bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Pandemic and Exercise (COPE) trial: a multigroup pragmatic randomised controlled trial examining effects of app-based at-home exercise programs on depressive symptoms
Authors: Puterman Eli , Hives Benjamin , Mazara Nicole , Grishin Nikol , Webster Joshua , Hutton Stacey , Koehle Michael Stephen , Liu Yan , Beauchamp Mark R 
Published: September 2021

BackgroundThe number of adults across the globe with significant depressive symptoms has grown substantially during the COVID-19 pandemic. The extant literature supports exercise as a potent behaviour that can significantly reduce depressive symptoms in clinical and non-clinical populations.ObjectiveUsing a suite of mobile applications, at-home exercise, including high intensity interval training (HIIT) and/or yoga, was completed to reduce depressive symptoms in the general population in the early months of the pandemic.MethodsA 6-week, parallel, multiarm, pragmatic randomised controlled trial was completed with four groups: (1) HIIT, (2) Yoga, (3) HIIT+yoga, and (4) waitlist control (WLC). Low active, English-speaking, non-retired Canadians aged 18–64 years were included. Depressive symptoms were measured at baseline and weekly following randomisation.ResultsA total of 334 participants were randomised to one of four groups. No differences in depressive symptoms were evident at baseline. The results of latent growth modelling showed significant treatment effects in depressive symptoms for each active group compared with the WLC, with small effect sizes (ESs) in the community-based sample of participants. Treatment groups were not significantly different from each other. Effect sizes were very large (eg, week 6 ES range=−2.34 to −2.52) when restricting the analysis only to participants with high depressive symptoms at baseline.ConclusionsAt-home exercise is a potent behaviour to improve mental health in adults during the pandemic, especially in those with increased levels of depressive symptoms. Promotion of at-home exercise may be a global public health target with important personal, social and economic implications as the world emerges scathed by the pandemic.Trial registration numberNCT04400279.
Social determinants of health impacting adherence to diabetic retinopathy examinations
Authors: Cai Cindy X , Li Yixuan , Zeger Scott L , McCarthy Melissa L 
Published: September 2021

IntroductionThis study evaluates the association of multidimensional social determinants of health (SDoH) with non-adherence to diabetic retinopathy examinations.Research design and methodsThis was a post-hoc subgroup analysis of adults with diabetes in a prospective cohort study of enrollees in the Washington, DC Medicaid program. At study enrollment, participants were given a comprehensive SDoH survey based on the WHO SDoH model. Adherence to recommended dilated diabetic retinopathy examinations, as determined by qualifying Current Procedural Terminology codes in the insurance claims, was defined as having at least one eye examination in the 2-year period following study enrollment.ResultsOf the 8943 participants enrolled in the prospective study, 1492 (64% female, 91% non-Hispanic Black) were included in this post-hoc subgroup analysis. 47.7% (n=712) were adherent to the recommended biennial diabetic eye examinations. Not having a regular provider (eg, a primary care physician) and having poor housing conditions (eg, overcrowded, inadequate heating) were associated with decreased odds of adherence to diabetic eye examinations (0.45 (95% CI 0.31 to 0.64) and 0.70 (95% CI 0.53 to 0.94), respectively) in the multivariate logistic regression analysis controlling for age, sex, race/ethnicity, overall health status using the Chronic Disability Payment System, diabetes severity using the Diabetes Complications Severity Index, history of eye disease, and history of diabetic eye disease treatment.ConclusionsA multidimensional evaluation of SDoH revealed barriers that impact adherence to diabetic retinopathy examinations. Having poor housing conditions and not having a regular provider were associated with poor adherence. A brief SDoH assessment could be incorporated into routine clinical care to identify social risks and connect patients with the necessary resources to improve adherence to diabetic retinopathy examinations.
The role of trained champions in sustaining and spreading nutrition care improvements in hospital: qualitative interviews following an implementation study
Authors: Laur Celia , Bell Jack , Valaitis Renata , Ray Sumantra , Keller Heather 
Published: September 2021

