bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the Personal Responsibility Scale for adolescents
Authors: Mergler Amanda , Shield Paul 
Published: June 2016

ABSTRACTIncreasing interest by policy makers and educators in enhancing the non‐cognitive factors that impact on the wellbeing of young people across the school years requires valid and reliable measurement scales. This paper reports the psychometric development of the Personal Responsibility Scale drawing on a preliminary 34‐item measure developed using data from focus groups with secondary students in Australia. This scale was then administered to 513 students across Years 9–12. Exploratory factor analysis identified three factors, ‘personal accountability’, ‘behavioural and emotional control’, and ‘cognitive control’. Structural equation modelling was used to examine the congeneric measurement models for these factors. The multidimensional nature of the personal responsibility construct was then examined through multilevel confirmatory factor analysis. These analyses supported a three‐factor structure to propose a final 15‐item scale. Additional validation requirements, future research possibilities, and implications of this study are addressed.
Changes of junctions of endothelial cells in coronary sclerosis: A review
Authors: Zhang Li‐Zi , Lei Sun 
Published: June 2016

AbstractAtherosclerosis, the major cause of cardiovascular diseases, has been a leading contributor to morbidity and mortality in the United States and it has been on the rise globally. Endothelial cell–cell junctions are critical for vascular integrity and maintenance of vascular function. Endothelial cell junctions dysfunction is the onset step of future coronary events and coronary artery disease.
Characteristics and risk factors of hospital acquired — Methicillin-resistant Staphylococcus aureus (HA-MRSA) infection of pediatric patients in a tertiary care hospital in Riyadh, Saudi Arabia
Authors: Alrabiah Khalid , Al Alola Sulaiman , Al Banyan Esam , Al Shaalan Mohammad , Al Johani Sameera 
Published: June 2016

Background and objectives:
The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infections has been steadily increasing. These infections are considered to be either hospital-acquired MRSA (HA-MRSA) or community-acquired MRSA (CA-MRSA). Children are at higher risk of infection than adults. HA-MRSA has been reported to have more serious outcomes than CA-MRSA. However, there are not enough studies in Saudi Arabia to study the characteristics of HA-MRSA in children. We aim to describe the characteristics of HA-MRSA infection, including risk factors, culture site, clinical manifestations, complications, and outcomes among pediatric patients in a tertiary care hospital in Riyadh, Saudi Arabia.

Design and settings:
This is a retrospective chart review study. It was conducted in King Abdu-laziz medical city in Riyadh.

Patients and methods:
The study included all patients 14 years of age or younger who were culture-positive from any site in the body during the period from January 1,2009 to December 31,2011. The time of culture compared to admission time was used to differentiate between CA-MRSA (within 72 h of admission) and HA-MRSA (more than 72 h after admission). The final sample size was 39 patients.

Results:
We found HA-MRSA to be more common in males and those with risk factors such as previous surgery and previous hospitalization. Patients had a high Pediatric intensive care unit (PICU) admission rate and were commonly septic with positive blood cultures. Seventy-four percent of patients fully recovered, 10% recovered with complications and 15% died.

Conclusion:
HA-MRSA is an infection that can cause serious complications and a high rate of PICU admissions. Clinical manifestations such as shock are associated with higher mortality and morbidity rates. Special care should be given to those admitted to PICU, as they have high rates of mortality and morbidity.
Function and expression study uncovered hepatocyte plasma membrane ecto-ATP synthase as a novel player in liver regeneration
Authors: Taurino Federica , Giannoccaro Caterina , Sardanelli Anna Maria , Cavallo Alessandro , De Luca Elisa , Santacroce Salvatore , Papa Sergio , Zanotti Franco , Gnoni Antonio 
Published: June 2016

