bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Culturally and Linguistically Responsive Vocabulary Approach for Young Latino Dual Language Learners
Authors: Méndez Lucía I. , Crais Elizabeth R. , Castro Dina C. , Kainz Kirsten 
Published: December 2014

PurposeThis study examined the role of the language of vocabulary instruction in promoting English vocabulary in preschool Latino dual language learners (DLLs). The authors compared the effectiveness of delivering a single evidence-informed vocabulary approach using English as the language of vocabulary instruction (English culturally responsive [ECR]) versus using a bilingual modality that strategically combined Spanish and English (culturally and linguistically responsive [CLR]).MethodForty-two DLL Spanish-speaking preschoolers were randomly assigned to the ECR group (n= 22) or CLR group (n= 20). Thirty English words were presented during small-group shared readings in their preschools 3 times a week for 5 weeks. Multilevel models were used to examine group differences in postinstruction scores on 2 Spanish and 2 English vocabulary assessments at instruction end and follow-up.ResultsChildren receiving instruction in the CLR bilingual modality had significantly higher posttest scores (than those receiving the ECR English-only instruction) on Spanish and English vocabulary assessments at instruction end and on the Spanish vocabulary assessment at follow-up, even after controlling for preinstruction scores.ConclusionsThe results provide additional evidence of the benefits of strategically combining the first and second language to promote English and Spanish vocabulary development in this population. Future directions for research and clinical applications are discussed.
Differential Diagnosis of Children with Suspected Childhood Apraxia of Speech
Authors: Murray Elizabeth , McCabe Patricia , Heard Robert , Ballard Kirrie J. 
Published: December 2014

Purpose
The gold standard for diagnosing childhood apraxia of speech (CAS) is expert judgment of perceptual features. The aim of this study was to identify a set of objective measures that differentiate CAS from other speech disorders.

Method
Seventy-two children (4–12 years of age) diagnosed with suspected CAS by community speech-language pathologists were screened. Forty-seven participants underwent diagnostic assessment including presence or absence of perceptual CAS features. Twenty-eight children met two sets of diagnostic criteria for CAS (American Speech-Language-Hearing Association, 2007b; Shriberg, Potter, & Strand, 2009); another 4 met the CAS criteria with comorbidity. Fifteen were categorized as non-CAS with phonological impairment, submucous cleft, or dysarthria. Following this, 24 different measures from the diagnostic assessment were rated by blinded raters. Multivariate discriminant function analysis was used to identify the combination of measures that best predicted expert diagnoses.

Results
The discriminant function analysis model, including syllable segregation, lexical stress matches, percentage phonemes correct from a polysyllabic picture-naming task, and articulatory accuracy on repetition of /pətəkə/, reached 91% diagnostic accuracy against expert diagnosis.

Conclusions
Polysyllabic production accuracy and an oral motor examination that includes diadochokinesis may be sufficient to reliably identify CAS and rule out structural abnormality or dysarthria. Testing with a larger unselected sample is required.

Supplemental Material

https://doi.org/10.23641/asha.6170495
Phonetics Exercises Using the Alvin Experiment-Control Software
Authors: Hillenbrand James M. , Gayvert Robert T. , Clark Michael J. 
Published: December 2014

Purpose
Exercises are described that were designed to provide practice in phonetic transcription for students taking an introductory phonetics course. The goal was to allow instructors to offload much of the drill that would otherwise need to be covered in class or handled with paper-and-pencil tasks using text rather than speech as input.

Method
The exercises were developed using Alvin, a general-purpose software package for experiment design and control. The simplest exercises help students learn sound–symbol associations. For example, a vowel-transcription exercise presents listeners with consonant–vowel–consonant syllables on each trial; students are asked to choose among buttons labeled with phonetic symbols for 12 vowels. Several word-transcription exercises are included in which students hear a word and are asked to enter a phonetic transcription. Immediate feedback is provided for all of the exercises. An explanation of the methods that are used to create exercises is provided.

Results
Although no formal evaluation was conducted, comments on course evaluations suggest that most students found the exercises to be useful.

