bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes
Authors: Mehta Rohan S , Petit Robert A , Read Timothy D , Weissman Daniel B 
Published: June 2023

AbstractBacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package that allows for the computation of our method.
Examining differential success in recruitment using respondent driven sampling (RDS) in a multi-site study of gay, bisexual and other men who have sex with men
Authors: Sang Jordan M. , Gholamian Bita , Wang Lu , Barath Justin , Noor Syed W. , Lachowsky Nathan J. , Hart Trevor A. , Cox Joseph , Lambert Gilles , Grace Daniel , Skakoon-Sparling Shayna , Lal Allan , Parlette Abbie , Apelian Herak , Jollimore Jody , Hogg Robert S. , Moore David M. 
Published: June 2023

Abstract
Background
The Engage Study is a longitudinal biobehavioral cohort study of gay, bisexual and other men who have sex with men (GBM) in Toronto, Montreal, and Vancouver. Baseline data (2,449 participants) were collected from February 2017 - August 2019 using respondent-driven sampling (RDS). Recruitment in Montreal required fewer seeds, had a much shorter recruitment period, and recruited the largest sample.

Methods
To better understand why RDS recruitment was more successful in Montreal compared to other sites, we conducted an analysis to examine RDS recruitment characteristics for GBM in each of the three study sites, explore demographic characteristics and measures of homophily, that is, the tendency of individuals to recruit other study participants who are like themselves, and compared motivations for study participation.

Results
Montreal had the greatest proportion of participants over the age of 45 (29.1% in Montreal, 24.6% in Vancouver, and 21.0% in Toronto) and the highest homophily for this age group, but homophily was high across the three cities. Montreal also reported the lowest percentage of participants with an annual income greater or equal to $60,000 (7.9% in Montreal, 13.1% in Vancouver and 10.6% in Toronto), but homophily was similar across all three cities. The majority of participants indicated interest in sexual health and HIV as the main reason for participating (36.1% in Montreal, 34.7% in Vancouver, and 29.8% in Toronto). Financial interest as the main reason for participation was low (12.7% in Montreal, 10.6% in Vancouver, and 5.7% in Toronto).

Conclusion
Taken together, although we found some differences in study demographic characteristics and homophily scores, we were unable to fully explain the different recruitment success based on the data available. Our study underlines the fact that success of RDS implementation may vary by unknown factors, and that researchers should be proactive and flexible to account for variability.
Diagnostic stewardship to limit repeat plasma cytomegalovirus viral load testing
Authors: Trirattanapikul Akeatit , Pasomsub Ekawat , Siriyotha Sukanya , Pattanaprateep Oraluck , Phuphuakrat Angsana 
Published: June 2023

Abstract
Background
Frequent serial monitoring of plasma cytomegalovirus (CMV) viral load caused unnecessary budgets for laboratory testing without changes in treatment. We aimed to implement diagnostic stewardship to limit CMV viral load testing at appropriate intervals.

Methods
A quasi-experimental study was performed. To avoid unnecessary plasma CMV viral load testing, the inpatient electronic pop-up reminder was launched in 2021. In cases with plasma CMV viral load testing was ordered in intervals of less than five days, telephone interview and feedback were performed. Pre-post intervention data was compared in terms of clinical and monetary outcomes. The rate of plasma CMV viral load testing performed in intervals of less than five days was compared between 2021 and 2019 using the Poisson regression model.

Results
After the protocol implementation, there was a significant decrease in the rate of plasma CMV viral load test orders in intervals of less than five days from 17.5% to 8.0% [incidence rate ratio 0.40, p < 0.001]. There was no statistically significant difference in the incidence of CMV DNAemia and CMV disease (p = 0.407 and 0.602, respectively). As a result, the hospital could save the costs of plasma CMV viral load testing per 1,000 patients performed with intervals of less than five days from 2,646,048.11 to 1,360,062.89 Thai Baht.

