bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges in the Implementation of the Rajasthan Pneumoconiosis Policy
Authors: Chaturvedi Oshi , Mantri Neha , Joshi Nitin Kumar , Goel Akhil Dhnaesh , Jain Yogesh Kumar , Gupta Manoj Kumar , Manda Balwant , Bhardwaj Pankaj 
Published: September 2022

Abstract

Objectives
“Silicosis” is a leading cause of occupational morbidity globally. In Rajasthan, India silicosis has been recognized as an epidemic, resulting in the development of a new pneumoconiosis policy in 2019. This study was conducted to provide an overview of the policy implementation regarding the detection, prevention, and control of silicosis.

Methods
A qualitative study was carried out in the Jodhpur district of Western Rajasthan in which stakeholders were interviewed. Themes were identified regarding prevention, detection, diagnosis, and certification, and organized by stakeholder role. Data were retrieved from the Silicosis Grant Disbursement Portal of the Government of Rajasthan to present an overview of the existing system for detection, prevention, and control of silicosis and to determine the delays in various aspects.

Results
A total of 35 stakeholders were interviewed. There was low awareness regarding the prevention, detection, diagnosis, and rehabilitation of silicosis amongst multiple stakeholders. There is a need for robust enforcement in mining units regarding silicosis prevention and screening. Unregistered mining activities and migration of mineworkers are major challenges in the detection of silicosis cases. Misdiagnosis and low notification rates prevent workers from accessing resources. There are myriad reasons for delays in workers receiving diagnosis and benefits, which have systemic roots but can be uprooted through rigorous implementation of the legislative provisions.

Conclusion
There are several well-established pieces of legislation to protect the rights of mineworkers; however, there are gaps in the effective implementation of various provisions that require immediate attention to address the challenges faced during the prevention, detection, diagnosis, and rehabilitation of workers with silicosis.
Systematic comparison of ranking aggregation methods for gene lists in experimental results
Authors: Wang Bo , Law Andy , Regan Tim , Parkinson Nicholas , Cole Joby , Russell Clark D , Dockrell David H , Gutmann Michael U , Baillie J Kenneth 
Published: September 2022

Abstract

Motivation
A common experimental output in biomedical science is a list of genes implicated in a given biological process or disease. The gene lists resulting from a group of studies answering the same, or similar, questions can be combined by ranking aggregation methods to find a consensus or a more reliable answer. Evaluating a ranking aggregation method on a specific type of data before using it is required to support the reliability since the property of a dataset can influence the performance of an algorithm. Such evaluation on gene lists is usually based on a simulated database because of the lack of a known truth for real data. However, simulated datasets tend to be too small compared to experimental data and neglect key features, including heterogeneity of quality, relevance and the inclusion of unranked lists.

Results
In this study, a group of existing methods and their variations that are suitable for meta-analysis of gene lists are compared using simulated and real data. Simulated data were used to explore the performance of the aggregation methods as a function of emulating the common scenarios of real genomic data, with various heterogeneity of quality, noise level and a mix of unranked and ranked data using 20 000 possible entities. In addition to the evaluation with simulated data, a comparison using real genomic data on the SARS-CoV-2 virus, cancer (non-small cell lung cancer) and bacteria (macrophage apoptosis) was performed. We summarize the results of our evaluation in a simple flowchart to select a ranking aggregation method, and in an automated implementation using the meta-analysis by information content algorithm to infer heterogeneity of data quality across input datasets.

Availability and implementation
The code for simulated data generation and running edited version of algorithms: https://github.com/baillielab/comparison_of_RA_methods. Code to perform an optimal selection of methods based on the results of this review, using the MAIC algorithm to infer the characteristics of an input dataset, can be downloaded here: https://github.com/baillielab/maic. An online service for running MAIC: https://baillielab.net/maic.

