bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Quantitative Characterization of the Spatial Distribution of Brain Metastases from Breast Cancer and Respective Molecular Subtypes
Authors: Mahmoodifar Saeedeh , Pangal Dhiraj J. , Cardinal Tyler , Craig David , Simon Thomas , Tew Ben Yi , Yang Wensha , Chang Eric , Yu Min , Neman Josh , Mason Jeremy , Toga Arthur , Salhia Bodour , Zada Gabriel , Newton Paul K. 
Published: July 2022

1.AbstractBrain metastases (BM) remain a significant cause of morbidity and mortality in breast cancer (BC) patients. Specific factors promoting the process of BM and predilection for selected neuro-anatomical regions remain unknown, yet may have major implications for prevention or treatment. Anatomical spatial distributions of BM from BC suggest a predominance of metastases in the hindbrain and cerebellum. Systematic approaches to quantifying BM location or location-based analyses based on molecular subtypes, however, remain largely unavailable. We analyzed stereotactic Cartesian coordinates derived from 134 patients undergoing gamma-knife radiosurgery (GKRS) for treatment of 407 breast cancer BMs to quantitatively study BM spatial distribution along principal component axes and by intrinsic molecular subtype (ER,PR,Herceptin). We corroborated that BC BMs show a consistent propensity to arise posteriorly and caudally, and that Her2+ tumors are relatively more likely to arise medially rather than laterally. To compare the distributions among varying BC molecular subtypes, we used the notion of mutual information, which revealed that the ER-PR-Her2+ and ER-PR-Her2-subtypes showed the smallest amount of mutual information and were most molecularly distinct. Using kernel density estimators, we found a propensity for triple negative BC to arise in more superiorly or cranially situated BMs. BM location maps according to vascular and anatomical distributions using cartesian coordinates to aid in systematic classification of tumor locations were additionally developed. Further characterization of these patterns may have major impacts on treatment or management of cancer patients.SignificanceThe quantitative spatial distribution of breast cancer metastases to the brain, and the effects of breast cancer molecular subtype on distribution frequencies remain poorly understood. We present a novel and shareable workflow for characterizing and comparing spatial distributions of BM which may aid in identifying therapeutic or diagnostic targets and interactions with the tumor microenvironment.
Polygenic Risk Score Comparative Analyses Reveals Risk Disparity of Genetic Predisposition to Chronic Kidney Disease- A Multi Ancestry Approach
Authors: Sharma Varun , Sharma Indu , Gupta Love , Rastogi Garima , Sharma Anuka 
Published: July 2022

AbstractPolygenic Risk Score (PRS) models are used extensively to find the population/individual risk towards disease. These predictive scores are of great help as risk scores if predicted earlier the life of individual can be saved from the chronic/ complex diseases. In this empirical assessments study, the polygenic risk score was calculated in three different ancestries (SAS, EAS and African Americans) based on more than three hundred markers. The risk score we observed indicated that average population risk scores are varied but on cumulating the ancestries the average risk score increased ∼1.3 times than individual population average risk. The parameter which varies greatly while calculating the PRS is the ancestry; it should be prerequisite that individuals of same ancestry should be taken as a one population groups while calculating the scores.
Decisional Needs and Patient Treatment Preferences for Heart Failure Medications: Scoping Review Protocol
Authors: Turgeon Ricky D. , Barry Arden R. , MacDonald Blair 
Published: July 2022

