bluuebunny/crossref_metadata_2025_split huggingface dataset:
Who May Benefit From Armeo Power Treatment? A Neurophysiological Approach to Predict Neurorehabilitation Outcomes
Authors: Calabrò Rocco Salvatore , Russo Margherita , Naro Antonino , Milardi Demetrio , Balletta Tina , Leo Antonino , Filoni Serena , Bramanti Placido 
Published: February 2016

AbstractBackgroundThe Armeo Power, a rehabilitation exoskeleton that allows early treatment of motor disabilities, provides intelligent arm support in a large 3‐dimensional work space, thus enabling patients to perform intensive, repetitive, and goal‐oriented exercises. This device could efficiently induce new connections and facilitate plasticity phenomena potentiation. Knowledge of the potential brain plasticity reservoir after brain damage constitutes a prerequisite for an optimal rehabilitation strategy.ObjectiveTo identify potential neurophysiologic markers predicting the responsiveness of stroke patients to upper limb robotic treatment.DesignProspective cohort study.SettingBehavioral and Robotic Neurorehabilitation Laboratory of IRCCS Centro Neurolesi Bonino‐Pulejo, Messina, Italy.PatientsWe enrolled 35 patients who had sustained a first‐ever ischemic supratentorial stroke at least 2 months before enrollment and had unilateral hemiplegia.MethodsAll patients underwent 40 Armeo Power training sessions that lasted 1 hour each (ie, 5 times a week for 8 weeks).Main Outcome MeasurementsWe assessed the spasticity and motor function of the upper limb by means of the Modified Ashworth scale and Fugl‐Meyer assessment, respectively. Moreover, we evaluated the cortical excitability and plasticity potential of the bilateral primary motor areas in response to the repetitive paired associative stimulation paradigm using transcranial magnetic stimulation and Armeo Power kinematic parameters.ResultsThe patients who showed significant repetitive paired associative stimulation aftereffects at baseline exhibited an evident increase of cortical plasticity in the affected hemisphere (motor evoked potential amplitude increase, P = .03), a decrease of interhemispheric inhibition (affected hemisphere cortical silent period duration decrease, P = .01; unaffected hemisphere cortical silent period duration increase, P = .004; repetitive paired associative stimulation aftereffect increase, P = .008). Such findings were paralleled by clinical improvements (Fugl‐Meyer, P = .04) and Armeo Power kinematic improvements (elbow flexion/extension, P = .02; shoulder range of movement, P = .002).ConclusionsOur data suggest that use of Armeo Power may improve upper limb motor function recovery as predicted by reshaping of cortical and transcallosal plasticity, according to the baseline cortical excitability.Level of EvidenceIV
A Case Series: The Identification of Buried Bumper Syndrome With Abdominal Computed Tomography Scan in Two Severely Brain Injured Rehabilitation Patients
Authors: Krull Christine M.P. , Dennison Andrew C. 
Published: February 2016

AbstractBuried bumper syndrome is a potentially dangerous complication related to percutaneous endoscopic gastrostomy tube placement. Early diagnosis of this condition is important to avoid further complications related to subcutaneous or intraperitoneal administration of tube feedings. However, diagnosis in persons with altered mental status due to brain injury is challenging because of the patient's lack of ability to communicate and report symptoms. We present 2 case studies that demonstrate both the importance of early diagnosis and management and the lack of adequate sensitivity of a Gastrografin‐aided kidney, ureter, and bladder (KUB) study.
metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis
Authors: Cichonska Anna , Rousu Juho , Marttinen Pekka , Kangas Antti J. , Soininen Pasi , Lehtimäki Terho , Raitakari Olli T. , Järvelin Marjo-Riitta , Salomaa Veikko , Ala-Korpela Mika , Ripatti Samuli , Pirinen Matti 
Published: February 2016

