bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malaria Vectors Tend to Avoid the Indoor-Based Vector Control Tools in Wonji Sugar Estate, Oromia, Ethiopia
Authors: Lelisa Kidane , Golassa Lemu , Woldehawariat Yitbarek , Dugassa Sisay 
Published: August 2024

Background: There is a paucity of data regarding resting habits and comparison of the physiological states of Anopheles mosquito populations from indoor and outdoor collection venues in Ethiopia. Therefore, this study aims to investigate resting behavior and age structure of the malaria vectors in Wonji Sugar Estate. Methods: Longitudinal entomological study was conducted at Wonji Sugar Estate from July 2018 to June 2020. Pyrethrum spray catches (PSC), Pit Shelter (PIT), and Oral Aspirators were used to collect adult Anopheles species from various resting sites. Mosquitoes were identified to the species using morphological keys. Finally, the resting behavior of Anopheles mosquitoes were determined using standard protocol. Results: A total of 1406 mosquitoes were collected from indoor and outdoor resting venues, with the outdoor resting population being significantly higher ( F = 8.296, P = .04). The number of half-gravid/gravid Anopheles species collected from outdoors was higher than that from indoor resting venues ( F = 35.612, P = .00). Eight two percent of the indoor sampled Anopheles species left the indoor venue before completing their gonotrophic cycle. Anopheles pharoensis and An. coustani cx. exhibited exophily rate of 83.4% and 100%, respectively. The overall parity rate of Anopheles gambiae s.l. was 45.7%. The highest parity rate, daily survival rate, and longevity of Anopheles gambiae s.l. was 66.7%, 0.874, and 7.399 days, respectively. Anopheles gambiae s.l. reached the infective stages for Plasmodium falciparum and P. vivax in February 2019. Conlusion: Anopheles mosquitoes, including the major malaria vector Anopheles gambiae s.l., showed predominantly exophilic habits, underscoring the need for outdoor vector control strategies in addition to indoor-based interventions. The increase in the nulliparous population indicates a higher risk of vector-human contact. Meanwhile, the extended lifespan of Anopheles gambiae s.l. observed during the dry season could increase the risk of infectious bites.
The Healthy Timing and Spacing of Pregnancies (HTSP) project: improving family planning in Siaya County, Kenya
Authors: Otchere Susan A. , Moraa Isabellah , Rotich Vincent , Omunyidde Stephen , Jillson Kimberly Q. 
Published: August 2024

Background: Religious leaders are influential and can impact the uptake of family planning (FP). In this study of the Healthy Timing and Spacing of Pregnancies (HTSP) project, led in Siaya County, Kenya, from September 2017 to June 2019, we present findings from the project’s evaluation, to determine changes in knowledge of the key HTSP messages; changes in the proportion of community members who correctly identify at least three methods of contraception; changes in knowledge of healthy child spacing; and changes in modern contraceptive prevalence rate. Methods: This is a two-staged ( baseline and endline) cross-sectional study, designed to assess the knowledge, practice, and coverage of HTSP/FP services. Primary data was collected using a questionnaire adapted from the United States Agency for International Development. Focus group discussion participants included men, women, representatives of community groups, faith leaders, and community heath volunteers. Frequencies were calculated from the ODK platform. Bivariate analytics (paired t test) were performed. Results: At baseline, women respondents aged 20–29 years constituted 66.3% of the women participants, dropping to 60.9% at endline. Women aged 30–34 years constituted 11.9% and 22% of the entire women respondents, at baseline and endline, respectively. Men aged 20–29 constituted 45.2% of all men respondents at baseline, and 35.4% at endline. There were statistically significant increases in the knowledge of modern contraceptives among women ( p = 0.0342), faith leaders ( p = 0.0464), and the entire population ( p = 0.0097), from baseline to endline. Conclusion: The HTSP model identifies success factors for FP interventions in Kenya and other low- and middle-income countries where faith leaders and community stakeholders are influential, and that women and faith leaders are much more easily impacted positively with these efforts, as measured by increased knowledge and awareness of modern contraceptive methods, compared with men.
Utility of pan-bacterial and pan-fungal PCR in endophthalmitis: case report and review of the literature
Authors: Ercanbrack Carson W. , Rahal Dania A. , Chauhan Muhammad Z. , Jabbehdari Sayena , Uwaydat Sami H. 
Published: August 2024

Abstract
Background
Endophthalmitis is a clinical diagnosis but identification of the disease-causing agent or agents allows for a more tailored treatment. This is routinely done through intraocular fluid cultures and staining. However, culture-negative endophthalmitis is a relatively common occurrence, and a causative organism cannot be identified. Thus, further diagnostic testing, such as pan-bacterial and pan-fungal polymerase chain reactions (PCRs), may be required.

