bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimicrobial susceptibility and molecular typing of MRSA in cystic fibrosis
Authors: Champion E.A. , Miller M.B. , Popowitch E.B. , Hobbs M.M. , Saiman L. , Muhlebach M.S. ,   for the STAR‐CF Study Team
Published: June 2013

SummaryObjectivesThe prevalence of methicillin‐resistant Staphylococcus aureus (MRSA) in cystic fibrosis (CF) patients in the United States is approximately 25%. Little is known about the relative proportion of hospital‐ versus community‐associated strains or the antimicrobial susceptibility of MRSA in different CF centers. We hypothesized that the majority of MRSA isolates obtained from children with CF are those endemic in the hospital and that those associated with community acquisition (SCCmec IV) would be more resistant than typically seen in non‐CF MRSA isolates.MethodsWe studied MRSA strains from seven pediatric CF centers to determine the clonal distribution based on DNA sequencing of the staphylococcal protein A gene (spa typing), the type of staphylococcal chromosomal cassette mec (SCCmec), and the proportion of strains with Panton‐Valentine leukocidin (PVL). Antimicrobial susceptibility to systemic and topical antibiotics was compared between different MRSA types.ResultsWe analyzed 277 MRSA isolates from unique patients (mean age 11.15 ± 4.77 years, 55% male). Seventy % of isolates were SCCmec II PVL negative and the remainder SCCmec IV. Overall 17% MRSA strains were PVL positive (all SCCmec IV). Spa typing of 118 isolates showed most of the SCCmec II strains being t002, while SCCmec IV PVL positive isolates were t008, and SCCmec IV PVL negative isolates represented a variety of spa‐types. The proportions of SCCmec II strains and spa‐types were similar among centers. Overall rates of resistance to trimethoprim–sulfamethoxazole (4%), tetracycline (7%), tigecycline (0.4%), linezolid (0.4%) as well as fosfomycin (0.4%), fusidic acid (3%), and mupirocin (1%) were low. No strains were resistant to vancomycin. SCCmec II strains had higher rates of resistance to ciprofloxacin and clindamycin (P < 0.001) than SCCmec IV strains.ConclusionsIn this U.S. study, most MRSA isolates in the pediatric CF population were SCCmec II PVL negative. Rates of resistance were low, including to older and orally available antibiotics such as trimethoprim–sulfamethoxazole. Pediatr Pulmonol. 2014; 49:230–237. © 2013 Wiley Periodicals, Inc.
Science Interests in Preschool Boys and Girls: Relations to Later Self‐Concept and Science Achievement
Authors: LEIBHAM MARY BETH , ALEXANDER JOYCE M. , JOHNSON KATHY E. 
Published: June 2013

ABSTRACTAlthough young children display various types of interests, little is known regarding the potential impact of these interests on subsequent learning and development. Of particular importance is the question of whether or not children's early interests are instrumental in their later academic achievement. The current study fills this gap in the interest literature by longitudinally investigating the relationship between 116 children's early science interests and their subsequent self‐concepts and science‐related academic achievement, with particular emphasis placed on gender. The intensity and content of children's science interests between the ages of 4 and 6 (i.e., preschool interests) and between the ages of 6 and 8 (i.e., elementary school interests) were used as predictors of age 8 self‐concept and science achievement. Boys displayed higher overall levels of science interests than girls, though interest was not related to boys’ self‐concepts. Girls’ early intense science interests were related to higher science self‐concepts at age 8. In addition, early interests predicted science achievement in girls but not in boys. In conclusion, it appears that early science interest may be a critical supporting factor for girls in fostering positive self‐concepts and higher science achievement scores. © 2013 Wiley Periodicals, Inc. Sci Ed 97:574–593, 2013
The RNase II/RNB family of exoribonucleases: putting the ‘Dis’ in disease
Authors: Reis Filipa P. , Pobre Vânia , Silva Inês J. , Malecki Michal , Arraiano Cecília M. 
Published: June 2013

Important findings over the last years have shed new light onto the mechanistic details of RNA degradation by members of the RNase II/RNB family of exoribonucleases. Members of this family have been shown to be involved in growth, normal chloroplast biogenesis, mitotic control and cancer. Recently, different publications have linked human orthologs (Dis3 and Dis3L2) to important human diseases. This article describes the structural and biochemical characteristics of members of this family of enzymes, and the physiological implications that relate them with disease. WIREs RNA 2013, 4:607–615. doi: 10.1002/wrna.1180This article is categorized under:

RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
RNA Turnover and Surveillance > Regulation of RNA Stability
RNA in Disease and Development > RNA in Disease
Microsatellite marker‐based assessment of the biodiversity of native bioethanol yeast strains
Authors: Antonangelo Ana Teresa B. F. , Alonso Diego P. , Ribolla Paulo E. M. , Colombi Débora 
Published: June 2013