Supplementary information
Supplementary data are available at Bioinformatics online.
PoCUS in nephrology: a new tool to improve our diagnostic skills
Authors: Romero-González Gregorio , Manrique Joaquin , Slon-Roblero María F , Husain-Syed Faeq , De la Espriella Rafael , Ferrari Fiorenza , Bover Jordi , Ortiz Alberto , Ronco Claudio 
Published: September 2022

ABSTRACT
Point-of-Care Ultrasonography (PoCUS) aims to include a fifth pillar (insonation) in the classical physical examination in order to obtain images to answer specific questions by the clinician at the patient's bedside, allowing rapid identification of structural or functional abnormalities, enabling more accurate volume assessment and supporting diagnosis, as well as guiding procedures. In recent years, PoCUS has started becoming a valuable tool in day-to-day clinical practice, adopted by healthcare professionals from various medical specialties, never replacing physical examination but improving patient and medical care and experience. Renal patients represent a wide range of diseases, which lends PoCUS a special role as a valuable tool in different scenarios, not only for volume-related information but also for the assessment of a wide range of acute and chronic conditions, enhancing the sensitivity of conventional physical examination in nephrology. PoCUS in the hands of a nephrologist is a precision medicine tool.
Multi-species meta-analysis identifies transcriptional signatures associated with cardiac endothelial responses in the ischaemic heart
Authors: Li Ziwen , Solomonidis Emmanouil G , Berkeley Bronwyn , Tang Michelle Nga Huen , Stewart Katherine Ross , Perez-Vicencio Daniel , McCracken Ian R , Spiroski Ana-Mishel , Gray Gillian A , Barton Anna K , Sellers Stephanie L , Riley Paul R , Baker Andrew H , Brittan Mairi 
Published: September 2022

AbstractAimMyocardial infarction remains the leading cause of heart failure. The adult human heart lacks the capacity to undergo endogenous regeneration. New blood vessel growth is integral to regenerative medicine necessitating a comprehensive understanding of the pathways that regulate vascular regeneration. We sought to define the transcriptomic dynamics of coronary endothelial cells following ischaemic injuries in the developing and adult mouse and human heart and to identify new mechanistic insights and targets for cardiovascular regeneration.Methods and resultsWe carried out a comprehensive meta-analysis of integrated single-cell RNA-sequencing data of coronary vascular endothelial cells from the developing and adult mouse and human heart spanning healthy and acute and chronic ischaemic cardiac disease. We identified species-conserved gene regulatory pathways aligned to endogenous neovascularization. We annotated injury-associated temporal shifts of the endothelial transcriptome and validated four genes: VEGF-C, KLF4, EGR1, and ZFP36. Moreover, we showed that ZFP36 regulates human coronary endothelial cell proliferation and defined that VEGF-C administration in vivo enhances clonal expansion of the cardiac vasculature post-myocardial infarction. Finally, we constructed a coronary endothelial cell meta-atlas, CrescENDO, to empower future in-depth research to target pathways associated with coronary neovascularization.ConclusionWe present a high-resolution single-cell meta-atlas of healthy and injured coronary endothelial cells in the mouse and human heart, revealing a suite of novel targets with great potential to promote vascular regeneration, and providing a rich resource for therapeutic development.
Moving beyond ‘infancy’: towards a cross-fertilization between EMI and EAP scholarship
Authors: Wingate Ursula , Hakim Angela 
Published: September 2022

Abstract
Growth in the provision of English medium instruction (EMI) has led to a significant increase in publications on EMI. Several publications claim that EMI is a young field that is still at the level of ‘infancy’ in areas such as language-related student support and teacher education. This raises the question why EMI appears not to draw on research and practices from English for academic purposes (EAP), a discipline with a longer history of enquiry into English-medium education. In this paper, we explore convergences between EMI and EAP in the areas of student support, collaboration between language teachers and subject teachers, and teacher education, and suggest some EAP theories and practices that EMI might usefully draw on. We conclude by stressing the need for cross-fertilization between EMI and EAP scholarship and for a joined research agenda that aims to produce more systematic empirical evidence of the benefits of discipline-specific academic language and literacy development.
Frequent vegetable consumption is inversely associated with hypertension among indigenous Africans
Authors: Akpa Onoja Matthew , Okekunle Akinkunmi Paul , Asowata Osahon Jeffery , Chikowore Tinashe , Mohamed Shukri F , Sarfo Fred , Akinyemi Rufus , Akpalu Albert , Wahab Kolawole , Obiako Reginald , Komolafe Morenikeji , Owolabi Lukman , Osaigbovo Godwin O , Ogbole Godwin , Tiwari Hemant K , Akinyemi Joshua , Fakunle Adekunle , Uvere Ezinne , Adeoye Abiodun M , Lackland Daniel , Arnett Donna K , Ovbiagele Bruce , Ramsay Michèle , Owolabi Mayowa 
Published: September 2022

