bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree
Authors: Alda Fernando , Ludt William B , Elías Diego J , McMahan Caleb D , Chakrabarty Prosanta 
Published: July 2021

AbstractChoosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here, we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different data sets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel data set of ultraconserved elements (UCEs) and a recently published exon data set of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent data sets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting and nonphylogenetic signals. For UCEs, high levels of incomplete lineage sorting were found to be the major cause of gene tree discordance, whereas, for exons, nonphylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.
Genetic architecture modulates diet-induced hepatic mRNA and miRNA expression profiles in Diversity Outbred mice
Authors: Que Excel , James Kristen L , Coffey Alisha R , Smallwood Tangi L , Albright Jody , Huda M Nazmul , Pomp Daniel , Sethupathy Praveen , Bennett Brian J 
Published: July 2021

Abstract
Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here, we performed global hepatic eQTL and microRNA expression quantitative trait loci (mirQTL) analysis in a population of Diversity Outbred mice fed two different diets. We identified several key features of eQTL and mirQTL, namely differences in the mode of genetic regulation (cis or trans) between mRNA and miRNA. Approximately 50% of mirQTL are regulated by a trans-acting factor, compared to ∼25% of eQTL. We note differences in the heritability of mRNA and miRNA expression and variance explained by each eQTL or mirQTL. In general, cis-acting variants affecting mRNA or miRNA expression explain more phenotypic variance than trans-acting variants. Finally, we investigated the effect of diet on the genetic architecture of eQTL and mirQTL, highlighting the critical effects of environment on both eQTL and mirQTL. Overall, these data underscore the complex genetic regulation of two well-characterized RNA classes (mRNA and miRNA) that have critical roles in the regulation of clinical traits and disease susceptibility
Designing drug shops for young women in Tanzania: applying human-centred design to facilitate access to HIV self-testing and contraception
Authors: Hunter Lauren A , McCoy Sandra I , Rao Aarthi , Mnyippembe Agatha , Hassan Kassim , Njau Prosper , Mfaume Rashid , Liu Jenny X 
Published: July 2021

AbstractAdolescent and young adult women in sub-Saharan Africa experience barriers to sexual and reproductive health (SRH) services that elevate their risk of human immunodeficiency virus (HIV) acquisition and unintended pregnancy. Community drug shops may be effective distribution points to connect young women with SRH products. Thus, we used human-centred design (HCD) to create drug shops where young women could access HIV self-testing and contraception in Shinyanga, Tanzania. Enhancing the HCD process with behavioural science, we collected diverse data (i.e. 18 in-depth interviews, 9 ‘shadowing’ interviews, 6 shop observations, 6 focus groups) to understand the latent needs and motivations of young women and drug shopkeepers, brainstormed creative solutions and iteratively refined and tested solutions for acceptability, feasibility and cultural fit. We found a widespread moral imperative to control young women’s behaviour via misinformation about SRH, community gossip and financial control. Young women often engaged in mundane shopping at the behest of others. At drug shops, few SRH products were deemed appropriate for unmarried women, and many reactively sought SRH products only after engaging in higher risk behaviours. In response to these insights, we designed the ‘Malkia Klabu’ (‘Queen Club’) loyalty programme through which young women could earn mystery prizes by shopping at drug shops and discreetly request free SRH products, including HIV self-test kits, by pointing at symbols on loyalty cards. Our HCD approach increases the likelihood that the intervention will address the specific needs and preferences of both drug shopkeepers and young women. We will evaluate its effectiveness in a randomized trial.
Organizational structure and human agency within the South African health system: a qualitative case study of health promotion
Authors: Rwafa-Ponela Teurai , Goudge Jane , Christofides Nicola 
Published: July 2021