AbstractIntroductionTreatment decisions regarding heart failure with reduced ejection fraction (HFrEF; ejection fraction ≤40%) pharmacotherapy are complex. Decision aids can bridge this knowledge-to-practice gap and improve the integration of patients’ preferences and values for patient-centered care. However, little is known about the preferences and decisional needs of patients regarding these medications. The objectives of this scoping review are to identify, map and synthesize the literature evaluating the decisional needs, treatment preferences and values of patients making decisions regarding HFrEF medications.Methods and AnalysisWe will search MEDLINE, Embase, CINAHL (inception-April 2022), bibliographies of included studies and relevant reviews, Web of Science ‘cited references’, cocites.com, clinicaltrials.gov, Epistemonikos, and the Ottawa Decision Aid Inventory, without language restriction. We will include qualitative, quantitative, and mixed-methods studies that describe patient and clinician decisional needs, or patient treatment preferences or values regarding HFrEF medications guided by the Ottawa Decision Support Framework, or decision aids to support HFrEF medication decisions. One author will perform all searches and upload results to Covidence. Two review authors will independently screen retrieved article titles and abstracts for inclusion, review full-text for final inclusion, and extract data from included articles and decision aids using a standardized data extraction form. We will present a graphical abstract mapping what is known about decisional needs and patient preferences and values, decisional support interventions, and decisional outcomes regarding HFrEF medications. We will also describe extracted data in narrative and tabular format to address the scoping review objectives, and discuss implications for practice and subsequent research in the field of shared decision-making for HFrEF.Ethics and DisseminationResearch ethics board approval is not required for this scoping review of published data. We will present the findings at relevant conferences, publish a peer-reviewed manuscript, and disseminate results via institutional and partner social media platforms.Strengths and limitations of this studyThis scoping review will systematically identify, map and synthesize the decisional needs, treatment preferences and values of patients regarding heart failure medication decisions.We have developed a comprehensive search strategy to identify qualitative, quantitative and mixed-methods studies (published and unpublished), as well as decision aids.The review will follow methodology outlined in the Joanna Briggs Institute Manual for Evidence Synthesis and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews reporting guidelines.The results of the scoping review will ultimately be limited by available studies; however, preliminary searches have identified several eligible studies.
Polymorphic Inverted Repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana
Authors: Arce Agustín L. , Mencia Regina , Cambiagno Damian A. , Lang Patricia L. , Liu Chang , Burbano Hernán A. , Weigel Detlef , Manavella Pablo A. 
Published: July 2022

AbstractTransposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable elements (TEs) can be activated during stress conditions and subsequently insert into gene-rich regions. TE-derived inverted repeats (IRs) are commonly found near plant genes, where they affect host gene expression with potentially positive effects on adaptation. However, the molecular mechanisms by which these IRs control gene expression is unclear in most cases. Here, we identify in the Arabidopsis thaliana genome hundreds of IRs located near genes that are transcribed by RNA Polymerase II, resulting in the production of 24-nt small RNAs that trigger methylation of the IRs. The expression of these IRs is associated with drastic changes in the local 3D chromatin organization, which alter the expression pattern of the hosting genes. Notably, the presence and structure of many IRs differ between A. thaliana accessions. Capture-C sequencing experiments revealed that such variation changes short-range chromatin interactions, which translates into changes in gene expression patterns. CRISPR/Cas9-mediated disruption of two of such IRs leads to a switch in genome topology and gene expression, with phenotypic consequences. Our data demonstrate that the insertion of an IR near a gene provides an anchor point for chromatin interactions that can profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.
Visual explanations for the detection of diabetic retinopathy from retinal fundus images
Authors: Boreiko Valentyn , Ilanchezian Indu , Seçkin Ayhan Murat , Müller Sarah , Koch Lisa M. , Faber Hanna , Berens Philipp , Hein Matthias 
Published: July 2022