BackgroundMany patients are already malnourished when admitted to hospital. Barriers and facilitators to nutrition care in hospital have been identified and successful interventions developed; however, few studies have explored how to sustain and spread improvements. The More-2-Eat phase 1 study involved five hospitals across Canada implementing nutrition care improvements, while phase 2 implemented a scalable model using trained champions, audit and feedback, a community of practice with external mentorship and an implementation toolkit in 10 hospitals (four continuing from phase 1). Process measures showed that screening and assessment from phase 1 were sustained for at least 4 years. The objective of this study was to help explain how these nutrition care improvements were sustained and spread by understanding the role of the trained champions, and to confirm and expand on themes identified in phase 1.MethodsSemistructured telephone interviews were conducted with champions from each phase 2 hospital and recordings transcribed verbatim. To explore the champion role, transcripts were deductively coded to the 3C model of Concept, Competence and Capacity. Phase 2 transcripts were also deductively coded to themes identified in phase 1 interviews and focus groups.ResultsTen interviews (n=14 champions) were conducted. To sustain and spread nutrition care improvements, champions needed to understand theConceptsof change management, implementation, adaptation, sustainability and spread in order to embed changes into routine practice. Champions also needed theCompetence, including the skills to identify, support and empower new champions, thus sharing the responsibility.Capacity, including time, resources and leadership support, was the most important facilitator for staying engaged, and the most challenging. All themes identified in qualitative interviews in phase 1 were applicable 4 years later and were mentioned by new phase 2 hospitals. There was increased emphasis on audit and feedback, and the need for standardisation to support embedding into current practice.ConclusionTrained local champions were required for implementation. By understanding key concepts, with appropriate and evolving competence and capacity, champions supported sustainability and spread of nutrition care improvements. Understanding the role of champions in supporting implementation, spread and sustainability of nutrition care improvements can help other hospitals when planning for and implementing these improvements.Trial registration numberNCT02800304,NCT03391752.
Molecular characterisation of pancreatic ductal adenocarcinoma withNTRKfusions and review of the literature
Authors: Allen Michael J , Zhang Amy , Bavi Prashant , Kim Jaeseung C , Jang Gun Ho , Kelly Deirdre , Perera Sheron , Denroche Rob E , Notta Faiyaz , Wilson Julie M , Dodd Anna , Ramotar Stephanie , Hutchinson Shawn , Fischer Sandra E , Grant Robert C , Gallinger Steven , Knox Jennifer J , O'Kane Grainne M 
Published: September 2021

AimsThe majority of pancreatic ductal adenocarcinomas (PDACs) harbour oncogenic mutations inKRASwith variants inTP53,CDKN2AandSMAD4also prevalent. The presence of oncogenic fusions includingNTRKfusions are rare but important to identify. Here we ascertain the prevalence ofNTRKfusions and document their genomic characteristics in a large series of PDAC.MethodsWhole genome sequencing and RNAseq were performed on a series of patients with resected or locally advanced/metastatic PDAC collected between 2008 and 2020 at a single institution. A subset of specimens underwent immunohistochemistry (IHC) analysis. Clinical and molecular characterisation and IHC sensitivity and specificity were evaluated.Results400 patients were included (resected n=167; locally advanced/metastatic n=233). Three patients were identified as harbouring anNTRKfusion, twoEML4-NTRK3(KRAS-WT) and a single novelKANK1-NTRK3fusion. The latter occurring in the presence of a subclonalKRASmutation. Typical PDAC drivers were present including mutations inTP53andCDKN2A. Substitution base signatures and tumour mutational burden were similar to typical PDAC. The prevalence ofNTRKfusions was 0.8% (3/400), while inKRASwild-type tumours, it was 6.25% (2/32). DNA prediction alone documented six false-positive cases. RNA analysis correctly identified the in-frame fusion transcripts. IHC analysis was negative in theKANK1-NTRK3fusion but positive in aEML4-NTRK3case, highlighting lower sensitivity of IHC.ConclusionNTRKfusions are rare; however, with emerging therapeutic options targeting these fusions, detection is vital. Reflex testing forKRASmutations and subsequent RNA-based screening could help identify these cases in PDAC.
Frequency of microsatellite instability (MSI) in upper tract urothelial carcinoma: comparison of the Bethesda panel and the Idylla MSI assay in a consecutively collected, multi-institutional cohort
Authors: Kullmann Friederike , Strissel Pamela L , Strick Reiner , Stoehr Robert , Eckstein Markus , Bertz Simone , Wullich Bernd , Sikic Danijel , Wach Sven , Taubert Helge , Olbert Peter , Heers Hendrik , Lara María Fernanda , Macias Maria Luisa , Matas-Rico Elisa , Lozano Maria José , Prieto Daniel , Hierro Isabel , van Doeveren Thomas , Bieche Ivan , Masliah-Planchon Julien , Beaurepere Romane , Boormans Joost L , Allory Yves , Herrera-Imbroda Bernardo , Hartmann Arndt , Weyerer Veronika 
Published: September 2021

