bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global perspective on social stratification in science
Authors: Akbaritabar Aliakbar , Castro Torres Andrés Felipe , Larivière Vincent 
Published: July 2024

AbstractTo study stratification among scientists, we reconstruct the career-long trajectories of 8.2 million scientists worldwide using 12 bibliometric measures of productivity, geographical mobility, collaboration, and research impact. While most previous studies examined these variables in isolation, we study their relationships using Multiple Correspondence and Cluster Analysis. We group authors according to their bibliometric performance and academic age across six macro fields of science, and analyze co-authorship networks and detect collaboration communities of different sizes. We found a stratified structure in terms of academic age and bibliometric classes, with a small top class and large middle and bottom classes in all collaboration communities. Results are robust to community detection algorithms used and do not depend on authors’ gender. These results imply that increased productivity, impact, and collaboration are driven by a relatively small group that accounts for a large share of academic outputs, i.e., the top class. Mobility indicators are the only exception with bottom classes contributing similar or larger shares. We also show that those at the top succeed by collaborating with various authors from other classes and age groups. Nevertheless, they are benefiting disproportionately from these collaborations which may have implications for persisting stratification in academia.
Two-tier architecture-based grading for pancreatic cancer outperforms traditional grading
Authors: Dao Andre , Orr Christine Elizabeth , Nyi Nyi May-Phyo , Wang Tao 
Published: July 2024

Abstract

Objectives
A novel architecture-based grading system for pancreatic ductal adenocarcinoma (PDAC) is tested against traditional grading.

Methods
A total of 103 PDAC resections were graded by College of American Pathologists/American Joint Committee on Cancer (CAP/AJCC) guidelines and by a system using an architectural pattern (dispersed larger duct = low grade vs dense smaller duct = high grade). Survival analyses and interobserver variability were assessed. In total, 114 cases from a public data set were used for validation.

Results
Median overall survivals were 15 and 36 months for architectural high-grade and low-grade cases, respectively (P &lt; .001). Conversely, CAP/AJCC grading showed no survival difference between well-differentiated and moderately differentiated tumors (P = .545). Architecture-based grading remained prognostically significant for recurrence-free survival (P = .004), but CAP/AJCC grading was not (P = .226). Adjusted for stage and margin status, architectural high-grade PDACs showed a hazard ratio of 2.69 relative to low grade (P &lt; .001) for survival. The validation cohort confirmed prognostic differences in overall (P &lt; .001) and recurrence-free survival (P = .027) for the architecture-based system, outperforming CAP/AJCC grading. Architecture-based grading exhibited a Cohen’s ĸ value of 0.710 (substantial agreement), superior to traditional grading (0.488, moderate agreement).

Conclusions
Grading PDAC based on architectural pattern results in superior prognostication and reproducibility vs CAP/AJCC grading.
The significance of extensive HPV genotyping for cervical high-grade neoplasia among women with atypical glandular cells
Authors: Tang Xiao , Zilla Megan L , Jiang Wei , He Yanmei , Starr David , Li Lei , Tong Lingling , Wang Cheng , Wang Wei , Yang Kaixuan , Yin Rutie , Zhao Chengquan 
Published: July 2024

Abstract

Objectives
To examine the associated risk of cervical intraepithelial neoplasm grade 3+ (CIN3+) lesions in patients with AGC and extensive human papillomavirus (HPV) genotyping.

Methods
Cases with atypical glandular cell (AGC) interpretation on a Papanicolaou (Pap) test were identified along with associated extensive HPV genotyping and histologic follow-up results.

Results
Within this cohort of 469,694 Pap tests, 0.4% were diagnosed as AGCs. In total, 1267 cases had concurrent high-risk HPV (hrHPV) genotyping, and 40.3% were hrHPV positive. The percentage of AGC cases with cervical CIN3+ on histologic follow-up was 52.2% when hrHPV was positive, whereas it was 4.9% with a negative hrHPV result. The top 5 hrHPV genotypes associated with cervical CIN3+ in this cohort were HPV16, HPV18, HPV58, HPV52, and HPV33. Indeed, 92.8% of the hrHPV-associated CIN3+ lesions identified in this cohort were positive for at least one of these HPV genotypes. The sensitivity of detecting cervical CIN3+ lesions was 85.6% with the top 5 hrHPV genotypes (HPV16/18/58/52/33) and only increased to 89.0% when the additional 12 genotypes were included.

