bluuebunny/crossref_metadata_2025_split huggingface dataset:
Audiometric Thresholds: Stimulus Considerations in Sound Field and Under Earphones
Authors: Norrix Linda W. , Anderson Alora 
Published: August 2015

Purpose
This study evaluates a new stimulus, FREquency Specific Hearing assessment (FRESH) noise, to obtain hearing thresholds and reviews the potential pitfalls of using narrow band noise.

Method
Twelve adults with simulated gradually sloping hearing loss and 12 adults with steeply sloping hearing loss participated. Hearing thresholds were measured in sound field and under a supraaural earphone for FRESH noise, warbled tones, and narrowband noise. Pure-tone thresholds were also measured under the supraaural earphone.

Results
FRESH noise thresholds were similar to pure-tone and warbled-tone thresholds regardless of audiometric configuration. For the group with gradually sloping hearing loss, thresholds obtained with narrowband noise were approximately 4 dB better than those obtained with the other test stimuli. For the group with steeply sloping hearing loss, narrowband noise significantly underestimated hearing thresholds—the steeper the hearing loss, the greater the underestimation.

Conclusions
When hearing loss is suspected, FRESH noise is appropriate for accurately determining audiometric thresholds in sound field and under earphones. A wider band, attention-getting stimulus such as narrowband noise can result in thresholds that are inaccurate. Clinical decision making regarding choice of test stimulus is discussed.
Relationships Between Formant Frequencies of Sustained Vowels and Tongue Contours Measured by Ultrasonography
Authors: Lee Shao-Hsuan , Yu Jen-Fang , Hsieh Yu-Hsiang , Lee Guo-She 
Published: August 2015

Purpose
The purpose of this study was to explore the formant–articulation relationships in corner vowels by acoustic analysis of speech signals and measuring tongue contour using ultrasonography.

Method

Eighteen healthy adults (8 men, 10 women), aged between 20 and 40 years, were enrolled. Speech signals of sustained vowels /ɑ/, /i/, and /u/ were recorded to obtain the first 2 formant frequencies. Tongue height, tongue advancement, and lengths of posterior tongue surface (L
PTS
) and anterior oral cavity (L
AOC
) were obtained using ultrasound image processing technique in order to examine the resonance mechanism of the oral vocal tract.

Results

L
PTS
and L
AOC
, as well as mean frequencies of the first and second formants, showed significant differences between sexes and among vowels. The first formant significantly and better correlated with L
PTS
than with tongue height (
r
= –.78,
p
< .001, Pearson's correlation). The correlation of the second formant with L
AOC
(
r
= –.85,
p
< .001) was also significant and better than the correlation with tongue advancement. Sex, however, did not show significant correlation with the formant frequencies.

Conclusions
Ultrasonographic measurements of tongue contour correlated well to the formant frequencies. The results stressed the importance of tongue shaping in articulation. Although more studies are necessary in clinical implications, disorders associated with abnormal tongue shaping may be the target applications in the future.
“My World Has Expanded Even Though I'm Stuck at Home”: Experiences of Individuals With Amyotrophic Lateral Sclerosis Who Use Augmentative and Alternative Communication and Social Media
Authors: Caron Jessica , Light Janice 
Published: August 2015

Purpose
This study aimed to expand the current understanding of how persons with amyotrophic lateral sclerosis (pALS) use augmentative and alternative communication and social media to address their communication needs.

Method
An online focus group was used to investigate the experiences of 9 pALS who use augmentative and alternative communication and social media. Questions posed to the group related to (a) current use of social media, (b) advantages of social media, (c) barriers to independent use, (d) supports to independent use, and (e) recommendations for developers, policy makers, and other pALS.

Results
Participants primarily reported that use of social media was a beneficial tool that provided increased communication opportunities, connections to communication partners, and networks of support. Specific results are discussed with reference to the research as well as implications for practice and recommendations for future research.

Conclusions
As individuals with ALS experience loss of function, some communication modes may no longer be viable. Providing access to different modes of communication, including social media, can allow independence, participation and better quality of life.
A Drawing Task to Assess Emotion Inference in Language-Impaired Children
Authors: Vendeville Nathalie , Blanc Nathalie , Brechet Claire 
Published: August 2015

Purpose
Studies investigating the ability of children with language impairment (LI) to infer emotions rely on verbal responses (which can be challenging for these children) and/or the selection of a card representing an emotion (which limits the response range). In contrast, a drawing task might allow a broad spectrum of responses without involving language. This study used a drawing task to compare the ability to make emotional inferences in children with and without LI.

