bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical practice competence and associated factors among undergraduate midwifery and nursing sciences students at Bahir Dar city, Northwest Ethiopia
Authors: Yezengaw Telksew Yelma , Debella Adera , Animen Simachew , Aklilu Almaz , Feyisa Wondu , Hailu Mickiale , Sime Betelhem , Mohammed Ahmed , Deressa Alemayehu , Mussa Ibsa , Alemu Addisu , Mezmur Haymanot , Lami Magarsa , Eyeberu Addis 
Published: November 2023

Background:
Competence describes actions that will be demonstrated or observed and assessed while competency refers to the skill itself. Following appropriate theoretical and practical training, clinical experience is required to achieve the highest level of clinical competence. It is estimated that many women and newborns die each year due to a lack of qualified health professional around the world. As a result, the purpose of this study was to determine the prevalence and factors influencing clinical competency in the study area.

Methods:
An Institutional-based cross-sectional study was conducted from 12 August to 12 September 2022, among 403 undergraduate health sciences students of Bahir Dar University. Participants were approached through simple random sampling technique. Data were collected using a pre-tested structured questionnaire through a face-to-face interview, and entered into Epidata version 3.1 and analyzed using SPSS version 22. The prevalence was reported using proportion with 95% CI and summary measures. Predictors were assessed using a multivariable logistic regression analysis model and reported using an adjusted odds ratio (AOR) with 95% CI. Statistical significance was declared at P value less than 0.05.

Results:
Overall, the prevalence of clinical practice competency was 36.5% [95% CI; 33.5, 39.1]. Students who were provided a logbook (AOR=5.40, 95% CI 2.91, 10.02), adequate clinical cases in the clinical practice placement (AOR=2.72, 95% CI 1.60, 4.60), preceptor show different procedures (AOR=2.50, 95% CI 1.33, 4.71), student’s confidence during conducting procedure (AOR=4.16, 95% CI 1.67, 10.35) and the suitability of the way of teaching to the learning styles of students during skills demonstration (AOR=2.10, 95% CI 1.00, 4.40) were factors statistically associated with clinical practice competence.

Conclusions:
According to this study, more than three out of every five participants were found to be clinically incompetent. Providing logbooks, adequate clinical cases, preceptors showing different procedures, students’ confidence, and suitability of the way of teaching to the learning styles of students were significantly associated with clinical practice competence. Implementing logbooks, selecting clinical sites, enhancing the confidence of students, preferred teaching/learning styles, and clinical preceptor support were important to improve the clinical competence of students.
Effect of Duration of Feminizing Hormone Therapy on Facial Fat Volumes
Authors: Moghadam Shahrzad , Roca Yvonne , LaGuardia Jonnby S. , Huang Kelly X. , Chin Madeline G. , Bedar Meiwand , Fadich Sarah K. , Lee Justine C. 
Published: November 2023

Background:
Gender-affirming feminizing hormone therapy induces body fat redistribution. However, the amount and timing of facial fat changes in response to feminizing hormone therapy are unknown, despite being relevant to counseling and surgical planning for facial gender-affirming surgery. The authors assessed the influence of feminizing hormone therapy duration on malar and temporal fat volume.

Methods:
Malar and temporal fat volumes were compared using computed tomography in transfeminine patients (age, 20 to 29 years; body mass index, 18.5 to 24.9) treated with feminizing hormone therapy for less than 2 years versus 2 years or longer. Patients with previous surgical or nonsurgical facial soft-tissue interventions were excluded. Multivariable linear regressions evaluated the contribution of hormone therapy duration to malar and temporal fat volumes.

Results:
A total of 45 patients were included, 30 (66.7%) treated with feminizing hormone therapy for 2 years or longer and 15 (33.3%) treated for less than 2 years (median [interquartile range], 44.5 [33.5 to 65.6] versus 15.0 [11.0 to 18.0] months; P < 0.001). Patients treated with hormone therapy for 2 years or longer demonstrated a 1.6-fold greater malar fat volume (5.5 [4.2 to 6.3] versus 3.4 [2.3 to 4.2] cm3; P < 0.001) and 1.4-fold greater temporal fat volume (2.8 [2.4 to 3.6] cm3 versus 2.0 [1.7 to 2.4] cm3; P = 0.01) compared with those treated for less than 2 years. When accounting for other contributory variables, such as body mass index, skull size, and total soft-tissue depth, in multivariable linear regression models, hormone therapy duration of 2 years or longer independently predicted higher malar (β = 0.51, P < 0.001) and temporal (β = 0.32, P = 0.02) fat volumes.

