bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the genomic region under epigenetic regulation during non‐alcoholic fatty liver disease progression
Authors: Hotta Kikuko , Kitamoto Takuya , Kitamoto Aya , Ogawa Yuji , Honda Yasushi , Kessoku Takaomi , Yoneda Masato , Imajo Kento , Tomeno Wataru , Saito Satoru , Nakajima Atsushi 
Published: October 2017

AimThe progression of non‐alcoholic fatty liver disease (NAFLD) is affected by epigenetics. We undertook co‐methylation and differentially methylated region (DMR) analyses to identify the genomic region that is under epigenetic regulation during NAFLD progression.MethodsWe collected liver biopsy specimens from 60 Japanese patients with NAFLD and classified these into mild (fibrosis stages 0–2) or advanced (fibrosis stages 3–4) NAFLD. We carried out a genome‐wide DNA methylation analysis and identified the differentially methylated CpGs between mild and advanced NAFLD. Differentially methylated regions with multiple consecutive differentially methylated CpGs between mild and advanced NAFLD were extracted.ResultsCo‐methylation analysis showed that individual differentially methylated CpG sites were clustered into three modules. The CpG sites clustered in one module were hypomethylated in advanced NAFLD and their annotated genes were enriched for “immune system” function. The CpG sites in another module were hypermethylated and their annotated genes were enriched for “mitochondria” or “lipid particle”, and “lipid metabolism” or “oxidoreductase activity”. Hypomethylated DMRs included tumorigenesis‐related genes (FGFR2, PTGFRN, and ZBTB38), the expressions of which are upregulated in advanced NAFLD. Tumor suppressor MGMT had two DMRs and was downregulated. Conversely, FBLIM1 and CYR61, encoding proteins that reduce cell proliferation, showed hypomethylated DMRs and were upregulated. Expression of the antioxidant gene NQO1 was upregulated, with a hypomethylated DMR. The DMR containing cancer‐related MIR21 was hypomethylated in advanced NAFLD.ConclusionsCo‐methylation and DMR analyses suggest that the NAFLD liver undergoes mitochondrial dysfunction, decreased lipid metabolism, and impaired oxidoreductase activity, and acquires tumorigenic potential at the epigenetic level.
Personal Lending Relationships
Authors: KAROLYI STEPHEN ADAM 
Published: October 2017

ABSTRACTI identify the effects of personal relationships on loan contracting using executive deaths and retirements at other firms as a source of exogenous variation in executive turnover. After plausibly exogenous turnover, borrowers choose lenders with which their new executives have personal relationships 4.1 times as frequently, and loans from these lenders have 20 basis points lower spreads and 12.5% larger amounts. Personal relationships benefit firms across loan terms, especially during macroeconomic downturns. Increased financial flexibility from personal relationships insulated firms from financial shocks during the recent financial crisis: they exhibited less constrained investment and were less likely to layoff employees.
APETALA 2‐domain‐containing transcription factors: focusing on abscisic acid and gibberellins antagonism
Authors: Shu Kai , Zhou Wenguan , Yang Wenyu 
Published: October 2017

SummaryThe phytohormones abscisic acid (ABA) and gibberellin (GA) antagonistically mediate diverse plant developmental processes including seed dormancy and germination, root development, and flowering time control, and thus the optimal balance between ABA and GA is essential for plant growth and development. Although more than a half and one century have passed since the initial discoveries of ABA and GA, respectively, the precise mechanisms underlying ABA–GA antagonism still need further investigation. Emerging evidence indicates that two APETALA 2 (AP2)‐domain‐containing transcription factors (ATFs), ABI4 in Arabidopsis and OsAP2‐39 in rice, play key roles in ABA and GA antagonism. These two transcription factors precisely regulate the transcription pattern of ABA and GA biosynthesis or inactivation genes, mediating ABA and GA levels. In this Viewpoint article, we try to shed light on the effects of ATFs on ABA–GA antagonism, and summarize the overlapping but distinct biological functions of these ATFs in the antagonism between ABA and GA. Finally, we strongly propose that further research is needed into the detailed roles of additional numerous ATFs in ABA and GA crosstalk, which will improve our understanding of the antagonism between these two phytohormones.
Perceptions of Risk and Vulnerability Following Exposure to a Major Natural Disaster: The Calgary Flood of 2013
Authors: Tanner Alexa , Árvai Joseph 
Published: October 2017