Body
There are now newer, other testing modalities, specifically pan-bacterial and pan-fungal PCRs, that may allow ophthalmologists to isolate a causative agent when quantitative PCRs and cultures remain negative. We present a case report in which pan-fungal PCR was the only test, amongst quantitative PCRs, cultures, and biopsies, that was able to identify a pathogen in endophthalmitis. Pan-PCR has unique advantages over quantitative PCR in that it does not have a propensity for false-positive results due to contamination. Conversely, pan-PCR has drawbacks, including its inability to detect viruses and parasites and its increased turnaround time and cost. Based on two large retrospective studies, pan-PCR was determined not to be recommended in routine cases of systemic infection as it does not typically add value to the diagnostic workup and does not change the treatment course in most cases. However, in cases like the one presented, pan-bacterial and pan-fungal PCRs may be considered if empiric treatment fails or if the infective organism cannot be isolated. If pan-PCR remains negative or endophthalmitis continues to persist, an even newer form of testing, next-generation sequencing, may aid in the diagnostic workup of culture-negative endophthalmitis.

Conclusion
Pan-bacterial and pan-fungal PCR testing is a relatively new diagnostic tool with unique advantages and drawbacks compared to traditional culturing and PCR methods. Similar to the tests’ use in non-ophthalmic systemic infections, pan-bacterial and pan-fungal PCRs are unlikely to become the initial diagnosis test and completely replace culture methods. However, they can provide useful diagnostic information if an infectious agent is unable to be identified with traditional methods or if empiric treatment of endophthalmitis continues to fail.
RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs
Authors: Leonard Alexander S. , Mapel Xena M. , Pausch Hubert 
Published: August 2024

Abstract
Background
Association testing between molecular phenotypes and genomic variants can help to understand how genotype affects phenotype. RNA sequencing provides access to molecular phenotypes such as gene expression and alternative splicing while DNA sequencing or microarray genotyping are the prevailing options to obtain genomic variants.

Results
We genotype variants for 74 male Braunvieh cattle from both DNA (~ 13-fold coverage) and deep total RNA sequencing from testis, vas deferens, and epididymis tissue (~ 250 million reads per tissue). We show that RNA sequencing can be used to identify approximately 40% of variants (7–10 million) called from DNA sequencing, with over 80% precision. Within highly expressed coding regions, over 92% of expected variants were called with nearly 98% precision. Allele-specific expression and putative post-transcriptional modifications negatively impact variant genotyping accuracy from RNA sequencing and contribute to RNA-DNA differences. Variants called from RNA sequencing detect roughly 75% of eGenes identified using variants called from DNA sequencing, demonstrating a nearly 2-fold enrichment of eQTL variants. We observe a moderate-to-strong correlation in nominal association p-values (Spearman ρ2 ~ 0.6), although only 9% of eGenes have the same top associated variant.

Conclusions
We find hundreds of thousands of RNA-DNA differences in variants called from RNA and DNA sequencing on the same individuals. We identify several highly significant eQTL when using RNA sequencing variant genotypes which are not found with DNA sequencing variant genotypes, suggesting that using RNA sequencing variant genotypes for association testing results in an increased number of false positives. Our findings demonstrate that caution must be exercised beyond filtering for variant quality or imputation accuracy when analysing or imputing variants called from RNA sequencing.
Association mapping with a diverse population of Puccinia graminis f. sp. tritici identified avirulence loci interacting with the barley Rpg1 stem rust resistance gene
Authors: Upadhaya Arjun , Upadhaya Sudha G. C. , Brueggeman Robert 
Published: August 2024

Abstract
Background
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada.

Methods and results
To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus.

Conclusions
The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.
Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing
Authors: Sime Amsale Melkamu , Kifle Bezayit Amare , Woldesemayat Adugna Abdi , Gemeda Mesfin Tafesse 
Published: August 2024

Abstract
Background
The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.

