bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shiny-Seq: advanced guided transcriptome analysis
Authors: Sundararajan Zenitha , Knoll Rainer , Hombach Peter , Becker Matthias , Schultze Joachim L. , Ulas Thomas 
Published: June 2019

Abstract
Objective

Over the last years, Next Generation Sequencing has generated huge amounts of gene expression data supporting research to answer biological and medical questions. While several tools and advanced guided analysis pipelines were designed for this purpose, some require programming skills and others lack the support for many important features that enable more comprehensive data analysis.

Results

We present the tool Shiny-Seq. It has many new features such as batch effect evaluation and removal, quality check with several visualization options, enrichment analysis with multiple biological databases, identification of patterns using advanced methods such as weighted gene co-expression network analysis, summarizing analysis as power point presentation and all results as tables via one click feature. The source code is published on GitHub (https://github.com/schultzelab/Shiny-Seq) with the code licensed under GPLv3. Shiny-Seq is written in R using the Shiny framework. In addition, the application is hosted on a public website hosted by shinyapps.io server (https://schultzelab.shinyapps.io/Shiny-Seq/) and as a Docker image https://hub.docker.com/r/makaho/shiny-seq.
Applying person-centred care to support trial recruitment and retention in a randomised trial for patients with refractory breathlessness and advanced disease: a qualitative study.
Authors: Lovell Natasha , Etkind Simon N , Bajwah Sabrina , Maddocks Matthew , Higginson Irene J 
Published: June 2019

Abstract
Background
Recruitment and retention in clinical trials remains an important challenge, particularly in the context of advanced illness. It is important to understand what affects retention to improve trial quality, minimise attrition and reduce missing data. Person centred care (PCC) has been shown to improve patient outcomes in advanced disease or complex needs. Therefore, we considered whether the same principles could be applied to clinical trials. This study aimed to explore what influenced participants to take part and remain in a feasibility trial of mirtazapine for chronic breathlessness.

Methods
Qualitative study embedded within a double blind randomised trial. Participants with cancer, Chronic Obstructive Pulmonary Disease (COPD), Interstitial Lung Disease (ILD), or Chronic Heart Failure (CHF), with a Modified Medical Research Council Dyspnoea Scale grade 3/4 were recruited from three UK sites. A purposive subsample completed qualitative interviews after the trial. Interviews were analysed using thematic analysis. Results were interpreted in relation to the core elements of PCC.

Results
22 participants were interviewed. 11 had a diagnosis of COPD, 8 ILD, 2 CHF, and 1 lung cancer. Median age was 71 years (56-84). 16 were male. 20 had completed the trial, 2 withdrew due to adverse effects. Three main themes were identified as important for recruitment and retention; the relationship between patient and professional, the context, and potential benefit to self and others. Within ‘relationships’ the personal attributes of the researcher, and continuity of research team were identified as particularly important when considering why people remained in the trial. We interpreted results in relation to PCC and developed a model of the person centred trial.

Conclusions
We propose that a PCC approach can improve recruitment and retention in clinical trials. The importance of the relationship between the patient and professional, and continuity within the research team has implications for future funding of clinical trials, the focus of which is often based on monthly recruitment targets and not on retention. Future work should aim to evaluate this model across other settings and in countries outside of the United Kingdom.

Trial registration
Registry name: ISRCTN
Registration number: ISRCTN32236160
Date of registration: 13/06/2016
Association of lifestyle factors with blood lipids and inflammation in adults aged 40 years and above: a population-based cross-sectional study in Taiwan
Authors: Muga Miriam Adoyo , Owili Patrick Opiyo , Hsu Chien-Yeh , Chao Jane C-J 
Published: June 2019

Abstract
Background

Lifestyle factors were associated with an increased risk of cardiovascular disease (CVD) occurrence. We explored the associations between lifestyle factors and CVD risk factors, and assessed the interactive effects of lifestyle factors on CVD risk factors.

Methods

A cross-sectional data of 114,082 (57,680 men and 56,402 women) middle-aged adults and elderly in Taiwan were collected from 2001 to 2010. Logistic regression analysis was used to assess the associations between lifestyle factors and CVD risk factors. The relative excess risk due to interaction (RERI) and the attributable proportion due to interaction were used to explore the interactive effect of lifestyle factors on CVD risk factors.