Conclusions
The diagnostic stewardship program is safe and helpful in reducing unnecessary plasma CMV viral load testing and costs.
Neuropsychological, neuroimaging and autopsy findings of butane encephalopathy
Authors: Yun Jaeseob , Jang Sung Hwan , Cho Huiran , Lee Myung Jun , Jung Na-Yeon , Lee Jae-Hyeok , Shin Jin-Hong , Lee Young Min , Yoon Jin A , Pak Kyoungjune , Ko Junkyeung , Lee Jae Meen , Hwang Chungsu , Ahn Jae Woo , Sung Suk , Choi Kyung-Un , Huh Gi Yeong , Kim Eun-Joo 
Published: June 2023

Abstract
Background
Butane is an aliphatic hydrocarbon used in various commercial products. While numerous reports of sudden cardiac-related deaths from butane inhalation have been described, butane-associated acute encephalopathy has rarely been reported.

Case presentation
A 38-year-old man presented with cognitive dysfunction after butane gas inhalation. Neuropsychological test results showed impairments in verbal and visual memory, and frontal executive function. Diffusion weighted MRI revealed symmetric high-signal changes in the bilateral hippocampus and globus pallidus. FDG-PET demonstrated decreased glucose metabolism in the bilateral precuneus and occipital areas and the left temporal region. At the 8-month follow-up, he showed still significant deficits in memory and frontal functions. Diffuse cortical atrophy with white matter hyperintensities and extensive glucose hypometabolism were detected on follow-up MRI and FDG-PET, respectively. Brain autopsy demonstrated necrosis and cavitary lesions in the globus pallidus.

Conclusions
Only a few cases of butane encephalopathy have been reported to date. Brain lesions associated with butane encephalopathy include lesions in the bilateral thalamus, insula, putamen, and cerebellum. To the best of our knowledge, this is the first report on bilateral hippocampal and globus pallidal involvement in acute butane encephalopathy. The pathophysiology of central nervous system complications induced by butane intoxication is not yet fully understood. However, the direct toxic effects of butane or anoxic injury secondary to cardiac arrest or respiratory depression have been suggested as possible mechanisms of edematous changes in the brain after butane intoxication.
Socioeconomic and geographical inequalities in using skilled birth attendants during delivery in Bangladesh over two decades
Authors: Chowdhury Syed Sharaf Ahmed , Kundu Satyajit , Sharif Azaz Bin 
Published: June 2023

AbstractBackgroundMaternal and neonatal mortality is a major public health concern globally. Evidence supports that skilled birth attendants (SBA) can significantly reduce maternal and neonatal mortality. Despite the improvement in SBA use, Bangladesh lacks evidence of equality in SBA use across socioeconomic and geographic regions. Therefore, we aim to estimate the trends and magnitude of inequality in SBA use in Bangladesh over the last two decades.MethodsData from the last 5 rounds of Bangladesh Demographic and Health Surveys (BDHS; 2017-18, 2014, 2011, 2007, and 2004) were used to measure the inequalities in the SBA use utilizing the WHO’s Health Equity Assessment Toolkit (HEAT) software. Inequality was assessed by four summary measures, namely, Population Attributable Risk (PAR), Population Attributable Fraction (PAF), Difference (D), and Ratio (R) based on the four equity dimensions: wealth status, education level, place of residence, and subnational regions (divisions). Point estimates and a 95% confidence interval (CI) were reported for each measure.ResultsAn increasing trend in the overall prevalence of SBA use was observed (From 15.6% in 2004 to 52.9% in 2017). We found significant inequalities in SBA use in every wave of BDHS (from 2004 to 2017), with the result concentrating on the rich (in 2017, PAF: 57.1; 95% CI: 52.5–61.7), educated (in 2017, PAR: 9.9; 95% CI: 5.2–14.5), and people from urban areas (in 2017, PAF: 28.0; 95% CI: 26.4–29.5). We also identified geographic disparities in SBA use favoring Khulna and Dhaka divisions (in 2017, PAR: 10.2; 95% CI: 5.7–14.7). Our study also observed inequality in using SBA among Bangladeshi women decreased over time.ConclusionTo increase SBA use and to decrease inequality in all four equity dimensions, disadvantaged sub-groups should be prioritized in policies and planning for program implementation.
Clinical outcome analysis of modified B-Lynch sutures in the fundus uteri and part of the corpus uteri for the prevention of intraoperative haemorrhage during caesarean delivery in women with twin pregnancy: a retrospective study
Authors: Shi Chunbo , Chen Jinliang , Chen Aner 
Published: June 2023

Abstract
Objective
To explore the efficacy of modified B-Lynch sutures in the fundus uteri and part of the corpus uteri for the prevention of intraoperative haemorrhage during caesarean delivery in women with twin pregnancy.