AbstractIn medical image classification tasks like the detection of diabetic retinopathy from retinal fundus images, it is highly desirable to get visual explanations for the decisions of black-box deep neural networks (DNNs). However, gradient-based saliency methods often fail to highlight the diseased image regions reliably. On the other hand, adversarially robust models have more interpretable gradients than plain models but suffer typically from a significant drop in accuracy, which is unacceptable for clinical practice. Here, we show that one can get the best of both worlds by ensembling a plain and an adversarially robust model: maintaining high accuracy but having improved visual explanations. Also, our ensemble produces meaningful visual counterfactuals which are complementary to existing saliency-based techniques. Code is available under https://github.com/valentyn1boreiko/Fundus_VCEs.
Association between nursing home crowding and outbreak-associated respiratory infection and death prior to the COVID-19 pandemic between 2014 and 2019 in Ontario, Canada
Authors: Leece Pamela , Whelan Michael , Costa Andrew P. , Daneman Nick , Johnstone Jennie , McGeer Allison , Rochon Paula , Schwartz Kevin L. , Brown Kevin A. 
Published: July 2022

AbstractImportanceResident crowding in nursing homes is associated with larger SARS-CoV-2 outbreaks. However, this association has not been previously documented for non-SARS-CoV-2 respiratory infections.ObjectiveWe sought to measure the association between nursing home crowding and respiratory infections in Ontario nursing homes prior to the COVID-19 pandemic.Design, Setting, and ParticipantsWe conducted a retrospective cohort study of nursing home residents in Ontario, Canada over a five-year period prior to the COVID-19 pandemic, between September 2014 and August 2019.ExposureUsing administrative data, we estimated the crowding index equal to the mean number of residents per bedroom and bathroom (residents / [0.5*bedrooms+0.5*bathrooms]).OutcomesThe incidence of outbreak-associated infections and mortality per 100 nursing home residents per year. We also examined infection and mortality outcomes for outbreaks due to 7 specific pathogens: coronaviruses (OC43, 229E, NL63, HKU1), influenza A, influenza B, human metapneumovirus, parainfluenza virus, respiratory syncytial virus, rhinovirus/enterovirus.ResultsThere was one or more respiratory outbreak in 93.9% (588/626) nursing homes in Ontario. There were 4,921 outbreaks involving 64,829 cases of respiratory infection, and 1,969 deaths. Outbreaks attributable to a single identified pathogen were principally caused by influenza A (29%), rhinovirus (11.7%), influenza B (8.1%), and respiratory syncytial virus (6.1%). Among homes, 42.7% (251/588) homes had a high crowding index (≥ 2.0). After adjustment, more crowded homes had higher outbreak-associated respiratory infection incidence (aRR 1.89; 95% 1.64-2.18) and mortality incidence (aRR 2.28; 95% 1.84-2.84). More crowded homes had higher adjusted estimates of the incidence of infection and mortality for each of the 7 respiratory pathogens examined.Conclusions and RelevanceResidents of crowded nursing homes experienced more respiratory-outbreak infections and mortality due to influenza and other non-SARS-CoV-2 respiratory pathogens. Decreasing crowding in nursing homes is an important patient safety target beyond the COVID-19 pandemic.
Gaps and complex structurally variant loci in phased genome assemblies
Authors: Porubsky David , Vollger Mitchell R. , Harvey William T. , Rozanski Allison N. , Ebert Peter , Hickey Glenn , Hasenfeld Patrick , Sanders Ashley D. , Stober Catherine ,   The Human Pangenome Reference Consortium, Korbel Jan O. , Paten Benedict , Marschall Tobias , Eichler Evan E. 
Published: July 2022

ABSTRACTThere has been tremendous progress in the production of phased genome assemblies by combining long-read data with parental information or linking read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than ~140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 77 phased and assembled human genomes (154 unique haplotypes). We find that trio-based approaches using HiFi are the current gold standard although chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. We find two-thirds of defined contig ends cluster near the largest and most identical repeats [including segmental duplications (35.4%) or satellite DNA (22.3%) or to regions enriched in GA/AT rich DNA (27.4%)]. As a result, 1513 protein-coding genes overlap assembly gaps in at least one haplotype and 231 are recurrently disrupted or missing from five or more haplotypes. In addition, we estimate that 6-7 Mbp of DNA are incorrectly orientated per haplotype irrespective of whether trio-free or trio-based approaches are employed. 81% of such misorientations correspond tobona fidelarge inversion polymorphisms in the human species, most of which are flanked by large identical segmental duplications. In addition, we also identify large-scale alignment discontinuities consistent with an 11.9 Mbp deletion and 161.4 Mbp of insertion per human haploid genome. While 99% of this variation corresponds to satellite DNA, we identify 230 regions of the euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Although not completely resolved, these regions include copy number polymorphic and biomedically relevant genic regions where complete resolution and a pangenome representation will be most useful, yet most challenging, to realize.
Knowledge of calories and its influencing factors: evidence from a fast-growing developing country
Authors: Cheah Yong Kang , Lim Kuang Kuay , Ismail Hasimah , Salleh Ruhaya , Kee Chee Cheong , Lim Kuang Hock 
Published: July 2022

