bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paediatric First-Time Patella Dislocators: An Approach to Conservative Management
Authors: Yet Lam Kai , Collin Looi , Arjandas Mahadev 
Published: January 2017

Background First-time lateral patella dislocations are generally treated nonoperatively. However, the ideal form of conservative management and immobilization remains unknown. We compare the clinical outcomes after different immobilization methods. Methods Paediatric-age patients that met our inclusion criteria, and presenting with a first episode of lateral patella dislocation to our hospital from 2006 to 2013, were enrolled. Different immobilization methods included brace, backslab, or cylinder cast. A retrospective review was performed to compare bracing against other immobilization methods, using a primary outcome measure of redislocation rate, and secondary outcome measures like progression to surgery, range-of-motion, pain, and weight-bearing status. Results A total of 142 patients (with 147 affected knees) with minimum 1 -year follow-up were included in the study. Bracing was found to be superior to other immobilization methods in preventing repeat dislocations, and need for subsequent surgery. At 6 weeks, patients treated with the backslab had the highest incidence of pain. There were no differences with regards to range-of-motion or weight-bearing status. Conclusion We recommend the use of a brace, with a progressive rehabilitation protocol in the management of first-time lateral patella dislocators. This study is also unique, in that it specifically addresses nonoperative management of first time patella dislocators in a paediatric-age population group.
Surgical Repair of Moderate Ischemic Mitral Regurgitation—A Systematic Review and Meta-analysis
Authors: Aggarwal Saurabh , Reddy Yogesh , Alla Venkata , Baskaran Janani , Kanmanthareddy Arun , Suri Rakesh , Anantha Narayanan Mahesh 
Published: January 2017

Introduction Moderate mitral regurgitation (MR) of ischemic etiology has been associated with worse outcomes after coronary artery bypass grafting (CABG). Studies comparing concomitant mitral valve replacement/repair (MVR/Re) with CABG and standalone CABG have reported conflicting results. We performed a systematic review and meta-analysis of the published literature.
Patients and Methods We searched using PubMed, Cochrane, EMBASE, CINAHL, and Google scholar databases from January 1960 to June 2016 for clinical trials comparing CABG to CABG + MVR/Re for moderate MR. Pooled risk ratio or mean difference (MD) with 95% confidence intervals (CI) for individual outcomes were calculated using random effects model and heterogeneity was assessed using Cochrane's Q-statistic.
Results A total of 11 studies were included. Mean follow-up was 35.3 months. All-cause mortality (Mantel–Haenszel [MH] risk ratio [RR]: 0.96, 95% CI: 0.75–1.24, p = 0.775), early mortality (MH RR: 0.65, 95% CI: 0.39–1.07, p = 0.092), and stroke rates (MH RR 0.65, 95% CI: 0.21–2.03, p = 0.464) were similar between CABG and CABG + MVR/Re groups. Adverse event at follow-up was lower with CABG (MH RR: 0.90, 95% CI: 0.61–1.32, p = 0.584). MD of change from baseline in left ventricular (LV) end-systolic dimension (MD: − 2.50, 95% CI: − 5.21 to − 0.21, p = 0.071) and LV ejection fraction (MD: 0.48, 95% CI: − 2.48 to 3.44, p = 0.750) were not significantly different between the groups. Incidence of moderate MR (MH RR: 3.24, 95% CI: 1.79–5.89, p < 0.001) was higher in the CABG only group.
Conclusion Addition of MVR/Re to CABG in patients with moderate ischemic MR did not result in improvement in early or overall mortality, stroke risk, or intermediate markers of LV function when compared with CABG alone.
Dynamical theory of shear bands in structural glasses
Authors: Wisitsorasak Apiwat , Wolynes Peter G. 
Published: January 2017

Significance
When glasses are under imposed stresses or strains, they are subject to plastic deformation. Unlike their crystal counterparts, shear within the glasses localizes in thin bands, known as shear bands. Forming the shear bands can lead to structural failure of the whole sample and prevent using glasses as structural materials. In this work, we show how shear bands arise dynamically by the coupling of activated dynamics of configurationally rearranging regions with elastic strain transport. This result also explains the non-Newtonian flow of glasses.
miRmine: a database of human miRNA expression profiles
Authors: Panwar Bharat , Omenn Gilbert S , Guan Yuanfang 
Published: January 2017

Abstract

Motivation
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly.