Methods
This retrospective analysis covers the clinical data of 40 women with postpartum haemorrhage caused by uterine inertia during caesarean section in women with twin pregnancy in our hospital from January 2018 to May 2022. These women were divided into the group with modified B-Lynch sutures at the fundus and part of the corpus uteri (Group A, 20 patients) and the group with classic B-Lynch sutures (Group B, 20 patients) according to the treatment received. The treatment effect and safety of the two uterine compression sutures were compared.

Results
In this study, no statistically significant differences were found in the outcomes of haemostasis or intraoperative and 24-h postoperative blood loss between the two uterine compression suture groups (P > 0.05). Compared to Group B, Group A showed a significantly reduced operative time, postoperative hospital stay, puerperal morbidity rate, pain score and duration of lochia.

Conclusion
Modified B-Lynch sutures at the fundus and part of the corpus uteri can achieve a haemostatic effect similar to that of the classic B-Lynch suture, while it allows for a shortened operative time and reduced postoperative complications. Modified B-Lynch sutures can serve as a safe, rapid and effective haemostatic method for the prevention and treatment of postpartum haemorrhage during caesarean section in women with twin pregnancy, showing certain validity for promotion in clinics.
Diagnostic and prognostic value of deregulated long non-coding RNA RPPH1 in patients with severe community-acquired pneumonia: a retrospective cohort study
Authors: Su Pengtao , Hu Pengbo , Xu Ling , Zhang Bing 
Published: June 2023

Abstract
Background
Severe community-acquired pneumonia (SCAP) is one of the most common critical and acute diseases in the respiratory and acute medicine department. The expression and significance of lncRNA RPPH1 (RPPH1) in SCAP were assessed aiming to explore a biomarker assisting in the screening and management of SCAP.

Methods
This study is a retrospective study enrolled 97 SCAP patients, 102 mild community-acquired pneumonia (MCAP) patients, and 65 healthy individuals. The serum expression of RPPH1 of study subjects was evaluated using PCR. The diagnostic and prognostic significance of RPPH1 in SCAP was evaluated by ROC and Cox analyses. Meanwhile, the correlation of RPPH1 with patients’ clinicopathological features was evaluated by spearman correlation analysis to evaluate its role in assessing disease severity.

Results
A significant downregulation of RPPH1 was observed in the serum of SCAP patients compared with MCAP and healthy individuals. RPPH1 was positively correlated with ALB (r = 0.74) and negatively correlated with C-reactive protein (r = -0.69), neutrophil-to-lymphocyte ratio (r = -0.88), procalcitonin (r = -0.74), and neutrophil (r = -0.84) of SCAP patients, which are associated with the development and severity of SCAP. Additionally, reduced RPPH1 was closely associated with the 28-day development-free survival of SCAP patients and served as an adverse prognostic indicator together with procalcitonin.

Conclusions
Downregulated RPPH1 in SCAP could act as a diagnostic biomarker screening SCAP from healthy and MCAP individuals and act as a prognostic biomarker predicting patients’ disease conditions and outcomes. The demonstrated significance of RPPH1 in SCAP could assist the clinical antibiotic therapies of SCAP patients.
Effect of continuous chelation on the dentinal tubule penetration of a calcium silicate–based root canal sealer: a confocal laser microscopy study
Authors: Hassan Reham , Roshdy Nehal Nabil 
Published: June 2023

Abstract
Background
This study aimed to evaluate the effect of various irrigation protocols on the penetration depth of a calcium silicate–based sealer into dentinal tubules using confocal laser scanning microscopy (CLSM).