Conclusions
In patients with an AGC Pap, the risk of having a cervical CIN3+ lesion is greatly increased by positivity for hrHPV types 16, 18, 58, 52, and/or 33. Incorporating comprehensive HPV genotyping into AGC cytology allows for refined risk stratification and more tailored management strategies.
Risk and Protective Factors of Probable Binge Eating Disorder in US Military Spouses: Findings From the Millennium Cohort Family Study
Authors: Ray Travis N , Esquivel Alejandro P , McMaster Hope S , Jacobson Isabel G , Maguen Shira , Cohort Family Study Team for the Millennium 
Published: July 2024

Abstract
Binge eating disorder (BED) is a public health concern that has received little research attention in military families. Further research is needed to identify risk and protective factors to inform intervention and prevention efforts. This longitudinal study examined predictors of probable BED in a sample of U.S. military spouses (N = 5,269). Data were derived from the Millennium Cohort Family Study, which included baseline assessments of risk and protective factors and a follow-up assessment of probable BED approximately 3 years later. Results of a multivariable logistic regression model indicated that spouses with probable posttraumatic stress disorder, adverse childhood experiences, or who were former smokers had increased risk of probable BED at follow-up. Spouses whose service member had a deployment with combat exposure, or had not deployed, had higher risk of probable BED than spouses whose service member deployed without combat exposure. Age &gt;34 years was the only protective factor to emerge as significant in the adjusted model. Results highlighted the need for interventions to improve psychoeducation and coping skills in military spouses, which may mitigate BED symptoms stemming from military-related stressors (e.g., combat deployment) or prior trauma, especially once maladaptive coping mechanisms (e.g., smoking) have ceased.
Pharmacotherapy considerations for pediatric acute agitation management in the emergency department
Authors: Mills Kimberly P , Kemper Megan , Charatcharungkiat Natchanan , Hoganson George M 
Published: July 2024

Abstract

Purpose
To review the current literature regarding the pharmacological management of acute agitation in pediatric patients and practical considerations when comparing agents for empiric use in the emergency department (ED).

Summary
ED providers play an integral role in the management of acute agitation in pediatric patients. The development of acute agitation is multifactorial, and patients may quickly escalate upon arrival or while boarding in the ED. Non-pharmacological de-escalation strategies should be prioritized. If a patient poses a safety risk to themself or staff members, the administration of pharmacological treatment may be necessary to target the underlying cause and allow for the patient to safely engage in assessment and treatment. There is limited guidance regarding medication selection and dosing for acute agitation in pediatrics despite being a key facet of multimodal management.

Conclusion
The literature regarding pharmacotherapy for acute agitation management in pediatric patients remains scarce. Medications utilized vary depending on institutional practice as well as provider preference. Evidence suggests that implementing an institutional protocol for pediatric acute agitation in the ED may improve patient outcomes. Additional studies are needed optimize the pharmacological management of acute pediatric agitation and patient outcomes in the ED.
consICA: an R package for robust reference-free deconvolution of multi-omics data
Authors: Chepeleva Maryna , Kaoma Tony , Zinovyev Andrei , Toth Reka , Nazarov Petr V 
Published: July 2024

Abstract

Motivation
Deciphering molecular signals from omics data helps understanding cellular processes and disease progression. Effective algorithms for extracting these signals are essential, with a strong emphasis on robustness and reproducibility.

