bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards greater transparency in neurodevelopmental disorders research: use of a proposed workflow and propensity scores to facilitate selection of matched groups
Authors: Bang Janet Y. , Sharda Megha , Nadig Aparna S. 
Published: July 2020

Abstract
Background
Matching is one commonly utilized method in quasi-experimental designs involving individuals with neurodevelopmental disorders (NDD). This method ensures two or more groups (e.g., individuals with an NDD versus neurotypical individuals) are balanced on pre-existing covariates (e.g., IQ), enabling researchers to interpret performance on outcome measures as being attributed to group membership. While much attention has been paid to the statistical criteria of how to assess whether groups are well-matched, relatively little attention has been given to a crucial prior step: the selection of the individuals that are included in matched groups. The selection of individuals is often an undocumented process, which can invite unintentional, arbitrary, and biased decision-making. Limited documentation can result in findings that have limited reproducibility and replicability and thereby have poor potential for generalization to the broader population. Especially given the heterogeneity of individuals with NDDs, interpretation of research findings depends on minimizing bias at all stages of data collection and analysis.

Results
In the spirit of open science, this tutorial demonstrates how a workflow can be used to provide a transparent, reproducible, and replicable process to select individuals for matched groups. Our workflow includes the following key steps: Assess data, Select covariates, Conduct matching, and Diagnose matching. Our sample dataset is from children with autism spectrum disorder (ASD; n = 25) and typically developing children (n = 43) but can be adapted to comparisons of any two groups in quasi-experimental designs. We work through this method to conduct and document matching using propensity scores implemented with the R package MatchIt. Data and code are publicly available, and a template for this workflow is provided in the Additional file 1 as well as on a public repository.

Conclusions
It is important to provide clear documentation regarding the selection process to establish matched groups. This documentation ensures better transparency in participant selection and data analysis in NDD research. We hope the adoption of such a workflow will ultimately advance our ability to replicate findings and help improve the lives of individuals with NDDs.
Optimization of a physical internet based supply chain using reinforcement learning
Authors: Puskás Eszter , Budai Ádám , Bohács Gábor 
Published: July 2020

AbstractPhysical Internet based supply chains create open, global logistics systems that enable new types of collaboration among participants. The open system allows the logistical examination of vehicle technology innovations such as the platooning concept. This article explores the multiple platoon collaboration. For the reconfiguration of two platoons a heuristic and a reinforcement learning (RL) based models have been developed. To our knowledge, this work is the first attempt to apply an RL-based decision model to solve the problem of controlling platoon cooperation. Vehicle exchange between platoons is provided by a virtual hub. Depending on the various input parameters, the efficiency of the model was examined through numerical examples in terms of the target function based on the transportation cost. Models using platoon reconfiguration are also compared to the cases where no vehicle exchange is implemented. We have found that a reinforcement learning based model provides a more efficient solution for high incoming vehicle numbers and low dispatch interval, although for low vehicle numbers heuristics model performs better.
Understanding the child-doctor relationship in research participation: a qualitative study
Authors: Luchtenberg Malou L. , Maeckelberghe Els L. M. , Locock Louise , Verhagen A. A. Eduard 
Published: July 2020

AbstractBackgroundChildren have reported that one reason for participating in research is to help their doctor. This is potentially harmful if associated with coercive consent but might be beneficial for recruitment. We aimed to explore children’s perceptions of the child-doctor relationship in research.MethodsThis is a multicenter qualitative study with semi structured interviews performed between 2010 and 2011 (United Kingdom) and 2017–2019 (the Netherlands). Interviews took place nationwide at children’s homes. We performed a secondary analysis of the two datasets, combining an amplified analysis aimed to enlarge our dataset, and a supplementary analysis, which is a more in-depth investigation of emergent themes that were not fully addressed in the original studies. All participants had been involved in decisions about research participation, either as healthy volunteers, or as patients. Recruitment was aimed for a purposive maximum variation sample, and continued until data saturation occurred. We have studied how children perceived the child-doctor relationship in research. Interviews were audiotaped or videotaped, transcribed verbatim, and thematically analyzed using Atlas.ti software.ResultsIn total, 52 children were recruited aged 9 to 18, 29 in the United Kingdom and 23 in the Netherlands. Children’s decision-making depended strongly on support by research professionals, both in giving consent and during participation. Often, their treating physician was involved in the research process. Familiarity and trust were important and related to the extent to which children thought doctors understood their situation, were medically competent, showed support and care, and gave priority to the individual child’s safety. A trusting relationship led to a feeling of mutuality and enhanced children’s confidence. This resulted in improving their experiences throughout the entire research process. None of the participants reported that they felt compelled to participate in the research.ConclusionsThe child-doctor relationship in pediatric research should be characterized by familiarity and trust. This does not compromise children’s voluntary decision but enhances children’s confidence and might result in a feeling of mutuality. By addressing the participation of children as an iterative process during which treatment and research go hand in hand, the recruitment and participation of children in research can be improved.
Triglyceride–glucose index (TyG index) is a predictor of incident colorectal cancer: a population-based longitudinal study
Authors: Okamura Takuro , Hashimoto Yoshitaka , Hamaguchi Masahide , Obora Akihiro , Kojima Takao , Fukui Michiaki 
Published: July 2020

