bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Reliable Change Using 95% Credible Intervals for the Differences in Proportions: A Statistical Analysis for Case-Study Methodology
Authors: Unicomb Rachael , Colyvas Kim , Harrison Elisabeth , Hewat Sally 
Published: April 2015

Purpose
Case-study methodology studying change is often used in the field of speech-language pathology, but it can be criticized for not being statistically robust. Yet with the heterogeneous nature of many communication disorders, case studies allow clinicians and researchers to closely observe and report on change. Such information is valuable and can further inform large-scale experimental designs. In this research note, a statistical analysis for case-study data is outlined that employs a modification to the Reliable Change Index (Jacobson & Truax, 1991). The relationship between reliable change and clinical significance is discussed. Example data are used to guide the reader through the use and application of this analysis.

Method
A method of analysis is detailed that is suitable for assessing change in measures with binary categorical outcomes. The analysis is illustrated using data from one individual, measured before and after treatment for stuttering.

Conclusions
The application of this approach to assess change in categorical, binary data has potential application in speech-language pathology. It enables clinicians and researchers to analyze results from case studies for their statistical and clinical significance. This new method addresses a gap in the research design literature, that is, the lack of analysis methods for noncontinuous data (such as counts, rates, proportions of events) that may be used in case-study designs.
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
Authors: Will Sebastian , Otto Christina , Miladi Milad , Möhl Mathias , Backofen Rolf 
Published: April 2015

Abstract
Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time).
Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics.
Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE.
Contact: backofen@informatik.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Pitfalls in stock discrimination by shape analysis of otolith contours
Authors: Harbitz Alf , Albert Ole Thomas 
Published: April 2015

Abstract
This paper focuses on artefacts that may corrupt stock discrimination by shape analysis of otolith contours, how one can examine if such artefacts are important, and how they can be avoided. The scope focuses on Fourier transforms of contour points, the linear Fisher discrimination technique, and success rates based on cross validation by the “leave one out at a time” technique. The “zero-score” technique is introduced as a tool to examine the importance of a possible artefact, based on the theoretical result that the probability of correct classification of any otolith from either of two identical groups is zero. If one of the identical groups is exposed to a possible influential factor, e.g. a different smoothing, a high classification rate will reveal that this factor is an important artefact. The concept of a “lasso contour” is introduced that drastically reduces the impact of smoothing and provides a non-concave shape that enables a one-dimensional representation of the contour without ambiguities. Results are illustrated by comparison between Greenland halibut (Reinhardtius hippoglossoides) otolith contours from southern Greenland and Northeast Arctic waters. The conclusion is that the probability of correct classification of locality based on the original contours is too optimistic (77–79%), while the scores based on lasso contours are insensitive to smoothing and still optimistically high (68–70%).
Natural tracers reveal population structure of albacore (Thunnus alalunga) in the eastern North Pacific
Authors: Wells R. J. David , Kinney Michael J. , Kohin Suzanne , Dewar Heidi , Rooker Jay R. , Snodgrass Owyn E. 
Published: April 2015

Abstract
Chemical signatures in otoliths and muscle tissue of albacore (Thunnus alalunga) from two regions of the North Pacific were characterized to examine population structure. Regions included northern (offshore northwest United States and Canada, &gt;40°N) and southern (offshore southwest United States and Mexico, &lt;40°N) areas where albacore have demonstrated region-specific differences in movement and size at age. Juvenile (ages 1–4 years) albacore were collected from each region through recreational and commercial fisheries over a 5-year period (2009–2013). Three different otolith chemistry assays were performed, including whole otoliths (proxy for lifetime signature), otolith edge (recent signature), and otolith core (nursery signature). Whole otolith δ13C and δ18O showed similar δ13C and enriched δ18O (∼0.5‰) values for juvenile albacore collected in the southern region; classification success to the two regions ranged from 78 to 91% during each year (similar age classes). Otolith edge δ13C and δ18O showed similar results as whole otoliths, but no regional differences were found for otolith core chemistry. Incorporation of trace element concentrations from whole otoliths improved discrimination between regions to 90–100% classification success during each year of the study, with significantly higher Ba:Ca, Mg:Ca, and Mn:Ca in albacore otoliths from the northern region. Albacore from the southern region also displayed enriched muscle δ13C (∼1.21‰) and δ15N (∼0.85‰) values relative to fish of the same size range from the northern region. Discrimination success between the two regions across all years using muscle δ13C and δ15N was 91%. Ultimately, results from this study suggest regional separation of albacore in the eastern North Pacific warranting region-specific vital rates in future modelling efforts.
Worldwide distribution of the NS3 gene 80K polymorphism among circulating hepatitis C genotype 1 viruses: implication for simeprevir usage
Authors: Vidal Luãnna L. , Santos André F. , Soares Marcelo A. 
Published: April 2015