AbstractMany studies have examined the general public's flood risk perceptions in the aftermath of local and regional flooding. However, relatively few studies have focused on large‐scale events that affect tens of thousands of people within an urban center. Similarly, in spite of previous research on flood risks, unresolved questions persist regarding the variables that might influence perceptions of risk and vulnerability, along with management preferences. In light of the opportunities presented by these knowledge gaps, the research reported here examined public perceptions of flood risk and vulnerability, and management preferences, within the city of Calgary in the aftermath of extensive flooding in 2013. Our findings, which come from an online survey of residents, reveal that direct experience with flooding is not a differentiating factor for risk perceptions when comparing evacuees with nonevacuees who might all experience future risks. However, we do find that judgments about vulnerability—as a function of how people perceive physical distance—do differ according to one's evacuation experience. Our results also indicate that concern about climate change is an important predictor of flood risk perceptions, as is trust in government risk managers. In terms of mitigation preferences, our results reveal differences in support for large infrastructure projects based on whether respondents feel they might actually benefit from them.
A Swedish national adoption study of risk of irritable bowel syndrome (IBS)
Authors: Waehrens Rasmus , Zöller Bengt , Sundquist Jan , Sundquist Kristina , Pirouzifard MirNabi 
Published: October 2017

ObjectivesIrritable bowel syndrome (IBS) clusters in families, but the familial risk of IBS has not been determined in adoptees. Studying adoptees and their biological and adoptive parents is a strong study design for separating genetic from environmental causes of familial clustering. This nationwide study aimed to separate the biological (genetic) and familial environmental contribution to the familial transmission of IBS.MethodsWe performed a family study for Swedish-born adoptees born from 1951 until 1995, and their biological and adoptive parents. The Swedish Multigeneration Register was linked to the Hospital Register (inpatients and outpatients) for the period 1964–2012 and the Swedish Outpatient Care Register for 2001–2012, and the Swedish Primary Healthcare register for 1989–2012. ORs for IBS were calculated for adoptees with an affected biological parent with IBS compared with adoptees without a biological parent with IBS. The OR for IBS was also determined in adoptees with an adoptive parent with IBS compared with adoptees without an adoptive parent with IBS. Heritabilityh2(±SE) was also determined.ResultsThe ORs for IBS were 1.67 in adoptees (95% CI 1.06 to 2.62) of biological parents diagnosed with IBS. The ORs for IBS were 0.88 in adoptees (95% CI 0.48 to 1.63) of adoptive parents diagnosed with IBS. The heritability was 19.5%±8.5%.ConclusionsThe present study indicates that biological (genetic) factors are important for the familial clustering of IBS. The heritability calculated is in the range from twin studies and suggests that heritability may be estimated in adoptees.
The effects of a household conditional cash transfer programme on coverage and quality of antenatal care: a secondary analysis of Indonesia’s pilot programme
Authors: Triyana Margaret , Shankar Anuraj H 
Published: October 2017

