bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative genomic analyses reveal putative cell type-specific targets of the Drosophila ets transcription factor Pointed
Authors: Bollepogu Raja Komal Kumar , Yeung Kelvin , Shim Yoon-Kyung , Mardon Graeme 
Published: January 2024

AbstractThe Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is the downstream effector of the Epidermal growth factor receptor (Egfr) pathway and is required for cell cycle progression, specification, and differentiation of most cell types in the larval eye disc. Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we employed an integrated approach by combining genome-wide single cell and bulk data to identify putative cell type-specific Pnt targets. First, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Next, we integrated ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) to reveal 157 putative cell type-specific Pnt targets that may help mediate unique cell type responses upon Egfr-induced differentiation. Finally, our integrated data also predicts cell type-specific functional enhancers that were not reported previously. Together, our study provides a greatly expanded list of putative cell type-specific Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Egfr signaling.
Genome-wide association study for stayability at different calvings in Nellore beef cattle
Authors: Silva Diogo Osmar , Fernandes Júnior Gerardo Alves , Fonseca Larissa Fernanda Simielli , Mota Lúcio Flávio Macedo , Bresolin Tiago , Carvalheiro Roberto , de Albuquerque Lucia Galvão 
Published: January 2024

Abstract
Backgrounding
Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal’s life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female’s productive life.

Results
The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant.

Conclusion
Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.
High frequency of antimicrobial resistance in Salmonella and Escherichia coli causing diarrheal diseases at the Yirimadio community health facility, Mali
Authors: Diarra Bintou , Guindo Ibréhima , Koné Boī , Dembélé Maīmouna , Cissé Ibrahim , Thiam Souleymane , Konaté Kadidia , Tékété Mamadou , Maīga Almoustapha , Maīga Oumou , Timbiné Lassina , Djimde Abdoulaye 
Published: January 2024

Abstract
Background
Diarrhoea is a public health problem, especially in developing countries where it is the second leading cause of child mortality. In Low Income Countries like in Mali, self-medication and inappropriate use of antibiotics due to the scarcity of complementary diagnostic systems can lead to the development of multidrug-resistant bacteria causing diarrhoea. The objective of this work was to determine the microorganisms responsible for diarrhoea in children under 15 years of age and to characterize their sensitivity to a panel of antibiotics used in a peri-urban community in Mali. The study involved outpatient children visiting the Yirimadio Community Health Centre and diagnosed with diarrhoea. Stool samples from those patients were collected and analysed by conventional stools culture and the susceptibility to antibiotics of detected bacteria was determined by the disc diffusion method in an agar medium.

Result
Overall, 554 patients were included. Children under the age of 3 years accounted for 88.8% (492 of 554) of our study population. Two bacterial species were isolated in this study, Escherichia coli 31.8% (176 of 554) and Salmonella 2.9% (16 of 554). In the 176, E. coli strains resistance to amoxicillin and to cotrimoxazole was seen in 93.8% (165 of 176) and 92.6% ( 163 of 176), respectively. The ESBL resistance phenotype accounted for 39,8% (70 of 176) of E. coli. Sixteen (16) strains of Salmonella were found, of which one strain (6.3%) was resistant to amoxicillin and to amoxicillin + clavulanic acid. Another one was resistant to chloramphenicol (6.3%). Two strains of Salmonella were resistant to cotrimoxazole (12.5%) and two others were resistant to cefoxitin (12.5%).

Conclusions
The data suggest that E. coli is frequently involved in diarrhoea in children under 3 years of age in this peri-urban setting of Bamako, Mali, with a high rate of resistance to amoxicillin and cotrimoxazole, the most widely used antibiotics in the management of diarrhoea in this setting.
Transcatheter aortic valve implantation versus surgical aortic valve replacement for pure aortic regurgitation: a systematic review and meta-analysis of 33,484 patients
Authors: Elkasaby Mohamed Hamouda , Khalefa Basma Badrawy , Yassin Mazen Negmeldin Aly , Alabdallat Yasmeen Jamal , Atia Ahmed , Altobaishat Obieda , Omar Islam , Hussein Amany 
Published: January 2024

Abstract
Introduction
The published studies comparing transcatheter aortic valve implantation (TAVI) and surgical aortic valve replacement (SAVR) in pure aortic regurgitation (AR) are conflicting. We conducted this systematic review and meta-analysis to compare TAVI with SAVR in pure AR.