Conclusion:
Feminizing hormone therapy increases malar and temporal fat volumes by approximately 2 cm3 and 0.8 cm3 for each area, respectively, after 2 years of treatment.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
A National Assessment of Racial and Ethnic Disparities in Cleft Lip Repair
Authors: Peck Connor J. , Parsaei Yassmin , Jazayeri Hossein E. , Desai Mayur M. , Lopez Joseph , Uribe Flavio A. , Steinbacher Derek 
Published: November 2023

Purpose:
The authors examined the effects of race and ethnicity on the likelihood of experiencing delays to surgery, postoperative surgical complications, and prolonged hospital length of stay (LOS) after primary cleft lip repair.

Methods:
Patients who underwent cleft lip repair were identified in the 2006 through 2012 Kids’ Inpatient Database. Primary outcomes were defined as treatment after 6 months of age, any surgical complication, LOS greater than 1 day, and total hospital charges. Multivariable analyses were performed to adjust for sociodemographic and clinical characteristics that might account for differences in outcomes.

Results:
There were 5,927 eligible patients with cleft lip: 3,724 White, 1,316 Hispanic, 279 Black, 277 Asian or Pacific Islander, and 331 other (including American Indian or Alaska Native, multiple races, or races/ethnicities not specified within the dataset). Across all outcomes, there were significant unadjusted differences (P < 0.001) by race and ethnicity, with White children having the lowest odds of delayed surgery, complications, and prolonged LOS, and the lowest charges. Multivariable analyses suggested that differences in baseline health status may account for much of this disparity in combination with factors such as income, insurance type, and location. Even after adjusting for covariates, significantly increased odds of delayed surgery and higher charges remained for Hispanic and Asian or Pacific Islander patients.

Conclusion:
There are significant differences in the odds of delays, complications, prolonged hospital stays, and total charges among patients with cleft lip of different races or ethnicities. Advocacy efforts to ameliorate disparity in early infant health may subsequently improve equity in cleft outcomes.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Risk, II.
Anatomy of the anterior ribs and the composition of the costal margin: A cadaver study
Authors: Patel Arjun , Privette Alicia , Bauman Zachary , Hansen Adam , Kubalak Steven , Eriksson Evert 
Published: November 2023

BACKGROUND
Traditional rib anatomy and costal margin teaching contends that the costal margin consists of a combined costal cartilage made up of ribs 7 to 10. Variations in 9th and 10th rib anatomy have been observed. We sought to evaluate the variability of interchondral joints and the make-up of the costal margin.

METHODS
Cadaveric dissections were performed to evaluate the anatomy of the anterior ribs and the composition of the costal margin. Experienced chest wall surgeons evaluated this anatomy through a standardized dissection and assessment. Dissection videos were performed to allow for further review/assessment.

RESULTS
Bilateral chest wall anatomy of 30 cadavers was evaluated (15 male, 15 female). The average age was 78 ± 12 years, and all patients were Caucasian. In all patients, the first rib attached to the manubrium, the second rib attached to the manubriosternal junction, and ribs 3 to 6 attached directly to the sternum. Interchondral joints were present between ribs 4/5—3%, 5/6—68%, 6/7—83%, 7/8—72%. Ribs combining to form a common costal cartilage via cartilaginous unions were observed between 6/7—3%, 7/8—45%, 8/9—30%, and 9/10—20%.
The 8th rib attached directly to the sternum without joining the 7th rib in 10% of cadavers. The 8th and 9th ribs had free tips in 45% and 60% of evaluations, respectively. The 10th rib was found to have a hooked tip in 25% of cases and was a floating rib without attachment to the 9th rib 52% of the time. Rib tip mobility was noted in ribs 8, 9, and 10 in 52%, 70%, and 90%, respectively.