Abstract

Aims
The relationship between vegetable consumption and hypertension occurrence remains poorly characterized in sub-Saharan Africa. This study assessed the association of vegetable consumption with odds of hypertension among indigenous Africans.

Methods and results
We harmonized data on prior vegetable consumption and hypertension occurrence (defined as one of the following conditions; systolic blood pressure ≥140 or diastolic blood pressure ≥90 mmHg or previous diagnosis or use of antihypertensive medications) from 16 445 participants across five African countries (Nigeria, South Africa, Kenya, Ghana and Burkina Faso) in the Stroke Investigative Research and Educational Network and Africa Wits-INDEPTH partnership for Genomic studies. Vegetable consumption (in servings/week) was classified as ‘low’ (&lt;6). ‘moderate’ (6–11), ‘sufficient’ (12–29), and ‘high’ (≥30). Odds ratios (ORs) and 95% confidence interval (CI) of hypertension were estimated by categories of vegetable consumption (using ‘low’ consumption as reference), adjusting for sex, age in years, family history of cardiovascular diseases, education, smoking, alcohol use, physical inactivity, body mass index, diabetes mellitus and dyslipidaemia using logistic regressions at P &lt; 0.05. The mean age of participants was 53.0 ( ± 10.7) years, and 7552 (45.9%) were males, whereas 7070 (42.9%) had hypertension. In addition, 6672(40.6%) participants had ‘low’ vegetable consumption, and 1758(10.7%) had ‘high’ vegetable consumption. Multivariable-adjusted OR for hypertension by distribution of vegetable consumption (using ‘low’ consumption as reference) were 1.03 (95% CI: 0.95, 1.12) for ‘moderate’ consumption; 0.80 (0.73, 0.88) for ‘sufficient’, and 0.81 (0.72, 0.92) for ‘high’ consumption, P-for-trend &lt;0.0001.

Conclusion
Indigenous Africans who consumed at least 12 servings of vegetables per week were less likely to be found hypertensive, particularly among males and young adults.
Regulation of Digital Platforms and the Digital Economy in Japan
Authors: Aso Tsukasa , Rademacher Christoph 
Published: September 2022

Abstract
The digital economy continues to evolve in Japan and around the world. Big data and personal information have significant economic value and require appropriate legal protection for both information providers and users. Digital platforms, as online intermediaries, occupy a particularly important position in relation to the handling of such information. While digital platforms can greatly benefit society by accumulating and structuring large amounts of data from diverse markets, they can also be prone to the lock-in effect, resulting in monopolies or oligopolies due to network effects. Therefore, digital platforms can have a detrimental effect on individuals and society if they do not operate appropriately. Potential issues include a lack of transparency and fairness of transactions, distribution of infringing content, and the mishandling of data and personal information. Policymakers across the globe recognize these issues, and various regulatory measures have been proposed and implemented. In this paper, we outline how Japan regulates issues related to digital platforms and the digital economy, and highlight some nuances of the Japanese law by comparing it with corresponding European systems.
Adaptive guided salp swarm algorithm with velocity clamping mechanism for solving optimization problems
Authors: Wang Zongshan , Ding Hongwei , Wang Jie , Hou Peng , Li Aishan , Yang Zhijun , Hu Xiang 
Published: September 2022