Methods
We searched PubMed, Embase, Web of Science (WOS), Scopus, and the Cochrane Library Central Register of Controlled Trials (CENTRAL) from inception until 23 June 2023. Review Manager was used for statistical analysis. The risk ratio (RR) with a 95% confidence interval (CI) was used to compare dichotomous outcomes. Continuous outcomes were compared using the mean difference (MD) and 95% CI. The inconsistency test (I2) assessed the heterogeneity. We used the Newcastle-Ottawa scale to assess the quality of included studies. We evaluated the strength of evidence using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) scale.

Results
We included six studies with 5633 patients in the TAVI group and 27,851 in SAVR. In-hospital mortality was comparable between TAVI and SAVR (RR = 0.89, 95% CI [0.56, 1.42], P = 0.63) (I2 = 86%, P < 0.001). TAVI was favored over SAVR regarding in-hospital stroke (RR = 0.50; 95% CI [0.39, 0.66], P < 0.001) (I2 = 11%, P = 0.34), in-hospital acute kidney injury (RR = 0.56; 95% CI: [0.41, 0.76], P < 0.001) (I2 = 91%, P < 0.001), major bleeding (RR = 0.23; 95% CI: [0.17, 0.32], P < 0.001) (I2 = 78%, P < 0.001), and shorter hospital say (MD = − 4.76 days; 95% CI: [− 5.27, − 4.25], P < 0.001) (I2 = 88%, P < 0.001). In contrast, TAVI was associated with a higher rate of pacemaker implantation (RR = 1.68; 95% CI: [1.50, 1.88], P < 0.001) (I2 = 0% P = 0.83).

Conclusion
TAVI reduces in-hospital stroke and is associated with better safety outcomes than SAVR in patients with pure AR.
Clinical characteristics and outcome of cardiac resynchronization therapy for heart failure in National Hospital of Sri Lanka from year 2005 to 2020 – a retrospective observational study
Authors: Iddagoda Hewage Don Sandun Prabath , Kuruppu Kuruppumullage Chamini Nuwansika , Dunuwille Asunga , Wijewardena Asanka , Gunawardena Rohan 
Published: January 2024

Abstract
Background
Cardiac resynchronization therapy (CRT) has been a well-established treatment modality for moderate to severe left ventricular systolic dysfunction with left ventricular desynchrony. This is the pioneering study that analyses the cohort who underwent CRT implantation at the National Hospital of Sri Lanka (NHSL) in Colombo from 2005 to 2020.

Objectives
This study was carried out to describe socio-demographic factors, improvements in clinical outcome (symptoms, electrocardiographic, and echocardiographic features), and post-CRT complications in the study population, as well as to determine the efficacy of CRT in heart failure.

Method
A retrospective observational study was conducted on all the living patients who had undergone CRT implantation from 2005 to 2020. The data was gathered from all the consented patients who visited the device programming clinic using a physician-administered questionnaire and clinical records. Data was analyzed using SPSS 25, and significant statistics were assessed with the McNemer test, the Student T test, and the Chi-Squared test.

Results
The study included 50 patients with a mean age of 52.82+/− 11.66 years and female predominance (56%, n = 28). Idiopathic dilated cardiomyopathy (50%, n = 25) was the leading etiological factor, followed by ischemic cardiomyopathy (28%, n = 14). Clinical symptoms have improved significantly with CRT implantation (p < 0.001). A significant improvement was found in NYHA functional class (p < 0.001, 95% CI = 0.072 to 0.284), QRS width (p < 0.001, 95% CI = 0.229 to 0.534), ejection fraction (p < 0.001, 95% CI = − 16.437 to − 8.504), and LV EDD (p < 0.001, 95% CI = 2.89 to 9.24). Post-CRT complications included lead malfunction (6%, n = 3) and chronic (14%, n = 7), bleeding or hematoma (2%, n = 1), pocket erosion or infection (6%, n = 3), and infective endocarditis (2%, n = 1).