CONCLUSION
Interchondral joints are common between ribs 5 and 8. Significant variability exists in the chest wall and costal margin compared with traditional teaching. It is important for chest wall surgeons treating diseases of the costal margin to appreciate this anatomic variability.
Spastic Paraplegia Type 7-Associated Optic Neuropathy: A Case Series
Authors: Bell Carter A. , Ko Melissa W. , Mackay Devin D. , Bursztyn Lulu L. C. D. , Grossman Scott N. 
Published: November 2023

Background:
Hereditary optic neuropathies comprise a group of clinically and genetically heterogeneous disorders. Optic neuropathy has been previously reported in families with spastic paraplegia type 7 (SPG7) gene mutations. However, the typical time course and clinical presentation of SPG7-associated optic neuropathy is poorly understood. We report a series of 5 patients harboring pathogenic SPG7 mutations who originally presented to a neuro-ophthalmology clinic with symptoms of optic neuropathy.

Methods:
Retrospective case series of 5 patients with pathogenic SPG7 mutations and optic atrophy from 3 neuro-ophthalmology clinics. Demographic, clinical, diagnostic, and treatment data were collected and reported by the clinician authors.

Results:
Five patients ranging in age from 8 to 48 years were evaluated in the neuro-ophthalmology clinic. Although there were variable clinical presentations for each subject, all noted progressive vision loss, typically bilateral, and several also had previous diagnoses of peripheral neuropathy (e.g., Guillain-Barré Syndrome). Patients underwent neuro-ophthalmic examinations and testing with visual fields and optic coherence tomography of the retinal nerve fiber layer. Genetic testing revealed pathogenic variants in the SPG7 gene.

Conclusions:
Five patients presented to the neuro-ophthalmology clinic with progressive vision loss and were diagnosed with optic atrophy. Although each patient harbored an SPG7 mutation, this cohort was phenotypically and genotypically heterogeneous. Three patients carried the Ala510Val variant. The patients demonstrated varying degrees of visual acuity and visual field loss, although evaluations were completed during different stages of disease progression. Four patients had a previous diagnosis of peripheral neuropathy. This raises the prospect that a single pathogenic variant of SPG7 may be associated with peripheral neuropathy in addition to optic neuropathy. These results support the consideration of SPG7 testing in patients with high suspicion for genetic optic neuropathy, as manifested by symmetric papillomacular bundle damage without clear etiology on initial workup. Applied judiciously, genetic testing, including for SPG7, may help clarify the cause of unexplained progressive optic neuropathies.
Constructing genotype and phenotype network helps reveal disease heritability and phenome-wide association studies
Authors: Cao Xuewei , Zhu Lirong , Liang Xiaoyu , Zhang Shuanglin , Sha Qiuying 
Published: November 2023

AbstractAnalyses of a bipartite Genotype and Phenotype Network (GPN), linking the genetic variants and phenotypes based on statistical associations, provide an integrative approach to elucidate the complexities of genetic relationships across diseases and identify pleiotropic loci. In this study, we first assess contributions to constructing a well-defined GPN with a clear representation of genetic associations by comparing the network properties with a random network, including connectivity, centrality, and community structure. Next, we construct network topology annotations of genetic variants that quantify the possibility of pleiotropy and apply stratified linkage disequilibrium (LD) score regression to 12 highly genetically correlated phenotypes to identify enriched annotations. The constructed network topology annotations are informative for disease heritability after conditioning on a broad set of functional annotations from the baseline-LD model. Finally, we extend our discussion to include an application of bipartite GPN in phenome-wide association studies (PheWAS). The community detection method can be used to obtain a priori grouping of phenotypes detected from GPN based on the shared genetic architecture, then jointly test the association between multiple phenotypes in each network module and one genetic variant to discover the cross-phenotype associations and pleiotropy. Significance thresholds for PheWAS are adjusted for multiple testing by applying the false discovery rate (FDR) control approach. Extensive simulation studies and analyses of 633 electronic health record (EHR)-derived phenotypes in the UK Biobank GWAS summary dataset reveal that most multiple phenotype association tests based on GPN can well-control FDR and identify more significant genetic variants compared with the tests based on UK Biobank categories.
Estimating Between Country Migration in Pneumococcal Populations
Authors: Belman Sophie , Pesonen Henri , Croucher Nicholas J. , Bentley Stephen D. , Corander Jukka 
Published: November 2023