Results
The microbial diversity based on small subunit (SSU) rRNA analysis revealed the dominance of the bacterial domain representing 81.82% and 92.31% in the studied samples. Furthermore, the phylum composition result indicated the dominance of the phyla Proteobacteria (23.08%, 27.27%), Actinobacteria (11.36%, 20.51%), and Acidobacteria (10.26%, 15.91%). The study also identified unassigned bacteria which might have a unique potential for biopolymer hydrolysis. The metagenomic study revealed that 100,244 and 65,356 genes were predicted from the two distinct samples. A total number of 1806 CAZyme genes were identified, among annotated CAZymes, 758 had a known enzyme assigned to CAZymes. Glycoside hydrolases (GHs) CAZyme family contained most of the CAZyme genes with known enzymes such as β-glucosidase, endo-β-1,4-mannanase, exo-β-1,4-glucanase, α-L-arabinofuranosidase and oligoxyloglucan reducing end-specific cellobiohydrolase. On the other hand, 1048 of the identified CAZyme genes were putative CAZyme genes with unknown enzymatical activity and the majority of which belong to the GHs family.

Conclusions
In general, the identified putative CAZymes genes open up an opportunity for the discovery of new enzymes responsible for hydrolyzing biopolymers utilized for biofuel energy generation. This finding is used as a first-hand piece of evidence to serve as a benchmark for further and comprehensive studies to unveil novel classes of bio-economically valuable genes and their encoded products.
Person-centered care for common mental disorders in Ontario’s primary care patient-centered medical homes: a qualitative study of provider perspectives
Authors: Menear Matthew , Ashcroft Rachelle , Dahrouge Simone , Silveira Jose , Booton Jocelyn , Emode Monica , McKenzie Kwame 
Published: August 2024

Abstract
Background
For more than a decade, the Patient-Centered Medical Home model has been a guiding vision for the modernization of primary care systems. In Canada, Ontario’s Family Health Teams (FHTs) were designed in the mid-2000s with the medical home model in mind. These primary care clinics aim to provide accessible, comprehensive, and person-centered primary care services to communities across Ontario. Their services typically include mental health care for people experiencing common mental disorders, such as depression and anxiety disorders. It remains unclear, however, whether the mental health care delivered within FHTs is consistent with person-centered care approaches. In the current study, we aimed to explore the perspectives of FHT providers on the care delivered to people with common mental disorders to determine whether, and to what extent, they believed this care was person-centered.

Methods
We conducted a qualitative grounded theory study involving interviews with 65 health professionals and administrators from 18 FHTs across Ontario. Transcripts were coded using a three-step process of initial, focused, and axial coding that mixed inductive and deductive approaches informed by sensitizing concepts on person-centeredness.

Results
Practices and challenges associated with the delivery of mental health care in a person-centered way were captured by several themes regrouped into five domains: (1) patient as unique person, (2) patient-provider relationship, (3) sharing power and responsibility, (4) connecting to family and community, and (5) creating person-centered care environments. FHT providers perceived that they delivered person-centered care by delivering mental health care that was responsive, flexible, and consistent with biopsychosocial approaches. They emphasized the importance of creating long-lasting relationships with patients grounded in empathy and trust. Their challenges included being able to ensure continuity of care, adequately prioritizing patients’ mental health issues, and meaningfully engaging patients and families as partners in care.

Conclusions
Our findings suggest that FHT providers have adopted a range of person-centered practices for people with common mental disorders. However, greater attention to practices such as shared decision making, supporting self-management, and involving families in care would strengthen person-centeredness and bring teams closer to the Patient-Centered Medical Home vision.
Development of a self-assessment tool to address the functioning of community-dwelling older adults in general practice: a validation study of the EFA23 questionnaire
Authors: Rink Laura , Floto Caroline , Apel Katharina , Weiss Maren , Stegmeier Elmar , Kühlein Thomas , Sebastião Maria 
Published: August 2024

Abstract
Background
Multimorbidity is increasingly prevalent among ageing patients, leading to reduced daily functioning. To address the challenges posed by multimorbidity in older adults, a person- and context-centred approach is needed. This study aimed to develop a questionnaire as a self-assessment tool for older adults focusing on functioning in general practice based on the International Classification of Functioning, Disability and Health (ICF).

Methods
A mixed-methods approach was employed in the development and validation of the German EFA23 (Erfassung Funktionaler Gesundheit im Alter – 23 Fragen; Assessing Functional Health in Old Age – 23 questions) questionnaire. Based on an ICF subset developed in a preparatory phase and consensus study, questionnaire items were formulated and tested in a qualitative pretest, followed by a validation study. A workshop with general practitioners (GPs) was held to develop a supplementary manual for GPs on how to interpret the questionnaire results and discuss them with the patients.