Results

The interaction between alcohol consumption and smoking exhibited an excess risk of high triglycerides (RERI = 0.21; 95% CI: 0.14 – 0.29), and that of alcohol consumption and physical activity had an excess risk of high LDL-cholesterol (RERI = 0.11; 95% CI: 0.06 – 0.16) and high blood glucose (RERI = 0.05; 95% CI: 0.01 – 0.11). Alcohol consumption and vegetable-rich diet (intake of high vegetables with no or low meat) had an excess risk of high LDL-cholesterol and low HDL-cholesterol, but a reduced risk of high triglycerides (RERI = -0.10; 95% CI: -0.17 – -0.04). Smoking and physical activity had an increased risk of high blood glucose and a reduced risk of low HDL-cholesterol. Smoking and vegetable-rich diet reduced the risk of high triglycerides (RERI = -0.11; 95% CI: -0.18 – -0.04), high blood glucose (RERI = -0.14; 95% CI: -0.21 – -0.07) and low HDL-cholesterol (RERI = -0.10; 95% CI: -0.19 – -0.01).

Conclusions

The interaction between smoking, alcohol consumption, physical activity and diet were associated with lipid profile and blood glucose, hence there was an interaction between these lifestyle factors in an additive scale. Public health promotion should therefore consider multifaceted promotional activities that are likely to make a positive impact on the health status of the Taiwanese population.
An outbreak of norovirus-related acute gastroenteritis associated with delivery food in Guangzhou, southern China
Authors: Lu Ying , Ma Mengmeng , Wang Hui , Wang Dahu , Chen Chun , Jing Qinlong , Geng Jinmei , Li Tiegang , Zhang Zhoubin , Yang Zhicong 
Published: June 2019

Abstract
Objectives
Large numbers of students at a school located in Guangzhou city developed a sudden onset of symptoms of diarrhea and vomiting. In order to control the outbreak, an epidemiological investigation was conducted to determine the pathogen, sources of infection, route of transmission and risk factors.
Methods
The study population consisted of probable cases and confirmed cases. An active search was conducted for cases among all students, teachers and other staff members. A case control study was carried out using online standardised questionnaires. Data were obtained regarding demographic characteristics, gastrointestinal symptoms, personal hygiene habits, history of contact with a person with diarrhea and/or vomiting and dining place in the past 3 days. Rectal swabs or stool specimens of the cases, food handlers and environmental smear swab samples were collected to detect potential intestinal viruses and bacteria. Odds ratios (ORs) and 95% confidence intervals were calculated.
Results
A total of 157 cases fit the definition of the probable case, including 46 cases of laboratory-confirmed norovirus infection between March 8 and March 22, 2018. The proportion of the students who had eaten delivery food three days before the onset of disease in the case group was 2.69 times that in the control group (95%CI: 1.88-3.85). Intake of take-out food three days before, exposure to similar cases 72 hours before onset and case in the same dormitory were risk factors. A total of 20 rectal swabs samples from students, 10 rectal swabs from food handlers and 2 environmental swabs samples of out-campus restaurant were tested positive for norovirus (GⅡ).
Conclusions
The outbreak of norovirus infectious diarrhea was determined. Food handling practices carries potential risk of acute gastroenteritis outbreaks due to a lack of surveillance and supervision. More attention should be paid to the monitoring and supervision of food handlers to reduce the incidence of norovirus-related acute gastroenteritis associated with delivery food.
The intersection of developmental vulnerability and socioeconomic disadvantage on access to health care for preschool aged children: evidence for the inverse-care law
Authors: Woolfenden Sue , Galea Claire , Badland Hannah , Smithers-Sheedy Hayley , Williams Katrina , Kavanagh Anne , Reddihough Dinah , Goldfeld Sharon , Lingam Raghu , Badawi Nadia , O'Connor Meredith 
Published: June 2019