AimsUpper tract urothelial carcinoma (UTUC) is a rare malignancy with a poor prognosis which occurs sporadically or in few cases results from a genetic disorder called Lynch syndrome. Recently, examination of microsatellite instability (MSI) has gained importance as a biomarker: MSI tumours are associated with a better response to immunomodulative therapies. Limited data are known about the prevalence of MSI in UTUC. New detection methods using the fully automated Idylla MSI Assay facilitate analysis of increased patient numbers.MethodsWe investigated the frequency of MSI in a multi-institutional cohort of 243 consecutively collected UTUC samples using standard methodology (Bethesda panel), along with immunohistochemistry of mismatch repair (MMR) proteins. The same tumour cohort was retested using the Idylla MSI Assay by Biocartis.ResultsUsing standard methodology, 230/243 tumours were detected as microsatellite stable (MSS), 4/243 tumours as MSI and 9/243 samples as invalid. In comparison, the Idylla MSI Assay identified four additional tumours as MSS, equalling 234/243 tumours; 4/243 were classified as MSI and only 5/243 cases as invalid. At the immunohistochemical level, MSI results were supported in all available cases with a loss in MMR proteins. The overall concordance between the standard and the Idylla MSI Assay was 98.35%. Time to result differed between 3 hours for Idylla MSI Assay and 2 days with the standard methodology.ConclusionOur data indicate a low incidence rate of MSI tumours in patients with UTUC. Furthermore, our findings highlight that Idylla MSI Assay can be applied as an alternative method of MSI analysis for UTUC.
Homelessness in early adulthood and biomedical risk factors by middle-age: the 1970 British Cohort Study
Authors: White James W , Hamer Mark , Batty G David 
Published: September 2021

BackgroundHomelessness has been linked to premature mortality but the relationship with biomedical risk factors is uncertain.MethodsWe analysed data from 8581 participants in the 1970 British Birth Cohort Study. Homelessness and type of experience were self-reported at 30 years of age. Nine biomarkers outcomes were collected at 46 years of age: body mass index (BMI), blood pressure, total and high-density cholesterol, triglycerides, glycated haemoglobin, C-reactive protein (CRP), insulin-like growth factor 1 and we computed the 10-year risk for coronary heart disease.ResultsBy 30 years of age, 5.8% of participants had been homeless with sofa surfing the most common experience (4.3%). Homelessness was associated with socioeconomic disadvantage, mental health problems and substance use in early adulthood, but these differences were not expressed in biomarkers. After accounting for early adulthood characteristics, residing in a bed and breakfast was associated with a higher BMI (0.59, 95% CI 0.13 to 1.05) and CRP (0.16, 95% CI 0.04 to 0.29), squatting with a lower BMI (−1.69, 95% CI –3.08 to −0.21) and rough sleeping with a higher 10-year risk of coronary heart disease (0.03, 95% CI 0.01 to 0.05).ConclusionsExposure to homelessness in early adulthood was essentially unrelated to biomarkers in middle age. Inconsistent links were found for specific types of experience.
Longitudinal thalamic white and grey matter changes associated with visual hallucinations in Parkinson’s disease
Authors: Zarkali Angeliki , McColgan Peter , Leyland Louise Ann , Lees Andrew John , Weil Rimona Sharon 
Published: September 2021