Results
R/Bioconductor package consICA implements consensus independent component analysis (ICA)—a data-driven deconvolution method to decompose heterogeneous omics data and extract features suitable for patient stratification and multimodal data integration. The method separates biologically relevant molecular signals from technical effects and provides information about the cellular composition and biological processes. Build-in annotation, survival analysis, and report generation provide useful tools for the interpretation of extracted signals. The implementation of parallel computing in the package ensures efficient analysis using modern multicore systems. The package offers a reproducible and efficient data-driven solution for the analysis of complex molecular profiles, with significant implications for cancer research.

Availability and implementation
The package is implemented in R and available under MIT license at Bioconductor (https://bioconductor.org/packages/consICA) or at GitHub (https://github.com/biomod-lih/consICA).
Automated, image-based quantification of peroxisome characteristics with perox-per-cell
Authors: Neal Maxwell L , Shukla Nandini , Mast Fred D , Farré Jean-Claude , Pacio Therese M , Raney-Plourde Katelyn E , Prasad Sumedh , Subramani Suresh , Aitchison John D 
Published: July 2024

Abstract

Summary
perox-per-cell automates cumbersome, image-based data collection tasks often encountered in peroxisome research. The software processes microscopy images to quantify peroxisome features in yeast cells. It uses off-the-shelf image processing tools to automatically segment cells and peroxisomes and then outputs quantitative metrics including peroxisome counts per cell and spatial areas. In validation tests, we found that perox-per-cell output agrees well with manually quantified peroxisomal counts and cell instances, thereby enabling high-throughput quantification of peroxisomal characteristics.

Availability and implementation
The software is coded in Python. Compiled executables and source code are available at https://github.com/AitchisonLab/perox-per-cell.
Drawing mitochondrial genomes with circularMT
Authors: Goodman Simon J , Carr Ian M 
Published: July 2024

Abstract

Summary
Mitochondrial DNA sequences are used extensively in phylogeographic and phylogenetic studies for a wide range of organisms. With the advent of low-cost, high-throughput “next generation” DNA sequencing, and user-friendly bioinformatics pipelines for generating and annotating whole mitochondrial genome assemblies, the analysis of whole mitochondrial genomes has become an important component of phylogenomic studies for taxa with high species diversity but limited coverage for other genomic resources. An important step in characterizing de novo mitochondrial genome assemblies is to evaluate and describe structural rearrangements relative to reference taxa. Accessible tools are needed to help visualize gene and non-coding feature complement, their order, and strand orientation. However, there are few dedicated applications that generate high-quality genome diagrams. Here we present circularMT and circularMT-console that allow users to create highly customizable, publication-quality images, of linear and circular mitochondrial genome maps, either individually or integrated into an analysis pipeline.

Availability and implementation
Both applications are implemented in C#, with binaries, source code, and user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319).
Causal inference with hidden mediators
Authors: Ghassami Amiremad , Yang Alan , Shpitser Ilya , Tchetgen Tchetgen Eric 
Published: July 2024

Summary
Proximal causal inference was recently proposed as a framework to identify causal effects from observational data in the presence of hidden confounders for which proxies are available. In this paper, we extend the proximal causal inference approach to settings where identification of causal effects hinges upon a set of mediators that are not observed, yet error prone proxies of the hidden mediators are measured. Specifically, (i) we establish causal hidden mediation analysis, which extends classical causal mediation analysis methods for identifying natural direct and indirect effects under no unmeasured confounding to a setting where the mediator of interest is hidden, but proxies of it are available; (ii) we establish a hidden front-door criterion, criterion to allow for hidden mediators for which proxies are available; (iii) we show that the identification of a certain causal effect called the population intervention indirect effect remains possible with hidden mediators in settings where challenges in (i) and (ii) might co-exist. We view (i)–(iii) as important steps towards the practical application of front-door criteria and mediation analysis as mediators are almost always measured with error and, thus, the most one can hope for in practice is that the measurements are at best proxies of mediating mechanisms. We propose identification approaches for the parameters of interest in our considered models. For the estimation aspect, we propose an influence function-based estimation method and provide an analysis for the robustness of the estimators.
Effective Interventions to Reduce Burnout in Social Workers: A Systematic Review
Authors: Bryce Carl , Povey Rachel , Oliver Mike , Cooke Richard 
Published: July 2024