Abstract
Motivation: A dominant approach to genetic association studies is to perform univariate tests between genotype-phenotype pairs. However, analyzing related traits together increases statistical power, and certain complex associations become detectable only when several variants are tested jointly. Currently, modest sample sizes of individual cohorts, and restricted availability of individual-level genotype-phenotype data across the cohorts limit conducting multivariate tests.
Results: We introduce metaCCA, a computational framework for summary statistics-based analysis of a single or multiple studies that allows multivariate representation of both genotype and phenotype. It extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.
Multivariate meta-analysis of two Finnish studies of nuclear magnetic resonance metabolomics by metaCCA, using standard univariate output from the program SNPTEST, shows an excellent agreement with the pooled individual-level analysis of original data. Motivated by strong multivariate signals in the lipid genes tested, we envision that multivariate association testing using metaCCA has a great potential to provide novel insights from already published summary statistics from high-throughput phenotyping technologies.
Availability and implementation: Code is available at https://github.com/aalto-ics-kepaco
Contacts: anna.cichonska@helsinki.fi or matti.pirinen@helsinki.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
fqtools: an efficient software suite for modern FASTQ file manipulation
Authors: Droop Alastair P. 
Published: February 2016

Abstract
Summary: Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.
Availability and implementation: fqtools is open source and is available at: https://github.com/alastair-droop/fqtools.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: a.p.droop@leeds.ac.uk
Coala: an R framework for coalescent simulation
Authors: Staab Paul R. , Metzler Dirk 
Published: February 2016

Abstract
Summary: Simulation programs based on the coalescent efficiently generate genetic data according to a given model of evolution. We present coala, an R package for calling coalescent simulators with a unified syntax. It can execute simulations with several programs, calculate additional summary statistics and combine multiple simulations to create biologically more realistic data.
Availability and implementation: The package is publicly available on CRAN and on https://github.com/statgenlmu/coala under the conditions of the MIT license.
Contact: metzler@bio.lmu.de
A web application for sample size and power calculation in case-control microbiome studies
Authors: Mattiello Federico , Verbist Bie , Faust Karoline , Raes Jeroen , Shannon William D. , Bijnens Luc , Thas Olivier 
Published: February 2016

AbstractSummary: When designing a case-control study to investigate differences in microbial composition, it is fundamental to assess the sample sizes needed to detect an hypothesized difference with sufficient statistical power. Our application includes power calculation for (i) a recoded version of the two-sample generalized Wald test of the ‘HMP’ R-package for comparing community composition, and (ii) the Wilcoxon-Mann-Whitney test for comparing operational taxonomic unit-specific abundances between two samples (optional). The simulation-based power calculations make use of the Dirichlet-Multinomial model to describe and generate abundances. The web interface allows for easy specification of sample and effect sizes. As an illustration of our application, we compared the statistical power of the two tests, with and without stratification of samples. We observed that statistical power increases considerably when stratification is employed, meaning that less samples are needed to detect the same effect size with the same power.Availability and implementation: The web interface is written in R code using Shiny (RStudio Inc., 2016) and it is available at https://fedematt.shinyapps.io/shinyMB. The R code for the recoded generalized Wald test can be found at https://github.com/mafed/msWaldHMP.Contact: Federico.Mattiello@UGent.be
Mass-Observation, Left Intellectuals and the Politics of Everyday Life
Authors: Campsie Alexandre 
Published: February 2016

Abstract
This article examines the careers of a number of left thinkers who broke with the Communist Party of Great Britain in the late 1930s, committing themselves instead to a ‘politics of everyday life’ based on social investigation. Central to this moment was the social research organisation Mass-Observation, the sociologists of which argued that democracy should be built around the vibrancy and irreverence they identified in ordinary culture. This ambition gained its fullest application during the 1940s, as a number of former M-O researchers became influential in the social reconstruction effort, in Labour Party policy circles and, later, in post-war academic sociology. By tracing the sociological arguments of unaligned left intellectuals from the 1930s to the 1950s, this article emphasises the rich plurality of influences at play within British progressive thought in the mid-twentieth century—influences which spanned the worlds of far-left activism, literature, art, the social sciences, town planning and parliamentary politics. It also helps us to reassess the genesis of the first ‘New Left’ in 1956. This is often hailed as the moment when British socialists first started to appreciate ordinary culture, freed from political dogmatism. In fact, left intellectuals had been engaging with the politics of everyday life for at least two decades previously. Indeed, the nostalgic accent which some New Left writers placed on the traditional working-class group was but one facet of a more heterogeneous political tradition—one concerned to think beyond ‘class’ altogether, and to examine how culture operated at the level of the individual.
Star Wars: Response to Simonson, Winer/Fader, and Kozinets
Authors: de Langhe Bart , Fernbach Philip M. , Lichtenstein Donald R. 
Published: February 2016

