bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Computer System and Vowel Loading on Measures of Nasalance
Authors: Awan Shaheen N. , Omlor Kristin , Watts Christopher R. 
Published: April 2011

Purpose
The purpose of this study was to determine similarities and differences in nasalance scores observed with different computerized nasalance systems in the context of vowel-loaded sentences.

Methodology
Subjects were 46 Caucasian adults with no perceived hyper- or hyponasality. Nasalance scores were obtained using the Nasometer 6200 (Kay Elemetrics Corp.), the Nasometer II 6400 (Kay Elemetrics Corp.), and the NasalView (Tiger DRS, Inc.) for sentences loaded with mixed, high front, high back, low front, or low back vowels.

Results
Measures of nasalance obtained with the NasalView were significantly higher than those obtained with the Nasometer 6200, and the measures of nasalance obtained with the Nasometer 6200 were significantly higher than those obtained with the Nasometer II 6400. However, similar effects of vowel loading on measures of nasalance were observed, regardless of system. For all systems, the high front vowel sentence tended to result in higher measures of nasalance than did the high back, low front, and low back vowel sentences—the mixed vowel sentence tended to have a higher degree of nasalance than did any of the other sentences.

Conclusions
Although nasalance data computed using different systems are not readily comparable, all three systems that were evaluated produced similar effects of vowel loading on nasalance. Increased nasalance for high front versus low back vowels may be due to factors such as increased oral impedance, reduced radiated oral sound pressure, possible increases in airflow via the nasal cavity, and increased transpalatal nasalance.
Bimodal Hearing and Speech Perception With a Competing Talker
Authors: Pyschny Verena , Landwehr Markus , Hahn Moritz , Walger Martin , von Wedel Hasso , Meister Hartmut 
Published: April 2011

Purpose
The objective of the study was to investigate the influence of bimodal stimulation upon hearing ability for speech recognition in the presence of a single competing talker.

Method
Speech recognition was measured in 3 listening conditions: hearing aid (HA) alone, cochlear implant (CI) alone, and both devices together (CI + HA). To examine the use of low-frequency cues, the competing masker voice was manipulated with respect to fundamental frequency (F0) and formant frequencies. Twelve implanted adults were included in the study.

Results
Group results revealed only a relatively small benefit of CI + HA compared with the CI alone. A detailed analysis of errors, which was assumed to be an indicator for the release from masking, revealed that this benefit was not attributed to improved target–masker segregation. The variable determined to be responsible for segregating target and masker talkers was a large difference in F0 of the voices. This held true for all CI alone, HA alone, and CI + HA listening conditions.

Conclusions
Bimodal hearing improved overall speech recognition of both the target and the masker. No evidence for better target–masker separation with bimodal fitting could be found.
Accuracy of the NDI Wave Speech Research System
Authors: Berry Jeffrey J. 
Published: April 2011

Purpose
This work provides a quantitative assessment of the positional tracking accuracy of the NDI Wave Speech Research System.

Method
Three experiments were completed: (a) static rigid-body tracking across different locations in the electromagnetic field volume, (b) dynamic rigid-body tracking across different locations within the electromagnetic field volume, and (c) human jaw-movement tracking during speech. Rigid-body experiments were completed for 4 different instrumentation settings, permuting 2 electromagnetic field volume sizes with and without automated reference sensor processing.

Results

Within the anthropometrically pertinent “near field” (< 200 mm) of the NDI Wave field generator, at the 300-mm
3
volume setting, 88% of dynamic positional errors were < 0.5 mm and 98% were < 1.0 mm. Extreme tracking errors (> 2 mm) occurred within the near field for < 1% of position samples. For human jaw-movement tracking, 95% of position samples had < 0.5 mm errors for 9 out of 10 subjects.

Conclusions

Static tracking accuracy is modestly superior to dynamic tracking accuracy. Dynamic tracking accuracy is best for the 300-mm
3
field setting in the 200-mm near field. The use of automated head correction has no deleterious effect on tracking. Tracking errors for jaw movements during speech are typically < 0.5 mm.
Effects of Voice Therapy on Relative Fundamental Frequency During Voicing Offset and Onset in Patients With Vocal Hyperfunction
Authors: Stepp Cara E. , Merchant Gabrielle R. , Heaton James T. , Hillman Robert E. 
Published: April 2011

Purpose
The purpose of this study was to determine whether the relative fundamental frequency (RFF) surrounding a voiceless consonant in patients with hyperfunctionally related voice disorders would normalize after a successful course of voice therapy.

Method
Pre- and posttherapy measurements of RFF were compared in 16 subjects undergoing voice therapy for voice disorders associated with vocal hyperfunction.