ATP synthase, canonically mitochondrially located, is reported to be ectopically expressed on the plasma membrane outer face of several cell types. We analysed, for the first time, the expression and catalytic activities of the ecto- and mitochondrial ATP synthase during liver regeneration. Liver regeneration was induced in rats by two-thirds partial hepatectomy. The protein level and the ATP synthase and/or hydrolase activities of the hepatocyte ecto- and mitochondrial ATP synthase were analysed on freshly isolated hepatocytes and mitochondria from control, sham-operated and partial hepatectomized rats. During the priming phase of liver regeneration, 3 h after partial hepatectomy, liver mitochondria showed a marked lowering of the ATP synthase protein level that was reflected in the impairment of both ATP synthesis and hydrolysis. The ecto-ATP synthase level, in 3 h partial hepatectomized hepatocytes, was decreased similarly to the level of the mitochondrial ATP synthase, associated with a lowering of the ecto-ATP hydrolase activity coupled to proton influx. Noteworthily, the ecto-ATP synthase activity coupled to proton efflux was completely inhibited in 3 h partial hepatectomized hepatocytes, even in the presence of a marked intracellular acidification that would sustain it as in control and sham-operated hepatocytes. At the end of the liver regeneration, 7 days after partial hepatectomy, the level and the catalytic activities of the ecto- and mitochondrial ATP synthase reached the control and sham-operated values. The specific modulation of hepatocyte ecto-ATP synthase catalytic activities during liver regeneration priming phase may modulate the extracellular ADP/ATP levels and/or proton influx/efflux trafficking, making hepatocyte ecto-ATP synthase a candidate for a novel player in the liver regeneration process.
bdvis: visualizing biodiversity data in R
Authors: Barve Vijay , Otegui Javier 
Published: June 2016

Abstract
Summary: Biodiversity studies are relying increasingly on primary biodiversity records (PBRs) for modelling and analysis. Because biodiversity data are frequently ‘harvested’—i.e. not collected by the researcher for that particular study, but obtained from data aggregators such as the Global Biodiversity Information Facility—researchers need to be aware of strengths and weaknesses of their data before they venture into further analysis. R is becoming a lingua franca of data exploration and analysis. Here, we describe an R package, bdvis, which facilitates efforts to understand the gaps and strengths of PBR data with quick and useful visualization functions.
Availability and Implementation: The full code of the R package bdvis, along with instructions on how to install and use it, is available via CRAN – The Comprehensive R Archive Network (http://cran.r-project.org/web/packages/bdvis/index.html) and in the corresponding author’s main GitHub repository: http://www.github.com/vijaybarve/bdvis. The source code is licensed under CC0
Contact: vijay.barve@gmail.com
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
Authors: Cuscó Pol , Filion Guillaume J. 
Published: June 2016

AbstractMotivation: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard method to investigate chromatin protein composition. As the number of community-available ChIP-seq profiles increases, it becomes more common to use data from different sources, which makes joint analysis challenging. Issues such as lack of reproducibility, heterogeneous quality and conflicts between replicates become evident when comparing datasets, especially when they are produced by different laboratories.Results: Here, we present Zerone, a ChIP-seq discretizer with built-in quality control. Zerone is powered by a Hidden Markov Model with zero-inflated negative multinomial emissions, which allows it to merge several replicates into a single discretized profile. To identify low quality or irreproducible data, we trained a Support Vector Machine and integrated it as part of the discretization process. The result is a classifier reaching 95% accuracy in detecting low quality profiles. We also introduce a graphical representation to compare discretization quality and we show that Zerone achieves outstanding accuracy. Finally, on current hardware, Zerone discretizes a ChIP-seq experiment on mammalian genomes in about 5 min using less than 700 MB of memory.Availability and Implementation: Zerone is available as a command line tool and as an R package. The C source code and R scripts can be downloaded from https://github.com/nanakiksc/zerone. The information to reproduce the benchmark and the figures is stored in a public Docker image that can be downloaded from https://hub.docker.com/r/nanakiksc/zerone/.Contact: guillaume.filion@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
The Glycome Analytics Platform: an integrative framework for glycobioinformatics
Authors: Barnett Christopher B. , Aoki-Kinoshita Kiyoko F. , Naidoo Kevin J. 
Published: June 2016

Abstract
Motivation: Complex carbohydrates play a central role in cellular communication and in disease development. O- and N-glycans, which are post-translationally attached to proteins and lipids, are sugar chains that are rooted, tree structures. Independent efforts to develop computational tools for analyzing complex carbohydrate structures have been designed to exploit specific databases requiring unique formatting and limited transferability. Attempts have been made at integrating these resources, yet it remains difficult to communicate and share data across several online resources. A disadvantage of the lack of coordination between development efforts is the inability of the user community to create reproducible analyses (workflows). The latter results in the more serious unreliability of glycomics metadata.
Results: In this paper, we realize the significance of connecting multiple online glycan resources that can be used to design reproducible experiments for obtaining, generating and analyzing cell glycomes. To address this, a suite of tools and utilities, have been integrated into the analytic functionality of the Galaxy bioinformatics platform to provide a Glycome Analytics Platform (GAP).
Using this platform, users can design in silico workflows to manipulate various formats of glycan sequences and analyze glycomes through access to web data and services. We illustrate the central functionality and features of the GAP by way of example; we analyze and compare the features of the N-glycan glycome of monocytic cells sourced from two separate data depositions.
This paper highlights the use of reproducible research methods for glycomics analysis and the GAP presents an opportunity for integrating tools in glycobioinformatics.
Availability and Implementation: This software is open-source and available online at https://bitbucket.org/scientificomputing/glycome-analytics-platform
Contacts: chris.barnett@uct.ac.za or kevin.naidoo@uct.ac.za
Supplementary information: Supplementary data are available at Bioinformatics online.
Biologic therapy in the management of asthma
Authors: McCracken Jennifer L. , Tripple Julia W. , Calhoun William J. 
Published: June 2016