Abstract
Despite international recognition of health promotion (HP) as a cost-effective way to improve population health, it is not highly regarded nor is it sufficiently institutionalized in many health systems. This diminishes its ability to deliver on its public health promises. This paper examined the role of organizational structure and human agency within the South African health system (drawing on Giddens’s structuration theory) in determining the extent of, and barriers to, the institutionalization of HP. We conducted a qualitative case study using a combination of in-depth interviews (n = 37), key informant interviews (n = 8) and one-day workshops (n = 5) with Department of Health (DoH) staff (HP and non-HP personnel) from national, provincial and district levels as well as external HP stakeholders. Within the South African health system, there are dedicated HP staffs, with no specified professional competencies or a coherent hierarchy of job titles. Allocated HP resources were frequently shifted to other programmes. This resulted in a disconnect between national and provincial levels, which impeded communication and opportunity to develop a shared vision and coherent programme. We found some examples of successful HP organization and implementation practices, such as the tobacco control legislation. Overall, HP staff had limited agency and were often unable to articulate the vision for HP. Uncertainty about the role of HP has led to powerlessness, and feelings of resentment have generated demotivation and moral distress. HP voices were seldom heard and were repressed by dominant curative-focused structures. If leaders of HP continue to be embedded in such an institution, there is little chance of driving an effective HP agenda. Therefore, there is a need to engage policy-makers to integrate HP into the health system fabric. Establishment of an independent HP foundation could be one mechanism to drive multi-sectoral collaboration, contribute to evidence-based HP research and further develop health in all policies through advocacy.
Genomic and pleiotropic analyses of resting QT interval identifies novel loci and overlap with atrial electrical disorders
Authors: van Duijvenboden Stefan , Ramírez Julia , Young William J , Orini Michele , Mifsud Borbala , Tinker Andrew , Lambiase Pier D , Munroe Patricia B 
Published: July 2021

AbstractThe resting QT interval, an electrocardiographic (ECG) measure of ventricular myocardial repolarization, is a heritable risk marker of cardiovascular mortality, but the mechanisms remain incompletely understood. Previously reported candidate genes have provided insights into the regulatory mechanisms of the QT interval. However, there are still important knowledge gaps. We aimed to gain new insights by (i) providing new candidate genes, (ii) identifying pleiotropic associations with other cardiovascular traits, and (iii) scanning for sexually dimorphic genetic effects. We conducted a genome-wide association analysis for resting QT interval with ~9.8 million variants in 52 107 individuals of European ancestry without known cardiovascular disease from the UK Biobank. We identified 40 loci, 13 of which were novel, including 2 potential sex-specific loci, explaining ~11% of the trait variance. Candidate genes at novel loci were involved in myocardial structure and arrhythmogenic cardiomyopathy. Investigation of pleiotropic effects of QT interval variants using phenome-wide association analyses in 302 000 unrelated individuals from the UK Biobank and pairwise genome-wide comparisons with other ECG and cardiac imaging traits revealed genetic overlap with atrial electrical pathology. These findings provide novel insights into how abnormal myocardial repolarization and increased cardiovascular mortality may be linked.
The International Human Genome Project
Authors: Birney Ewan 
Published: July 2021

Abstract
The human genome project was conceived and executed as an international project, due to both pragmatic and principled reasons. This internationality has served the project well, with the resulting human genome being freely available for all researchers in all countries. Over time the reference human genome will likely have to evolve to a graph genome, and tap into more diverse sequences worldwide. A similar international mindset underpins data analysis for the interpretation of the human genome from basic to clinical research.
Box lesion or bi-atrial lesion set for atrial fibrillation during thoracoscopic epicardial ablation
Authors: Zheng Zhe , Li Haojie , Liu Sheng , Gao Ge , Yu Chunyu , Lin Hengqiang , Meng Ying 
Published: July 2021

Abstract OBJECTIVESThoracoscopic epicardial ablation with a limited lesion set led to suboptimal results for advanced paroxysmal atrial fibrillation (AF) or persistent AF. Whether additional right atrial lesions improve the result is unclear.METHODSWe conducted a retrospective study involving 80 consecutive patients with paroxysmal or persistent AF, left atrial (LA) dilation (LA diameter &gt;40 mm) and failed prior interventional ablation (40 patients, 50%) who underwent thoracoscopic epicardial ablation with box lesions (36 patients) or bi-atrial (BA) lesion (44 patients) in our institution. Freedom from atrial tachyarrhythmias after the procedures was compared between the box lesion group and BA lesion group.RESULTSBaseline differences included more patients with persistent AF (86.4% vs 47.2%) and larger left atrium [48.00 (44.00–50.75) vs 42.00 (41.25–44.00) mm] in the BA lesion group. There was no difference in procedural complications between the 2 groups. After a mean follow-up of 32 months, the freedom from atrial tachyarrhythmias off antiarrhythmic drugs at 6, 12 and 24 months was 77.2%, 77.2% and 77.2% in the BA lesion group and 69.4%, 50.0% and 40.6% in the box lesion group, respectively (P = 0.006). After adjustment for sex, age, body mass index, LA diameter, AF type, history of AF, and previous interventional ablation, BA lesion was an independent predictor of lower atrial tachyarrhythmia recurrence (hazard ratio 0.447, 95% confidential interval 0.208–0.963; P = 0.040).CONCLUSIONSCompared with the box lesion set, thoracoscopic epicardial ablation with BA lesion sets might provide better freedom from atrial tachyarrhythmias for paroxysmal or persistent AF with LA dilation. Randomized control trials are warranted to confirm the benefit of BA lesion sets in these patients.
Appropriateness of imaging decisions for low back pain presenting to the emergency department: a retrospective chart review study
Authors: Traeger Adrian C , Machado Gustavo C , Bath Sally , Tran Martin , Roper Lucinda , Oliveira Crystian , Peek Aimie , Coombs Danielle , Hall Amanda , Tcharkhedian Elise , Maher Chris G 
Published: July 2021