Abstract
Aim. Children who are developmentally vulnerable have greater health needs. Socioeconomic disadvantage not only increases this risk of developmental vulnerability but can be associated with less access to health services. Our aim was to compare health services use in children aged 4-5 years in Australia with and without developmentally vulnerability and consider the intersection of socioeconomic disadvantage on this relationship.
Method. Cross sectional data were collected from Wave 3 of the Longitudinal Study of Australian Children birth cohort when the children were aged 4-5 years. A composite variable for developmental vulnerability was designed by combining those children who were in the lowest 15% in the physical, socioemotional and/or learning outcome indices. Children were then subgrouped according to developmental vulnerability and disadvantage based on socioeconomic position (SEP) quintile (derived from parental education, occupation, household income). We defined SEP 1 the lowest quintile as ‘disadvantaged’ and SEP quintiles 2-5 as ‘not disadvantaged’. Multivariate regression was used to examine the intersection between health service use and developmental vulnerability and disadvantage using these composite variables.
Results The total number of children with information on developmental vulnerability in Wave 3 was 3967 (90% of the sample). A total of 1292 (32.6%) children were classified as developmentally vulnerable. 30.6% of children who were developmentally vulnerable came from families who were disadvantaged. Overall children who were developmentally vulnerable were reported to use more specialist/hospital health services than those who were not developmentally vulnerable (10-25 % vs 5-16%). Children who were developmentally vulnerable and not disadvantaged were 1.4-2.0 times more likely to have reported using a GP, paediatrician, other specialist, and Emergency Department compared with children who were developmentally vulnerable and disadvantaged.
Conclusion Preschool children who are developmentally vulnerable have a higher reported use of specialist and hospital services compared with those who are not developmentally vulnerable. There is evidence of an inverse care law; those who were not disadvantaged with and without developmental vulnerability are more likely to use health services compared with their counterparts who were disadvantaged.
Risk Stratification for Renal Ultrasonography in the Evaluation of Acute Kidney Injury
Authors: Tummalapalli Sri Lekha , Zech John , Cho Hyung J. , Goetz Celine 
Published: June 2019

Abstract
Abstract
Background
Renal ultrasounds (RUS) are commonly ordered in hospitalized patients with acute kidney injury (AKI), however clinical risk prediction could be used to inform which patients require imaging to rule out hydronephrosis. While risk stratification frameworks have been described, the role of nephrology consultation as an additional driver of RUS ordering has not been comprehensively studied.
Methods
We performed a cross-sectional study of hospitalized adults at a large, tertiary, academic medical center with AKI who had a RUS ordered. Predictors were high-risk, medium-risk, or low-risk category based on an existing risk stratification framework and RUS recommended by a consulting nephrology service. Outcomes were presence of unilateral or bilateral hydronephrosis and incidental findings on RUS.
Results
Two hundred and eighty-one patients were included in the study cohort; 111 (40%), 76 (27%), and 94 (33%) patients were in the high-, medium-, and low-risk groups for hydronephrosis, respectively, based on the risk stratification framework. Thirty-five patients (12%) were found to have hydronephrosis, of whom 86% were captured in the high-risk group. A nephrology consult was involved in 168 (60%) patients and RUS was recommended by the nephrology service in 95 (57%) cases. Of the 95 patients recommended for a RUS, 9 patients (9%) had hydronephrosis. Among the patients with a nephrology consultation, 9 (56%) of the 16 total patients with hydronephrosis were recommended to obtain a RUS.
Conclusions
We further validated a risk stratification framework for hydronephrosis and found that nephrology consultation was an additional driver of RUS ordering, but predicted hydronephrosis less well than the risk stratification framework. Our decision framework strengthens the argument for the use of risk stratification to improve upon consultant recommendations, reduce incidental findings, and decrease RUS overuse.
Identification of novel alternative splicing isoform biomarkers and their association with overall survival in colorectal cancer
Authors: Jia Hongtao , Wang Aili , Lian Haifeng , Shen Yuanyuan , Wang Qian , Zhou Zhenru , Zhang Ranran , Li Kun , Liu Chengxia 
Published: June 2019