Results
We used 304 high-quality microRNA sequencing (miRNA-seq) datasets from NCBI-SRA and calculated expression profiles for different tissues and cell-lines. In each miRNA-seq dataset, we found an average of more than 500 miRNAs with higher than 5x coverage, and we explored the top five highly expressed miRNAs in each tissue and cell-line. This user-friendly miRmine database has options to retrieve expression profiles of single or multiple miRNAs for a specific tissue or cell-line, either normal or with disease information. Results can be displayed in multiple interactive, graphical and downloadable formats.

Availability and Implementation
http://guanlab.ccmb.med.umich.edu/mirmine

Supplementary information
Supplementary data are available at Bioinformatics online.
aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments
Authors: Alonso Arnald , Lasseigne Brittany N , Williams Kelly , Nielsen Josh , Ramaker Ryne C , Hardigan Andrew A , Johnston Bobbi , Roberts Brian S , Cooper Sara J , Marsal Sara , Myers Richard M 
Published: January 2017

Abstract

Summary
The wide range of RNA-seq applications and their high-computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high-performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high-performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis.

Availability and documentation
https://github.com/HudsonAlpha/aRNAPipe; DOI: 10.5281/zenodo.202950

Supplementary information
Supplementary data are available at Bioinformatics online.
Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data
Authors: Peters Ruby , Benthem Muñiz Marta , Griffié Juliette , Williamson David J , Ashdown George W , Lorenz Christian D , Owen Dylan M 
Published: January 2017

AbstractMotivationUnlike conventional microscopy which produces pixelated images, SMLM produces data in the form of a list of localization coordinates—a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, the plasma membrane. While SMLM cluster analysis is now well developed, techniques for analyzing fibrous structures remain poorly explored.ResultsHere, we demonstrate a statistical methodology, based on Ripley’s K-function to quantitatively assess fibrous structures in 2D SMLM datasets. Using simulated data, we present the underlying theory to describe fiber spatial arrangements and show how these descriptions can be quantitatively derived from pointillist datasets. We also demonstrate the techniques on experimental data acquired using the image reconstruction by integrating exchangeable single-molecule localization (IRIS) approach to SMLM, in the context of the fibrous actin meshwork at the T cell immunological synapse, whose structure has been shown to be important for T cell activation.Availability and ImplementationFreely available on the web at https://github.com/RubyPeters/Angular-Ripleys-K. Implemented in MatLab.Supplementary informationSupplementary data are available at Bioinformatics online.
Incorporating technology to advance asthma controller adherence
Authors: Anderson William C. 
Published: January 2017

Purpose of review
Technological innovations, including text messaging, smart phone applications, and electronic monitoring devices, aimed at improving asthma controller adherence are being rapidly introduced both into clinical care and directly marketed to patients. This review analyzes recent clinical trials implementing these interventions, with a focus on their benefits and shortcomings.

Recent findings
Poor medication adherence continues to exert significant morbidity on patients with asthma. Objective, real-time measures to monitor adherence can overcome the limitations of prior methods, including self-report and prescription refills. Technological advances, especially those incorporating reminder systems, have demonstrated improved controller adherence. The increased adherence in these trials has not translated into consistent clinical improvement, including reducing hospitalizations, emergency department visits, and asthma exacerbations, possibly secondary to study design and poor inhalation technique.

Summary
Novel monitoring and reminder technology can augment patient medication adherence and provide clues to management before escalating therapy. Further studies are needed to investigate the overarching clinical impact of this technology, especially as it grows into routine clinical practice.
Management of preschool recurrent wheezing and asthma: a phenotype-based approach
Authors: Beigelman Avraham , Bacharier Leonard B. 
Published: January 2017

Purpose of review
The purpose of this review is to summarize the recent evidence on the management of preschool children with wheezing and asthma, and to propose a phenotype-based approach to the management of these children.

Recent findings
Recent studies have begun to identify populations of preschool children that are likely to benefit from inhaled corticosteroids (ICS) therapy and defined ICS regimens: daily ICS in preschool children with persistent asthma, and pre-emptive high-dose intermittent ICS among preschool children with intermittent disease reduce the risk of exacerbation. In addition, among preschool children with mild persistent asthma, the presence of aeroallergen sensitivity and/or blood eosinophil counts of 300/μL or greater are predictors of good response to daily ICS therapy. Other studies identified intermittent azithromycin as a therapy to prevent, and potentially to treat, acute exacerbations.
The uncertainty of the role of oral corticosteroids (OCS) as a therapy for acute exacerbations continues, as a recent meta-analysis showed that OCS did not prevent hospitalizations or urgent visits, and did not reduce the need for additional courses of OCS. Whereas previous epidemiologic studies suggested acetaminophen may increase risk of exacerbations, a clinical trial clearly demonstrated acetaminophen use, compared to ibuprofen use,does not increase exacerbation risk among preschool children with mild-persistent asthma.