Results

A 2-way analysis of variance showed a statistically significant effect of both cycle of vibration near the consonant and therapy phase (pre- vs. post-), with
p
< .001. A post hoc paired Student’s
t
test showed that posttherapy RFF measurements were significantly higher (more typical;
p
< .0001) than pretherapy measurements.

Conclusions
Prior to therapy, participants exhibited lowered RFF values, similar to those found previously (Stepp, Hillman, & Heaton, 2010). After successful completion of voice therapy, RFF values increased toward patterns seen previously in individuals with healthy typical voice. The goal of voice therapy in these patients was to reduce laryngeal muscle tension; therefore, the increase of RFF toward more typical values may be indicative of decreased baseline laryngeal muscle tension resulting from therapy. Results are discussed further in terms of necessary research to incorporate RFF as a clinical measure of vocal hyperfunction.
A novel high resolution ion wide angle spectrometer
Authors: Jung D. , Hörlein R. , Gautier D. C. , Letzring S. , Kiefer D. , Allinger K. , Albright B. J. , Shah R. , Palaniyappan S. , Yin L. , Fernández J. C. , Habs D. , Hegelich B. M. 
Published: April 2011

A novel ion wide angle spectrometer (iWASP) has been developed, which is capable of measuring angularly resolved energy distributions of protons and a second ion species, such as carbon C6 +, simultaneously. The energy resolution for protons and carbon ions is better than 10% at ∼50 MeV/nucleon and thus suitable for the study of novel laser-ion acceleration schemes aiming for ultrahigh particle energies. A wedged magnet design enables an acceptance angle of 30°(∼524 mrad) and high angular accuracy in the μrad range. First, results obtained at the LANL Trident laser facility are presented demonstrating high energy and angular resolution of this novel iWASP.
Direct observation of Young’s double-slit interferences in vibrationally resolved photoionization of diatomic molecules
Authors: Canton Sophie E. , Plésiat Etienne , Bozek John D. , Rude Bruce S. , Decleva Piero , Martín Fernando 
Published: April 2011

Vibrationally resolved valence-shell photoionization spectra of H
2
, N
2
and CO have been measured in the photon energy range 20–300 eV using third-generation synchrotron radiation. Young’s double-slit interferences lead to oscillations in the corresponding vibrational ratios, showing that the molecules behave as two-center electron-wave emitters and that the associated interferences leave their trace in the angle-integrated photoionization cross section. In contrast to previous work, the oscillations are directly observable in the experiment, thereby removing any possible ambiguity related to the introduction of external parameters or fitting functions. A straightforward extension of an original idea proposed by Cohen and Fano [Cohen HD, Fano U (1966)
Phys Rev
150:30] confirms this interpretation and shows that it is also valid for diatomic heteronuclear molecules. Results of accurate theoretical calculations are in excellent agreement with the experimental findings.
datPAV—an online processing, analysis and visualization tool for exploratory investigation of experimental data
Authors: Biswas Ambarish , Rao Raghuraj , Umashankar Shivshankar , Mynampati Kalyan C. , Reuben Sheela , Parab Gauri , Swarup Sanjay 
Published: April 2011

Abstract
Summary:Data processing, analysis and visualization (datPAV) is an exploratory tool that allows experimentalist to quickly assess the general characteristics of the data. This platform-independent software is designed as a generic tool to process and visualize data matrices. This tool explores organization of the data, detect errors and support basic statistical analyses. Processed data can be reused whereby different step-by-step data processing/analysis workflows can be created to carry out detailed investigation. The visualization option provides publication-ready graphics. Applications of this tool are demonstrated at the web site for three cases of metabolomics, environmental and hydrodynamic data analysis.
Availability: datPAV is available free for academic use at http://www.sdwa.nus.edu.sg/datPAV/.
Contact: sanjay@nus.edu.sg
Normalizing bead-based microRNA expression data: a measurement error model-based approach
Authors: Wang Bin , Wang Xiao−Feng , Xi Yaguang 
Published: April 2011

Abstract
Motivation: Compared with complementary DNA (cDNA) or messenger RNA (mRNA) microarray data, microRNA (miRNA) microarray data are harder to normalize due to the facts that the total number of miRNAs is small, and that the majority of miRNAs usually have low expression levels. In bead-based microarrays, the hybridization is completed in several pools. As a result, the number of miRNAs tested in each pool is even smaller, which poses extra difficulty to intrasample normalization and ultimately affects the quality of the final profiles assembled from various pools. In this article, we consider a measurement error model-based method for bead-based microarray intrasample normalization.
Results: In this study, results from quantitative real-time PCR (qRT-PCR) assays are used as ‘gold standards’ for validation. The performance of the proposed measurement error model-based method is evaluated via a simulation study and real bead-based miRNA expression data. Simulation results show that the new method performs well to assemble complete profiles from subprofiles from various pools. Compared with two intrasample normalization methods recommended by the manufacturer, the proposed approach produces more robust final complete profiles and results in better agreement with the qRT-PCR results in identifying differentially expressed miRNAs, and hence improves the reproducibility between the two microarray platforms. Meaningful results are obtained by the proposed intrasample normalization method, together with quantile normalization as a subsequent complemental intersample normalization method.
Availability: Datasets and R package are available at http://gauss.usouthal.edu/publ/beadsme/.
Contact: bwang@jaguar1.usouthal.edu
BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data
Authors: Yu Guoqiang , Zhang Bai , Bova G. Steven , Xu Jianfeng , Shih Ie−Ming , Wang Yue 
Published: April 2011