Abstract
Salp swarm algorithm (SSA) is a well-established population-based optimizer that exhibits strong exploration ability, but slow convergence and poor exploitation capability. In this paper, an endeavour is made to enhance the performance of the basic SSA. The new upgraded version of SSA named as ‘adaptive strategy-based SSA (ABSSA) algorithm’ is proposed in this paper. First, the exploratory scope and food source navigating commands of SSA are enriched using the inertia weight and boosted global best-guided mechanism. Next, a novel velocity clamping strategy is designed to efficiently stabilize the balance between the exploration and exploitation operations. In addition, an adaptive conversion parameter tactic is designed to modify the position update equation to effectively intensify the local exploitation competency and solution accuracy. The effectiveness of the proposed ABSSA algorithm is verified by a series of problems, including 23 classical benchmark functions, 29 complex optimization problems from CEC 2017, and five engineering design tasks. The experimental results show that the developed ABSSA approach performs significantly better than the standard SSA and other competitors. Moreover, ABSSA is implemented to handle path planning and obstacle avoidance (PPOA) tasks in autonomous mobile robots and compared with some swarm intelligent approach-based path planners. The experimental results indicate that the ABSSA-based PPOA method is a reliable path planning algorithm.
Infectious Disease Consults of Pseudomonas aeruginosa Bloodstream Infection and Impact on Health Outcomes
Authors: Ramanathan Swetha , Albarillo Fritzie S , Fitzpatrick Margaret A , Suda Katie J , Poggensee Linda , Vivo Amanda , Evans Martin E , Jones Makoto , Safdar Nasia , Pfeiffer Chris , Smith Bridget , Wilson Geneva , Evans Charlesnika T 
Published: September 2022

Abstract

Background
Infectious diseases (ID) consultation improves health outcomes for certain infections but has not been well described for Pseudomonas aeruginosa (PA) bloodstream infection (BSI). Therefore, the goal of this study was to examine ID consultation of inpatients with PA BSI and factors impacting outcomes.

Methods
This was a retrospective cohort study from January 1, 2012, to December 31, 2018, of adult hospitalized veterans with PA BSI and antibiotic treatment 2 days before through 5 days after the culture date. Multidrug-resistant (MDR) cultures were defined as cultures with resistance to at least 1 agent in ≥3 antimicrobial categories tested. Multivariable logistic regression models were fit to assess the impact of ID consults and adequate treatment on mortality.

Results
A total of 3256 patients had PA BSI, of whom 367 (11.3%) were multidrug resistant (MDR). Most were male (97.5%), over 65 years old (71.2%), and White (70.9%). Nearly one-fourth (n = 784, 23.3%) died during hospitalization, and 870 (25.8%) died within 30 days of their culture. Adjusted models showed that ID consultation was associated with decreased in-hospital (odds ratio [OR], 0.47; 95% CI, 0.39–0.56) and 30-day mortality (OR, 0.51; 95% CI, 0.42–0.62).

Conclusions
Consultation with ID physicians improves clinical outcomes such as in-hospital and 30-day mortality for patients with PA BSI. ID consultation provides value and should be considered for patients with PA BSI.
Perceptions and Experiences With Evidence-based Treatments Among People Who Use Opioids
Authors: Carlberg-Racich Suzanne , Sherrod Darielle , Swope Kristin , Brown Dannielle , Afshar Majid , Salisbury-Afshar Elizabeth 
Published: September 2022

Objectives
Even where treatment is available, people who use drugs (PWUD) may not seek help. Few published studies examine beliefs, experiences, and perceptions of evidence-based treatment among PWUD who are not actively engaged in care. This study aimed to explore the experiences of PWUD in considering or accessing treatment and gauge receptiveness to low-threshold treatment models.

Methods
A purposeful sample of participants actively using opioids and with previous interest in or experience with treatment was recruited from a harm reduction program in Chicago. Semistructured interviews were conducted to explore key phenomena while allowing for unanticipated themes. The instrument included questions about historical drug use, treatment experience, and perceptions of how to improve treatment access and services. Private interviews were audio recorded, transcribed, and double coded by 2 analysts. Queries of coded data were analyzed using issue-focused analysis to identify themes.