ObjectiveVisual hallucinations are common in Parkinson’s disease (PD) and associated with worse outcomes. Large-scale network imbalance is seen in PD-associated hallucinations, but mechanisms remain unclear. As the thalamus is critical in controlling cortical networks, structural thalamic changes could underlie network dysfunction in PD hallucinations.MethodsWe used whole-brain fixel-based analysis and cortical thickness measures to examine longitudinal white and grey matter changes in 76 patients with PD (15 hallucinators, 61 non-hallucinators) and 26 controls at baseline, and after 18 months. We compared white matter and cortical thickness, adjusting for age, gender, time-between-scans and intracranial volume. To assess thalamic changes, we extracted volumes for 50 thalamic subnuclei (25 each hemisphere) and mean fibre cross-section (FC) for white matter tracts originating in each subnucleus and examined longitudinal change in PD-hallucinators versus non-hallucinators.ResultsPD hallucinators showed white matter changes within the corpus callosum at baseline and extensive posterior tract involvement over time. Less extensive cortical thickness changes were only seen after follow-up. White matter connections from the right medial mediodorsal magnocellular thalamic nucleus showed reduced FC in PD hallucinators at baseline followed by volume reductions longitudinally. After follow-up, almost all thalamic subnuclei showed tract losses in PD hallucinators compared with non-hallucinators.InterpretationPD hallucinators show white matter loss particularly in posterior connections and in thalamic nuclei, over time with relatively preserved cortical thickness. The right medial mediodorsal thalamic nucleus shows both connectivity and volume loss in PD hallucinations. Our findings provide mechanistic insights into the drivers of network imbalance in PD hallucinations and potential therapeutic targets.
Ventricular–vascular coupling is predictive of adverse clinical outcome in paediatric pulmonary arterial hypertension
Authors: Dufva Melanie J , Ivy Dunbar , Campbell Kristen , Lam Aimee , Rauff Adam , Breeman Karel T N , Douwes Johannes M , Berger Rolf M F , Kheyfets Vitaly Oleg , Hunter Kendall 
Published: September 2021

AimsVentricular–vascular coupling, the ratio between the right ventricle’s contractile state (Ees) and its afterload (Ea), may be a useful metric in the management of paediatric pulmonary arterial hypertension (PAH). In this study we assess the prognostic capacity of the ventricular–vascular coupling ratio (Ees/Ea) derived using right ventricular (RV) pressure alone in children with PAH.MethodsOne hundred and thirty paediatric patients who were diagnosed with PAH via right heart catheterisation were retrospectively reviewed over a 10-year period. Maximum RV isovolumic pressure and end-systolic pressure were estimated using two single-beat methods from Takeuchiet al(Ees/Ea_(Takeuchi)) and from Kindet al(Ees/Ea_(Kind)) and used with an estimate of end-systolic pressure to compute ventricular–vascular coupling from pressure alone. Patients were identified as either idiopathic/hereditary PAH or associated PAH (IPAH/HPAH and APAH, respectively). Haemodynamic data, clinical functional class and clinical worsening outcomes—separated into soft (mild) and hard (severe) event categories—were assessed. Adverse soft events included functional class worsening, syncopal event, hospitalisation due to a proportional hazard-related event and haemoptysis. Hard events included death, transplantation, initiation of prostanoid therapy and hospitalisation for atrial septostomy and Pott’s shunt. Cox proportional hazard modelling was used to assess whether Ees/Eawas predictive of time-to-event.ResultsIn patients with IPAH/HPAH, Ees/Ea_(Kind) and Ees/Ea_(Takeuchi) were both independently associated with time to hard event (p=0.003 and p=0.001, respectively) and when adjusted for indexed pulmonary vascular resistance (p=0.032 and p=0.013, respectively). Neither Ees/Ea_(Kind) nor Ees/Ea_(Takeuchi) were associated with time to soft event. In patients with APAH, neither Ees/Ea_(Kind) nor Ees/Ea_(Takeuchi) were associated with time to hard event or soft event.ConclusionsEes/Eaderived from pressure alone is a strong independent predictor of adverse outcome and could be a potential powerful prognostic tool for paediatric PAH.
District-scale numerical analysis of settlements related to groundwater lowering in variable soil conditions
Authors: Peduto Dario , Prosperi Alfonso , Nicodemo Gianfranco , Korff Mandy 
Published: September 2021