Conclusions
Exercises were developed for use in an introductory phonetics course. The exercises can be used in their current form, they can be modified to suit individual needs, or new exercises can be developed.
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Authors: Shen Shihao , Park Juw Won , Lu Zhi-xiang , Lin Lan , Henry Michael D. , Wu Ying Nian , Zhou Qing , Xing Yi 
Published: December 2014

Significance
Alternative splicing (AS) is an important mechanism of eukaryotic gene regulation. Deep RNA sequencing (RNA-Seq) has become a powerful approach for quantitative profiling of AS. With the increasing capacity of high-throughput sequencers, it has become common for RNA-Seq studies of AS to examine multiple biological replicates. We developed rMATS, a new statistical method for robust and flexible detection of differential AS from replicate RNA-Seq data. Besides the analysis of unpaired replicates, rMATS includes a model specifically designed for paired replicates, such as case–control matched pairs in clinical RNA-Seq datasets. We expect rMATS will be useful for genome-wide studies of AS in diverse research projects. Our data also provide new insights about the experimental design for RNA-Seq studies of AS.
Retrieval of Enterobacteriaceae drug targets using singular value decomposition
Authors: Silvério-Machado Rita , Couto Bráulio R. G. M. , dos Santos Marcos A. 
Published: December 2014

Abstract
Motivation: The identification of potential drug target proteins in bacteria is important in pharmaceutical research for the development of new antibiotics to combat bacterial agents that cause diseases.
Results: A new model that combines the singular value decomposition (SVD) technique with biological filters composed of a set of protein properties associated with bacterial drug targets and similarity to protein-coding essential genes of Escherichia coli (strain K12) has been created to predict potential antibiotic drug targets in the Enterobacteriaceae family. This model identified 99 potential drug target proteins in the studied family, which exhibit eight different functions and are protein-coding essential genes or similar to protein-coding essential genes of E.coli (strain K12), indicating that the disruption of the activities of these proteins is critical for cells. Proteins from bacteria with described drug resistance were found among the retrieved candidates. These candidates have no similarity to the human proteome, therefore exhibiting the advantage of causing no adverse effects or at least no known adverse effects on humans.
Contact: rita_silverio@hotmail.com.
Supplementary information: Supplementary data are available at Bioinformatics online.
Adaptive settings for the nearest-neighbor particle tracking algorithm
Authors: Mazzaferri Javier , Roy Joannie , Lefrancois Stephane , Costantino Santiago 
Published: December 2014

Abstract
Background: The performance of the single particle tracking (SPT) nearest-neighbor algorithm is determined by parameters that need to be set according to the characteristics of the time series under study. Inhomogeneous systems, where these characteristics fluctuate spatially, are poorly tracked when parameters are set globally.
Results: We present a novel SPT approach that adapts the well-known nearest-neighbor tracking algorithm to the local density of particles to overcome the problems of inhomogeneity.
Conclusions: We demonstrate the performance improvement provided by the proposed method using numerical simulations and experimental data and compare its performance with state of the art SPT algorithms.
Availability and implementation: The algorithms proposed here, are released under the GNU General Public License and are freely available on the web at http://sourceforge.net/p/adaptivespt.
Contact: javier.mazzaferri@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model
Authors: Tsoi Lam C. , Elder James T. , Abecasis Goncalo R. 
Published: December 2014

Abstract
Motivation: Pathway analysis to reveal biological mechanisms for results from genetic association studies have great potential to better understand complex traits with major human disease impact. However, current approaches have not been optimized to maximize statistical power to identify enriched functions/pathways, especially when the genetic data derives from studies using platforms (e.g. Immunochip and Metabochip) customized to have pre-selected markers from previously identified top-rank loci. We present here a novel approach, called Minimum distance-based Enrichment Analysis for Genetic Association (MEAGA), with the potential to address both of these important concerns.
Results: MEAGA performs enrichment analysis using graphical algorithms to identify sub-graphs among genes and measure their closeness in interaction database. It also incorporates a statistic summarizing the numbers and total distances of the sub-graphs, depicting the overlap between observed genetic signals and defined function/pathway gene-sets. MEAGA uses sampling technique to approximate empirical and multiple testing-corrected P-values. We show in simulation studies that MEAGA is more powerful compared to count-based strategies in identifying disease-associated functions/pathways, and the increase in power is influenced by the shortest distances among associated genes in the interactome. We applied MEAGA to the results of a meta-analysis of psoriasis using Immunochip datasets, and showed that associated genes are significantly enriched in immune-related functions and closer with each other in the protein–protein interaction network.
Availability and implementation: http://genome.sph.umich.edu/wiki/MEAGA
Contact: tsoi.teen@gmail.com or goncalo@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data
Authors: Wise Aaron , Bar-Joseph Ziv 
Published: December 2014