Summary
Recent studies have shown potential for phenotypic-driven therapies for the management of preschool children with asthma. Targeting airway bacteria has emerged as a promising therapeutic approach, but its effect on antibiotic resistance still needs to be investigated. Finally, more studies are required to evaluate if oral corticosteroids provide any benefits for acute episodic wheeze.
Asthma guidelines: the Global Initiative for Asthma in relation to national guidelines
Authors: Becker Allan B. , Abrams Elissa M. 
Published: January 2017

Purpose of review
To compare and contrast national asthma guidelines with the Global Initiative for Asthma (GINA) strategy for asthma management and prevention.

Recent findings
The common goal of GINA and national asthma guidelines is to improve asthma care using the best evidence available from published data. This evidence-based approach has evolved from an initial perspective of expert opinion but with that evolution has not always considered the breadth of asthma phenotypes. GINA and national guidelines differ in a number of ways. GINA reviews available data and updates the core document and recommendations based on the latest data on a yearly basis to offer local, regional and national guidelines materials needed for knowledge mobilization. It remains the purview of those organizations to structure and implement those locally appropriate guidelines.

Summary
Both GINA and national guidelines have furthered asthma care to narrow the care gap from what is known to how asthma care is delivered, hopefully in a more directed, personalized manner. As well, both GINA and national guidelines have helped to shape the direction of research for the future benefit of children and their families.
Childhood asthma is a risk factor for the development of chronic obstructive pulmonary disease
Authors: McGeachie Michael J. 
Published: January 2017

Purpose of review
This review will catalog the many recent longitudinal studies that have investigated the relationship between asthma and lung function, or the persistence and trajectories of lung function deficits.

Recent findings
Recent work has reported on 50-year follow-ups of some prominent population cohorts. A history of asthma confers a 10–30-fold risk of chronic obstructive pulmonary disease. Individuals reaching a reduced maximum growth of forced expiratory volume in 1 s in early adulthood are at risk for early or more severe chronic obstructive pulmonary disease (COPD).

Summary
Taken together, there is a wealth of overlapping cohort studies of lung function, asthma and COPD. These show that asthma is associated with reduced lung function, which may start in infancy or prenatally, persists through childhood and adulthood and predisposes for early or more severe COPD.
Comparisons in Muscle Function and Training Rehabilitation Outcomes Between Avoidance-Endurance Model Subgroups
Authors: Fehrmann Elisabeth , Tuechler Kerstin , Kienbacher Thomas , Mair Patrick , Spreitzer Juliane , Fischer Linda , Kollmitzer Josef , Ebenbichler Gerold 
Published: January 2017

Objectives:
Evidence suggests that chronic low back pain patients with fear-avoidance (FAR) or endurance behavior are at risk of treatment failure and pain maintenance, with bodily overuse or underuse being assumed as mediating mechanisms for pain chronification. This study sought to examine whether or not the avoidance-endurance model subgroups, FAR, distress-endurers (DER), eustress-endurers (EER), and adaptive responders (AR), differed in physical measures and outcomes after training therapy.

Materials and Methods:
A total of 137 chronic low back pain patients were assessed before, at the end of, and 6 months after a 6-month rehabilitation training. Patients performed maximum back extension strength and trunk range-of-motion measures, flexion-relaxation tests, and completed the following questionnaires: Avoidance-Endurance Questionnaire, Roland-Morris Disability Questionnaire, Pain Disability Index, 36-Item Short-Form Health Survey, International Physical Activity Questionnaire, and visual analog scale. Statistical analysis included cluster analysis, analysis of covariances, and mixed-effects models.

Results:
At baseline, avoidance-endurance model subgroups did not differ in physical measures and activity levels. At the end of training, patients’ back-related health was significantly improved in all subgroups. However, the DER and the FAR were found to be more impaired before and after the intervention compared with EER and AR, as indicated by a higher pain intensity, higher disability levels, lower quality of life, and inferior working capacity.