Method
Twenty-two children with LI and 22 typically developing children ages 6 to 10 years were assessed in school during 3 sessions. They were asked to listen to audio stories. At specific moments, the experimenter stopped the recording and asked children to complete the drawing of a face to depict the emotion felt by the story's character. Three adult study-blind judges were subsequently asked to evaluate the expressiveness of the drawings.

Results
Children with LI had more difficulty than typically developing children making emotional inferences. Children with LI also made more errors of different valence than their typically developing peers.

Conclusion
Our findings confirm that children with LI show difficulty in producing emotional inferences, even when performing a drawing task—a relatively language-free response mode.
Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose–response data
Authors: Mpindi John-Patrick , Swapnil Potdar , Dmitrii Bychkov , Jani Saarela , Saeed Khalid , Wennerberg Krister , Aittokallio Tero , Östling Päivi , Kallioniemi Olli 
Published: August 2015

Abstract
Motivation: Most data analysis tools for high-throughput screening (HTS) seek to uncover interesting hits for further analysis. They typically assume a low hit rate per plate. Hit rates can be dramatically higher in secondary screening, RNAi screening and in drug sensitivity testing using biologically active drugs. In particular, drug sensitivity testing on primary cells is often based on dose–response experiments, which pose a more stringent requirement for data quality and for intra- and inter-plate variation. Here, we compared common plate normalization and noise-reduction methods, including the B-score and the Loess a local polynomial fit method under high hit-rate scenarios of drug sensitivity testing. We generated simulated 384-well plate HTS datasets, each with 71 plates having a range of 20 (5%) to 160 (42%) hits per plate, with controls placed either at the edge of the plates or in a scattered configuration.
Results: We identified 20% (77/384) as the critical hit-rate after which the normalizations started to perform poorly. Results from real drug testing experiments supported this estimation. In particular, the B-score resulted in incorrect normalization of high hit-rate plates, leading to poor data quality, which could be attributed to its dependency on the median polish algorithm. We conclude that a combination of a scattered layout of controls per plate and normalization using a polynomial least squares fit method, such as Loess helps to reduce column, row and edge effects in HTS experiments with high hit-rates and is optimal for generating accurate dose–response curves.
Contact: john.mpindi@helsinki.fi
Availability and implementation, Supplementary information: R code and Supplementary data are available at Bioinformatics online.
Accurate disulfide-bonding network predictions improveab initiostructure prediction of cysteine-rich proteins
Authors: Yang Jing , He Bao-Ji , Jang Richard , Zhang Yang , Shen Hong-Bin 
Published: August 2015

AbstractMotivation: Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g. &gt;3 bonds, is too low to effectively assist structure assembly simulations.Results: We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins.Availability and implementation: http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/Contact: zhng@umich.edu or hbshen@sjtu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Reducing bias due to noise and attenuation in open-ocean echo integration data
Authors: Ryan Tim E. , Downie Ryan A. , Kloser Rudy J. , Keith Gordon 
Published: August 2015

Abstract
Measurements of mean volume backscattering strength (Sv, dB re 1 m−1) at ocean-basin scale were made using 38-kHz hull-mounted echosounders on ships of opportunity as part of Australia's Integrated Marine Observing System. The data were collected on vessels of various designs, none of which were purposely built for collecting high-quality acoustic data. A full range of weather extremes affected the quality of the data and could cause large biases in Sv. To remove first-order biases and improve processing efficiency, a sequence of new and existing data processing filters were applied in a semi-automated procedure. These filters were designed to mitigate the effects of three types of noise: impulsive (less than one ping), transient (multiple pings), and background (hours or longer). A filter was also applied to identify signals that were attenuated by air bubbles beneath the transducer. These filters were applied to data from transits across the Southwest Pacific, Indian, and Southern Oceans to produce quality-controlled Sv datasets that are now available from a publicly accessible repository. These filters may be relevant to other open-ocean acoustic observing endeavours, and one or more could be used to mitigate bias in data from a range of acoustic applications.
Contrasting effects of ocean acidification on the microbial food web under different trophic conditions
Authors: Sala M. M. , Aparicio F. L. , Balagué V. , Boras J. A. , Borrull E. , Cardelús C. , Cros L. , Gomes A. , López-Sanz A. , Malits A. , Martínez R. A. , Mestre M. , Movilla J. , Sarmento H. , Vázquez-Domínguez E. , Vaqué D. , Pinhassi J. , Calbet A. , Calvo E. , Gasol J. M. , Pelejero C. , Marrasé C. 
Published: August 2015