Conclusion
According to the study, CRT significantly improves both clinical and functional outcomes in patients with moderate to severe heart failure.
Exploring trial publication and research waste in COVID-19 randomised trials of hydroxychloroquine, corticosteroids, and vitamin D: a meta-epidemiological cohort study
Authors: Fincham Lisa , Hohlfeld Ameer , Clarke Mike , Kredo Tamara , McCaul Michael 
Published: January 2024

Abstract
Background
The global research response to the COVID-19 pandemic was impressive, but also led to an infodemic and considerable research waste. Registered, but unpublished trials added to this noise. We aimed to determine the proportion of registered randomised trials of common COVID-19 treatments that were published and to describe the characteristics of these trials to examine the association between trial characteristics, publication status and research waste.

Methods
This meta-epidemiological cohort study used a sample of randomised trials of corticosteroids, hydroxychloroquine or vitamin D as treatments for COVID-19, registered between 1 November 2019 and 31 December 2021 and available via the WHO ICTRP portal. We searched for the trials’ published results up to 20 October 2022. We extracted the trial characteristics, analysing with descriptive statistics. We performed univariate logistic regression to examine the association between trials’ characteristics and publication status, followed by multiple logistic regression using significant characteristics to assess the association between trial characteristics and publication status.

Results
We identified 357 eligible trials on ICTRP. Of these, 107 (30%) had published or made their results available publicly by 20 October 2022, while 250 (70%) had not been published or shared their results publicly. Multiple logistic regression analysis showed that a larger target sample size was a significant positive predictor of publication with target sample sizes above 300 almost tripling the odds of publication (aOR: 2.75, 95% CI: 1.35 to 5.62).

Conclusions
Less than one third of registered trials made their results public and our findings identified that many trialists had not updated their trial registry entry with the trial status, results or both. Failure to share trial results publicly is a disservice to patients, clinicians and policy makers and adds to research waste.
The impact of endoscopist performance and patient factors on distal adenoma detection and colorectal cancer incidence
Authors: Power Sharon , Wooldrage Kate , Saunders Brian P. , Cross Amanda J. 
Published: January 2024

Abstract
Background
High quality endoscopy is key for detecting and removing precursor lesions to colorectal cancer (CRC). Adenoma detection rates (ADRs) measure endoscopist performance. Improving other components of examinations could increase adenoma detection.

Aims
To investigate how endoscopist performance at flexible sigmoidoscopy (FS) affects adenoma detection and CRC incidence.

Methods
Among 34,139 participants receiving FS screening by the main endoscopist at one of 13 centres in the UK FS Screening Trial, median follow-up was 17 years. Factors examined included family history of CRC, bowel preparation quality, insertion and withdrawal time, bowel segment reached, patient pain and ADR. Odds ratios (OR) for distal adenoma detection were estimated by logistic regression. Hazard ratios (HR) for distal CRC incidence were estimated by Cox regression.

Results
At screening, 4,104 participants had distal adenomas detected and 168 participants developed distal CRC during follow-up. In multivariable models, a family history of CRC (yes vs. no: OR 1.40, 95%CI 1.21–1.62), good or adequate bowel preparation quality (vs. excellent: OR 0.84, 95%CI 0.74–0.95; OR 0.56, 95%CI 0.49–0.65, respectively) and longer insertion and withdrawal times (≥ 4.00 vs. < 2.00 min: OR 1.96, 95%CI 1.68–2.29; OR 32.79, 95%CI 28.22–38.11, respectively) were associated with adenoma detection. Being screened by endoscopists with low or intermediate ADRs, compared to high ADRs, was positively associated with CRC incidence (multivariable: HR 4.71, 95%CI 2.65–8.38; HR 2.16, 95%CI 1.22–3.81, respectively).