Discussion:
Although FAR and DER did not differ in physical measures or activity levels from EER and AR, they demonstrated poor lower back-related health at baseline and after intervention. Thus, future research should elucidate as to which additional interventions could optimize their health.
Treatment Adherence in Child and Adolescent Chronic Migraine Patients
Authors: Kroon Van Diest Ashley M. , Ramsey Rachelle R. , Kashikar-Zuck Susmita , Slater Shalonda , Hommel Kevin , Kroner John W. , LeCates Susan , Kabbouche Marielle A. , O’Brien Hope L. , Kacperski Joanne , Allen Janelle R. , Peugh James , Hershey Andrew D. , Powers Scott W. 
Published: January 2017

Objectives:To examine treatment adherence among children and adolescents with chronic migraine who volunteered to be in a clinical trial using 3 measures: treatment session attendance, therapy homework completion, and preventive medication use by daily diary.Materials and Methods:Analyses are secondary from a trial of 135 youth aged 10 to 17 years diagnosed with chronic migraine and with a Pediatric Migraine Disability Score over 20. Participants were randomly assigned to cognitive-behavioral therapy plus amitriptyline (CBT+A, N=64) or headache education plus amitriptyline (HE+A, N=71). Therapists recorded session attendance. Completion of homework/practice between sessions was reported to therapists by patients. Patients reported preventive medication adherence using a daily headache diary.Results:Mean session attendance adherence out of 10 treatment sessions was 95% for CBT+A and 99% for HE+A. CBT+A participants reported completing a mean of 90% of home practice of CBT skills between the 10 sessions. Participants reported taking amitriptyline daily at a mean level of 90% when missing diaries were excluded and 79% when missing diaries were considered as missed doses of medication.Discussion:Our findings demonstrate that youth with chronic migraine who agree to be a part of a clinical trial do quite well at attending therapy sessions, and report that they are adherent to completing home/practice between sessions and taking medication. These results lend further support to consideration of CBT+A as a first-line treatment for youth with chronic migraine and suggest that measurement of adherence when this treatment is provided in practice will be important.
Pain Beliefs and Quality of Life in Young People With Disabilities and Bothersome Pain
Authors: Miró Jordi , Solé Ester , Gertz Kevin , Jensen Mark P. , Engel Joyce M. 
Published: January 2017

Objectives:
Pain beliefs have been hypothesized to play an important role in pediatric pain. However, research examining the associations between pain-related beliefs and measures of function in youths with disabilities is limited.

Methods:
In total, 84 youths (mean age, 14.26 y; SD, 3.27) with physical disabilities who indicated they also had bothersome pain were interviewed and asked to rate their average pain intensity in the past week and to complete measures of pain-related beliefs and health-related quality of life.

Results:
A number of pain beliefs were associated with different physical and psychosocial function domains, although different beliefs appeared to play different roles, depending on the function domain examined. Across all of the health-related quality-of-life domains studied, a belief that pain is influenced by one’s emotions was associated with lower levels of function. No differences were found in pain beliefs related to age. In addition, a small difference in pain beliefs was found for sex; specifically, girls were more likely than boys to endorse the belief that pain is influenced by emotions.

Discussion:
The findings provide new information regarding the role that pain beliefs have in predicting function and have important clinical implications regarding how youth with physical disabilities and pain might be most effectively treated.
A Quality Improvement Collaborative Program for Neonatal Pain Management in Japan
Authors: Ozawa Mio , Yokoo Kyoko , Funaba Yuuki , Fukushima Sayo , Fukuhara Rie , Uchida Mieko , Aiba Satoru , Doi Miki , Nishimura Akira , Hayakawa Masahiro , Nishimura Yutaka , Oohira Mitsuko 
Published: January 2017

Background:
Neonatal pain management guidelines have been released; however, there is insufficient systematic institutional support for the adoption of evidence-based pain management in Japan.

Purpose:
To evaluate the impact of a collaborative quality improvement program on the implementation of pain management improvements in Japanese neonatal intensive care units (NICUs).

Methods:
Seven Japanese level III NICUs participated in a neonatal pain management quality improvement program based on an Institute for Healthcare Improvement collaborative model. The NICUs developed evidence-based practice points for pain management and implemented these over a 12-month period. Changes were introduced through a series of Plan-Do-Study-Act cycles, and throughout the process, pain management quality indicators were tracked as performance measures. Jonckheere's trend test and the Cochran-Armitage test for trend were used to examine the changes in quality indicator implementations over time (baseline, 3 months, 6 months, and 12 months).

Findings:
Baseline pain management data from the 7 sites revealed substantial opportunities for improvement of pain management, and testing changes in the NICU setting resulted in measurable improvements in pain management. During the intervention phase, all participating sites introduced new pain assessment tools, and all sites developed electronic medical record forms to capture pain score, interventions, and infant responses to interventions.

Implications for Practice:
The use of collaborative quality improvement techniques played a key role in improving pain management in the NICUs.

Implications for Research:
Collaborative improvement programs provide an attractive strategy for solving evidence-practice gaps in the NICU setting.