Abstract
Social workers are at risk of developing burnout, which is associated with many adverse implications including increased risk of depression. A number of intervention studies have aimed to reduce burnout in this population; however, a systematic review of the evidence has yet to be performed. This review therefore aimed to fill that gap. A comprehensive search of major academic databases was conducted and the inclusion criteria were interventions that reported pre- and post-measures of burnout outcomes within a population of qualified social workers. Of the 2,456 records identified, nine were included in the review. Results showed that a number of burnout interventions have been developed for social workers, including mindfulness-based interventions, group-based skills training, exercise and taking a sabbatical. However, the overall quality of the studies was poor and therefore definitive recommendations for effective interventions could not be offered. Mindfulness-based and group skills development interventions warrant further investigation and organisational or institutional change to tackle burnout, alongside individual-level interventions, is crucial. It was concluded that future burnout intervention researchers should implement a greater methodological rigour, use theory to underpin intervention approaches, adopt a longitudinal design where possible, and administer validated measures of burnout.
Uromodulin and progression of IgA nephropathy
Authors: Chen Zijin , Xu Lin-lin , Du Wen , Ouyang Yan , Gu Xiangchen , Fang Zhengying , Yu Xialian , Li Junru , Xie Lin , Jin Yuanmeng , Ma Jun , Wang Zhaohui , Pan Xiaoxia , Zhang Wen , Ren Hong , Wang Weiming , Chen Xiaonong , Zhou Xu-jie , Zhang Hong , Chen Nan , Xie Jingyuan 
Published: July 2024

ABSTRACT

Background
This study investigates the link between genetic variants associated with kidney function and immunoglobulin A (IgA) nephropathy (IgAN) progression.

Methods
We recruited 961 biopsy-proven IgAN patients and 651 non-IgAN end-stage renal disease (ESRD) patients from Ruijin Hospital. Clinical and renal pathological data were collected. The primary outcome was the time to ESRD. A healthy population was defined as estimated glomerular filtration rate &gt;60 mL/min/1.73 m2 without albuminuria or hematuria. Fifteen single-nucleotide polymorphisms (SNPs) were selected from a genome-wide association study of kidney function and genotyped by the SNaPshot. Immunohistochemistry in renal tissue and ELISA in urine samples were performed to explore the potential functions of genetic variations.

Results
The rs77924615-G was independently associated with an increased risk for ESRD in IgAN patients after adjustments for clinical and pathologic indices, and treatment (adjusted hazard ratio 2.10; 95% confidence interval 1.14–3.88). No significant differences in ESRD-free survival time were found among different genotypes in non-IgAN ESRD patients (log-rank, P = .480). Moreover, rs77924615 exhibited allele-specific enhancer activity by dual-luciferase reporter assay. Accordingly, the urinary uromodulin–creatinine ratio (uUCR) was significantly higher in healthy individuals with rs77924615 AG or GG than in individuals with AA. Furthermore, uromodulin expression in tubular epithelial cells was higher in patients with rs77924615 AG or GG. Finally, we confirmed that an increased uUCR (P = .009) was associated with faster IgAN progression.

Conclusion
The SNP rs77924615, which modulates the enhancer activity of the UMOD gene, is associated with renal function deterioration in IgAN patients by increasing uromodulin levels in both the renal tubular epithelium and urine.
Stenting of aortic coarctation before coronary artery bypass surgery in an adult with acute myocardial infarction: a case report
Authors: Tomasino Marco , Valente Filipa , Rello Sabatè Pau , Martì Aguasca Gerard , Miranda Barrio Berta 
Published: July 2024

Abstract

Background
Aortic coarctation is a major risk factor for high blood pressure and atherosclerotic disease development. Evidence is lacking regarding the treatment of acute coronary syndrome in patients with untreated aortic coarctation.

Case summary
A 50-year-old male with a history of hypertension, diabetes, and haemodynamically significant untreated aortic coarctation presented to the emergency department with non-ST-elevation acute myocardial infarction. Coronary catheterization showed severe three-vessel disease. The aortic coarctation was addressed percutaneously using a covered CP stent. A quadruple coronary artery bypass surgery was conducted the following day. He was discharged home 10 days after surgery.