Abstract
Motivation: Current methods for reconstructing dynamic regulatory networks are focused on modeling a single response network using model organisms or cell lines. Unlike these models or cell lines, humans differ in their background expression profiles due to age, genetics and life factors. In addition, there are often differences in start and end times for time series human data and in the rate of progress based on the specific individual. Thus, new methods are required to integrate time series data from multiple individuals when modeling and constructing disease response networks.
Results: We developed Scalable Models for the Analysis of Regulation from Time Series (SMARTS), a method integrating static and time series data from multiple individuals to reconstruct condition-specific response networks in an unsupervised way. Using probabilistic graphical models, SMARTS iterates between reconstructing different regulatory networks and assigning individuals to these networks, taking into account varying individual start times and response rates. These models can be used to group different sets of patients and to identify transcription factors that differentiate the observed responses between these groups. We applied SMARTS to analyze human response to influenza and mouse brain development. In both cases, it was able to greatly improve baseline groupings while identifying key relevant TFs that differ between the groups. Several of these groupings and TFs are known to regulate the relevant processes while others represent novel hypotheses regarding immune response and development.
Availability and implementation: Software and Supplementary information are available at http://sb.cs.cmu.edu/smarts/.
Contact: zivbj@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements
Authors: Hwang Yih-Chii , Lin Chiao-Feng , Valladares Otto , Malamon John , Kuksa Pavel P. , Zheng Qi , Gregory Brian D. , Wang Li-San 
Published: December 2014

Abstract
Summary: We implemented a high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA–DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer–target gene relationships.
Availability and implementation: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine. The source code is freely available under the MIT license for academic and nonprofit use. The source code and instructions are available at the Wang lab website (http://wanglab.pcbi.upenn.edu/hippie/). It is also provided as an Amazon Machine Image to be used directly on Amazon Cloud with minimal installation.
Contact: lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu
Supplementary information: Supplementary Material is available at Bioinformatics online.
QuASAR: quantitative allele-specific analysis of reads
Authors: Harvey Chris T. , Moyerbrailean Gregory A. , Davis Gordon O. , Wen Xiaoquan , Luca Francesca , Pique-Regi Roger 
Published: December 2014

Abstract
Motivation: Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls.
Results: We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available.
Availability and implementation: http://github.com/piquelab/QuASAR.
Contact: fluca@wayne.edu or rpique@wayne.edu
Supplementary information: Supplementary Material is available at Bioinformatics online.
GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences
Authors: Sato Tetsuya , Suyama Mikita 
Published: December 2014

Abstract
Summary: Genome sequence alignments provide valuable information on many aspects of molecular biological processes. In this study, we developed a web server, GenomeCons, for manipulating multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence analyses. This server facilitates the visual inspection of multiple genome sequence alignments for a set of genomic intervals at a time. This allows the user to examine how these sites are evolutionarily conserved over time for their functional importance. The server also reports consensus sequences for the input genomic intervals, which can be applied to downstream analyses such as the identification of common motifs in the regions determined by ChIP-seq experiments.
Availability and implementation: GenomeCons is freely accessible at http://bioinfo.sls.kyushu-u.ac.jp/genomecons/
Contact: mikita@bioreg.kyushu-u.ac.jp
Semiconductor sequencing: how many flows do you need?
Authors: Budczies Jan , Bockmayr Michael , Treue Denise , Klauschen Frederick , Denkert Carsten 
Published: December 2014