Abstract

Background
Imaging for low back pain is widely regarded as a target for efforts to reduce low-value care.

Objective
We aimed to estimate the prevalence of the overuse and underuse of lumbar imaging in patients presenting with low back pain to the emergency department (ED).

Methods
This was a retrospective chart review study of five public hospital EDs in Sydney, Australia, in 2019–20. We reviewed the clinical charts of consecutive adult patients who presented with a complaint of low back pain and extracted clinical features relevant to a decision to request lumbar imaging. We estimated the proportion of encounters where a decision to request lumbar imaging was inappropriate (overuse) or where a clinician did not request an appropriate and informative lumbar imaging test when indicated (underuse).

Results
Six hundred and forty-nine patients presented with a complaint of low back pain, of which 158 (24.3%) were referred for imaging. Seventy-nine (12.2%) had a combination of features suggesting that lumbar imaging was indicated according to clinical guidelines. The prevalence of overuse and underuse of lumbar imaging was 8.8% (57 of 649 cases, 95% CI 6.8–11.2%) and 4.3% (28 of 649 cases, 95% CI 3.0–6.1%), respectively. Thirteen cases were classified as underuse because the patients were referred for uninformative imaging modalities (e.g. referred for radiography for suspected cauda equina syndrome).

Conclusion
In this study of emergency care, there was evidence of not only overuse of lumbar imaging but also underuse through failure to request lumbar imaging when indicated or referral for an uninformative imaging modality. These three issues seem more important targets for quality improvement than solely focusing on overuse.
Assemblages of Necrophagous Blow Flies (Diptera: Calliphoridae) in Four Contrasting Ecoregions of Los Angeles County, California, United States
Authors: Cumming Royce T , Dufek Matias I 
Published: July 2021

Abstract
An ecological study to evaluate necrophagous species richness, abundance, and diversity was conducted in four contrasting ecoregions of Los Angeles County, California, United States: a highly anthropized area, two moderately populated areas, and a sparsely populated area. Our hypothesis states that there will be higher abundance of exotic species in greatly anthropized ecoregions and higher diversity of native calliphorid flies in sparsely populated sites. A total of 2,883 blow flies belonging to 12 species were captured from the four ecoregions. The exotic Chrysomya rufifacies (Macquart) (Diptera: Calliphoridae) was the most abundant species, representing 72.84% of all Calliphoridae collected. The highest abundance was in the highly anthropized ecoregion. Differences of the blow fly assemblages across environmentally and anthropically different ecoregions were found, and that the relative abundance of the exotic species increased with anthropization. Our results suggest that both anthropization and elevation alter the structure of blow fly assemblages, modifying the abundance and species richness of Calliphoridae. The results of this study support the hypothesis of biotic homogenization, since we found a higher proportional abundance of exotic species and lower diversity of native blow flies in ecoregions heavily modified by human action. Additionally, the hypothesis of intermediate disturbance was supported as the highest diversity was found in the ecoregion with moderate anthropization mixed with natural elements. This is the first study to conduct an intensive survey of the Calliphoridae assemblages in Los Angeles County, which can be potentially used as a tool in human and veterinary health and forensic sciences.
Reducing manual operation time to obtain a segmentation learning model for volume electron microscopy using stepwise deep learning with manual correction
Authors: Konishi Kohki , Nonaka Takao , Takei Shunsuke , Ohta Keisuke , Nishioka Hideo , Suga Mitsuo 
Published: July 2021