Conclusions
Bowel preparation quality and longer insertion and withdrawal time are key for improving distal adenoma detection. Higher ADRs were associated with a lower risk of distal CRC.
Targeted metabolomics reveals plasma short-chain fatty acids are associated with metabolic dysfunction-associated steatotic liver disease
Authors: Thing Mira , Werge Mikkel Parsberg , Kimer Nina , Hetland Liv Eline , Rashu Elias Badal , Nabilou Puria , Junker Anders Ellekaer , Galsgaard Elisabeth Douglas , Bendtsen Flemming , Laupsa-Borge Johnny , McCann Adrian , Gluud Lise Lotte 
Published: January 2024

Abstract
Background
Alterations in the production of short-chain fatty acids (SCFAs) may reflect disturbances in the gut microbiota and have been linked to metabolic dysfunction-associated steatotic liver disease (MASLD). We assessed plasma SCFAs in patients with MASLD and healthy controls.

Methods
Fasting venous blood samples were collected and eight SCFAs were measured using gas chromatography-tandem mass spectrometry (GC-MS/MS). Relative between-group differences in circulating SCFA concentrations were estimated by linear regression, and the relation between SCFA concentrations, MASLD, and fibrosis severity was investigated using logistic regression.

Results
The study includes 100 patients with MASLD (51% with mild/no fibrosis and 49% with significant fibrosis) and 50 healthy controls. Compared with healthy controls, MASLD patients had higher plasma concentrations of propionate (21.8%, 95% CI 3.33 to 43.6, p = 0.02), formate (21.9%, 95% CI 6.99 to 38.9, p = 0.003), valerate (35.7%, 95% CI 4.53 to 76.2, p = 0.02), and α-methylbutyrate (16.2%, 95% CI 3.66 to 30.3, p = 0.01) but lower plasma acetate concentrations (− 30.0%, 95% CI − 40.4 to − 17.9, p < 0.001). Among patients with MASLD, significant fibrosis was positively associated with propionate (p = 0.02), butyrate (p = 0.03), valerate (p = 0.03), and α-methylbutyrate (p = 0.02). Six of eight SCFAs were significantly increased in F4 fibrosis.

Conclusions
In the present study, SCFAs were associated with MASLD and fibrosis severity, but further research is needed to elucidate the potential mechanisms underlying our observations and to assess the possible benefit of therapies modulating gut microbiota.
Activities of daily living limitations and the use of physical examination among older adults with informal care in China: do gender and residence make differences?
Authors: Luo Jingjing , Zhao Dan , Gao Tingting , Sun Jingjie , Li Peilong , Wang Xuehong , Wang Xueqing , Chai Shujun , Li Jiayan , Zhou Chengchao 
Published: January 2024

Abstract
Background
This study investigated the relationship between activities of daily living (ADL) limitations and the use of physical examination among older adults receiving informal care, and to further examine whether this relationship varies by gender and urban-rural areas.

Methods
The data in this study were obtained from the sixth Health Service of Shandong province, China. In total, 8,358 older adults aged 60 years or older who received informal care were included in the analysis. Binary logistic regression models were conducted to explore the association between ADL limitations and the use of physical examination and examine the differences between gender and urban-rural areas.

Results
The prevalence of limitations in ADL and physical examination utilization rate among older adults receiving informal care in Shandong Province were 14.12% and 72.31%, respectively. After adjusting for confounders, ADL limitations were negatively correlated with the utilization of physical examination services among older adults receiving informal care (OR = 0.74, 95% CI: 0.64, 0.87, P < 0.001), and there were gender and rural-urban differences. The association between ADL limitations and the use of physical examination was statistically significant in older women receiving informal care (OR = 0.65, 95% CI: 0.53, 0.80, P < 0.001). And only among urban older adults receiving informal care, those with ADL limitations had lower utilization of physical examination services than participants without ADL limitations (OR = 0.59, 95% CI: 0.47, 0.74, P < 0.001).