AbstractStreptococcus pneumoniae(the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus to take a foothold in a country depends on existing population configuration, the extent of vaccine implementation, as well as human mobility since it is a human obligate bacterium. To shed light on its international movement, we used extensive genome data from the Global Pneumococcal Sequencing (GPS) project and estimated migration parameters between multiple countries in Africa. Data on allele frequencies of polymorphisms at housekeeping-like loci for multiple different lineages circulating in the populations of South Africa, Malawi, Kenya, and The Gambia were used to calculate the fixation index (Fst) between countries. We then further used these summaries to fit migration coalescent models with the likelihood-free inference algorithms available in the ELFI software package. Synthetic data were additionally used to validate the inference approach. Our results demonstrate country-pair specific migration patterns and heterogeneity in the extent of migration between different lineages. Our approach demonstrates that coalescent models can be effectively used for inferring migration rates for bacterial species and lineages provided sufficiently granular population genomics surveillance data. Further it can demonstrate the connectivity of respiratory disease agents between countries to inform intervention policy in the longer term.
Genomically integrated orthogonal translation inEscherichia coli, a new synthetic auxotrophic chassis with altered genetic code, genetic firewall, and enhanced protein expression
Authors: Karbalaei-Heidari Hamid Reza , Budisa Nediljko 
Published: November 2023

AbstractIn the last three decades, genetic code engineering has expanded protein biosynthesis options from the natural set of 20 canonical amino acids to over 250 non-canonical amino acids (ncAAs). This progress involves rewiring of protein translation by establishing Orthogonal Translation Systems (OTS) through orthogonal pairs. Traditionally encoded on plasmid vectors, these systems are often unstable and burdensome in large-scale fermentations. To moving forward from academia to reliable technology, it is crucial to integrate OTS genetic modules stably into a molecular chassis with a defined genome background. Here, we demonstrate genomically integrated OTS inEscherichia coli, creating a synthetic auxotrophic chassis with an altered genetic code. Using CRISPR-associated transposase tool (CASTs), we targeted multiple genome sites, inserting OTS components (enzymes, tRNA genes) non-disruptively. Our OTS system demonstrated site-specific incorporation ofm-oNB-Dopa through in-frame amber stop codon readthrough, enabling the expression of smart underwater bioglues. Simple metabolic labelling, introducing fluoroproline analogs enhancing conformational stability during orthogonal translation, further bolstered system robustness. These chassis, equipped also with synthetic auxotrophy form-oNB-Dopa, serve as a built-in genetic barrier (genetic firewall), ensuring safe bioproduction in genetically isolated settings.Graphical AbstractOne-sentence AbstractCRISPR-assisted transposition has enabled the development of a robust and biosafe Escherichia coli-based chassis with genomically integrated orthogonal translation components, enhancing synthetic protein production and laying the foundation for the transition of this research field from academia to reliable technology.
Adaptation to ER Stress by Slt2, Counterpart of Human MAP Kinase ERK1/2, via Enhancing Splicing and Translation ofHAC1mRNA inSaccharomyces cerevisiae
Authors: Uppala Jagadeesh Kumar , Chakraborty Anish , George Jasmine , Mayer Kimberly Ann , Ghosh Chandrima , Dey Ritisha , Chaluvally-Raghavan Pradeep , Dey Madhusudan 
Published: November 2023