ObjectiveTo analyse the effectiveness of a household conditional cash transfer programme (CCT) on antenatal care (ANC) coverage reported by women and ANC quality reported by midwives.DesignThe CCT was piloted as a cluster randomised control trial in 2007. Intent-to-treat parameters were estimated using linear regression and logistic regression.SettingSecondary analysis of the longitudinal CCT impact evaluation survey, conducted in 2007 and 2009. This included 6869 pregnancies and 1407 midwives in 180 control subdistricts and 180 treated subdistricts in Indonesia.Outcome measuresANC component coverage index, a composite measure of each ANC service component as self-reported by women, and ANC provider quality index, a composite measure of ANC service provided as self-reported by midwives. Each index was created by principal component analysis (PCA). Specific ANC component items were also assessed.ResultsThe CCT was associated with improved ANC component coverage index by 0.07 SD (95% CI 0.002 to 0.141). Women were more likely to receive the following assessments: weight (OR 1.56 (95% CI 1.25 to 1.95)), height (OR 1.41 (95% CI 1.247 to 1.947)), blood pressure (OR 1.36 (95% CI 1.045 to 1.761)), fundal height measurements (OR 1.65 (95% CI 1.372 to 1.992)), fetal heart beat monitoring (OR 1.29 (95% CI 1.006 to 1.653)), external pelvic examination (OR 1.28 (95% CI 1.086 to 1.505)), iron-folic acid pills (OR 1.42 (95% CI 1.081 to 1.859)) and information on pregnancy complications (OR 2.09 (95% CI 1.724 to 2.551)). On the supply side, the CCT had no significant effect on the ANC provider quality index based on reports from midwives.ConclusionsThe CCT programme improved ANC coverage for women, but midwives did not improve ANC quality. The results suggest that enhanced ANC utilisation may not be sufficient to improve health outcomes, and steps to improve ANC quality are essential for programme impact.
Effects of advanced life support versus basic life support on the mortality rates of patients with trauma in prehospital settings: a study protocol for a systematic review and meta-analysis
Authors: Kondo Yutaka , Fukuda Tatsuma , Uchimido Ryo , Hifumi Toru , Hayashida Kei 
Published: October 2017

IntroductionAdvanced life support (ALS) is thought to be associated with improved survival in prehospital trauma care when compared with basic life support (BLS). However, evidence on the benefits of prehospital ALS for patients with trauma is controversial. Therefore, we aim to clarify if ALS improves mortality in patients with trauma when compared with BLS by conducting a systematic review and meta-analysis of the recent literature.Methods and analysisWe will perform searches in PubMed, Embase and the Cochrane Central Register of Controlled Trials for published observational studies, controlled before-and-after studies, randomised controlled trials and other controlled trials conducted in humans and published until March 2017. We will screen search results, assess study selection, extract data and assess the risk of bias in duplicate; disagreements will be resolved through discussions. Data from clinically homogeneous studies will be pooled using a random-effects meta-analysis, heterogeneity of effects will be assessed using the χ2test of homogeneity, and any observed heterogeneity will be quantified using the I2statistic. Last, the Grading of Recommendations Assessment, Development and Evaluation approach will be used to rate the quality of the evidence.Ethics and disseminationOur study does not require ethical approval as it is based on findings of previously published articles. Results will be disseminated through publication in a peer-reviewed journal, presentations at relevant conferences and publications for patient information.Trial registration numberPROSPERO (International Prospective Register of Systematic Reviews) registration number CRD42017054389.
Reaching consensus on reporting patient and public involvement (PPI) in research: methods and lessons learned from the development of reporting guidelines
Authors: Brett Jo , Staniszewska Sophie , Simera Iveta , Seers Kate , Mockford Carole , Goodlad Susan , Altman Doug , Moher David , Barber Rosemary , Denegri Simon , Entwistle Andrew Robert , Littlejohns Peter , Morris Christopher , Suleman Rashida , Thomas Victoria , Tysall Colin 
Published: October 2017

IntroductionPatient and public involvement (PPI) is inconsistently reported in health and social care research. Improving the quality of how PPI is reported is critical in developing a higher quality evidence base to gain a better insight into the methods and impact of PPI. This paper describes the methods used to develop and gain consensus on guidelines for reporting PPI in research studies (updated version of the Guidance for Reporting Patient and Public Involvement (GRIPP2)).MethodsThere were three key stages in the development of GRIPP2: identification of key items for the guideline from systematic review evidence of the impact of PPI on health research and health services, a three-phase online Delphi survey with a diverse sample of experts in PPI to gain consensus on included items and a face-to-face consensus meeting to finalise and reach definitive agreement on GRIPP2. Challenges and lessons learnt during the development of the reporting guidelines are reported.DiscussionThe process of reaching consensus is vital within the development of guidelines and policy directions, although debate around how best to reach consensus is still needed. This paper discusses the critical stages of consensus development as applied to the development of consensus for GRIPP2 and discusses the benefits and challenges of consensus development.
Key factors of case management interventions for frequent users of healthcare services: a thematic analysis review
Authors: Hudon Catherine , Chouinard Maud-Christine , Lambert Mireille , Diadiou Fatoumata , Bouliane Danielle , Beaudin Jérémie 
Published: October 2017

