bluuebunny/crossref_metadata_2025_split huggingface dataset:
Condom use consistency among South African HIV serodiscordant couples following an HIV risk-reduction intervention
Authors: Mashaphu Sibongile , Wyatt Gail E , Zhang Muyu , Liu Honghu 
Published: March 2022

Background: Although there are several ways to transmit HIV, condomless sex remains the primary mode in sub-Saharan Africa, including South Africa, with KwaZulu-Natal Province being one of the epicentres of HIV infection. This study explored the use of condoms in serodiscordant couples who were exposed to an HIV-risk reduction intervention that aimed to improve condom use and reduce the spread of HIV. Methods: A Total of 30 couples completed a paper-based questionnaire on their demographics and general health at baseline and 3 months, plus a semi-structured questionnaire with four domains. An analysis of HIV knowledge, condom use, condom use attitudes and protection perceptions about how other serodiscordant couples behave was conducted following a 12-week HIV risk reduction intervention. Participants were randomised 2:1 into intervention and control groups. Results: Condom use increased from 55% at baseline to 73.7% ( p = .0047) at 3 months for the intervention group and condom use in the last 7 days increased from 53% to 86% ( p = .0117). For the control group, condom use remained low at the 3 months follow up period ( p = .625). HIV knowledge improved significantly from baseline to 3 months for the intervention group ( p < .0001), as well as the control group ( p = .0005). Negative HIV condom use attitude scores in both groups decreased significantly from baseline to 3 months; intervention group ( p = .0059) and control group ( p = .0007). Conclusion: HIV knowledge and condom use improved significantly, while negative condom use attitudes and HIV protection perceptions decreased significantly following exposure to a risk-reduction intervention, suggesting that HIV preventive interventions should focus on partnership interventions.
Can mechanism of injury improve trauma diversion? A retrospective cross-sectional study
Authors: Yeung Wai Hung , Wong John Kit Shing , Tsui Kwok Leung , Lam Tommy Shing Kit , Lui Chun Tat , Lau Chu Leung 
Published: March 2022

Objective: The objective of this study was to determine the impact of adding selected mechanism of injury (MOI) to the existing trauma diversion criteria adopted in Hong Kong. Method: This is a cross-sectional study based on the trauma registry of New Territory West Cluster (NTWC) of Hospital Authority from January 2017 to December 2019. All adult patients aged 18 years or above were recruited if their injury occurred in the catchment area of Pok Oi Hospital (POH) or Tin Shui Wai Hospital (TSWH). Performance of the protocol before and after MOI criteria being added in terms of over-diversion and under-diversion rate was determined. Model discrimination was evaluated by plotting the receiver operating characteristic curve, and the area under the curve was compared before and after MOI criteria added. Net reclassification improvement and integrated discrimination improvement indices were evaluated. Result: A total of 502 patients were included for analysis. Before MOI criteria were added, the over-diversion rate and under-diversion rate were 31.1% and 54.7%, respectively. After MOI criteria were added, the over-diversion rate and under-diversion rate were 33.1% and 34.3%, respectively. The receiver operating characteristic curve of current primary trauma diversion (PTD) criteria had an area under the curve of 66.9% (95% confidence interval: 63%–71%). After adding MOI criteria, the new receiver operating characteristic curve yielded an area under the curve of 73.7% (95% confidence interval: 70%–78%), which is significantly better (p < 0.001). Net reclassification improvement and integrated discrimination improvement indices indicated that including MOI criteria would improve the model prediction. Conclusion: Adding mechanism of injury can improve trauma diversion protocol performance.
Prediction of cardiac autonomic neuropathy using a machine learning model in patients with diabetes
Authors: Abdalrada Ahmad Shaker , Abawajy Jemal , Al-Quraishi Tahsien , Islam Sheikh Mohammed Shariful 
Published: March 2022