Abstract

Objectives
Several direct-acting agents against the hepatitis C virus (HCV) NS3 protease and NS5b polymerase have been developed in recent years to improve treatment of this viral infection. Of these, simeprevir is currently recommended for HCV genotype 1 and 4 infections, but genotypic assessment for the presence of 80K is required prior to simeprevir administration due to the reduced susceptibility of genotype 1 viruses carrying that polymorphism. Because the prevalence of 80K at baseline in genotype 1 viruses varies between reports, we wanted to assess its worldwide prevalence.

Methods
Over 3000 HCV genotype 1 sequences reported from drug-naive subjects distributed around the world were retrieved from the HCV Los Alamos and GenBank databases. These were categorized into subtypes and geographical provenance (continent and country), and the presence of the 80K and 80R polymorphisms was visually inspected and counted.

Results
Disparate prevalence of 80K was observed depending on the country/continent analysed. While in resource-rich areas (USA, Western Europe and Australia) a high prevalence of 80K was seen in HCV subtype 1a, in emerging countries, such as Brazil, this prevalence was very low (&lt;1%). HCV subtype 1b sequences from France also displayed a significant occurrence of 80K (6.1%). 80R, on the other hand, was negligible worldwide.

Conclusions
The genotypic assessment of 80K in HCV subtype 1a prior to simeprevir administration in emerging countries with significant numbers of HCV infection is questionable, while it should be performed for subtype 1b in certain developed countries.
Measuring the equation of state of the high-z intergalactic medium using curvature statistics
Authors: Padmanabhan Hamsa , Srianand R. , Choudhury T. Roy 
Published: April 2015

Abstract
Using hydrodynamical simulations, we explore the use of the mean and percentiles of the curvature distribution function to recover the equation of state of the high-z (2 &lt; z &lt; 4) intergalactic medium (IGM). We find that the mean and percentiles of the absolute curvature distribution exhibit tight correlation with the temperatures measured at respective characteristic overdensities $\bar{\Delta }_i$s at each redshift. Hence, they provide complementary probes of the same underlying temperature–density distribution, and can in principle be used to simultaneously recover both parameters T0 and γ of the IGM effective equation of state. We quantify the associated errors in the recovered parameters T0 and γ from the intrinsic scatter in the characteristic overdensities and the uncertainties in the curvature measurement.
Endoscopic Incision for the Treatment of Refractory Esophageal Anastomotic Strictures in Children
Authors: Tan Yuyong , Zhang Jie , Zhou Junfeng , Duan Tianying , Liu Deliang 
Published: April 2015

ABSTRACTObjectives:The aim of the present study was to assess the safety and efficacy of endoscopic incision (EI) for the treatment of refractory anastomotic esophageal strictures in pediatric patients.Methods:We retrospectively reviewed the medical records of pediatric patients with refractory anastomotic strictures after surgical repair of esophageal atresia who underwent ≥3 sessions of endoscopic treatments (dilation and/or stenting). They were treated with EI alone or together with esophageal stenting. Efficacy and safety were evaluated during periodical follow‐up.Results:All of the 7 children received the procedure successfully with the operation time of 15 to 60 minutes. Four of them received EI alone, whereas the other 3 received EI with esophageal stenting (EIES). The symptoms remitted in all of the patients, and the dysphagia score decreased from 3–4 to 0–1 during follow‐up from 1 to 21 months. The average diameter of stricture was enlarged from 3 mm (range 2–5 mm) to 10.6 mm (range 8–12 mm). One patient suffered from chest pain, which resolved within 3 days. Patient 1 had recurrence 11 months after EIES, and patient 6 had recurrence 3 months after EI. They all underwent an additional EI to maintain patency. No severe complications were observed during operation and periodical follow‐up.Conclusions:EI is safe and appears effective for refractory esophageal anastomotic strictures in children in the short term. Large comparative studies are warranted to further confirm our findings. The long‐term follow‐up is necessary for assessing the long‐term efficacy of the new technique.
Water Load Test in Childhood Functional Abdominal Pain
Authors: Ozaki Roberto Koity Fujihara , Soares Ana Cristina Fontenele , da Graça Leite Speridião Patricia , Batista de Morais Mauro 
Published: April 2015