Abstract
Background
Colorectal cancer (CRC), which is related with insulin resistance, is a one of the most common cancers. Triglyceride-glucose index (TyG index) was made for a marker of insulin resistance. We conducted the investigation of association between TyG index and incident CRC.

Methods
We examined the affect of TyG index on incident CRC in this historical cohort study of 27,944 (16,454 men and 11,490 women) participants. TyG index was calculated as ln [fasting triglycerides (mg/dL) × fasting plasma glucose (mg/dL)/2]. The impact of TyG index on incident CRC was investigated using Cox proportional hazard models, adjusting for sex, age, body mass index, smoking status, alcohol consumption, exercise, systolic blood pressure and creatinine. The covariate-adjusted receiver operating characteristic (ROC) curve calculated the area under the curve (AUC) and cut-off value of TyG index for the incidence of CRC.

Results
During the median 4.4-year follow-up, 116 participants were diagnosed as CRC. The cumulative incidence rate of CRC were 0.4%. In Cox proportional hazard model, the HRs of TyG index were 1.38 (95% Confidence interval (CI), 1.00–1.91, p = 0.049) after adjusting for covariates. In the covariate-adjusted ROC curve analysis, the cut-off value of TyG index for incident CRC was 8.272 (AUC 0.687 (95%CI, 0.637–737, sensitivity = 0.620, specificity = 0.668, p < 0.001)).

Conclusions
TyG index can predict the onset of CRC. For early detection of CRC, we should encourage people with high TyG index to undergo screening for CRC.
Evaluation of antenatal risk factors for postpartum depression: a secondary cohort analysis of the cluster-randomised GeliS trial
Authors: Johar Hamimatunnisa , Hoffmann Julia , Günther Julia , Atasoy Seryan , Stecher Lynne , Spies Monika , Hauner Hans , Ladwig Karl-Heinz 
Published: July 2020

Abstract
Background
Maternal weight variables are important predictors of postpartum depression (PPD). While preliminary evidence points to an association between pre-pregnancy obesity and PPD, the role of excessive gestational weight gain (GWG) on PPD is less studied. In this secondary cohort analysis of the German ‘healthy living in pregnancy’ (GeliS) trial, we aimed to investigate associations between weight-related variables and PPD and to assess the influence of GWG on the risk for PPD.

Methods
We included women with normal weight, overweight, and obesity (BMI 18.5–40.0 kg/m2). Symptoms of PPD were assessed 6–8 weeks postpartum using the Edinburgh Postnatal Depression Scale. Pre-pregnancy BMI was self-reported. During the course of pregnancy, weight was measured at gynaecological practices within regular check-ups. GWG was defined as the difference between the last measured weight before delivery and the first measured weight at the time of recruitment (≤ 12th week of gestation). Excessive GWG was classified according to the Institute of Medicine. Multiple logistic regression analyses were used to estimate the odds of PPD in relation to pre-pregnancy BMI, GWG, and excessive GWG adjusting for important confounders.

Results
Of the total 1583 participants, 45.6% (n = 722) showed excessive GWG and 7.9% (n = 138) experienced PPD. Pre-pregnancy BMI (per 5-unit increase; OR = 1.23, 95% CI 1.08–1.41, p = 0.002) and pre-pregnancy overweight or obesity were significantly positively associated with the odds of developing PPD, particularly among women with an antenatal history of anxiety or depressive symptoms (overweight: OR = 1.93, 95% CI = 1.15–3.22, p = 0.01; obesity: OR = 2.11, 95% CI = 1.13–3.96, p = 0.02). Sociodemographic or lifestyle factors did not additively influence the odds of having PPD. In fully adjusted models, there was no significant evidence that GWG or the occurrence of excessive GWG increased the odds of experiencing PPD (excessive vs. non-excessive: OR = 3.48, 95% CI 0.35–34.94; GWG per 1 kg increase: OR = 1.16, 95% CI 0.94–1.44).

Conclusion
Pre-pregnancy overweight or obesity is associated with PPD independent of concurrent risk factors. History of anxiety or depressive symptoms suggests a stress-induced link between pre-pregnancy weight and PPD.