PurposeThis study examines sociodemographic and lifestyle factors associated with knowledge of calories.Design/methodology/approachData were analysed from the Komuniti Sihat Pembina Negara (KOSPEN) 2016. Logistic regressions were used to examine the effects of sociodemographic and lifestyle factors on knowledge of the definition of calories, recommended caloric intake and the effect of calories on body weight.FindingsThe results revealed that large proportions of respondents did not know the definition of calories (51.33%), recommended caloric intake (95.50%) and the effect of calories on body weight (64.89%). The proportions of respondents having knowledge of calories varied by income, gender, ethnicity, educational level, marital status, employment status, urbanization of states, smoking status and awareness of body mass index (BMI). Respondents were less likely to have knowledge of calories if they were low-income earners, non-Malays, less-educated, unemployed, smokers and unaware of their BMI.Practical implicationsSociodemographic and lifestyle factors play an important role in affecting knowledge of calories. Policymakers should make a concerted effort to improve knowledge of calories among adults with different sociodemographic backgrounds and lifestyle profiles.Originality/valueThis study provides several contributions to the literature: (1) The country of interest is Malaysia, where the prevalence of obesity is high and studies related to knowledge of calories are lacking. (2) In addition to knowledge of recommended caloric intake, knowledge of the definition of calories and the effect of calories on body weight factors are considered. (3) Apart from sociodemographic variables, smoking behaviour and awareness of BMI variables are included in the analyses.
Mobile banking service quality and customer value co-creation intention: a moderated mediated model
Authors: Hijazi Rawa 
Published: July 2022

PurposeThe objective of this paper is to explore the possible impact of mobile banking service quality (MBSQ) on customer value co-creation intention (CVCI).Design/methodology/approachA questionnaire was administered to research participants from Jordan. A total of 562 valid questionnaires were analysed. Mediation and moderation evaluations were performed in order to examine the function performed by MBSQ, customer engagement (CE), and social presence as determinants of CVCI. Structural equation modeling of type covariance-SEM using AMOS software was employed for the analysis.FindingsThe research results verify the proposition that MBSQ, CE, and social presence can all influence. In addition, the mediating role of customer engagement in respect of the relationship between MBSQ and CVCI is also confirmed in this research.Practical implicationsThis research is of use to bank managers who must allocate resources during the development of m-banking platforms, wherein value co-creation in banking can be promoted.Originality/valueThis study comprises an original contribution to current scholarship in the field of m-banking through its examination of the impact of customer engagement with m-banking. Moreover, this research augments current literature pertaining to the function of MBSQ in relation to CVCI as tempered by customer engagement and social presence.
Chaordic destination image formulation through gastronomy perspectives: evidence from Greece
Authors: Pappas Nikolaos , Michopoulou Eleni , Farmaki Anna , Leivadiotaki Emmanouela 
Published: July 2022

Purpose
This study aims to evaluate the complex behaviour of tourists in terms of the formulation of destination image related to its gastronomy. Through the examination of gastronomic image, memorability of experiences and food personality traits such as neophobia and neophilia, this research investigates the chaordic (chaos versus order) systems and provides specific pathways that formulate the gastronomic destination image.

