bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Randomized Controlled Trial for Children With Childhood Apraxia of Speech Comparing Rapid Syllable Transition Treatment and the Nuffield Dyspraxia Programme–Third Edition
Authors: Murray Elizabeth , McCabe Patricia , Ballard Kirrie J. 
Published: March 2015

PurposeThis randomized controlled trial compared the experimental Rapid Syllable Transition (ReST) treatment to the Nuffield Dyspraxia Programme–Third Edition (NDP3; Williams & Stephens, 2004), used widely in clinical practice in Australia and the United Kingdom. Both programs aim to improve speech motor planning/programming for children with apraxia of speech (CAS), but they differ in types of stimuli used, level of stimulus complexity at initiation of treatment, and the principles of motor learning that they apply.MethodTreatment was delivered to 26 children with mild to severe CAS aged 4–12 years through trained and supervised speech-language pathology students in 1-hr sessions, 4 days a week for 3 weeks at a university clinic. Articulation and prosodic accuracy were assessed at pretreatment, 1 week, 1 month, and 4 months posttreatment using blinded independent assessors to compare treatment, maintenance, and generalization effects.ResultsThe ReST and NDP3 treatments demonstrated large treatment effects. ReST maintained treatment gains from 1-week to 4-months posttreatment more effectively than the NDP3. Significant generalization to untreated stimuli was observed for both ReST and NDP3.ConclusionsReST and NDP3 have strong evidence of treatment and generalization gains in children with CAS when delivered intensively. Overall, ReST has greater external evidence from multiple sources but both treatments have support for clinical use.Supplemental Materialhttps://doi.org/10.23641/asha.6170300
Proficiency and Linguistic Complexity Influence Speech Motor Control and Performance in Spanish Language Learners
Authors: Nip Ignatius S. B. , Blumenfeld Henrike K. 
Published: March 2015

Purpose
Second-language (L2) production requires greater cognitive resources to inhibit the native language and to retrieve less robust lexical representations. The current investigation identifies how proficiency and linguistic complexity, specifically syntactic and lexical factors, influence speech motor control and performance.

Method

Speech movements of 29 native English speakers with low or high proficiency in Spanish were recorded while producing simple and syntactically complex sentences in English and Spanish. Sentences were loaded with cognate (e.g.,
baby–bebé
) or noncognate (e.g.,
dog–perro
) words. Effects of proficiency, lexicality (cognate vs. noncognate), and syntactic complexity on maximum speed, range of movement, duration, and speech movement variability were examined.

Results
In general, speakers with lower L2 proficiency differed in their speech motor control and performance from speakers with higher L2 proficiency. Speakers with higher L2 proficiency generally had less speech movement variability, shorter phrase durations, greater maximum speeds, and greater ranges of movement. In addition, lexicality and syntactic complexity affected speech motor control and performance.

Conclusions
L2 proficiency, lexicality, and syntactic complexity influence speech motor control and performance in adult L2 learners. Information about relationships between speech motor control, language proficiency, and cognitive–linguistic demands may be used to assess and treat bilingual clients and language learners.
Vocabulary Instruction onSesame Street: A Content Analysis of the Word on the Street Initiative
Authors: Larson Anne L. , Rahn Naomi L. 
Published: March 2015

PurposeAuthors of this content analysis examined howSesame Street's Word on the Street initiative aligns with research-based practices for selecting and teaching vocabulary to young children and considered how speech-language pathologists can use educational media to supplement traditional vocabulary instruction.MethodStudy authors used a well-established vocabulary selection hierarchy to analyze 170 target words across 7 seasons of Word on the Street to judge appropriateness for preschool vocabulary instruction. The authors then coded vocabulary instruction across 96 episodes to determine frequency and types of teaching strategies used within this educational program.ResultsTarget word selection was appropriate in 77% of episodes. Some instructional strategies were used frequently (e.g., exposure to a word, examples, and nonexamples), whereas others were used rarely (e.g., definitions, active learning). Across episodes, there was substantial variability in how many opportunities children had to learn words.ConclusionsVocabulary instruction during Word on the Street could be improved by targeting only high-utility words, maximizing learning opportunities during all segments, and increasing strategies that promote deep processing. Although research is needed to examine word learning during Word on the Street, speech-language pathologists may find selected segments targeting Tier 2 words useful for augmenting traditional intervention approaches.
Impfpräventable Erkrankungen: Wissen, Einstellung und Impfstatus von Medizinstudierenden
Authors: Petersen S. , Roggendorf H. , Wicker S. 
Published: March 2015