AbstractWe investigated the effects of an increase in dissolved CO2 on the microbial communities of the Mediterranean Sea during two mesocosm experiments in two contrasting seasons: winter, at the peak of the annual phytoplankton bloom, and summer, under low nutrient conditions. The experiments included treatments with acidification and nutrient addition, and combinations of the two. We followed the effects of ocean acidification (OA) on the abundance of the main groups of microorganisms (diatoms, dinoflagellates, nanoeukaryotes, picoeukaryotes, cyanobacteria, and heterotrophic bacteria) and on bacterial activity, leucine incorporation, and extracellular enzyme activity. Our results showed a clear stimulation effect of OA on the abundance of small phytoplankton (pico- and nanoeukaryotes), independently of the season and nutrient availability. A large number of the measured variables showed significant positive effects of acidification in summer compared with winter, when the effects were sometimes negative. Effects of OA were more conspicuous when nutrient concentrations were low. Our results therefore suggest that microbial communities in oligotrophic waters are considerably affected by OA, whereas microbes in more productive waters are less affected. The overall enhancing effect of acidification on eukaryotic pico- and nanophytoplankton, in comparison with the non-significant or even negative response to nutrient-rich conditions of larger groups and autotrophic prokaryotes, suggests a shift towards medium-sized producers in a future acidified ocean.
The first four-color photometric investigation of the W UMa type contact binary V868 Monocerotis
Authors: Xiao Zhou , Shengbang Qian , Jiajia He , Jia Zhang , Linqiao Jiang 
Published: August 2015

Abstract
The first four-color light-curves of V868 Monocerotis in the B, V, Rc, and Ic bands are presented and analyzed by using the 2013 version of the Wilson–Devinney method. It is discovered that V868 Mon is an A-subtype contact binary (f = 58.9%), with a large temperature difference of 916 K between the two components. Using the eight new data of the times of light minimum determined by the authors together with those collected from literature, the authors found that the general trend of the observed−calculated (O − C) curve shows an upward parabolic variation that corresponds to a long-term increase in the orbital period at a rate of dP/dt = 9.38 × 10−7 d yr−1. The continuous increase may be caused by a mass transfer from the less massive component to the more massive one.
MicroRNA-21 Mediates Isoflurane-induced Cardioprotection against Ischemia–Reperfusion Injury via Akt/Nitric Oxide Synthase/Mitochondrial Permeability Transition Pore Pathway
Authors: Qiao Shigang , Olson Jessica M. , Paterson Mark , Yan Yasheng , Zaja Ivan , Liu Yanan , Riess Matthias L. , Kersten Judy R. , Liang Mingyu , Warltier David C. , Bosnjak Zeljko J. , Ge Zhi-Dong 
Published: August 2015

AbstractAbstract
Isoflurane protects mouse hearts from myocardial ischemia/reperfusion injury by a microRNA-21-dependent mechanism. The results of this article open a new area of investigation into epigenetic mechanisms of volatile anesthetic-induced cardiac protection.

Background:
The role of microRNA-21 in isoflurane-induced cardioprotection is unknown. The authors addressed this issue by using microRNA-21 knockout mice and explored the underlying mechanisms.

Methods:
C57BL/6 and microRNA-21 knockout mice were echocardiographically examined. Mouse hearts underwent 30 min of ischemia followed by 2 h of reperfusion in vivo or ex vivo in the presence or absence of 1.0 minimum alveolar concentration of isoflurane administered before ischemia. Cardiac Akt, endothelial nitric oxide synthase (eNOS), and neuronal nitric oxide synthase (nNOS) proteins were determined by Western blot analysis. Opening of the mitochondrial permeability transition pore (mPTP) in cardiomyocytes was induced by photoexcitation-generated oxidative stress and detected by rapid dissipation of tetramethylrhodamine ethyl ester fluorescence using a confocal microscope.

Results:
Genetic disruption of miR-21 gene did not alter phenotype of the left ventricle, baseline cardiac function, area at risk, and the ratios of phosphorylated-Akt/Akt, phosphorylated-eNOS/eNOS, and phosphorylated-nNOS/nNOS. Isoflurane decreased infarct size from 54 ± 10% in control to 36 ± 10% (P < 0.05, n = 8 mice per group), improved cardiac function after reperfusion, and increased the ratios of phosphorylated-Akt/AKT, phosphorylated-eNOS/eNOS, and phosphorylated-nNOS/nNOS in C57BL/6 mice subjected to ischemia–reperfusion injury. These beneficial effects of isoflurane were lost in microRNA-21 knockout mice. There were no significant differences in time of the mPTP opening induced by photoexcitation-generated oxidative stress in cardiomyocytes isolated between C57BL/6 and microRNA-21 knockout mice. Isoflurane significantly delayed mPTP opening in cardiomyocytes from C57BL/6 but not from microRNA-21 knockout mice.