Results
A total of 69 items were developed and tested in the qualitative pretest with 15 respondents, resulting in 37 items for the validation study. The validation study, involving 237 older adults, showed the presence of one significant principal component. It demonstrated good internal consistency (Cronbach’s alpha = 0.967) and construct validity, showing positive correlations with established assessment tools. Descriptive statistics showed differences between the means of self-assessment by patients and an external GP assessment. The final EFA23 questionnaire consists of 23 items assessing limitations in functioning.

Conclusions
The EFA23 questionnaire can be used as a valid self-assessment instrument to measure functioning in older adults, supporting a person- and context-centred approach in general practice.
COVID-19 infection and 2-year mortality in nursing home residents who survived the first wave of the pandemic
Authors: Sanchez Manuel , Courtois-Amiot Pauline , Herrault Vincent , Allart Hélène , Eischen Philippe , Chetaille Fabienne , Lepineux Denise , de Cathelineau Castille , Raynaud-Simon Agathe 
Published: August 2024

Abstract
Background
During the first COVID-19 pandemic wave (1st CoPW), nursing homes (NHs) experienced a high rate of COVID-19 infection and death. Residents who survived the COVID-19 infection may have become frailer. This study aimed to determine the predictive value of having a COVID-19 infection during the 1st CoPW for 2-year mortality in NH residents.

Methods
This was a retrospective study conducted in three NHs. Residents who had survived the 1st CoPW (March to May 2020) were included. The diagnosis of COVID-19 was based on the results of a positive reverse transcriptase-polymerase chain reaction test. The collected data also included age, sex, length of residence in the NH, disability status, legal guardianship status, nutritional status, need for texture-modified food, hospitalization or Emergency Department visits during lockdown and SARS-COV2 vaccination status during the follow-up. Non-adjusted and adjusted Cox models were used to analyse factors associated with 2-year post-1st CoPW mortality.

Results
Among the 315 CoPW1 survivors (72% female, mean age 88 years, 48% with severe disability), 35% presented with COVID-19. Having a history of COVID-19 was not associated with 2-year mortality: hazard ratio (HR) [95% confidence interval] = 0.96 [0.81–1.13], p = 0.62. The factors independently associated with 2-year mortality were older age (for each additional year, HR = 1.05 [1.03–1.08], p < 0.01), severe disability vs. moderate or no disability (HR = 1.35 [1.12–1.63], p < 0.01) and severe malnutrition vs. no malnutrition (HR = 1.29 [1.04–1.60], p = 0.02). Considering that vaccination campaign started during the follow-up, mortality was associated with severe malnutrition before and severe disability after the start of the campaign. Vaccination was independently associated with better survival (HR 0.71 [0.55–0.93], p = 0.02).

Conclusions
Having survived a COVID-19 infection during the 1st CoPW did not affect subsequent 2-year survival in older adults living in NHs. Severe malnutrition and disability remained strong predictor of mortality in this population, whereas vaccination was associated to better survival.
Factors associated with self-reports of limitations in activities of daily living among Medicare Fee-for-Service recipients
Authors: Hays Ron D. , Haas Ann , Haviland Amelia M. , Martino Steven C. , Orr Nate , Binion Joy , Elliott Marc N. 
Published: August 2024

Abstract
Background
Physical function is an important indicator of physical health and predicts mortality. This study identified characteristics associated with limitations in Medicare recipients' activities of daily living.

Methods
2019 Consumer Assessment of Healthcare Providers and Systems Fee-for-Service Medicare Survey data: 79,725 respondents (34% response rate) who were 65 and older and 53% female; 7% Black, 5% Hispanic, 4% Asian American, Native Hawaiian, or other Pacific Islander, 2% Multiracial, 1% American Indian/Alaskan Native; 35% with high school education or less. Walking, getting in and out of chairs, bathing, dressing, toileting, and eating (scored as having no difficulty versus being able to do with difficulty or unable to do) and a scale of these items were regressed on patient characteristics.

Results
After adjustment for all characteristics, function limitations were found for those who smoked (effect sizes of significant associations range .04-.13), had chronic health conditions (.02-.33), were 85 years or older (.09-.46), needed assistance completing the survey (.32–1.29), were female (.05-.07), and had low income and assets (.15-.47).

Conclusions
These nationally representative U.S. estimates of physical function characteristics are useful for interventions for vulnerable population subgroups.