Discussion
We describe a successful sequential approach involving the percutaneous repair of a native aortic coarctation followed by a surgical myocardial revascularization in the context of acute coronary syndrome. Discussion within a multidisciplinary Heart Team is key in patients with such complexity.
Long-term prognostic impact of fasting plasma glucose and myocardial flow reserve beyond other risk factors and heart disease phenotypes
Authors: Filidei Elena , Caselli Chiara , Menichetti Luca , Poli Michela , Petroni Debora , Guiducci Letizia , Sorace Oreste , Pisani Patrizia , Pardini Silvia , Bonora Danilo , Giorgetti Assuero , Gimelli Alessia , Neglia Danilo 
Published: July 2024

Abstract
Cardiometabolic risk factors, including high fasting plasma glucose (hFPG), are emerging prognostic determinants in patients with coronary artery disease (CAD) or heart failure (HF). Coronary microvascular dysfunction might be a comprehensive risk predictor in these patients. The purpose of this study was to assess whether hFPG and global myocardial blood flow (MBF) reserve measured by positron emission tomography (PET), expressing global coronary function, predict long-term prognosis beyond other risk factors and presence of obstructive CAD or left ventricular (LV) dysfunction associated with HF. We retrospectively collected long-term follow-up data in 103 patients (mean age 61 ± 10 years, 74 males) with stable chest pain or dyspnoea who underwent cardiac PET/computerized tomography and coronary angiography. Disease phenotypes included obstructive CAD (35%), LV dysfunction without obstructive CAD (43%), or none (22%). At multivariable logistic regression analysis, MBF reserve lower than the median value (OR 1.8, 95% CI 1.5–2.2) was significantly associated with male gender (OR 3.45, 95% CI 1.21–9.83) and hFPG (OR 3.87, 95% CI 1.17–12.84) among all risk factors. In a median follow-up of 10.9 years (interquartile range 7.8–13.9), 39 patients (37.8%) died (13.6% cardiac death). At multivariable Cox analyses including all risk factors and disease phenotypes, age (HR 1.07, 95% CI 1.02–1.12), hFPG (HR 2.18, 95% CI 1.02–4.63), and depressed MBF reserve (HR 4.47, 95% CI 1.96–10.18) were independent predictors of death (global χ2 37.41, P = 0.0004). These results suggest a strong long-term prognostic role of hFPG and depressed MBF reserve in a high-risk population of patients with a high prevalence of obstructive CAD or HF.
Materials writing as a vehicle for teacher learning
Authors: Yang Shanshan , Sato Masatoshi , Shu Dingfang , Wang Beilei 
Published: July 2024

Abstract
This study explored how secondary school EFL teachers engaged in professional learning opportunities when they participated in the development of ELT materials. While increasing research has examined language teaching materials and teacher learning, the two research fields have remained largely disconnected, hindering the potential of materials writing for professional learning. With eight teachers as focal participants, the data included in-depth interviews, written reflections, and official documents. Findings showed that the EFL teachers took advantage of materials writing for their professional learning in the areas of policy, theory, and practice. Their engagement with the national curriculum standards, language, and language learning theories, together with local classroom realities in relation to teaching materials, reciprocally interacted with their professional learning. Based on the findings, we recommend that professional development programs include materials writing by localizing the content, clarifying its objectives, teaming teachers with researchers, and creating feedback loops.
Highly contiguous genome assembly of Drosophila prolongata—a model for evolution of sexual dimorphism and male-specific innovations
Authors: Luecke David , Luo Yige , Krzystek Halina , Jones Corbin , Kopp Artyom 
Published: July 2024

Abstract
Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of Southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi–C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2 Mb) genome assembly of 220 Mb. The repetitive content of the genome is 24.6%, the plurality of which are long terminal repeats retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, genome-wide association studies (GWAS), and other genomic analyses.