Methods
Twenty single-rooted mandibular premolars were endodontically prepared and divided into the following two groups according to the irrigation protocol used (n = 10): Group I: NaOCl + EDTA and Group II: continuous chelation (NaOCl/Dual Rinse). Obturation was performed with the warm vertical compaction technique using TotalFill HiFlow bioceramic sealer mixed with a fluorophore dye. Samples were observed using CLSM at 10× to measure the percentage of sealer penetration and its maximum depth into the dentinal tubules. Data were analysed using one-way ANOVA followed by Tukey’s post-hoc test. The significance level was set at p < 0.05 within all tests.

Results
Comparing the overall results of all sections tested, no statistically significant differences existed between the groups regarding the percentage of sealer penetration (p = 0.612) and maximum depth of penetration (p > 0.05).

Conclusions
With both types of irrigation used, dentinal tubule penetration was higher in the coronal section than in the apical section. Continuous chelation using NaOCl/Dual Rinse HEDP performed better in the coronal segments, while irrigation using NaOCl + EDTA promoted a higher percentage of sealer penetration in the apical segment.
Risk of uterine leiomyomata with menstrual and reproductive factors in premenopausal women: Korea nurses’ health study
Authors: Song Sihan , Park Soojin , Song Bo Mi , Lee Jung Eun , Cha Chiyoung , Park Hyun-Young 
Published: June 2023

Abstract
Background
Uterine leiomyomata (UL) are benign smooth muscle tumors that may cause significant morbidity in women of reproductive age. This study aimed to investigate the relationship of menstrual and reproductive factors with the risk of UL in premenopausal women.

Methods
This prospective study included 7,360 premenopausal women aged 22–48 years who were part of the Korea Nurses’ Health Study. Information on the menstrual cycle and reproductive history was assessed between 2014 and 2016, and self-reported cases of UL were obtained through 2021. Cox proportional hazards models were used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs).

Results
During 32,072 person-years of follow-up, 447 incident cases of UL were reported. After adjusting for other risk factors, women with late age at menarche had a lower incidence of UL (≥ 16 vs. 12–13 years: HR 0.68; 95% CI 0.47–0.99; p for trend = 0.026). The risk of UL was inversely associated with current menstrual cycle length (≥ 40 or too irregular to estimate vs. 26–31 days: HR 0.40; 95% CI 0.24–0.66) and cycle length at ages 18–22 years (HR 0.45; 95% CI 0.31–0.67; p for trend < 0.001, each). Parous women had lower risk of UL than nulliparous women (HR 0.40; 95% CI 0.30–0.53) and women who were aged 29–30 years at first birth had a lower risk of UL than those who were aged ≤ 28 years at first birth (HR 0.58; 95% CI 0.34–0.98). There was no significant association of the number of births or breastfeeding with the risk of UL among parous women. Neither a history of infertility nor oral contraceptive use was associated with the risk of UL.

Conclusions
Our results suggest that age at menarche, menstrual cycle length, parity, and age at first birth are inversely associated with the risk of UL in premenopausal Korean women. Future studies are warranted to confirm the long-term effects of menstrual and reproductive factors on women’s health.
Clinical effects of Emblica officinalis fruit consumption on cardiovascular disease risk factors: a systematic review and meta-analysis
Authors: Brown Paul D. S. , Ketter Nicole , Vis-Dunbar Mathew , Sakakibara Brodie M. 
Published: June 2023

Abstract
Background
Emblica officinalis (EO) fruit consumption has been found to have a beneficial effect on cardiovascular disease (CVD) physiological risk factors in preliminary clinical intervention trials; however, questions remain regarding the overall effectiveness of EO on CVD risk. The purpose of this systematic review and meta-analysis is to: 1) systematically describe the clinical research examining EO; and 2) quantitatively assess the effects of EO on CVD physiological risk factors.