Purpose of review
Current asthma management relies on inhaled corticosteroids, but some asthma is not well controlled with inhaled steroids alone or in combination with long-acting bronchodilators or leukotriene pathway inhibitors. The field of biologic therapy has grown dramatically in the past two decades, with current availability of three molecules, with two distinct and highly selective approaches to interfering with the allergic and eosinophilic airway inflammation common to most asthma. This review summarizes current and future options for incorporating biologic therapy into the overall management of asthma.

Recent findings
Two new biologic agents have been recently introduced in the United States market, supported by well controlled, randomized clinical trials. These trials have provided insight into the types of patients who are most likely to benefit from these novel agents.

Summary
In asthma patients with frequent exacerbations, the addition of a biologic agent targeting the interleukin-5 pathway, or immunoglobulin E, can significantly reduce exacerbations and improve asthma control. The clinical predictors of utility of specific agents overlap with one another, highlighting the importance of clinical judgment in the overall management of this complex disorder.
Comparisons of outcomes with food immunotherapy strategies: efficacy, dosing, adverse effects, and tolerance
Authors: Yanagida Noriyuki , Sato Sakura , Asaumi Tomoyuki , Ebisawa Motohiro 
Published: June 2016

Purpose of review
In the recent decade, oral immunotherapy has been studied in many clinical trials and entails many problems including a low efficacy for real tolerance and a high rate of induced symptoms. The optimal dose for inducing tolerance is unknown. The aim of this review was to clarify the efficacy and safety of oral immunotherapy, focusing on low doses.

Recent findings
We reviewed articles published in a few years or articles dealing with oral immunotherapy focusing on a low dose. We summarize recent articles on oral immunotherapy and those focusing on low doses.

Summary
Although lower doses for oral immunotherapy appear to cause fewer adverse reactions and be more effective than strict elimination, this strategy may be less effective than oral immunotherapy involving larger doses. The optimal dose for inducing tolerance is still unknown.
Tears for the City
Authors: Dunlap Ruby 
Published: June 2016

ABSTRACT:
Most nurses can describe a memorable patient, one who moved them deeply, and one who made them remember why they chose nursing as a calling. Thinking of a population with an emotional connection is usually more difficult. Current nursing practice includes the ability to serve a population or community as client. This article describes core functions of public health—assessment, policy development, and assurance, while offering biblical resources the Christian nurse has to consider a population with the same compassion as one does an individual.
The use of β-blockers is associated with a lower risk of developing hepatocellular carcinoma in patients with cirrhosis
Authors: Herrera Iván , Pascual Sonia , Zapater Pedro , Carnicer Fernando , Bellot Pablo , María Palazón José 
Published: June 2016

Introduction
Patients with cirrhosis by hepatitis C virus infection treated with β-blockers (BB) have been shown to have a reduced incidence of hepatocellular carcinoma (HCC). Also, an association between propranolol therapy and lower incidence of other tumors has been described.

Aim
To analyze the incidence of HCC according to BB treatment in cirrhosis of any cause.

Patients and methods
Cirrhotic patients included in the program for early detection of HCC were followed. Patients’ data were prospectively registered, including transplantation and death. Patients were classified as chronically taken or not BB and the proportions of patients who remained free of tumor from the diagnosis of cirrhosis until the end of follow-up were compared using Kaplan–Meier analysis and the Breslow test.

Results
A total of 173 patients (73 treated and 100 untreated BB) were followed. The median duration of follow-up was 11 years. There were no differences between both groups in the overall survival, number of deaths, or liver transplant.
Overall, 28 patients developed HCC during the follow-up, 20 patients who were untreated and eight patients treated with BB. The cumulative proportion of cases of HCC between untreated and treated with BB from the diagnosis of cirrhosis was statistically significant (6 vs. 3%, at 5 years; 19 vs. 6% at 10 years; 24 vs. 16% at 15 years; P=0.048). Multivariate analyses showed BB intake as the only significant variable associated with the development of HCC.