Trial registration
NCT01958307, ClinicalTrials.gov, retrospectively registered on 9 October 2013.
Clinical trials to assess adjuvant therapeutics for severe malaria
Authors: Varo Rosauro , Erice Clara , Johnson Sydney , Bassat Quique , Kain Kevin C. 
Published: July 2020

AbstractDespite potent anti-malarial treatment, mortality rates associated with severe falciparum malaria remain high. To attempt to improve outcome, several trials have assessed a variety of potential adjunctive therapeutics, however none to date has been shown to be beneficial. This may be due, at least partly, to the therapeutics chosen and clinical trial design used. Here, we highlight three themes that could facilitate the choice and evaluation of putative adjuvant interventions for severe malaria, paving the way for their assessment in randomized controlled trials. Most clinical trials of adjunctive therapeutics to date have been underpowered due to the large number of participants required to reach mortality endpoints, rendering these study designs challenging and expensive to conduct. These limitations may be mitigated by the use of risk-stratification of participants and application of surrogate endpoints. Appropriate surrogate endpoints include direct measures of pathways causally involved in the pathobiology of severe and fatal malaria, including markers of host immune and endothelial activation and microcirculatory dysfunction. We propose using circulating markers of these pathways to identify high-risk participants that would be most likely to benefit from adjunctive therapy, and further by adopting these biomarkers as surrogate endpoints; moreover, choosing interventions that target deleterious host immune responses that directly contribute to microcirculatory dysfunction, multi-organ dysfunction and death; and, finally, prioritizing where possible, drugs that act on these pathways that are already approved by the FDA, or other regulators, for other indications, and are known to be safe in target populations, including children. An emerging understanding of the critical role of the host response in severe malaria pathogenesis may facilitate both clinical trial design and the search of effective adjunctive therapeutics.
“Bayis Ilh Tus – a strong breath” a community-based research project to estimate the prevalence of chronic obstructive pulmonary disease in remote and rural first nations communities in Canada: research protocol
Authors: Turner Justin , Holyk Travis , Bartlett Karen , Rathburn Benna , Karlen Barbara , Ervin Francis , Wilson Jennifer , Camp Pat G. 
Published: July 2020

Abstract
Background
Respiratory health conditions appear to be more common among First Nations people versus non-First Nations people in Canada. However, the prevalence of chronic obstructive pulmonary disease (COPD) and its associated risk factors in First Nations communities are unknown. This project aims to estimate the prevalence of COPD in several First Nations communities in British Columbia, Canada and to characterize respiratory symptoms, COPD risk factors, and healthcare utilization.

Methods
This project is approved by both the University of British Columbia and Carrier Sekani Family Services Research Ethics Boards. We will randomly sample 220 adults, 30 years and older, from 11 participating First Nations. Each participant will complete pre- and post-bronchodilator spirometry tests and the adapted American Thoracic Society Epidemiological Questionnaire with items about smoking history, respiratory symptoms, co-morbidities, and exposures, in order to identify the presence of COPD and its associated individual, occupational, and community risk factors. Homes will be assessed for air quality measures including particulate matter, carbon monoxide and carbon dioxide, and humidity. Health care utilization will be abstracted from the electronic medical record.

Discussion
This is the first project in Canada to estimate the prevalence of COPD in First Nations communities using a random-sampling approach to recruitment. Additionally, although this study will collect detailed information on smoking history, we will also characterize past and current risk factors beyond cigarette smoking. Finally, our methodology ensures that the benefits to the communities are realized during the study period. Individual results will be shared with individuals and health providers to facilitate care. Air quality results will be sent to each Nation’s governing council to facilitate remediation where necessary.

Trial registration
The study has been retrospectively registered at clinicaltrials.gov (NCT04105088).
miR-541 serves as a prognostic biomarker of osteosarcoma and its regulatory effect on tumor cell proliferation, migration and invasion by targeting TGIF2
Authors: Liu Chunlei , Yi Xiuling 
Published: July 2020

Abstract
Background
Several studies reported the dysregulation of miR-541 in the progression of some human malignancies. Osteosarcoma (OS) is one of the most common primary malignant bone tumors. This study aimed to assess the expression and clinical significance of miR-541 in OS patients and explore the biological function of miR-541 in tumor progression.

Methods
Expression of miR-541 was detected by quantitative real-time PCR, and its prognostic value was evaluated using Kaplan-Meier survival analysis. The biological function of miR-541 was examined by analyzing its effects on OS cell proliferation, migration and invasion. Additionally, the underlying potential target of miR-541 was predicated and analyzed.