Background: Cardiac autonomic neuropathy (CAN) is a diabetes-related complication with increasing prevalence and remains challenging to detect in clinical settings. Machine learning (ML) approaches have the potential to predict CAN using clinical data. In this study, we aimed to develop and evaluate the performance of an ML model to predict early CAN occurrence in patients with diabetes. Methods: We used the diabetes complications screening research initiative data set containing 200 CAN-related tests on more than 2000 participants with type 2 diabetes in Australia. Data were collected on peripheral nerve functions, Ewing’s tests, blood biochemistry, demographics, and medical history. The ML model was validated using 10-fold cross-validation, of which 90% were used in training the model and the remaining 10% was used in evaluating the performance of the model. Predictive accuracy was assessed by area under the receiver operating curve, and sensitivity, specificity, positive predictive value, and negative predictive value. Results: Of the 237 patients included, 105 were diagnosed with an early stage of CAN while the remaining 132 were healthy. The ML model showed outstanding performance for CAN prediction with receiver operating characteristic curve of 0.962 [95% confidence interval (CI) = 0.939–0.984], 87.34% accuracy, and 87.12% sensitivity. There was a significant and positive association between the ML model and CAN occurrence ( p < 0.001). Conclusion: Our ML model has the potential to detect CAN at an early stage using Ewing’s tests. This model might be useful for healthcare providers for predicting the occurrence of CAN in patients with diabetes, monitoring the progression, and providing timely intervention.
Factors influencing utilization of early postnatal care services among postpartum women in Yirgalem town, Sidama Regional State, Ethiopia
Authors: Dona Aregahegn , Tulicha Tsedeke , Arsicha Admasu , Dabaro Desalegn 
Published: March 2022

Objective: Providing postnatal care services at right time could help to reduce maternal and newborn deaths. Thus, this study aimed to assess the factors influencing the utilization of early postnatal care services among postpartum women in Yirgalem town, Sidama Regional State, Ethiopia. Methods: A community-based cross-sectional study was done using structured and interviewer-administered questionnaires among randomly selected 306 postpartum women. Data were cleaned, coded, and entered into EpiData-3.1, and exported to Statistical Package for Social Science-21 for analysis. Descriptive statistics, bivariable, and multivariable logistic regression analysis were done. A p-value ⩽ 0.05 was used to consider statistically significant variables. Results: Generally, 202 (66.7%) visited a health facility for postpartum care. The prevalence of early postnatal care service utilization was 45.5% (95% confidence interval = 39.9–50.5). Mainly practiced services were physical examination (37%) and family planning (31%) services. Having formal education (adjusted odds ratio = 3.6; 95% confidence interval = 1.7–7.4), having antenatal care (adjusted odds ratio = 3.5; 95% confidence interval = 1.6–7.6), institutional delivery (adjusted odds ratio = 2.3; 95% confidence interval = 1.2–4.7), and getting advice from healthcare provider (adjusted odds ratio = 18.69; 95% confidence interval = 9.19–37.99) were factors significantly associated with early postnatal care service utilization. Conclusion: The practice of early postnatal care needs more attention in the study area. Improving the educational status of the women, strengthening healthcare providers’ counseling on the benefits of postnatal care, and inspiring pregnant women to use antenatal care and institutional delivery services will improve the use of postnatal care services on time.
Tension Control UCL Reconstruction With Internal Brace Augmentation
Authors: Yalcin Sercan , Maier Jacob , Schickendantz Mark , Frangiamore Salvatore 
Published: March 2022