Abstract
Alternative splicing is an important mechanism of regulating eukaryotic gene expression. Understanding the most common alternative splicing events in colorectal cancer (CRC) will help developing diagnostic, prognostic or therapeutic tools in CRC. Publicly available RNA-seq data of 31 pairs of CRC and normal tissues and 18 pairs of metastatic and normal tissues were used to identify alternative splicing events using PSI and DEXSeq methods. The highly significant splicing events were used to search a database of The Cancer Genome Atlas (TCGA). We identified alternative splicing events in 10 genes marking the signature of CRC (more inclusion of CLK1-E4, COL6A3-E6, CD44v8-10, alternative first exon regulation of ARHGEF9, CHEK1, HKDC1 and HNF4A) or metastasis (decrease of SERPINA1-E1a, CALD-E5b, E6 and FBLN2-E9). Except for CHEK1, all other 9 splicing events were confirmed by TCGA data with 382 CRC tumors and 52 normal controls. Two splicing events (COL6A3 and HKDC1) were found to be significantly associated with patient overall survival. The alternative splicing signatures of the 10 genes are highly consistent with previous reports and/or relevant to cancer biology. The significant association of higher expression of the COL6A3 E5-E6 junction and HKDC1 E1-E2 with better overall survival was firstly reported. This study might be of significant value in the future biomarker, prognosis marker and therapeutics development of CRC.
What Anthropological Reflexivity Is/Was All About? A Methodological Formalization
Authors: Milenković Miloš 
Published: June 2019

In this study, I suggest that reflexivity in anthropology can be viewed as a coordinative definition that helped anthropology survive its three crises – the crisis of ethnographic representation, the crisis of scientific realism, and the crisis of anthropological authority. In addition, reflexivity, in a specific sense, can be taken as a substitute for experiment, a subsititute even better than com­parative studies, and can thus help fulfill the long dream of consolidating an­thropology on firm scientific grounds (a dream I believe is, though, no longer necessary).
This text should be understood as a part of a series of studies that strive towards the methodological formalization of supposedly formalization-resis­tant concepts of postmodern anthropology. In reality, reflexive anthropology became postmodern science only by admitting to be experimental art, but the question is who would understand and, more importantly, finance and apply this concept? The incorporation of reflexivity into the core of anthropology enabled it to finally achieve the status of science, in the most conservative and general methodological sense. Therefore, the anti-postmodern frustration pre­sent in some relatively recent debates, examples of which we can see in this volume, is neither methodologically nor pragmatically founded. Reflexivity can only be useful, not harmful to the discipline, even from the standpoint of traditional, problem-applicative concepts of method. The only remaining as­signment is to reformulate it so it could be applied by methodological tradi­tionalists as well.
Cognitive “Boy stories”: urban folklore and urban topographies
Authors: Žikić Bojan 
Published: June 2019

The culturally cognitive perception of Belgrade’s topographies is considered through its deployment, symbolic use and narrative foundation. As the explanatory material-one football-media incident, the use of certain areas of the city in a spectacle-ceremonial manner, knowledge and lore of certain elements of the Belgrade topographies and the organization of «the football Belgrade»-were considered.
The attitude is taken that the topography of a city is a multifaceted cultural constituent, whose structure of particular meaning, as a part of cultural communication, is determined by the very fact it is an urban space. Physical aspects of spatial-ness are reduced to relationism, i.e. it has a meaning for the cultural communication only when the elements of urban topographies are brought into correlation. Other characteristics of physical spatial-ness are irrelevant for such communication. Meaning relations in which elements of urban topographies exist are formed on the very fact of them being urban, that is, the afore mentioned denotation that is ascribed to space, stems from those cultural features and artifacts that are associated in a given milieu with certain concrete elements of urban topographies.
MODELLING SENSITIVE ISSUES ON SUCCESSIVE WAVES
Authors: Priyanka Kumari , Trisandhya Pidugu 
Published: June 2019