Design/methodology/approach
Using fuzzy-set qualitative comparative analysis (fsQCA), this study examines the chaordic relations amongst memorable tourism experiences (MTEs), gastronomic neophobia and neophilia and gastronomic image upon the formulation of destination image. This study also includes two grouping variables (nationality [stratified], age).

Findings
Three sufficient configurations were revealed that can lead to the formulation of destination image, explaining the attributional gastronomic decision-making of holidaymakers. These solutions concern: food personality traits, generated experience and gastronomic image.

Research limitations/implications
In spite of the need for examining the complexity and the chaordic systems in the gastronomic domain, the lack of a sufficient number of studies using fsQCA hinders its full potential. The complete lack of gastronomic studies using this method highlights the necessity of its use for research in the respective field.

Originality/value
This study explores the complexity of how food-related personality traits influence the attainment of MTEs and the formulation of gastronomic image and how the chaordic systems influence the overall image of a destination.
Workplace ostracism and employee silence in service organizations: the moderating role of negative reciprocity beliefs
Authors: Yao Liu , Ayub Arslan , Ishaq Mustafa , Arif Sania , Fatima Tehreem , Sohail Hafiz M. 
Published: July 2022

PurposeEmployee silence is a pervasive workplace phenomenon that can cause severe economic losses to service organizations. Drawing on conservation of resource theory, the present research aims to investigate interpersonal antecedents of employee silence, specifically workplace ostracism while considering the moderating role of negative reciprocity beliefs (NRBs).Design/methodology/approachTwo-wave data collected from 355 employees working in service organizations in Pakistan supported the theorized model. The study used SmartPLS (v 3.2.7) to examine the measurement model and the structural model.FindingsAs projected, the authors found that workplace ostracism was positively related to acquiescence silence and defensive silence, but not related to prosocial silence. Besides, this study’s findings supported two-way interaction involving workplace ostracism and NRB on acquiescence silence and defensive silence, but not on prosocial silence. In particular, the presence of high NRB makes the adverse effects of workplace ostracism even worse.Originality/valueThis study explores the boundary conditions under which employee silence is more likely or less likely to occur. This just makes the current research all the more salient that why and when ostracized employees resort to remain silent in the workplace.
Resilience in healthcare supply chains: a review of the UK’s response to the COVID19 pandemic
Authors: Sawyerr Emmanuel , Harrison Christian 
Published: July 2022

PurposeThe purpose of this explorative research is to analyse the resilience of the United Kingdom's (UK) healthcare supply chains from a customer’s perspective in the light of the coronavirus pandemic.Design/methodology/approachUsing the capabilities of preparedness, robustness, recovery and adaptability as the foundational percept for supply chain resilience, 22 healthcare professionals in 17 of the UK's National Health Scheme (NHS) Trusts were interviewed to explore their personal and organisational approaches adopted relative to the provision of eye protection, gloves, gowns, aprons, masks and respirators. The Dynamic Capabilities View is mapped to the resilience capabilities and used to analyse the data from a transformational supply chain research perspective.FindingsThe supply chains were largely unprepared, which was not particularly surprising even though the availability of gloves was significantly better compared to the other personal protective equipment (PPE). Techniques adopted to ensure robustness and recovery revealed the use of unsanctioned methods such as extended use of PPE beyond recommended use, redefinition of guidelines, protocols and procedures by infection control and the use of expired PPE – all of which compromised customer well-being.Research limitations/implicationsAs the paper views resilience through the lens of customers, it does not provide the perspectives of the supply chain practitioners as to the reasons for the findings and the challenges within these supply chains.Practical implicationsThe compromise of the well-being of healthcare workers due to the vulnerabilities of healthcare supply chains is highlighted to managers and prescriptions for post-disruption adaptability are made.Originality/valueThis paper introduces transformative research to supply chain resilience research by uniquely looking at resilience from the customers' well-being perspective.