Background: Ulnar collateral ligament (UCL) rupture is a common injury, particularly in throwing athletes. It occurs either in the acute setting or due to repetitive microtrauma. UCL reconstruction has been a successful treatment with proper patient selection. A number of different surgical techniques have been described in the literature. We developed a novel surgical technique using internal brace augmentation to address the 2 most common causes of failure: suture failure and bone tunnel fracture. Indications: To provide information about this novel UCL reconstruction technique. Technique Description: The palmaris longus graft is harvested and prepared to be used as the autograft. A 5-cm curved incision is made over the medial epicondyle of the humerus. The UCL reconstruction is then performed using the double suspensory reconstruction technique followed by an internal brace augmentation. Results: Excellent clinical outcomes and high return to sports rates have been reported after UCL reconstruction. In this novel technique, the addition of the internal brace provides secondary interference fixation of the graft on the humeral side along with the additional support the brace itself provides. Discussion/Conclusion: Using internal brace augmentation increases the stability of the UCL reconstruction while preventing suture failure and bone tunnel fracture.
Prevalence of heavy chain MGUS by race and family history risk groups using a high-sensitivity screening method
Authors: Vachon Celine M. , Murray Josiah , Allmer Cristine , Larson Dirk , Norman Aaron D. , Sinnwell Jason P. , Dispenzieri Angela , Kleinstern Geffen , Visram Alissa , Kyle Robert A. , Rajkumar S. Vincent , Slager Susan L. , Kumar Shaji K. , Murray David L. 
Published: March 2022

Abstract
Mass-spectrometry (MS) assays detect lower levels of monoclonal proteins and result in earlier detection of monoclonal gammopathy of undetermined significance (MGUS). We examined heavy chain MGUS prevalence using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS among 3 risk groups, ages 50 or older: 327 African Americans (AA) and 1223 European Americans (EA) from a clinical biobank and 1093 unaffected first-degree relatives (FDR) of patients with hematologic disorders. Age- and sex-adjusted prevalence rates were directly standardized to 2010 United States population. Prevalence ratios were estimated for comparisons of AA and FDR to the EA group using the Poisson distribution. Results were also compared with population-based prevalence using conventional gel-based methods. Risk groups had similar sex and age distributions. MALDI-TOF MGUS prevalence was higher in the AA (16.5% [95% confidence interval (CI), 12.2%, 20.8%]) and FDR (18.3% [95% CI, 16.6%, 21.6%]) than in EA (10.8% [95% CI, 8.8%, 12.7%]), translating to prevalence ratios of 1.73 (95% CI, 1.31, 2.29) and 1.90 (95% CI, 1.55, 2.34), respectively. MALDI-TOF EA prevalence was over threefold higher than conventional estimates but showed similar age trends. Thus, the MALDI-TOF assay found greater numbers with MGUS but similar relative differences by race, family history, and age as prior studies.
Cystitis glandularis- rare cause of urinary bladder mass: case report and literature review
Authors: Ahmad Ahsan , Imbisat Md Zaid , Ranjan Nikhil , Tiwari Rajesh Kumar , Kumar Bipin , Khatoon Qurana 
Published: March 2022

Abstract
Background
Cystitis glandularis a rare benign proliferative disease of the urinary bladder mucosa is usually a microscopic finding and manifests rarely as a large visible macroscopic lesion of urinary bladder. Only few cases of cystitis glandularis presenting as urinary bladder mass in female patients have been reported in the literature. We are reporting a case of cystitis glandularis presenting as a urinary bladder mass in a very young female patient.
Case presentation.
Our patient, a young female 25 years of age presented in the Urology OPD with complaints of irritative lower urinary tract symptoms for two years and intermittent hematuria for one year. On evaluation, she was found to have a urinary bladder mass. Transurethral resection of her urinary bladder mass was done and on histopathological examination, it came out to be cystitis glandularis.

Conclusion
Clinical presentation of cystitis glandularis is variable. It may remain asymptomatic or could present as irritative lower urinary tract symptoms, hematuria, or mucus in the urine. It is normally a microscopic finding but could also present as an overt urinary bladder mass however this has been reported rarely in the literature.
A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes
Authors: Clark Lindsay V. , Mays Wittney , Lipka Alexander E. , Sacks Erik J. 
Published: March 2022

Abstract
Background
Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an effective tool for filtering loci but requires genotyping to be performed first at a high computational cost, whereas counting the number of sequence tags detected per genotype is computationally quick but very ineffective in inbred or polyploid populations. Therefore, new methods are needed for filtering paralogs.