Conclusions
Our study suggested that the relationship between ADL limitations and the use of physical examination among older adults receiving informal care differed by gender and urban-rural areas in Shandong, China. These findings implied that the government should provide more health resources and personalized physical examination service programs, especially to meet the differential needs of women and urban old adults receiving informal care, to contribute to the implementation of healthy aging strategies.
Comparison of anticholinergic burden with chronic polypharmacy on functional decline and mortality in Korean older people: a retrospective nationwide cohort study
Authors: Huh Youn , Kim Ye-Jee , Choi Jung-Yeon , Lee Ji Eun , Jung Hee-Won , Shin Cheol Min , Won Chang Won , Son Ki Young 
Published: January 2024

Abstract
Background
We aimed to evaluate the association of anticholinergic burden and chronic polypharmacy with the incidence of functional decline and all-cause mortality, and to determine the difference between anticholinergic burden and chronic polypharmacy among Korean older people.

Methods
This nationwide cohort study included 42,132 older people aged ≥ 65 years who underwent Korean National Health Insurance Service health examinations from 2007 to 2008. Odds ratios (ORs) and 95% confidence intervals (CIs) for abnormal Timed Up and Go (TUG) test results were assessed using multivariate logistic regression analyses. Hazard ratios (HRs) and 95% CIs for all-cause mortality until the end of 2015 were estimated using multivariable Cox proportional hazards regression analysis.

Results
Of the participants, 37.19% had abnormal TUG test results, and 7.66% of those died during the 5.7-year mean follow-up. The abnormal TUG test results OR increased by 27% among individuals with Korean Anticholinergic Burden Scale (KABS) scores ≥ 3 (OR 1.27, 95% CI 1.02–1.58) compared to those with KABS scores of 0. The HRs for all-cause mortality increased for individuals with higher KABS scores (P for trend < 0.001) or chronic polypharmacy (P for trend < 0.001) compared to those for individuals without these conditions. The combination of a higher KABS or chronic polypharmacy and abnormal TUG test results increased the risk of all-cause mortality (All P for trend < 0.001).

Conclusion
Anticholinergic drug burden shows a better association with functional decline than chronic polypharmacy, and the use of medications and functional decline may be important risk factors for all-cause mortality among older people.
Association between psychiatric disorders and glioma risk: evidence from Mendelian randomization analysis
Authors: Yang Wenzhuo , Han Yu , He Changjia , Zhong Sheng , Ren Fei , Chen Zhongping , Mou Yonggao , Sai Ke 
Published: January 2024

Abstract
Background
Observational studies have explored the association of psychiatric disorders and the risk of brain cancers. However, the causal effect of specific mental illness on glioma remains elusive due to the lack of solid evidence.

Methods
We performed a two-sample bidirectional Mendelian randomization (MR) analysis to explore the causal relationships between 5 common psychiatric disorders (schizophrenia, major depressive disorder, bipolar disorder, autism spectrum disorder, and panic disorder) and glioma. Summary statistics for psychiatric disorders and glioma were extracted from Psychiatric Genomics Consortium (PGC) and 8 genome-wide association study (GWAS) datasets respectively. We calculated the MR estimates for odds ratio of glioma associated with each psychiatric disorder by using inverse-variance weighting (IVW) method. Sensitivity analyses such as weighted median estimator, MR-Egger and MR-PRESSO were leveraged to assess the strength of causal inference.

Results
A total of 30,657 participants of European ancestry were included in this study. After correction for multiple testing, we found that genetically predicted schizophrenia was associated with a statistically significant increase in odds of non-glioblastoma multiforme (non-GBM) (OR = 1.13, 95% CI: 1.03–1.23, P = 0.0096). There is little evidence for the causal relationships between the other 4 psychiatric disorders with the risk of glioma.

Conclusions
In this MR analysis, we revealed an increased risk of non-GBM glioma in individuals with schizophrenia, which gives an insight into the etiology of glioma.