Conclusion
Cirrhotic patients treated with BB have a lower cumulative probability of developing HCC during the 10 years after the diagnosis of cirrhosis.
Control of the onset of puberty
Authors: Livadas Sarantis , Chrousos George P. 
Published: June 2016

Purpose of review
The mechanism of puberty initiation remains an enigma, despite extensive research in the field. Pulsatile pituitary gonadotropin secretion under the guidance of hypothalamic gonadotropin-releasing hormone (GnRH) constitutes a sine qua non for pubertal onset. In turn, the secretion of GnRH in the human hypothalamus is regulated by kisspeptin and its receptor as well as by permissive or opposing signals mediated by neurokinin B and dynorphin acting on their respective receptors. These three supra-GnRH regulators compose the Kisspeptin, Neurokinin B and Dynorhin neurons (KNDy) system, a key player in pubertal onset and progression.

Recent findings
The recent discovery that makorin ring finger protein 3 is also involved in puberty initiation provided further insights into the regulation of the KNDy pathway. In fact, the inhibitory (γ-amino butyric acid, neuropeptide Y, and RFamide-related peptide-3) and stimulatory signals (glutamate) acting upstream of KNDy called into question the role of makorin ring finger protein 3 as the gatekeeper of puberty. Meanwhile, the findings that ‘neuroestradiol’ produced locally and endocrine disruptors from the environment may influence GnRH secretion is intriguing. Finally, epigenetic mechanisms have been implicated in pubertal onset through recently discovered mechanisms.

Summary
The exact molecular machinery underlying puberty initiation in humans is under intensive investigation. In this review, we summarize research evidence in the field, while emphasizing the areas of uncertainty and underlining the impact of current information on the evolving theory regarding this fascinating phenomenon.
Resilience in Patients With Recent Diagnosis of a Schizophrenia Spectrum Disorder
Authors: Bozikas Vasilis P. , Parlapani Eleni , Holeva Vasiliki , Skemperi Eleni , Bargiota Stavroula I. , Kirla Danai , Rera Eirini , Garyfallos Georgios 
Published: June 2016

Abstract
This study focused on resilience in patients who recently received a diagnosis of schizophrenia spectrum disorder (SSD). Psychopathological symptoms, depressive symptoms, and hopelessness were considered as sources of stress in the context of psychosis. Forty-eight SSD patients (mean period between diagnosis and recruitment, 20.79 months) were enrolled. Psychopathological symptoms were assessed by the Positive and Negative Syndrome Scale, depression by the Calgary Depression Scale for Schizophrenia, hopelessness by the Beck Hopelessness Scale, and functioning by the Social and Occupational Functioning Scale. Resilience was evaluated by the Connor-Davidson Resilience Scale, which was additionally completed by 81 healthy controls. Patients demonstrated less resilience than did healthy participants. Female patients showed higher resilience levels and functioning than did males. High resilience levels were associated with less severe positive symptoms, general psychopathological symptoms, depression, and hopelessness. Apart from negative symptoms, results indicated that resilience may be a potential moderator of functioning. Thus, resilience-oriented interventions might constitute an additional therapeutic approach for SSD patients.
Gene-tree reconciliation with MUL-trees to resolve polyploidy events
Authors: Thomas Gregg W.C. , Hussain Ather S. , Hahn Matthew W. 
Published: June 2016

AbstractPolyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy.
Hipk is required for JAK/STAT activity and promotes hemocyte-derived tumorigenesis
Authors: Blaquiere Jessica A. , Wray Nathan B. , Verheyen Esther M. 
Published: June 2016

AbstractDysregulation of key signaling molecules and pathways are causative of many Human diseases and cancers. A point mutation in the Drosophila Janus kinase (calledhop) causes constitutive activation of the JAK/STAT pathway and results in blood cell tumours. We provide robust genetic evidence that Hipk is required for endogenous JAK/STAT activity. Overexpression of Hipk can phenocopy the effects of overactive JAK/STAT mutations and lead to melanized tumors and loss of Hipk can suppress the effects of hyperactive JAK/STAT. Furthermore, Hipk expression in blood cell progenitors causes tumors. PLA experiments show that Hipk can interact with the pathway effector Stat92E. Together our results show that Hipk is a novel factor required for effective JAK/STAT signaling.Summary StatementLoss ofhipkimpairs JAK/STAT activity in multiple tissue types and elevated Hipk leads to the formation of blood cell tumors in Drosophila.