Abstract
In de Langhe, Fernbach, and Lichtenstein (2016), we argue that consumers trust average user ratings as indicators of objective product performance much more than they should. This simple idea has provoked passionate commentaries from eminent researchers across three subdisciplines of marketing: experimental consumer research, modeling, and qualitative consumer research. Simonson challenges the premise of our research, asking whether objective performance even matters. We think it does and explain why in our response. Winer and Fader argue that our results are neither insightful nor important. We believe that their reaction is due to a fundamental misunderstanding of our goals, and we show that their criticisms do not hold up to scrutiny. Finally, Kozinets points out how narrow a slice of consumer experience our article covers. We agree, and build on his observations to reflect on some big-picture issues about the nature of research and the interaction between the subdisciplines.
Evolution of dispersion in the cosmic deuterium abundance
Authors: Dvorkin Irina , Vangioni Elisabeth , Silk Joseph , Petitjean Patrick , Olive Keith A. 
Published: February 2016

Abstract
Deuterium is created during big bang nucleosynthesis, and, in contrast to the other light stable nuclei, can only be destroyed thereafter by fusion in stellar interiors. In this Letter, we study the cosmic evolution of the deuterium abundance in the interstellar medium (ISM) and its dispersion using realistic galaxy evolution models. We find that models that reproduce the observed metal abundance are compatible with observations of the deuterium abundance in the local ISM and z ∼ 3 absorption line systems. In particular, we reproduce the low astration factor which we attribute to a low global star formation efficiency. We calculate the dispersion in deuterium abundance arising from different structure formation histories in different parts of the Universe. Our model also predicts a tight correlation between deuterium and metal abundances which could be used to measure the primordial deuterium abundance.
Long-Term Control of Human Immunodeficiency Virus-1 Replication Despite Extensive Resistance to Current Antiretroviral Regimens: Clonal Analysis of Resistance Mutations in Proviral Deoxyribonucleic Acid
Authors: Stella-Ascariz Natalia , Montejano Rocio , Martin-Vicente María , Mingorance Jesús , Pérez-Valero Ignacio , Bernardino José I. , Arribas Jose R. 
Published: February 2016

AbstractArchived resistance mutations compromise antiretroviral treatment. We have investigated 3 selected aviremic patients who had extensive historical resistance to their current regimen. All 3 patients underwent unstructured treatment interruptions associated to the re-emergence of wild-type virus before starting their current suppressive regimes. Almost all historical resistance mutations detected in plasma were found in circulating proviral deoxyribonucleic acid. None of the clones analyzed was fully resistant to the current antiretroviral regimen.
Application of Whole-Genome Sequencing to an Unusual Outbreak of Invasive Group A Streptococcal Disease
Authors: Galloway-Peña Jessica , Clement Meredith E. , Sharma Kuinkel Batu K. , Ruffin Felicia , Flores Anthony R. , Levinson Howard , Shelburne Samuel A. , Moore Zack , Fowler Vance G. 
Published: February 2016

Abstract
Whole-genome analysis was applied to investigate atypical point-source transmission of 2 invasive group A streptococcal (GAS) infections. Isolates were serotype M4, ST39, and genetically indistinguishable. Comparison with MGAS10750 revealed nonsynonymous polymorphisms in ropB and increased speB transcription. This study demonstrates the usefulness of whole-genome analyses for GAS outbreaks.
Absence of Pneumocystis jirovecii Colonization in Human Immunodeficiency Virus-Infected Individuals With and Without Airway Obstruction and With Undetectable Viral Load
Authors: Ronit Andreas , Klitbo Ditte Marie , Kildemoes Anna Overgaard , Benfield Thomas , Gerstoft Jan , Vestbo Jørgen , Jensen Jørgen Skov , Kurtzhals Jørgen , Nielsen Susanne Dam 
Published: February 2016