ABSTRACTThis cross‐sectional study evaluates the relations between the water load test in childhood functional gastrointestinal disorders with food intake and nutritional status. Patients with functional dyspepsia required a lower maximum water intake to produce fullness (n = 11, median = 380 mL) than patients with irritable bowel syndrome (n = 10, median = 695 mL) or functional abdominal pain (n = 10, median = 670 mL) (P < 0.05). Among patients who ingested ≤560 mL (n = 17) or >560 mL (n = 14) in the water load test, there was no relation between the maximum drinking capacity and food intake, body mass index, or height.
Laboratory Errors in a Pediatric Emergency Department Network
Authors: Lichenstein Richard , O’Connell Karen , Funai Tomohiko , Blumberg Stephen , Shaw Kathy , Ruddy Richard , Mahajan Prashant V. , Chamberlain James M. 
Published: April 2015

Objectives
To describe the types and severity of reported laboratory errors in pediatric emergency departments.

Methods
Retrospective review of incident reports classified as laboratory errors from July 2007 to June 2008 within the Pediatric Emergency Care Applied Research Network. Laboratory testing errors recorded included: delayed results or lost specimen, unlabeled specimens, wrong patient, failure to label specimen correctly, and other. The severity of laboratory-related incidents was characterized using the National Coordinating Council for Medication Error Reporting and Prevention severity classification system. Contributing factors were classified as environmental, equipment, human (employee), information technology systems, parent or guardian, or systems-based.

Results
A total of 335 (42.2%) laboratory reports were related to events in the preanalytic phase. Involved staff personnel were identified in 345 of the reports (43.5%). Nurses were identified in 179 (22.6%) and physicians in 38 (4.8%). The majority of laboratory errors [408 (51.5%)] were not associated with harm; 138 (17.4%) patients were harmed by the error; 136 (98.6%) patients were temporarily harmed and required treatment, and 1 (0.7%) patient was hospitalized or had their hospitalization prolonged with the event. Human factors 657 (82.8%) were the most common contributing factor.

Conclusions
Laboratory errors are a common cause of safety events in the pediatric ED. Most events are preanalytic and involve problems with specimens that are improperly collected, mislabeled, or lost. Although most events were not associated with harm, there is potential for significant injury.
Do Written Disclosures of Serious Events Increase Risk of Malpractice Claims? One Health Care System's Experience
Authors: Painter Lisa M. , Kidwell Kelley M. , Kidwell Richard P. , Janov Cheryl , Voinchet Robert G. , Simmons Richard L. , Wu Albert W. 
Published: April 2015

ObjectiveThis study aimed to determine whether Pennsylvania ACT 13 of 2002 (Mcare) requiring the written and verbal disclosure of “serious events” was accompanied by increased malpractice claims or compensation costs in a large U.S. health system.Main Outcomes and MeasuresThe primary outcome was the rate of malpractice claims. The secondary outcome was the amount paid for compensation of malpractice claims. The analyses tested the relationship between the rate of serious event disclosures and the outcome variables, adjusted for the year of the event, category of claim, and the degree of “harm” related to the event.ResultsThere were 15,028 serious event disclosures and 1302 total malpractice claims among 1,587,842 patients admitted to UPMC hospitals from May 17, 2002, to June 30, 2011. As the number of serious event disclosures increased, the number of malpractice claims per 1000 admissions remained between 0.62 and 1.03. Based on a matched analysis of claims that were disclosed and those that were not (195 pairs), disclosure status was significantly associated with increased claim payout (disclosures had 2.71 times the payout; 95% confidence interval, 1.56–4.72). Claims with higher harm levels H and I were independently associated with higher payouts than claims with lower harm levels A to D (11.15 times the payout; 95% confidence interval, 2.30–54.07).Conclusions and RelevanceImplementation of a mandated serious event disclosure law in Pennsylvania was not associated with an overall increase in malpractice claims filed. Among events of similar degree of harm, disclosed events had higher compensation paid compared with those that had not been disclosed.
Improved Compliance and Comprehension of a Surgical Safety Checklist With Customized Versus Standard Training: A Randomized Trial
Authors: Rakoff David , Akella Krishna , Guruvegowda Chandrashekar , Chhajwani Sunil , Seshadri SriKrishna , Sola Srikanth 
Published: April 2015

Objective
This study aimed to determine the effect of customized training versus standard readily available training on surgical safety checklist (SSCL) compliance and comprehension.