Abstract
Motivation: Semiconductor sequencing directly translates chemically encoded information (A, C, G or T) into voltage signals that are detected by a semiconductor device. Changes of pH value and thereby of the electric potential in the reaction well are detected during strand synthesis from nucleotides provided in cyclic repeated flows for each type of nucleotide. To minimize time requirement and costs, it is necessary to know the number of flows that are required for complete coverage of the templates.
Results: We calculate the number of required flows in a random sequence model and present exact expressions for cumulative distribution function, expected value and variance. Additionally, we provide an algorithm to calculate the number of required flows for a concrete list of amplicons using a BED file of genomic positions as input. We apply the algorithm to calculate the number of flows that are required to cover six amplicon panels that are used for targeted sequencing in cancer research. The upper bounds obtained for the number of flows allow to enhance the instrument throughput from two chips to three chips per day for four of these panels.
Availability and implementation: The algorithm for calculation of the flows was implemented in R and is available as package ionflows from the CRAN repository.
Contact: jan.budczies@charite.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Are the broad optical Balmer lines in PG 1613+658 from the central accretion disc?
Authors: Zhang Xue-Guang 
Published: December 2014

Abstract
In this letter, we report on the positive correlations between the broad-line width and broad-line flux for the broad Balmer lines of the active galactic nucleus (AGN) PG 1613+658, which has been observed for a long time. Rather than the expected negative correlations that come with the widely accepted virialization assumption for AGN broad emission-line regions (BLRs), the positive correlations indicate very different BLR structures of PG 1613+658 from the commonly considered BLR structures that are dominated by the equilibrium between radiation pressure and gas pressure. Therefore, it is preferable to assume that the observed broad single-peaked optical Balmer lines of PG 1613+658 originate from the accretion disc, because the mainly gravity-dominated disc-like BLRs with radial structures have few effects from radiation pressure.
The inefficiency of satellite accretion in forming extended star clusters
Authors: Bianchini Paolo , Renaud Florent , Gieles Mark , Varri Anna Lisa 
Published: December 2014

Abstract
The distinction between globular clusters and dwarf galaxies has been progressively blurred by the recent discoveries of several extended star clusters, with size (20–30 pc) and luminosity (−6 &lt; Mv &lt; −2) comparable to the one of the faint dwarf spheroidals. In order to explain their sparse structure, it has been suggested that they formed as star clusters in dwarf galaxy satellites that later accreted on to the Milky Way. If these clusters form in the centre of dwarf galaxies, they evolve in a tidally compressive environment where the contribution of the tides to the virial balance can become significant, and lead to a supervirial state and subsequent expansion of the cluster, once removed. Using N-body simulations, we show that a cluster formed in such an extreme environment undergoes a sizable expansion, during the drastic variation of the external tidal field due to the accretion process. However, we show that the expansion due to the removal of the compressive tides is not enough to explain the observed extended structure, since the stellar systems resulting from this process are always more compact than the corresponding clusters that expand in isolation due to two-body relaxation. We conclude that an accreted origin of extended globular clusters is unlikely to explain their large spatial extent, and rather favour the hypothesis that such clusters are already extended at the stage of their formation.
Non-linear mirror instability
Authors: Rincon F. , Schekochihin A. A. , Cowley S. C. 
Published: December 2014

Abstract
Slow dynamical changes in magnetic-field strength and invariance of the particles’ magnetic moments generate ubiquitous pressure anisotropies in weakly collisional, magnetized astrophysical plasmas. This renders them unstable to fast, small-scale mirror and firehose instabilities, which are capable of exerting feedback on the macroscale dynamics of the system. By way of a new asymptotic theory of the early non-linear evolution of the mirror instability in a plasma subject to slow shearing or compression, we show that the instability does not saturate quasi-linearly at a steady, low-amplitude level. Instead, the trapping of particles in small-scale mirrors leads to non-linear secular growth of magnetic perturbations, δB/B ∝ t2/3. Our theory explains recent collisionless simulation results, provides a prediction of the mirror evolution in weakly collisional plasmas and establishes a foundation for a theory of non-linear mirror dynamics with trapping, valid up to δB/B = O(1).