This study presents a novel framework in which numerical modelling contributes to the performance of district-scale, subsidence-induced damage assessment in cities where ground settlements affect entire quarters. Therein, the implementation of expeditious procedures offers geotechnical engineers the possibility of contributing beyond the typical site scale. For this purpose, several “typified” hydro-geomechanical-loading (HGL) models, which represent (simplified) scenarios of masonry buildings undergoing settlements, were set up to account for different predisposing or triggering factors (i.e., soil heterogeneity, loading conditions, and groundwater variations) of settlement occurrence in built-up areas. These models exploit multi-source, wide-area input datasets encompassing the hydro-mechanical properties of geomaterials, in situ investigations and measurements (e.g., groundwater levels in wells), and innovative remote sensing data (i.e., DInSAR techniques). With reference to a district in Rotterdam City (the Netherlands), which was built on “soft soils”, the numerical simulations of different scenarios (i) provide an overview of the comparative role of predisposing or triggering factors on settlement occurrence and (ii) allow assessments of the expected induced damage to masonry buildings over 30 years with the exploitation of fragility curves. Considering the widespread diffusion of such geohazards, the proposed approach could help prioritise (rather expensive) maintenance work to the built heritage within sustainable strategies for subsidence risk mitigation.
Towards an Anatomy of Software Craftsmanship
Authors: Sundelin Anders , Gonzalez-huerta Javier , Wnuk Krzysztof , Gorschek Tony 
Published: September 2021

Context:
The concept of software craftsmanship has early roots in computing, and in 2009, the Manifesto for Software Craftsmanship was formulated as a reaction to how the Agile methods were practiced and taught. But software craftsmanship has seldom been studied from a software engineering perspective.

Objective:
The objective of this article is to systematize an anatomy of software craftsmanship through literature studies and a longitudinal case study.

Method:
We performed a snowballing literature review based on an initial set of nine papers, resulting in 18 papers and 11 books. We also performed a case study following seven years of software development of a product for the financial market, eliciting qualitative, and quantitative results. We used thematic coding to synthesize the results into categories.

Results:
The resulting anatomy is centered around four themes, containing 17 principles and 47 hierarchical practices connected to the principles. We present the identified practices based on the experiences gathered from the case study, triangulating with the literature results.

Conclusion:
We provide our systematically derived anatomy of software craftsmanship with the goal of inspiring more research into the principles and practices of software craftsmanship and how these relate to other principles within software engineering in general.
SPI: Automated Identification of Security Patches via Commits
Authors: Zhou Yaqin , Siow Jing Kai , Wang Chenyu , Liu Shangqing , Liu Yang 
Published: September 2021

Security patches in open source software, providing security fixes to identified vulnerabilities, are crucial in protecting against cyber attacks. Security advisories and announcements are often publicly released to inform the users about potential security vulnerability. Despite the
National Vulnerability Database (NVD)
publishes identified vulnerabilities, a vast majority of vulnerabilities and their corresponding security patches remain beyond public exposure, e.g., in the open source libraries that are heavily relied on by developers. As many of these patches exist in open sourced projects, the problem of curating and gathering security patches can be difficult due to their hidden nature. An extensive and complete security patches dataset could help end-users such as security companies, e.g., building a security knowledge base, or researcher, e.g., aiding in vulnerability research.

To efficiently curate security patches including undisclosed patches at large scale and low cost, we propose a deep neural-network-based approach built upon commits of open source repositories. First, we design and build security patch datasets that include 38,291 security-related commits and 1,045
Common Vulnerabilities and Exposures (CVE)
patches from four large-scale C programming language libraries. We manually verify each commit, among the 38,291 security-related commits, to determine if they are security related.

We devise and implement a deep learning-based security patch identification system that consists of two composite neural networks: one commit-message neural network that utilizes pretrained word representations learned from our commits dataset and one code-revision neural network that takes code before revision and after revision and learns the distinction on the statement level. Our system leverages the power of the two networks for Security Patch Identification. Evaluation results show that our system significantly outperforms SVM and K-fold stacking algorithms. The result on the combined dataset achieves as high as 87.93% F1-score and precision of 86.24%.
We deployed our pipeline and learned model in an industrial production environment to evaluate the generalization ability of our approach. The industrial dataset consists of 298,917 commits from 410 new libraries that range from a wide functionalities. Our experiment results and observation on the industrial dataset proved that our approach can identify security patches effectively among open sourced projects.