Zusammenfassung
Ziel der Studie: Medizinisches Personal hat ein erhöhtes Infektionsrisiko und kann Infektionskrankheiten auf Patienten übertragen. Auch Medizinstudierende haben regelmäßigen Kontakt mit Patienten und sollten deswegen über den gleichen Immunschutz gegenüber impfpräventablen Infektionen wie medizinisches Personal verfügen. Ziel unserer Studie war das Wissen und die Einstellung zu arbeitsmedizinisch indizierten Impfungen sowie den Impfstaus der Medizinstudierenden zu erheben.
Methodik: Anonyme Fragebogenerhebung bei Medizinstudierenden des 4. vorklinischen Semesters der Goethe-Universität Frankfurt.
Ergebnisse und Schlussfolgerungen: Wenngleich eine hohe Akzeptanz der Medizinstudierenden hinsichtlich Impfungen festgestellt wurde, so ist das Wissen und der Impfstatus der Studierenden verbesserungswürdig. Bspw. wussten nur 46,4% der Medizinstudierenden, dass es eine generelle Influenzaimpfempfehlung für medizinisches Personal gibt und lediglich 76,8% der Studierenden gaben an, dass sie 2 Masernimpfungen erhalten hatten. Insgesamt 2/3 der Studierenden waren „sehr für Impfen“ bzw. „vollkommenen für Impfen“ und bewerteten die Wahrscheinlichkeit für ungeimpftes medizinisches Personal an einer arbeitsbedingten Infektion zu erkranken als „ziemlich groß“ bis „sehr groß“. Vor dem Hintergrund der positiven Grundeinstellung der Studierenden können – durch die Vermittlung von weiterem Wissen hinsichtlich impfpräventabler Infektionen und arbeitsbedingter Infektionsrisiken – mit einen konsequenten Impfangebot voraussichtlich hohe Impfquoten bei den Studierenden erreicht werden.
A Randomized Controlled Trial Comparing Transforaminal Lumbar Interbody Fusion and Uninstrumented Posterolateral Fusion in the Degenerative Lumbar Spine
Authors: Jalalpour Kourosh , Neumann Pavel , Johansson Christer , Hedlund Rune 
Published: March 2015

Study Design Randomized controlled trial. Objective Despite a large number of publications of outcomes after spinal fusion surgery, there is still no consensus on the efficacy of the several different fusion methods. The aim of this study was to determine whether transforaminal lumbar interbody fusion (TLIF) results in an improved clinical outcome compared with uninstrumented posterolateral fusion (PLF) in the surgical treatment for chronic low back pain. Methods This study included 135 patients with degenerative disk disease ( n = 96) or postdiskectomy syndrome ( n = 39). Inclusion criteria were at least 1 year of back pain with or without leg pain in patients aged 20 to 65 with one- or two-level disease. Exclusion criteria were sequestration of disk hernia, psychosocial instability, isthmic spondylolisthesis, drug abuse, and previous spine surgery other than diskectomy. Pain was assessed by visual analog scale (pain index). Functional disability was quantified by the disability rating index and Oswestry Disability Index. The global outcome was assessed by the patient and classified as much better, better, unchanged, or worse. The patients were randomized to conventional uninstrumented PLF ( n = 67) or TLIF ( n = 68). PLF was performed in a standardized fashion using autograft. TLIF was performed with pedicle titanium screw fixation and a porous tantalum interbody spacer with interbody and posterolateral autograft. The clinical outcome measurements were obtained preoperatively and at 12 and 24 months postoperatively. The 2-year follow-up rate was 98%. Results The two treatment groups improved significantly from preoperatively to 2 years’ follow-up. At final follow-up, the results in the TLIF group were significantly superior to those in the PLF group in pain index (2.0 versus 3.9, p = 0.007) and in disability rating index (22 versus 36, p = 0.003). The Oswestry Disability Index was better in the TLIF group (20 versus 28, p = 0.110, not significant). The global assessment was clearly superior in the TLIF group: 63% of patients scored “much better” in the TLIF group as compared with 48% in the PLF group ( p = 0.017). Conclusions The results of the current study support the use of TLIF rather than uninstrumented PLF in the surgical treatment of the degenerative lumbar spine. The less optimal outcome after uninstrumented PLF may be explained by the much higher reoperation rate.
Force-induced on-rate switching and modulation by mutations in gain-of-function von Willebrand diseases
Authors: Kim Jongseong , Hudson Nathan E. , Springer Timothy A. 
Published: March 2015