Abstract
Three-dimensional (3D) observation of a biological sample using serial-section electron microscopy is widely used. However, organelle segmentation requires a significant amount of manual time. Therefore, several studies have been conducted to improve organelle segmentation’s efficiency. One such promising method is 3D deep learning (DL), which is highly accurate. However, the creation of training data for 3D DL still requires manual time and effort. In this study, we developed a highly efficient integrated image segmentation tool that includes stepwise DL with manual correction. The tool has four functions: efficient tracers for annotation, model training/inference for organelle segmentation using a lightweight convolutional neural network, efficient proofreading and model refinement. We applied this tool to increase the training data step by step (stepwise annotation method) to segment the mitochondria in the cells of the cerebral cortex. We found that the stepwise annotation method reduced the manual operation time by one-third compared with the fully manual method, where all the training data were created manually. Moreover, we demonstrated that the F1 score, the metric of segmentation accuracy, was 0.9 by training the 3D DL model with these training data. The stepwise annotation method using this tool and the 3D DL model improved the segmentation efficiency of various organelles.
A pilot study to assess the need for new hospital pharmaceutical services in Algerian patients and physicians’ perspective
Authors: Chelghoum Mustapha , Khitri Walid , Kadouri Feriel , Chaouche Khedra 
Published: July 2021

Abstract

Objectives
The objective of this study was to assess the needs for pharmaceutical services from the perspectives of physicians and patients in the hospital setting and to contribute to the implementation of new hospital pharmacy activities.

Methods
A cross-sectional descriptive study was carried out among the doctors and patients encountered in hospital departments in Sidi Bel Abbès (Algeria); each service was evaluated using a Likert scale. Associated characteristics with an important need were evaluated by univariate analysis and binary logistic regression.

Key findings
All pharmaceutical services were important to the patients, particularly providing treatment advice and therapeutic education. Women presented an important need for insurance of the availability of pharmaceutical products (P = 0.02) and lifestyle and dietetic information (P = 0.05). High frequency of taking medication was associated with an important need for information about drug interactions (P = 0.005). Patient-oriented pharmaceutical services were not important to the physicians who considered drug information and therapeutic education to be the most important need.

Conclusions
To implement patient-centred services, it is important to improve the contact between pharmacists and physicians and to provide information about pharmaceutical services that can benefit patients. Implementation of new practices in university hospital is more feasible than in public health facilities.
Sevoflurane inhibits the apoptosis of hypoxia/reoxygenation-induced cardiomyocytes via regulating miR-27a-3p-mediated autophagy
Authors: Zhang Yang , Zhan Biming , Hu Ying , Chen Shibiao , Zhang Qin 
Published: July 2021

Abstract

Introduction
Sevoflurane (Sevo) prevents hypoxia/reoxygenation (H/R)-induced cardiomyocytes apoptosis. MiR-27a-3p expression is up-regulated in Sevo-treated hippocampal neurons.

Objective
This study explored whether the effect of Sevo on cardiomyocytes was mediated by miR-27a-3p.

Methods
The cardiomyocytes were cultured under H/R condition or pre-treated with Sevo, and further transfected with miR-27a-3p inhibitor or treated with an autophagy inhibitor 3-methyladenine (3-MA). Then the cell morphology was observed under an optical microscope. The cell viability and apoptosis were measured by MTT and flow cytometry. Expressions of miR-27a-3p, apoptosis-related, and autophagy-related factors were determined by western blot or RT-qPCR.

Key findings
Sevo improved the abnormal morphology, promoted the cell viability and the expressions of Bcl-2 and miR-27a-3p, but reduced the apoptosis and Bax and C-caspase-3 levels of H/R-induced cardiomyocytes. MiR-27a-3p inhibitor had an effect opposite to Sevo on the cardiomyocytes and further counteracted the effect of Sevo on the H/R-induced cardiomyocytes. Downregulation miR-27a-3p increased the expression of Beclin 1 and the ratio of LC3B-II to LC3B-I in H/R-induced cardiomyocytes. Furthermore, 3-MA had an opposite effect to miR-27a-3p inhibitor and further counteracted the effect of the miR-27a-3p inhibitor on H/R-induced cardiomyocytes.

Conclusion
Sevo inhibited the apoptosis of H/R-induced cardiomyocytes via regulating miR-27a-3p-mediated autophagy.