AbstractThis paper addresses the problem of estimation of population mean of sensitive character using non-sensitive auxiliary variable at current wave in two wave successive sampling. A general class of estimator is proposed and studied under randomized and scrambled response model. Many existing estimators have been modified to work for sensitive population mean estimation. The modified estimators became the members of proposed general class of estimators. The detail properties of all the estimators have been discussed. Their behaviour under randomized and scrambled response techniques have been elaborated. Numerical illustrations including simulation have been accompanied to judge the performance of different estimators. Finally suitable recommendations are forwarded.
NONRANDOMIZED RESPONSE MODEL FOR COMPLEX SURVEY DESIGNS
Authors: Arnab Raghunath , Shangodoyin Dahud Kehinde , Arcos Antonio 
Published: June 2019

Abstract
Warner’s randomized response (RR) model is used to collect sensitive information for a broad range of surveys, but it possesses several limitations such as lack of reproducibility, higher costs and it is not feasible for mail questionnaires. To overcome such difficulties, nonrandomized response (NRR) surveys have been proposed. The proposed NRR surveys are limited to simple random sampling with replacement (SRSWR) design. In this paper, NRR procedures are extended to complex survey designs in a unified setup, which is applicable to any sampling design and wider classes of estimators. Existing results for NRR can be derived from the proposed method as special cases.
ON THE SMOOTHED PARAMETRIC ESTIMATION OF MIXING PROPORTION UNDER FIXED DESIGN REGRESSION MODEL
Authors: Ramakrishnaiah Y. S. , Trivedi Manish , Satish Konda 
Published: June 2019

Abstract
The present paper revisits an estimator proposed by Boes (1966) – James (1978), herein called BJ estimator, which was constructed for estimating mixing proportion in a mixed model based on independent and identically distributed (i.i.d.) random samples, and also proposes a completely new (smoothed) estimator for mixing proportion based on independent and not identically distributed (non-i.i.d.) random samples. The proposed estimator is nonparametric in true sense based on known “kernel function” as described in the introduction. We investigated the following results of the smoothed estimator under the non-i.i.d. set-up such as (a) its small sample behaviour is compared with the unsmoothed version (BJ estimator) based on their mean square errors by using Monte-Carlo simulation, and established the percentage gain in precision of smoothed estimator over its unsmoothed version measured in terms of their mean square error, (b) its large sample properties such as almost surely (a.s.) convergence and asymptotic normality of these estimators are established in the present work. These results are completely new in the literature not only under the case of i.i.d., but also generalises to non-i.i.d. set-up.
Soil Salinity and Maize Growth under Cycle Irrigation in Coastal Soils
Authors: Huang Mingyi , Zhang Zhanyu , Sheng Zhuping , Zhu Chengli , Zhai Yaming , Lu Peirong , Brinkman Debra 
Published: June 2019

The coastal regions of eastern China have substantial potential for agricultural production. Freshwater scarcity makes the utilization of plentiful brackish water a vital issue in this area. We aim to assess the effects of cycle irrigation with fresh and brackish water on soil salinity and maize (Zea mays L.). A pot experiment was performed with two typical coastal soils (sandy loam and silt loam) and one local maize cultivar. The maize growing season was divided into three phases (development, mid‐, and later stage). Cycle irrigation was conducted using brackish water (5 g NaCl L−1) during one stage and freshwater for the remaining stages. Cycle irrigation using brackish water at the development stage caused both osmotic and ionic stresses on the maize, leading to significantly‐reduced evapotranspiration (ET), increased stem and leaf Na+/K+ ratio, and stunted growth. The decline of kernel number and 100‐grain weight resulted in severe yield loss. Cycle irrigation with brackish water at the mid‐stage induced less adverse effects on crop growth, while the decrease in kernel number remarkably reduced the yield. Cycle irrigation with brackish water at the later stage minimized the impacts of saline irrigation on soil salinity and maize productivity. Nonetheless, salt leaching by off‐season rainfall and low salinity water and soil salt monitoring should be considered before the next season. Compared to sandy loam soil, silt loam displayed higher soil salinization, and lower maize growth and yield. Additional field research is recommended to facilitate the reliable use of coastal soil and water resources.Core Ideas

Cycle irrigation with fresh and brackish water in two coastal soils is studied.
Cycle irrigation using brackish water is effective when freshwater is scarce.
Brackish water is proposed to be used at maize later reproductive stages.
Sandy loam soil is preferable for cycle irrigation compare to silt loam soil.