Abstract
Motivation: Identification of somatic DNA copy number alterations (CNAs) and significant consensus events (SCEs) in cancer genomes is a main task in discovering potential cancer-driving genes such as oncogenes and tumor suppressors. The recent development of SNP array technology has facilitated studies on copy number changes at a genome-wide scale with high resolution. However, existing copy number analysis methods are oblivious to normal cell contamination and cannot distinguish between contributions of cancerous and normal cells to the measured copy number signals. This contamination could significantly confound downstream analysis of CNAs and affect the power to detect SCEs in clinical samples.
Results: We report here a statistically principled in silico approach, Bayesian Analysis of COpy number Mixtures (BACOM), to accurately estimate genomic deletion type and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We tested the proposed method on two simulated datasets, two prostate cancer datasets and The Cancer Genome Atlas high-grade ovarian dataset, and obtained very promising results supported by the ground truth and biological plausibility. Moreover, based on a large number of comparative simulation studies, the proposed method gives significantly improved power to detect SCEs after in silico correction of normal tissue contamination. We develop a cross-platform open-source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues including relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, making it straightforward to include in existing data pipelines.
Availability: The cross-platform, stand-alone Java application, BACOM, the R interface, bacomR, all source code and the simulation data used in this article are freely available at authors' web site: http://www.cbil.ece.vt.edu/software.htm.
Contact: yuewang@vt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
PathScan: a tool for discerning mutational significance in groups of putative cancer genes
Authors: Wendl Michael C. , Wallis John W. , Lin Ling , Kandoth Cyriac , Mardis Elaine R. , Wilson Richard K. , Ding Li 
Published: April 2011

Abstract
Motivation: The expansion of cancer genome sequencing continues to stimulate development of analytical tools for inferring relationships between somatic changes and tumor development. Pathway associations are especially consequential, but existing algorithms are demonstrably inadequate.
Methods: Here, we propose the PathScan significance test for the scenario where pathway mutations collectively contribute to tumor development. Its design addresses two aspects that established methods neglect. First, we account for variations in gene length and the consequent differences in their mutation probabilities under the standard null hypothesis of random mutation. The associated spike in computational effort is mitigated by accurate convolution-based approximation. Second, we combine individual probabilities into a multiple-sample value using Fisher–Lancaster theory, thereby improving differentiation between a few highly mutated genes and many genes having only a few mutations apiece. We investigate accuracy, computational effort and power, reporting acceptable performance for each.
Results: As an example calculation, we re-analyze KEGG-based lung adenocarcinoma pathway mutations from the Tumor Sequencing Project. Our test recapitulates the most significant pathways and finds that others for which the original test battery was inconclusive are not actually significant. It also identifies the focal adhesion pathway as being significantly mutated, a finding consistent with earlier studies. We also expand this analysis to other databases: Reactome, BioCarta, Pfam, PID and SMART, finding additional hits in ErbB and EPHA signaling pathways and regulation of telomerase. All have implications and plausible mechanistic roles in cancer. Finally, we discuss aspects of extending the method to integrate gene-specific background rates and other types of genetic anomalies.
Availability: PathScan is implemented in Perl and is available from the Genome Institute at: http://genome.wustl.edu/software/pathscan.
Contact: mwendl@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
OTUbase: an R infrastructure package for operational taxonomic unit data
Authors: Beck Daniel , Settles Matt , Foster James A. 
Published: April 2011

Abstract
Summary: OTUbase is an R package designed to facilitate the analysis of operational taxonomic unit (OTU) data and sequence classification (taxonomic) data. Currently there are programs that will cluster sequence data into OTUs and/or classify sequence data into known taxonomies. However, there is a need for software that can take the summarized output of these programs and organize it into easily accessed and manipulated formats. OTUbase provides this structure and organization within R, to allow researchers to easily manipulate the data with the rich library of R packages currently available for additional analysis.
Availability: OTUbase is an R package available through Bioconductor. It can be found at http://www.bioconductor.org/packages/release/bioc/html/OTUbase.html.
Contact: msettles@uidaho.edu
MAISTAS: a tool for automatic structural evaluation of alternative splicing products
Authors: Floris Matteo , Raimondo Domenico , Leoni Guido , Orsini Massimiliano , Marcatili Paolo , Tramontano Anna 
Published: April 2011