Results
We introduce a novel statistic, Hind/HE, that uses the probability that two reads sampled from a genotype will belong to different alleles, instead of observed heterozygosity. The expected value of Hind/HE is the same across all loci in a dataset, regardless of read depth or allele frequency. In contrast to methods based on observed heterozygosity, it can be estimated and used for filtering loci prior to genotype calling. In addition to filtering paralogs, it can be used to filter loci with null alleles or high overdispersion, and identify individuals with unexpected ploidy and hybrid status. We demonstrate that the statistic is useful at read depths as low as five to 10, well below the depth needed for accurate genotype calling in polyploid and outcrossing species.

Conclusions
Our methodology for estimating Hind/HE across loci and individuals, as well as determining reasonable thresholds for filtering loci, is implemented in polyRAD v1.6, available at https://github.com/lvclark/polyRAD. In large sequencing datasets, we anticipate that the ability to filter markers and identify problematic individuals prior to genotype calling will save researchers considerable computational time.
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development
Authors: Fisher Malcolm E. , Segerdell Erik , Matentzoglu Nicolas , Nenni Mardi J. , Fortriede Joshua D. , Chu Stanley , Pells Troy J. , Osumi-Sutherland David , Chaturvedi Praneet , James-Zorn Christina , Sundararaj Nivitha , Lotay Vaneet S. , Ponferrada Virgilio , Wang Dong Zhuo , Kim Eugene , Agalakov Sergei , Arshinoff Bradley I. , Karimi Kamran , Vize Peter D. , Zorn Aaron M. 
Published: March 2022

AbstractBackgroundOntologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease.ResultsHere we present theXenopusphenotype ontology (XPO) to annotate phenotypic data from experiments inXenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from theXenopusAnatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data fromXenopusexperiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated.ConclusionsThe XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, theXenopusModel Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources.
Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens
Authors: Asadollahpour Nanaei Hojjat , Kharrati-Koopaee Hamed , Esmailizadeh Ali 
Published: March 2022

Abstract
Background
Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes. To detect genomic signatures of adaptation, we applied nucleotide diversity (θπ) and FST statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits.

Results
We assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (~ 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits.

Conclusions
The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate.
Genome-wide characterization and expression analysis of Erf gene family in cotton
Authors: Zafar Muhammad Mubashar , Rehman Abdul , Razzaq Abdul , Parvaiz Aqsa , Mustafa Ghulam , Sharif Faiza , Mo Huijuan , Youlu Yuan , Shakeel Amir , Ren Maozhi 
Published: March 2022

Abstract
Background
AP2/ERF transcription factors are important in a variety of biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, little study has been done on cotton’s AP2/ERF genes, although cotton is an essential fibre crop. We were able to examine the tissue and expression patterns of AP2/ERF genes in cotton on a genome-wide basis because of the recently published whole genome sequence of cotton. Genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed.

Results
A total of 118, 120, 213, 220 genes containing the sequence of single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Synteny and collinearity analysis revealed that segmental duplications may have played crucial roles in the expansion of the cotton ERF gene family, as well as tandem duplications played a minor role. Cis-acting elements of the promoter sites of Ghi-ERFs genes predict the involvement in multiple hormone responses and abiotic stresses. Transcriptome and qRT-PCR analysis revealed that Ghi-ERF-2D.6, Ghi-ERF-12D.13, Ghi-ERF-6D.1, Ghi-ERF-7A.6 and Ghi-ERF-11D.5 are candidate genes against salinity tolerance in upland cotton.

Conclusion
Overwhelmingly, the present study paves the way to better understand the evolution of cotton ERF genes and lays a foundation for future investigation of ERF genes in improving salinity stress tolerance in cotton.