Results
The expression of miR-541 was significantly decreased in OS tissues and cell lines. The deregulated expression of miR-541 in tumor tissues was associated with the overall survival of OS patients and was a potential independent prognostic indicator. In OS cells, the overexpression of miR-541 could inhibit cell proliferation, migration and invasion. The luciferase activity results indicated that TGIF2 was a potential target of miR-541.

Conclusion
The results of this study revealed that the decreased miR-541 expression in OS patients may serve as a prognostic biomarker, and that the overexpression of miR-541 in OS cells results in inhibited cell proliferation, migration and invasion, indicating the potential of miR-541 as a therapeutic target in OS treatment.
Malakoplakia of the gastrointestinal tract: clinicopathologic analysis of 23 cases
Authors: Lee Michael , Ko Huaibin Mabel , Rubino Anthony , Lee Hwajeong , Gill Ryan , Lagana Stephen M. 
Published: July 2020

Abstract
Background
Malakoplakia is an uncommon, tumor-like inflammatory disease characterized by impaired histiocytes that are unable to completely digest phagocytized bacteria. The genitourinary tract is the most common site of involvement, however, cases have also been described in the gastrointestinal tract, suggesting that it is the second most common site of involvement. This study investigates the clinical and histologic features of malakoplakia in the gastrointestinal tract.

Case presentation
For 23 gastrointestinal specimens (biopsies and resections) from patients with a pathologic diagnosis of malakoplakia, we recorded the gender, age, location, primary diagnosis, endoscopic or surgical indication, endoscopic/gross impression and immune status (immunocompromised vs. immunocompetent).

Conclusion
Malakoplakia occurred throughout the length of the gastrointestinal tract with most of the cases located in the sigmoid colon and rectum (n = 10); other sites included the transverse and descending colon (n = 4), stomach/gastroesophageal junction (n = 4), appendix (n = 2), cecum (n = 1), small bowel (n = 1), and the peri-anal area (n = 1). Endoscopically, these lesions most commonly appeared as polyps (n = 10) or masses (n = 5), other clinical endoscopic impressions varied from a thickened area/fibrosis to mucosal erythema. Most patients were immunocompromised due to a disease state (e.g. organ transplantation, cancer diagnosis, autoimmune condition) and/or medication effect. Eight patients with malakoplakia were on immunosuppressive medications (8/23, 35%). Common immunosuppressed disease states included cancer (n = 9), autoimmune disease (n = 5), status post organ transplantation (n = 4), diabetes (n = 5), infection/sepsis (n = 3), and HIV/AIDS (n = 1). Some patients had multiple co-morbidities (i.e. diabetes and organ transplant). Twenty-one patients with malakoplakia were in an immunosuppressive state (21/23, 91%).
Distribution of hygiene kits during a cholera outbreak in Kasaï-Oriental, Democratic Republic of Congo: a process evaluation
Authors: D’Mello-Guyett Lauren , Greenland Katie , Bonneville Sharla , D’hondt Rob , Mashako Maria , Gorski Alexandre , Verheyen Dorien , Van den Bergh Rafael , Maes Peter , Checchi Francesco , Cumming Oliver 
Published: July 2020

Abstract
Background
Cholera remains a leading cause of infectious disease outbreaks globally, and a major public health threat in complex emergencies. Hygiene kits distributed to cholera case-households have previously shown an effect in reducing cholera incidence and are recommended by Médecins Sans Frontières (MSF) for distribution to admitted patients and accompanying household members upon admission to health care facilities (HCFs).

Methods
This process evaluation documented the implementation, participant response and context of hygiene kit distribution by MSF during a 2018 cholera outbreak in Kasaï-Oriental, Democratic Republic of Congo (DRC). The study population comprised key informant interviews with seven MSF staff, 17 staff from other organisations and a random sample of 27 hygiene kit recipients. Structured observations were conducted of hygiene kit demonstrations and health promotion, and programme reports were analysed to triangulate data.

Results and conclusions
Between Week (W) 28–48 of the 2018 cholera outbreak in Kasaï-Oriental, there were 667 suspected cholera cases with a 5% case fatality rate (CFR). Across seven HCFs supported by MSF, 196 patients were admitted with suspected cholera between W43-W47 and hygiene kit were provided to patients upon admission and health promotion at the HCF was conducted to accompanying household contacts 5–6 times per day. Distribution of hygiene kits was limited and only 52% of admitted suspected cholera cases received a hygiene kit. The delay of the overall response, delayed supply and insufficient quantities of hygiene kits available limited the coverage and utility of the hygiene kits, and may have diminished the effectiveness of the intervention. The integration of a WASH intervention for cholera control at the point of patient admission is a growing trend and promising intervention for case-targeted cholera responses. However, the barriers identified in this study warrant consideration in subsequent cholera responses and further research is required to identify ways to improve implementation and delivery of this intervention.