Results
The sample (N = 40) approximated groups at highest risk of fatal overdose in Chicago, with more than 80% between the ages of 45 to 64 years, 65% African American, and 62% male identified. The majority had prior treatment experience, although all resumed use after completing or leaving treatment. The most prevalent barriers to treatment included structural barriers related to social determinants, lack of readiness for abstinence, burdensome intake procedures, and regulatory/programmatic requirements. Most participants expressed interest in low-threshold treatment.

Conclusions
Existing treatment barriers may be addressed by shifting to lower-threshold intake processes and/or outreach-based delivery of opioid agonist treatment. Engaging PWUD in efforts to create lower-threshold treatment programs is necessary to ensure that needs are met.
Extent of Disease on Visceral Peritoneal Surfaces of Mucinous Appendiceal Neoplasms Controls Survival
Authors: Sugarbaker Paul H. , Chang David 
Published: September 2022

Objective:
To determine causes of treatment failure of low-grade appendiceal mucinous neoplasms (LAMN).

Background:
For 3 decades, LAMN have been treated by cytoreductive surgery (CRS) and perioperative intraperitoneal chemotherapy. This combined treatment has resulted in a large change in the survival of these patients.

Methods:
A retrospective review of a prospectively maintained database was performed. A restricted cohort of patients with only LAMN histology and complete CRS were included in the statistical analysis.

Results:
Four hundred and fifty patients were available with a median follow-up of 15.3 years (range 10–35 years). The median age was 49.7 and there were 196 males (43.6%). The mean survival was 24.5 years. Extent of parietal peritonectomy, resection of uterus, ovaries and apex of vagina had no impact on survival. Variables that indicated an increased extent of disease on visceral peritoneal surfaces had a significant impact on survival. Early postoperative intraperitoneal chemotherapy with 5-fluorouracil did not augment hyperthermic intraperitoneal chemotherapy (HIPEC). Patients who required reoperation for recurrence or patients with class 4 adverse events had a reduced prognosis.

Conclusions:
The mean survival of LAMN treated by complete CRS and perioperative chemotherapy was 24.5 years. Extent of disease quantitated on visceral peritoneal surfaces by the extent of visceral resections was the variable associated with treatment failure. Peritonectomy plus HIPEC was able to control disease on parietal peritoneal surfaces. Not only a larger extent of disease but also its location on visceral peritoneal surfaces controlled survival.
Effect of Local Antibiotic Prophylaxis on Postoperative Deep Infection in Fracture Surgery: A Systematic Review and Meta-Analysis
Authors: Kruse Colin , Axelrod Daniel , Al-Mohrej Omar A. , Daniel Ryan , Johal Herman 
Published: September 2022

Objectives:
Despite the use of systemic antibiotic prophylaxis, postoperative infection after fracture surgery remains an issue. The purpose of this systematic review and meta-analysis was to evaluate the effect of locally applied antibiotics on deep infection in fracture surgery in both the open and closed fractures.

Data Sources:
A comprehensive search of MEDLINE, Embase, and PubMed was performed from the date of inception to April 15, 2021, and included studies in all languages.

Study Selection:
Cohort studies were eligible if they investigated the effect on the infection rate of local antibiotic prophylaxis on deep infection after fracture surgery.

Data Extraction:
This study was conducted according to the Cochrane Handbook for Systematic Reviews and reported as per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Risk of bias was assessed using version 2 of the Cochrane risk-of-bias tool for randomized trials and the Methodological Index for Nonrandomized Studies tool where applicable.

Data Synthesis:
An inverse variance random-effects model was the primary analysis model because of the anticipated diversity in the evaluated populations. Univariate models were used when a single outcome was of interest.

Conclusions:
The risk of deep infection was significantly reduced when local antibiotics were applied compared with the control group receiving systemic prophylaxis only. This beneficial effect was observed in open fractures but failed to reach statistical significance in closed fractures. This meta-analysis suggests that there may be a significant risk reduction in deep infection rate after fracture surgery when local antibiotics are added to standard systemic prophylaxis, particularly in open fractures. Further high-powered Level I studies are needed to support these findings.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.