Methods
The Pubmed, Embase, Web of Science, and Google Scholar electronic platforms were searched for relevant randomized controlled trials (RCTs) published until April 7, 2021. Studies were included if they involved adults (age ≥ 18 years) ingesting a form of EO fruit; included blood lipids, blood pressure, and/or inflammatory biomarkers as outcomes; had clearly defined intervention and control treatments with pre- and post-intervention data; were peer-reviewed; and were written in English. Studies were excluded if they compared EO with another risk reduction intervention without a usual care control group. RCTs were assessed for methodological quality using the Cochrane risk-of-bias version 2 (ROB2) tool, qualitatively described, and quantitatively evaluated using random and fixed effect meta-analysis models.

Results
A total of nine RCTs (n = 535 participants) were included for review. Included studies followed parallel-group (n = 6) and crossover (n = 3) designs, with EO dosage ranging from 500 mg/day to 1500 mg/day, and treatment duration ranging from 14 to 84 days. Meta-analyses revealed EO to have a significant composite effect at lowering low-density lipoprotein cholesterol (LDL-C; Mean difference (MD) = -15.08 mg/dL [95% Confidence interval (CI) = -25.43 to -4.73], I2 = 77%, prediction interval = -48.29 to 18.13), very low-density lipoprotein cholesterol (VLDL-C; MD = -5.43 mg/dL [95% CI = -8.37 to -2.49], I2 = 44%), triglycerides (TG; MD = -22.35 mg/dL [95% CI = -39.71 to -4.99], I2 = 62%, prediction interval = -73.47 to 28.77), and high-sensitivity C-reactive protein (hsCRP; MD = -1.70 mg/L [95% CI = -2.06 to -1.33], I2 = 0%) compared with placebo.

Conclusions
Due to statistical and clinical heterogeneity in the limited number of clinical trials to date, the promising effects of EO on physiologic CVD risk factors in this review should be interpreted with caution. Further research is needed to determine if EO offers an efficacious option for primary or secondary prevention of CVD as either monotherapy or adjunct to evidence-based dietary patterns and/or standard pharmacotherapy.
Discharge interventions for First Nations people with a chronic condition or injury: a systematic review
Authors: Coombes Julieann , Holland Andrew J.A , Ryder Courtney , Finlay Summer May , Hunter Kate , Bennett-Brook Keziah , Orcher Phillip , Scarcella Michele , Briscoe Karl , Forbes Dale , Jacques Madeleine , Maze Deborah , Porykali Bobby , Bourke Elizabeth , Kairuz Santos Camila A. 
Published: June 2023

Abstract
Background
Aboriginal and Torres Strait Islander peoples have a unique place in Australia as the original inhabitants of the land. Similar to other First Nations people globally, they experience a disproportionate burden of injury and chronic health conditions. Discharge planning ensures ongoing care to avoid complications and achieve better health outcomes. Analysing discharge interventions that have been implemented and evaluated globally for First Nations people with an injury or chronic conditions can inform the implementation of strategies to ensure optimal ongoing care for Aboriginal and Torres Strait Islander people.

Methods
A systematic review was conducted to analyse discharge interventions conducted globally among First Nations people who sustained an injury or suffered from a chronic condition. We included documents published in English between January 2010 and July 2022. We followed the reporting guidelines and criteria set in Preferred Reporting Items for Systematic Review (PRISMA). Two independent reviewers screened the articles and extracted data from eligible papers. A quality appraisal of the studies was conducted using the Mixed Methods Appraisal Tool and the CONSIDER statement.

Results
Four quantitative and one qualitative study out of 4504 records met inclusion criteria. Three studies used interventions involving trained health professionals coordinating follow-up appointments, linkage with community care services and patient training. One study used 48-hour post discharge telephone follow-up and the other text messages with prompts to attend check-ups. The studies that included health professional coordination of follow-up, linkage with community care and patient education resulted in decreased readmissions, emergency presentations, hospital length of stay and unattended appointments.

Conclusion
Further research on the field is needed to inform the design and delivery of effective programs to ensure quality health aftercare for First Nations people. We observed that discharge interventions in line with the principal domains of First Nations models of care including First Nations health workforce, accessible health services, holistic care, and self-determination were associated with better health outcomes.

Registration
This study was prospectively registered in PROSPERO (ID CRD42021254718).