ObjectiveThe aim of this paper was to identify the key factors of case management (CM) interventions among frequent users of healthcare services found in empirical studies of effectiveness.DesignThematic analysis review of CM studies.MethodsWe built on a previously published review that aimed to report the effectiveness of CM interventions for frequent users of healthcare services, using the Medline, Scopus and CINAHL databases covering the January 2004–December 2015 period, then updated to July 2017, with the keywords ‘CM’ and ‘frequent use’. We extracted factors of successful (n=7) and unsuccessful (n=6) CM interventions and conducted a mixed thematic analysis to synthesise findings. Chaudoir’s implementation of health innovations framework was used to organise results into four broad levels of factors: (1) ,environmental/organisational level, (2) practitioner level, (3) patient level and (4) programme level.ResultsAccess to, and close partnerships with, healthcare providers and community services resources were key factors of successful CM interventions that should target patients with the greatest needs and promote frequent contacts with the healthcare team. The selection and training of the case manager was also an important factor to foster patient engagement in CM. Coordination of care, self-management support and assistance with care navigation were key CM activities. The main issues reported by unsuccessful CM interventions were problems with case finding or lack of care integration.ConclusionsCM interventions for frequent users of healthcare services should ensure adequate case finding processes, rigorous selection and training of the case manager, sufficient intensity of the intervention, as well as good care integration among all partners. Other studies could further evaluate the influence of contextual factors on intervention impacts.
The STROBE extensions: protocol for a qualitative assessment of content and a survey of endorsement
Authors: Sharp Melissa K , Utrobičić Ana , Gómez Guadalupe , Cobo Erik , Wager Elizabeth , Hren Darko 
Published: October 2017

IntroductionThe STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) Statement was developed in response to inadequate reporting of observational studies. In recent years, several extensions to STROBE have been created to provide more nuanced field-specific guidance for authors. The content and the prevalence of extension endorsement have not yet been assessed. Accordingly, there are two aims: (1) to classify changes made in the extensions to identify strengths and weaknesses of the original STROBE checklist and (2) to determine the prevalence and typology of endorsement by journals in fields related to extensions.Methods and analysisTwo independent researchers will assess additions in each extension. Additions will be coded as ‘field specific’ (FS) or ‘not field specific’ (NFS). FS is defined as particularly relevant information for a single field and guidance provided generally cannot be extrapolated beyond that field. NFS is defined as information that reflects epidemiological or methodological tenets and can be generalised to most, if not all, types of observational research studies. Intraclass correlation will be calculated to measure reviewers’ concordance. On disagreement, consensus will be sought. Individual additions will be grouped by STROBE checklist items to identify the frequency and distribution of changes.Journals in fields related to extensions will be identified through National Library of Medicine PubMed Broad Subject Terms, screened for eligibility and further distilled via Ovid MEDLINE® search strategies for observational studies. Text describing endorsement will be extracted from each journal’s website. A classification scheme will be created for endorsement types and the prevalence of endorsement will be estimated. Analyses will use NVivo V.11 and SAS University Edition.Ethics and disseminationThis study does not require ethical approval as it does not involve human participants. This study has been preregistered on Open Science Framework.
Social-media-enabled learning in emergency medicine: a case study of the growth, engagement and impact of a free open access medical education blog
Authors: Carley Simon , Beardsell Iain , May Natalie , Crowe Liz , Baombe Janos , Grayson Alan , Carden Richard , Liebig Ashley , Gray Chris , Fisher Ross , Horner Daniel , Howard Laura , Body Richard 
Published: October 2017