AbstractUnfolded protein response (UPR) is a cellular strategy to increase the protein folding capacity of cells in response to stress within the endoplasmic reticulum (ER). In metazoan cells, three major UPR sensors Ire1, PERK and ATF6 work in concert by simultaneously activating intracellular signaling pathways and modulating a series of physiological processes such as attenuation of the general protein synthesis and expression of protein chaperones. In yeastSaccharomyces cerevisiae, Ire1 is known to be the only UPR sensor, which mediates splicing ofHAC1mRNA in the cytoplasm and derepresses its translation. Hac1 is a transcription factor that increases the expression of protein folding enzymes and chaperones, thus enhancing the protein folding capacity of cells. In this study, we provide compelling evidence that kinase Slt2 plays a significant role in facilitating both the splicing and translation ofHAC1mRNA, while also serving as a key mediator in the activation of UPR genes through an alternative route. We also provide evidence that human extracellular signal-regulated kinase 1 (ERK1) or ERK2 served as a functional substitute for yeast Slt2 in the context of UPR. Furthermore, ERK1 exhibits an enhanced activation in human primary cells when grown in the presence of ER stressor. These findings collectively suggest that Slt2 responds to ER stress by activating the Ire1 pathway as well as initiating a parallel signaling pathway.
Protocol for VIVALDI Social Care: Pilot Study to reduce Infections, Outbreaks and Antimicrobial Resistance in Care Homes for Older Adults
Authors: Krutikov M , Fry Z , Azmi B , Lezard C , Thorn K , Patefield G , Childe G , Hudson J , Stirrup O , Jhass A , Turner N , Cassell J , Flowers P , Hayward A , Copas A , Green M , Shallcross L 
Published: November 2023

AbstractCare home residents are vulnerable to severe outcomes from infections such as COVID-19 and influenza. However, measures to control outbreaks, such as care home closures to visitors and new admissions, have a detrimental impact on their quality of life. Many infections and outbreaks could be prevented but the first step is to measure them reliably. This is challenging in care homes due to the lack of data and research infrastructure. During the pandemic, the VIVALDI study measured COVID-19 infections in residents and staff by partnering with care providers and using routinely collected data. This study aims to establish sentinel surveillance and a research database to enable observational and future interventional studies in care homes. The project has been co-produced with care providers, staff, residents, relatives, and researchers.The study (October 2023 to March 2025) will explore the feasibility of establishing a network of 500-1500 care homes for older adults in England that is underpinned by a linked data platform. No data will be collected from staff. The cohort will be created by regularly extracting resident identifiers from Digital Social Care Records (DSCR), followed by pseudonymisation and linkage to routinely collected datasets.Following extensive consultation, we decided not to seek informed consent from residents for data collection, but they can ‘opt out’ of the study. Our goal is to be inclusive, and it is challenging to give every resident the opportunity to ‘opt in’ due to cognitive impairment and the requirement for consultees. The project, and all requests to use the data will be overseen by relatives, residents, staff, and care providers. The study has been provisionally approved by the Health Research Authority Confidentiality Advisory Group and the South-West Frenchay Research Ethics Committee. It is funded by the UK Health Security Agency.
The YTHDF1-3 proteins are bidirectionally influenced by the codon content of their mRNA targets
Authors: Moch Clara , Zou Limei , Pythoud Nicolas , Fillon Emilie , Bourgeois Gabrielle , Graille Marc , Carapito Christine , Chapat Clément 
Published: November 2023

ABSTRACTN6-methyladenosine (m6A) is the most abundant modification in eukaryotic mRNAs and plays critical roles in a broad variety of biological processes. Recognition of m6A by the YTHDF1-3 proteins results in the alteration of the translation efficiency and stability of methylated mRNAs, although their mode of action is still matter of debates. To decode the molecular basis of YTHDF1-3 action in human cells, we performed an unbiased proteomic screen of their full spectrum of interacting proteins using BioID (proximity-dependent biotin identification). Our systematic BioID mapping revealed that each YTHDF protein is a dynamic hub that associates with both mRNA silencing machineries and the translation apparatus. Based on this, we identified a direct interaction between YTHDF2 and the ribosomal protein RACK1, and found that the silencing activity of YTHDF2 is bidirectionally modulated by the codon content of its targeted mRNAs. Using a tethering reporter system that recapitulates this phenomenon, we confirmed that the three YTHDF proteins selectively repress mRNAs enriched in optimal codons, while they activate those enriched in non-optimal codons. Altogether, these results have important implications for understanding the underlying multiplicity of YTHDF1-3 and could reconcile seemingly contradictory data.