospital readmissions for asthma and COPD
Authors: Lopez Kevin , Li Huan , Lipkin-Moore Zachary , Kay Shannon , Rajeevan Haseena , Davis J. Lucian , Wilson F. Perry , Rochester Carolyn L. , Gomez Jose L. 
Published: December 2023

Abstract
Question
Severe asthma and COPD exacerbations requiring hospitalization are linked to increased disease morbidity and healthcare costs. We sought to identify Electronic Health Record (EHR) features of severe asthma and COPD exacerbations and evaluate the performance of four machine learning (ML) and one deep learning (DL) model in predicting readmissions using EHR data.

Study design and methods
Observational study between September 30, 2012, and December 31, 2017, of patients hospitalized with asthma and COPD exacerbations.

Results
This study included 5,794 patients, 1,893 with asthma and 3,901 with COPD. Patients with asthma were predominantly female (n = 1288 [68%]), 35% were Black (n = 669), and 25% (n = 479) were Hispanic. Black (44 vs. 33%, p = 0.01) and Hispanic patients (30 vs. 24%, p = 0.02) were more likely to be readmitted for asthma. Similarly, patients with COPD readmissions included a large percentage of Blacks (18 vs. 10%, p < 0.01) and Hispanics (8 vs. 5%, p < 0.01). To identify patients at high risk of readmission index hospitalization data of a subset of 2,682 patients, 777 with asthma and 1,905 with COPD, was analyzed with four ML models, and one DL model. We found that multilayer perceptron, the DL method, had the best sensitivity and specificity compared to the four ML methods implemented in the same dataset.

Interpretation
Multilayer perceptron, a deep learning method, had the best performance in predicting asthma and COPD readmissions, demonstrating that EHR and deep learning integration can improve high-risk patient detection.