AbstractBackgroundClinicians are increasingly using social media for professional development and education. In 2012, we developed the St.Emlyn’s blog, an open access resource dedicated to providing free education in the field of emergency medicine.ObjectiveTo describe the development and growth of this international emergency medicine blog.MethodWe present a narrative description of the development of St.Emlyn’s blog. Data on scope, impact and engagement were extracted from WordPress, Twitter and Google Analytics.ResultsThe St.Emlyn’s blog demonstrates a sustained growth in size and user engagement. Since inception in 2012, the site has been viewed over 1.25 million times with a linear year-on-year growth. We have published over 500 blog posts, each of which attracts a mean of 2466 views (range 382–69 671). The site has been viewed in nearly every country in the world, although the majority (&gt;75%) of visitors come from the USA, UK and Australia.SummaryThis case study of an emergency medicine blog quantifies the reach and engagement of social-media-enabled learning in emergency medicine.
Evaluation of the diversity of garden potato varieties grown in Canada using simple sequence repeat and morphology
Authors: Côté Marie-José , Leduc Lisa , Mecteau Mélanie , Yu Trevor , Guillemette Eliane , Fraser Nicole 
Published: October 2017

Garden potato varieties grown on more than 1.5 ha are subject to variety registration to be sold as seed potato in Canada. Prerequisites for the registration of varieties include the pedigree and breeding history as well as a morphological description. For most varieties, no pedigree or morphological description is available, and furthermore, some groups are essentially derived from one another. Therefore, a review to determine the genetic and morphological similarities and uniqueness of some of the garden potato varieties was initiated. Seven garden potato varieties grown over the largest areas in Canada were genotyped using a set of nine microsatellite [simple sequence repeat (SSR)] markers, resulting in six distinct SSR profiles. These varieties were also grown out for morphological description, providing supplementary information for the national registration and their monitoring during the seed certification process. To further assess the genetic similarities of garden or heritage varieties, 84 potato varieties were genotyped, and the unique SSR profiles of 62 varieties and six SSR profiles shared among the other 22 varieties were added to the Canadian Food Inspection Agency potato variety reference SSR profile collection. Furthermore, a set of blue varieties were described morphologically to evaluate the nature of morphological characteristic variation of varieties sharing the same SSR profile. Although all 14 varieties grown show some morphological differences, all varieties within each group sharing an SSR profile also clustered together based on morphological characteristics.
Single and sequential applications of dicamba for the control of glyphosate-resistant common ragweed in glyphosate- and dicamba-resistant soybean
Authors: Byker Holly P. , Van Wely Annemarie C. , Soltani Nadar , Lawton Mark B. , Robinson Darren E. , Sikkema Peter H. 
Published: October 2017

Confirmation of glyphosate-resistant (GR) weeds in southwestern Ontario has led to a change in weed management practices, particularly in soybean. Registered soil-applied herbicides have been identified that have activity on GR common ragweed; however, due to the long emergence period of common ragweed, additional postemergence options are required. The recent development of glyphosate- and dicamba-resistant soybean (Roundup Ready Xtend soybean) allows for the preplant and postemergence application of dicamba. Three field studies were conducted in Ontario, Canada, in a field with confirmed GR common ragweed. Glyphosate-resistant common ragweed interference resulted in 75% yield loss in soybean compared with the weed-free check. At 4 wk after application, dicamba tank-mixed with glyphosate applied preplant only, postemergence only, or preplant followed by postemergence controlled GR common ragweed up to 94%, 87%, and 99%, respectively. The availability of dicamba for use in glyphosate- and dicamba-resistant soybean will provide an additional mode of action for weed management in soybean.
Test Focus Selection for Integration Testing
Authors: Banitaan Shadi , Nygard Kendall E. , Magel Kenneth 
Published: October 2017

Object-oriented software systems contain large number of modules which make unit testing, integration testing, and system testing very difficult and challenging. While the aim of unit testing is to show that individual modules are working properly and the aim of the system testing is to determine whether the whole system meets its specifications, the aim of integration testing is to uncover errors in the interactions between system modules. However, it is generally impossible to test all connections between modules because of time and budget constraints. Thus, it is important to focus the testing on the connections presumed to be more error-prone. The goal of this work is to guide software testers where in a software system to focus when performing integration testing to save time and resources. This paper proposes a new approach to predict and rank error-prone connections. We use method level metrics that capture both dependencies and internal complexity of methods. We performed experiments on several Java applications and used error seeding techniques for evaluation. The experimental results showed that our approach is effective for selecting the test focus in integration testing.