Abstract
Pneumocystis jirovecii colonization has been associated with non-acquired immune deficiency syndrome (AIDS) pulmonary comorbidity. We used spirometry to measure pulmonary function and analyzed oral wash specimens by quantitative polymerase chain reaction (PCR), targeting the large mitochondrial ribosomal subunit. For sensitivity control, a blinded subsample was subjected to touch-down PCRs, targeting both large and small ribosomal subunits and the major surface glycoprotein. Pneumocystis jirovecii deoxyribonucleic acid (DNA) was detected in 1 of 156 (95% confidence interval, .1%–3.5%) virologically suppressed human immunodeficiency virus (HIV)-infected individuals confirmed by all PCR methods. Thus, prevalence of P jirovecii colonization was low and unlikely to be a major cause of pulmonary comorbidity in this group of well treated HIV-infected individuals.
The Effects of Acoustic Bandwidth on Simulated Bimodal Benefit in Children and Adults with Normal Hearing
Authors: Sheffield Sterling W. , Simha Michelle , Jahn Kelly N. , Gifford René H. 
Published: February 2016

Objectives:
The primary purpose of this study was to examine the effect of acoustic bandwidth on bimodal benefit for speech recognition in normal-hearing children with a cochlear implant (CI) simulation in one ear and low-pass filtered stimuli in the contralateral ear. The effect of acoustic bandwidth on bimodal benefit in children was compared with the pattern of adults with normal hearing. Our hypothesis was that children would require a wider acoustic bandwidth than adults to (1) derive bimodal benefit, and (2) obtain asymptotic bimodal benefit.

Design:
Nineteen children (6 to 12 years) and 10 adults with normal hearing participated in the study. Speech recognition was assessed via recorded sentences presented in a 20-talker babble. The AzBio female-talker sentences were used for the adults and the pediatric AzBio sentences (BabyBio) were used for the children. A CI simulation was presented to the right ear and low-pass filtered stimuli were presented to the left ear with the following cutoff frequencies: 250, 500, 750, 1000, and 1500 Hz.

Results:
The primary findings were (1) adults achieved higher performance than children when presented with only low-pass filtered acoustic stimuli, (2) adults and children performed similarly in all the simulated CI and bimodal conditions, (3) children gained significant bimodal benefit with the addition of low-pass filtered speech at 250 Hz, and (4) unlike previous studies completed with adult bimodal patients, adults and children with normal hearing gained additional significant bimodal benefit with cutoff frequencies up to 1500 Hz with most of the additional benefit gained with energy below 750 Hz.

Conclusions:
Acoustic bandwidth effects on simulated bimodal benefit were similar in children and adults with normal hearing. Should the current results generalize to children with CIs, these results suggest pediatric CI recipients may derive significant benefit from minimal acoustic hearing (<250 Hz) in the nonimplanted ear and increasing benefit with broader bandwidth. Knowledge of the effect of acoustic bandwidth on bimodal benefit in children may help direct clinical decisions regarding a second CI, continued bimodal hearing, and even optimizing acoustic amplification for the nonimplanted ear.
The Prevalence and the Incidence of Diagnosed Open-Angle Glaucoma and Diagnosed Angle-Closure Glaucoma: Changes From 2001 to 2010
Authors: Chiu Shin-Lin , Chu Chiao-Lee , Muo Chih-Hsin , Chen Chiu-Liang , Lan Shou-Jen 
Published: February 2016

Purpose:
To explore the trends in diagnosed open-angle glaucoma (OAG) and diagnosed angle-closure glaucoma (ACG) in Taiwan during the period of 2001 to 2010.

Materials and Methods:
Data were sourced from the National Longitudinal Health Insurance Database 2000 (LHID2000). The study population comprised all patients with a diagnosis of OAG or ACG (International Classification of Diseases, 9th Revision, Clinical Modification codes 365). Patients were stratified by their sex and age; differences in standardized incidence rates were compared between the stratified groups.

Results:
Throughout the study period, the prevalence of diagnosed OAG (slope=0.18, P<0.0001) and ACG (slope=0.09, P<0.0001) increased. Before 2005, the prevalence of ACG was higher than that of OAG; however, from 2005 to 2010, the prevalence of OAG was higher than that of ACG. The standardized incidence of diagnosed OAG increased insignificantly (slope=1.06, P=0.18), and that of diagnosed ACG decreased significantly (slope=−1.17, P=0.009). The prevalence and the incidence of OAG and ACG were the highest among people of advanced age. Women had higher standardized incidence rates of ACG during the study period. Men had higher standardized incidence rates of OAG in every year of the study with the exception of 2007.