Significance
Binding of von Willebrand factor (VWF) to platelets is regulated by hydrodynamic forces in the vasculature. VWF can sense force and can bind when the hydrodynamics change due to bleeding. We show that force application switches the A1 domain in VWF to a second state with faster on-rate for its binding partner on platelets, GPIbα. This provides a physiological mechanism for activating VWF binding to platelets at sites of bleeding. Moreover, force increases the effects of gain-of-function mutations found in von Willebrand disease (VWD) and platelet-type VWD by mechanically stabilizing bond formation and strength.
Hemoglobin βCys93 is essential for cardiovascular function and integrated response to hypoxia
Authors: Zhang Rongli , Hess Douglas T. , Qian Zhaoxia , Hausladen Alfred , Fonseca Fabio , Chaube Ruchi , Reynolds James D. , Stamler Jonathan S. 
Published: March 2015

Significance
Oxygen delivery by RBC Hb is essential for life. Just three amino acids in Hb are conserved in all mammals and birds, but only two of those are required to carry oxygen. The third, a Cys within the β-chain, βCys93, has been assigned a role in carrying nitric oxide, which mediates vasodilation. However, the physiological importance of RBC-mediated vasoregulation is unknown. We show that blood flow and tissue oxygenation are markedly impaired in mice with a βCys93Ala mutation. The βCys93Ala mutation also results in myocardial ischemia, cardiac decompensation, and enhanced mortality. These findings support a new view of the respiratory cycle wherein, remarkably, RBCs regulate blood flow and (βCys93NO)-Hb is necessary for adequate tissue oxygenation and normal cardiovascular function.
Resiliency as a factor protecting youths from risky behaviour: Moderating effects of gender and sport
Authors: Lipowski Mariusz , Lipowska Małgorzata , Jochimek Magdalena , Krokosz Daniel 
Published: March 2015

AbstractWe hypothesised that resiliency may protect adolescents against risky behaviours, and that both the practicing of sports, and gender are moderating variables in relationships between resiliency and risky behaviours. The study included 18‐year‐old pupils from a selection of secondary schools (n = 556). A total of 188 individuals practiced competitive sports and the remaining 368 participants were non‐athletes. The participants were examined with the Resiliency Assessment Scale for Children and Adolescents (SPP‐18) and with a survey containing questions and statements related to high‐risk “experiments with adulthood”. Adolescent athletes showed higher levels of resiliency than their peers. The power of the “Determination and Persistence in Action” effect on “Alcohol” scale differed significantly between male athletes and male non‐athletes. Only in the athletes groups were higher scores on this scale reflected by lower values on the “Drugs” scale. Moreover, it is possible to observe differences in undertaking risky behaviour between male and female athletes. The analysis of risky sexual behaviour suggests that sport is a risk factor for men, and a protective factor for women. These data suggest that consistent prophylactic and psycho‐educative activities, with a special attention to differences between genders, should be provided to all the adolescents, irrespective of their sport performance levels.
PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R
Authors: Grau Jan , Grosse Ivo , Keilwagen Jens 
Published: March 2015

Abstract
Summary: Precision-recall (PR) and receiver operating characteristic (ROC) curves are valuable measures of classifier performance. Here, we present the R-package PRROC, which allows for computing and visualizing both PR and ROC curves. In contrast to available R-packages, PRROC allows for computing PR and ROC curves and areas under these curves for soft-labeled data using a continuous interpolation between the points of PR curves. In addition, PRROC provides a generic plot function for generating publication-quality graphics of PR and ROC curves.
Availability and implementation: PRROC is available from CRAN and is licensed under GPL 3.
Contact: grau@informatik.uni-halle.de
Learning chromatin states with factorized information criteria
Authors: Hamada Michiaki , Ono Yukiteru , Fujimaki Ryohei , Asai Kiyoshi 
Published: March 2015

Abstract
Motivation: Recent studies have suggested that both the genome and the genome with epigenetic modifications, the so-called epigenome, play important roles in various biological functions, such as transcription and DNA replication, repair, and recombination. It is well known that specific combinations of histone modifications (e.g. methylations and acetylations) of nucleosomes induce chromatin states that correspond to specific functions of chromatin. Although the advent of next-generation sequencing (NGS) technologies enables measurement of epigenetic information for entire genomes at high-resolution, the variety of chromatin states has not been completely characterized.
Results: In this study, we propose a method to estimate the chromatin states indicated by genome-wide chromatin marks identified by NGS technologies. The proposed method automatically estimates the number of chromatin states and characterize each state on the basis of a hidden Markov model (HMM) in combination with a recently proposed model selection technique, factorized information criteria. The method is expected to provide an unbiased model because it relies on only two adjustable parameters and avoids heuristic procedures as much as possible. Computational experiments with simulated datasets show that our method automatically learns an appropriate model, even in cases where methods that rely on Bayesian information criteria fail to learn the model structures. In addition, we comprehensively compare our method to ChromHMM on three real datasets and show that our method estimates more chromatin states than ChromHMM for those datasets.
Availability and implementation: The details of the characterized chromatin states are available in the Supplementary information. The program is available on request.
Contact: mhamada@waseda.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival
Authors: Suo Chen , Hrydziuszko Olga , Lee Donghwan , Pramana Setia , Saputra Dhany , Joshi Himanshu , Calza Stefano , Pawitan Yudi 
Published: March 2015