Conclusions:
Isoflurane protects mouse hearts from ischemia–reperfusion injury by a microRNA-21-dependent mechanism. The Akt/NOS/mPTP pathway is involved in the microRNA-21-mediated protective effect of isoflurane.
Influence of Tracheal Obstruction on the Efficacy of Superimposed High-frequency Jet Ventilation and Single-frequency Jet Ventilation
Authors: Sütterlin Robert , LoMauro Antonella , Gandolfi Stefano , Priori Rita , Aliverti Andrea , Frykholm Peter , Larsson Anders 
Published: August 2015

AbstractAbstract
In a study of pigs with obstructed airway, superimposed high-frequency jet ventilation was superior over high-frequency jet ventilation in providing adequate oxygenation by increasing lung volume and carbon dioxide removal by increasing tidal volume even without increasing the risk of barotrauma.
Supplemental Digital Content is available in the text.

Background:
Both superimposed high-frequency jet ventilation (SHFJV) and single-frequency (high-frequency) jet ventilation (HFJV) have been used with success for airway surgery, but SHFJV has been found to provide higher lung volumes and better gas exchange than HFJV in unobstructed airways. The authors systematically compared the ventilation efficacy of SHFJV and HFJV at different ventilation frequencies in a model of tracheal obstruction and describe the frequency and obstruction dependence of SHFJV efficacy.

Methods:
Ten anesthetized animals (weight 25 to 31.5 kg) were alternately ventilated with SHFJV and HFJV at a set of different fHF from 50 to 600 min−1. Obstruction was created by insertion of interchangeable stents with ID 2 to 8 mm into the trachea. Chest wall volume was measured using optoelectronic plethysmography, airway pressures were recorded, and blood gases were analyzed repeatedly.

Results:
SHFJV provided greater than 1.6 times higher end-expiratory chest wall volume than HFJV, and tidal volume (VT) was always greater than 200 ml with SHFJV. Increase of fHF from 50 to 600 min−1 during HFJV resulted in a more than 30-fold VT decrease from 112 ml (97 to 130 ml) to negligible values and resulted in severe hypoxia and hypercapnia. During SHFJV, stent ID reduction from 8 to 2 mm increased end-expiratory chest wall volume by up to 3 times from approximately 100 to 300 ml and decreased VT by up to 4.2 times from approximately 470 to 110 ml. Oxygenation and ventilation were acceptable for 4 mm ID or more, but hypercapnia occurred with the 2 mm stent.

Conclusion:
In this in vivo porcine model of variable severe tracheal stenosis, SHFJV effectively increased lung volumes and maintained gas exchange and may be advantageous in severe airway obstruction.
Nursing home director of nursing leadership style and director of nursing-sensitive survey deficiencies
Authors: McKinney Selina H. , Corazzini Kirsten , Anderson Ruth A. , Sloane Richard , Castle Nicholas G. 
Published: August 2015

Background:
Nursing homes are becoming increasingly complex clinical environments because of rising resident acuity and expansion of postacute services within a context of historically poor quality performance. Discrete quality markers have been linked to director of nursing (DON) leadership behaviors. However, the impact of DON leadership across all measured areas of DON jurisdiction has not been tested using comprehensive domains of quality deficiencies.

Purpose:
The aim of this study was to examine the effects of DON leadership style including behaviors that facilitate the exchange of information between diverse people on care quality domains through the lens of complexity science.

Methodology:
Three thousand six hundred nine DONs completed leadership and intent-to-quit surveys. Quality markers that were deemed DON sensitive included all facility survey deficiencies in the domains of resident behaviors/facility practices, quality of life, nursing services, and quality of care. Logistic regression procedures estimated associations between variables.

Findings:
The odds of deficiencies for all DON sensitive survey domains were lower in facilities where DONs practiced complexity leadership including more staff input and shared decisional authority. DON quit intentions were aligned with higher odds of facility deficiencies across all domains.

Practice Implications:
Results supported the hypotheses that DONs using complexity leadership approaches by interacting more freely with staff, discussing resident issues, and sharing decision making produced better care outcomes from every DON sensitive metric assessed by Centers for Medicare and Medicaid Services. The mechanism linking poor quality with high DON quit intentions is an area for future research. Encouraging DON use of complexity leadership approaches has the potential to improve a broad swath of quality outcomes.
Fast and efficient QTL mapper for thousands of molecular phenotypes
Authors: Ongen Halit , Buil Alfonso , Brown Andrew Anand , Dermitzakis Emmanouil T. , Delaneau Olivier 
Published: August 2015

AbstractMotivationIn order to discover quantitative trait loci (QTLs), multi-dimensional genomic data sets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing.ResultsWe have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted p-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot data sets can be now easily analyzed an order of magnitude faster than previous approaches.AvailabilitySource code, binaries and comprehensive documentation of FastQTL are freely available to download athttp://fastqtl.sourceforge.net/.Contactolivier.delaneau@unige.ch