Abstract
Motivation: Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins.
Results: Here we describe a publicly available tool that, given a gene or a protein, retrieves and analyses all its annotated isoforms, provides users with three-dimensional models of the isoform(s) of his/her interest whenever possible and automatically assesses whether homology derived structural models correspond to plausible structures. This information is clearly relevant. When the homology model of some isoforms of a gene does not seem structurally plausible, the implications are that either they assume a structure unrelated to that of the other isoforms of the same gene with presumably significant functional differences, or do not correspond to functional products. We provide indications that the second hypothesis is likely to be true for a substantial fraction of the cases.
Availability: http://maistas.bioinformatica.crs4.it/.
Contact: anna.tramontano@uniromal.it
An overview of global catch statistics for inland fish
Authors: Welcomme Robin L. 
Published: April 2011

Abstract
Welcomme, R. L. 2011. An overview of global catch statistics for inland fish. – ICES Journal of Marine Science, 68: 1751–1756. The reported global inland fish catch passed 10 million tonnes in 2008, after almost linear growth from the early 1950s. The rise coincides with an increasing number of reports of falling catches resulting from environmental degradation. It is thought that catches from inland waters were underreported in the past because of constraints on collecting the relevant data. National approaches to data collection are not generally comparable and their accuracy not usually assessed. National data processing and reporting should be audited, and training undertaken to harmonize these activities. The apparently bigger catches probably result from better reporting of actual catches rather than any increase in the amount of fish landed. Current data are sufficient only for a general overview of global inland catches of fish, rather than for the detailed analysis needed for management, policy formulation, and the valuation of inland fisheries. There is a need for improved approaches to data collection and for historical catches to be corrected to account for changes in methodologies and reporting procedures.
Photoprotective Energy Dissipation Involves the Reorganization of Photosystem II Light-Harvesting Complexes in the Grana Membranes of Spinach Chloroplasts
Authors: Johnson Matthew P. , Goral Tomasz K. , Duffy Christopher D.P. , Brain Anthony P.R. , Mullineaux Conrad W. , Ruban Alexander V. 
Published: April 2011

Abstract
Plants must regulate their use of absorbed light energy on a minute-by-minute basis to maximize the efficiency of photosynthesis and to protect photosystem II (PSII) reaction centers from photooxidative damage. The regulation of light harvesting involves the photoprotective dissipation of excess absorbed light energy in the light-harvesting antenna complexes (LHCs) as heat. Here, we report an investigation into the structural basis of light-harvesting regulation in intact spinach (Spinacia oleracea) chloroplasts using freeze-fracture electron microscopy, combined with laser confocal microscopy employing the fluorescence recovery after photobleaching technique. The results demonstrate that formation of the photoprotective state requires a structural reorganization of the photosynthetic membrane involving dissociation of LHCII from PSII and its aggregation. The structural changes are manifested by a reduced mobility of LHC antenna chlorophyll proteins. It is demonstrated that these changes occur rapidly and reversibly within 5 min of illumination and dark relaxation, are dependent on ΔpH, and are enhanced by the deepoxidation of violaxanthin to zeaxanthin.
TheArabidopsis thalianaCheckpoint Kinase WEE1 Protects against Premature Vascular Differentiation during Replication Stress
Authors: Cools Toon , Iantcheva Anelia , Weimer Annika K. , Boens Shannah , Takahashi Naoki , Maes Sara , Van den Daele Hilde , Van Isterdael Gert , Schnittger Arp , De Veylder Lieven 
Published: April 2011

AbstractA sessile lifestyle forces plants to respond promptly to factors that affect their genomic integrity. Therefore, plants have developed checkpoint mechanisms to arrest cell cycle progression upon the occurrence of DNA stress, allowing the DNA to be repaired before onset of division. Previously, the WEE1 kinase had been demonstrated to be essential for delaying progression through the cell cycle in the presence of replication-inhibitory drugs, such as hydroxyurea. To understand the severe growth arrest of WEE1-deficient plants treated with hydroxyurea, a transcriptomics analysis was performed, indicating prolonged S-phase duration. A role for WEE1 during S phase was substantiated by its specific accumulation in replicating nuclei that suffered from DNA stress. Besides an extended replication phase, WEE1 knockout plants accumulated dead cells that were associated with premature vascular differentiation. Correspondingly, plants without functional WEE1 ectopically expressed the vascular differentiation marker VND7, and their vascular development was aberrant. We conclude that the growth arrest of WEE1-deficient plants is due to an extended cell cycle duration in combination with a premature onset of vascular cell differentiation. The latter implies that the plant WEE1 kinase acquired an indirect developmental function that is important for meristem maintenance upon replication stress.