Background
The success of the SSCL in reducing surgical mortality and morbidity depends largely on the degree of compliance among health care workers with the checklist's components. We hypothesized that a customized training program would improve comprehension of the SSCL components among health care workers.

Methods
We prospectively evaluated compliance and comprehension of a locally modified SSCL among surgeons, anesthesiologists, nurses, and perfusionists who were randomized to standard versus customized training in the department of cardiac and thoracic surgery. Standard training included videos, posters, and didactic sessions obtained from the World Health Organization. Customized training consisted of a department-specific orientation video (using local staff as actors), locally made posters, and didactic sessions. Comprehension was assessed by a written exam after each training program. Verbal and written compliance with the SSCL was measured within the operating theater by trained observers.

Results
We observed a total of 244 surgeries for SSCL compliance. Comprehension of the didactic material provided in the training programs was higher in the customized versus the standard training group (75% versus 30%; P < 0.0001). Verbal compliance was higher in the customized versus standard training groups (87% versus 49%; P < 0.0001). Written compliance was 100% for both the customized and standard training groups.

Conclusions
A customized training program improves verbal compliance and comprehension among health care workers when implementing an SSCL, compared with standard readily available training.
Use of loop‐mediated isothermal amplification to detect six groups of pathogens causing secondary lower respiratory bacterial infections in horses
Authors: Kinoshita Yuta , Niwa Hidekazu , Katayama Yoshinari 
Published: April 2015

ABSTRACTMicrobial substitution occasionally occurs following the administration of antimicrobials to horses that have pneumonia or pleuropneumonia. Four specific loop‐mediated isothermal amplification (LAMP) assays were developed to detect some equine respiratory pathogens, namely strains of the Bacteroides–Prevotella group, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Staphylococcus aureus. These four LAMP assays and two previously published LAMP assays targeting Escherichia coli or Pseudomonas aeruginosa were used on clinical respiratory specimens and a high accordance found between the results of the LAMP assays and bacterial culture. Use of these LAMP assays could enable rapid detection of pathogenic bacteria and swift administration of the appropriate antimicrobials.
Physicochemical control of bacterial and protist community composition and diversity in Antarctic sea ice
Authors: Torstensson Anders , Dinasquet Julie , Chierici Melissa , Fransson Agneta , Riemann Lasse , Wulff Angela 
Published: April 2015

SummaryDue to climate change, sea ice experiences changes in terms of extent and physical properties. In order to understand how sea ice microbial communities are affected by changes in physicochemical properties of the ice, we used 454‐sequencing of 16S and 18S rRNA genes to examine environmental control of microbial diversity and composition in Antarctic sea ice. We observed a high diversity and richness of bacteria, which were strongly negatively correlated with temperature and positively with brine salinity. We suggest that bacterial diversity in sea ice is mainly controlled by physicochemical properties of the ice, such as temperature and salinity, and that sea ice bacterial communities are sensitive to seasonal and environmental changes. For the first time in Antarctic interior sea ice, we observed a strong eukaryotic dominance of the dinoflagellate phylotype SL163A10, comprising 63% of the total sequences. This phylotype is known to be kleptoplastic and could be a significant primary producer in sea ice. We conclude that mixotrophic flagellates may play a greater role in the sea ice microbial ecosystem than previously believed, and not only during the polar night but also during summer when potential food sources are abundant.
Do Improvements in the Information Environment Enhance Insiders’ Ability to Learn from Outsiders?
Authors: LOUREIRO GILBERTO , TABOADA ALVARO G. 
Published: April 2015

ABSTRACTWe examine whether and how an exogenous shock to the information environment changes insiders’ ability to learn from outsiders. We document three main findings. First, we find an increase in investment‐to‐price sensitivity following the adoption of International Financial Reporting Standards (IFRS). Second, we show that the relation between the market reaction to M&A deal announcements and the likelihood of deal completion becomes stronger after IFRS adoption. Third, we find significant improvements in post‐acquisition operating and stock return performance post‐IFRS adoption. These results are more pronounced for firms that experienced significant increases in foreign institutional ownership around IFRS adoption, especially when these foreign investors are from countries that matter for the firm’s growth opportunities. Taken together, our findings suggest that insiders’ ability to learn from outsiders improves post‐IFRS, and this improved ability to learn from outsiders leads to real economic gains.