Abstract
Motivation: Genome and transcriptome analyses can be used to explore cancers comprehensively, and it is increasingly common to have multiple omics data measured from each individual. Furthermore, there are rich functional data such as predicted impact of mutations on protein coding and gene/protein networks. However, integration of the complex information across the different omics and functional data is still challenging. Clinical validation, particularly based on patient outcomes such as survival, is important for assessing the relevance of the integrated information and for comparing different procedures.
Results: An analysis pipeline is built for integrating genomic and transcriptomic alterations from whole-exome and RNA sequence data and functional data from protein function prediction and gene interaction networks. The method accumulates evidence for the functional implications of mutated potential driver genes found within and across patients. A driver-gene score (DGscore) is developed to capture the cumulative effect of such genes. To contribute to the score, a gene has to be frequently mutated, with high or moderate mutational impact at protein level, exhibiting an extreme expression and functionally linked to many differentially expressed neighbors in the functional gene network. The pipeline is applied to 60 matched tumor and normal samples of the same patient from The Cancer Genome Atlas breast-cancer project. In clinical validation, patients with high DGscores have worse survival than those with low scores (P = 0.001). Furthermore, the DGscore outperforms the established expression-based signatures MammaPrint and PAM50 in predicting patient survival. In conclusion, integration of mutation, expression and functional data allows identification of clinically relevant potential driver genes in cancer.
Availability and implementation: The documented pipeline including annotated sample scripts can be found in http://fafner.meb.ki.se/biostatwiki/driver-genes/.
Contact: yudi.pawitan@ki.se
Supplementary information: Supplementary data are available at Bioinformatics online.
Proper evaluation of alignment-free network comparison methods
Authors: Yaveroğlu Ömer Nebil , Milenković Tijana , Pržulj Nataša 
Published: March 2015

Abstract
Motivation: Network comparison is a computationally intractable problem with important applications in systems biology and other domains. A key challenge is to properly quantify similarity between wiring patterns of two networks in an alignment-free fashion. Also, alignment-based methods exist that aim to identify an actual node mapping between networks and as such serve a different purpose. Various alignment-free methods that use different global network properties (e.g. degree distribution) have been proposed. Methods based on small local subgraphs called graphlets perform the best in the alignment-free network comparison task, due to high level of topological detail that graphlets can capture. Among different graphlet-based methods, Graphlet Correlation Distance (GCD) was shown to be the most accurate for comparing networks. Recently, a new graphlet-based method called NetDis was proposed, which was claimed to be superior. We argue against this, as the performance of NetDis was not properly evaluated to position it correctly among the other alignment-free methods.
Results: We evaluate the performance of available alignment-free network comparison methods, including GCD and NetDis. We do this by measuring accuracy of each method (in a systematic precision-recall framework) in terms of how well the method can group (cluster) topologically similar networks. By testing this on both synthetic and real-world networks from different domains, we show that GCD remains the most accurate, noise-tolerant and computationally efficient alignment-free method. That is, we show that NetDis does not outperform the other methods, as originally claimed, while it is also computationally more expensive. Furthermore, since NetDis is dependent on the choice of a network null model (unlike the other graphlet-based methods), we show that its performance is highly sensitive to the choice of this parameter. Finally, we find that its performance is not independent on network sizes and densities, as originally claimed.
Contact: natasha@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
MeDuSa: a multi-draft based scaffolder
Authors: Bosi Emanuele , Donati Beatrice , Galardini Marco , Brunetti Sara , Sagot Marie-France , Lió Pietro , Crescenzi Pierluigi , Fani Renato , Fondi Marco 
Published: March 2015

Abstract
Motivation: Completing the genome sequence of an organism is an important task in comparative, functional and structural genomics. However, this remains a challenging issue from both a computational and an experimental viewpoint. Genome scaffolding (i.e. the process of ordering and orientating contigs) of de novo assemblies usually represents the first step in most genome finishing pipelines.
Results: In this article we present MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MeDuSa is highly accurate and, in most cases, outperforms traditional scaffolders. The possibility to use MeDuSa on eukaryotic datasets has also been evaluated, leading to interesting results.
Availability and implementation: MeDuSa web server: http://combo.dbe.unifi.it/medusa. A stand-alone version of the software can be downloaded from https://github.com/combogenomics/medusa/releases. All results presented in this work have been obtained with MeDuSa v. 1.3.
Contact: marco.fondi@unifi.it
Supplementary information: Supplementary data are available at Bioinformatics online.