Conclusions:
In Taiwan, ACG was more prevalent in women and OAG might be more prevalent in men. The prevalence of ACG was higher than that of OAG before 2005, but the prevalence of OAG has been higher than that of ACG since 2005.
Evaluation of Retinal Nerve Fiber Layer and Ganglion Cell Complex Thickness in Unilateral Exfoliation Syndrome Using Optical Coherence Tomography
Authors: Aydin Damla , Kusbeci Tuncay , Uzunel Umut D. , Orsel Tumay , Yuksel Bora 
Published: February 2016

Purpose:
To evaluate retinal nerve fiber layer (RNFL) and ganglion cell complex (GCC) thickness by using optical coherence tomography in unilateral exfoliation syndrome (XFS) and to assess whether exfoliation itself is an independent risk factor for glaucomatous optic nerve damage.

Materials and Methods:
Thirty exfoliative eyes of unilateral XFS cases, 30 fellow eyes of unilateral exfoliation, and 30 eyes of healthy subjects were enrolled the study. Peripapillary RNFL and macular GCC thickness measurements by Cirrus HD OCT (Carl Zeiss Meditec, Dublin, CA) were performed on all subjects.

Results:
RNFL thickness in superior quadrant was significantly different between groups (P=0.025) and it was thinner in XFS than healthy subjects (P=0.020). All GCC parameters except GCC thickness in inferior quadrant were significantly different between groups (P=0.110 for inferior quadrant, P<0.046 for other GCC parameters). GCC were thinner in XFS than healthy subjects except inferior and inferonasal quadrants (P=0.091, 0.051 for inferior and inferonasal quadrants, respectively, P<0.039 for other GCC parameters). Minimum GCC thickness, GCC thicknesses in superior, and inferonasal quadrants were significantly thinner in fellow eyes than healthy subjects (P=0.011, 0.013, 0.047, respectively).

Conclusions:
XFS is related with thinner RNFL and GCC even in normal intraocular pressure values, similar optic disc parameters and visual field results. XFS may be an independent risk factor for glaucomatous optic nerve damage. So, further studies are needed to evaluate whether exfoliation itself is an independent risk factor for optic nerve damage.
Repeatability of Spectral Domain Optical Coherence Tomography Measurements in High Myopia
Authors: Rao Harsha L. , Kumar Addepalli U. , Bonala Sampath R. , Yogesh Kadam , Lakshmi Bodduluri 
Published: February 2016

Purpose:
The purpose of this study was to compare the repeatability of spectral domain optical coherence tomography (SDOCT) parameters in high-myopic and emmetropic healthy subjects, and to evaluate the influence of axial length on the repeatability of SDOCT parameters in high myopia.

Methods:
In a prospective study, 93 eyes of 63 high-myopic subjects (spherical refractive error, −6 to −12 D; median age, 25 y) and 28 eyes of 14 emmetropic (spherical refractive error, 0 D; median age, 30 y) subjects underwent optic nerve head, retinal nerve fiber layer (RNFL), and ganglion cell complex imaging with SDOCT. For the repeatability analysis, 31 eyes of 31 high-myopic subjects and 14 eyes of 14 emmetropic subjects underwent 3 repeated scans in the same session.

Results:
Among the optic nerve head parameters, within-subject coefficient of variation (CVw) measurements of the disc area (0.6% vs. 0.2%), rim area (8.7 vs. 2.8), and rim volume (16.7 vs. 8.9) were significantly larger (worse) in high-myopic compared with the emmetropic subjects. CVw measurements of all RNFL (range, 1.7 to 22.4) and ganglion cell complex (range, 1.8 to 2.5) parameters in high-myopic subjects were comparable to that in emmetropic subjects (2.4 to 24.0 and 1.7 to 2.0, respectively). Axial length significantly affected the CVw of nasal (coefficient, 0.01; P=0.04) and average RNFL (coefficient, 0.004; P=0.001) parameters but not that of the other SDOCT parameters.

Conclusions:
Repeatabilities of most of the SDOCT parameters in high-myopic subjects were good and comparable to that of emmetropic subjects. This suggests that SDOCT can be useful for following up high-myopic glaucoma patients to detect progression.