AbstractAlthough many Brazilian sugar mills initiate the fermentation process by inoculating selected commercial Saccharomyces cerevisiae strains, the unsterile conditions of the industrial sugar cane ethanol fermentation process permit the constant entry of native yeast strains. Certain of those native strains are better adapted and tend to predominate over the initial strain, which may cause problems during fermentation. In the industrial fermentation process, yeast cells are often exposed to stressful environmental conditions, including prolonged cell recycling, ethanol toxicity and osmotic, oxidative or temperature stress. Little is known about these S. cerevisiae strains, although recent studies have demonstrated that heterogeneous genome architecture is exhibited by some selected well‐adapted Brazilian indigenous yeast strains that display high performance in bioethanol fermentation. In this study, 11 microsatellite markers were used to assess the genetic diversity and population structure of the native autochthonous S. cerevisiae strains in various Brazilian sugar mills. The resulting multilocus data were used to build a similarity‐based phenetic tree and to perform a Bayesian population structure analysis. The tree revealed the presence of great genetic diversity among the strains, which were arranged according to the place of origin and the collection year. The population structure analysis revealed genotypic differences among populations; in certain populations, these genotypic differences are combined to yield notably genotypically diverse individuals. The high yeast diversity observed among native S. cerevisiae strains provides new insights on the use of autochthonous high‐fitness strains with industrial characteristics as starter cultures at bioethanol plants. Copyright © 2013 John Wiley & Sons, Ltd.
Adjustment disorder with anxiety in old age: Comparing prevalence and clinical management in primary care and mental health care
Authors: Arbus C. , Hergueta T. , Duburcq A. , Saleh A. , Le Guern M.-E. , Robert P. , Camus V. 
Published: June 2013

AbstractPurpose:Adjustment disorder with anxiety (AjD-A) is a common cause of severe anxiety symptoms, but little is known about its prevalence in old age.Methods:This cross-sectional study examined the prevalence of AjD-A in outpatients over the age of 60 who consecutively consulted 34 general practitioners and 22 psychiatrists during a 2-week period. The diagnosis of AjD-A was obtained using the optional module for diagnostic of adjustment disorder of the Mini International Neuropsychiatric Interview (MINI). The study procedure also explored comorbid psychiatric conditions and documented recent past stressful life events, as well as social disability and current pharmacological and non-pharmacological management.Results:Overall, 3651 consecutive subjects were screened (2937 in primary care and 714 in mental health care). The prevalence rate of AjD-A was 3.7% (n = 136). Up to 39% (n = 53) of AjD-A subjects had a comorbid psychiatric condition, mostly of the anxious type. The most frequently stressful life event reported to be associated with the onset of AjD-A was personal illness or health problem (29%). More than 50% of the AjD-A patients were markedly to extremely disabled by their symptoms. Compared to patients who consulted psychiatrists, patients who were seen by primary care physicians were older, had obtained lower scores at the Hamilton Anxiety Rating Scale, benefited less frequently from non-pharmacological management and received benzodiazepines more frequently.Conclusions:AjD-A appears to be a significantly disabling cause of anxiety symptoms in community dwelling elderly persons, in particular those presenting personal health related problems. Improvement of early diagnosis and non-pharmacological management of AjD-A would contribute to limit risks of benzodiazepine overuse, particularly in primary care settings.
A note on the mirror-symmetric coherent structure in plane Couette flow
Authors: Nagata M. 
Published: June 2013

AbstractWe note that the mirror-symmetric solution in plane Couette flow, found recently by Gibson, Halcrow & Cvitanović (J. Fluid Mech., vol. 611, 2009, pp. 107–130) and Itano & Generalis (Phys. Rev. Lett., vol. 102, 2009, p. 114501), belongs to the solution group classified as ‘ribbon’ in rotating-plane Couette flow (RPCF). It represents a subcritical (in terms of the system rotation) solution at zero rotation rate on the three-dimensional tertiary flow branch which bifurcates from thesecondstreamwise-independent flow in RPCF. The way of its appearance is similar to that of the Nagata solution (J. Fluid Mech., vol. 217, 1990, pp. 519–527), which lies on the subcritical three-dimensional tertiary flow branch bifurcating from thefirststreamwise-independent flow in RPCF.
CEOs Under Fire: The Effects of Competition from Inside Directors on Forced CEO Turnover and CEO Compensation
Authors: Mobbs Shawn 
Published: June 2013

AbstractThis study examines board monitoring when a credible chief executive officer (CEO) replacement is on the board. Inside directors whose talents are in greater demand externally, as reflected by their holding outside directorships, are more likely to become CEOs, and their presence is associated with greater forced CEO turnover sensitivity to accounting performance and CEO compensation sensitivity to stock performance. These results reveal that certain insiders strengthen board monitoring by serving as a readily available CEO replacement and contradict the presumption that all insiders are under CEO control. Furthermore, the results persist when accounting for the endogenous firm selection of talented inside directors.
The effect of helium impurity addition on current sheath speed in argon-operated plasma focus using a tridimensional magnetic probe
Authors: PANAHI N. , MOHAMMADI M. A. , HEDYEH S. , RAWAT R. S. 
Published: June 2013

AbstractUsing the tridimensional magnetic probe, the current sheath velocity at 0.25 Torr is studied in Sahand, a Filippov-type plasma focus facility. The current sheath velocity in argon-filled plasma focus with different percentages of helium impurity at different operating voltages was studied. The highest average current sheath velocity of 12.26 ± 1.51 cm μs−1 at the top of the anode in the axial phase was achieved at 17 kV. Minimum average current sheath velocity is 5.24 ± 1.18 cm μs−1 at 12 kV with 80% argon + 20% helium as a working gas. The full width at half-maximum of peaks of the magnetic probe was found to be inversely related to the current sheath velocity, i.e. smaller at higher voltages for different impurity and decreased with increasing of impurity.
Continuous wavelet transform analysis for self-similarity properties of turbulence in magnetized DC glow discharge plasma
Authors: SARMA BORNALI , CHAUHAN SOURABH S. , WHARTON A. M. , IYENGAR A. N. SEKAR 
Published: June 2013

AbstractCharacterization of self-similarity properties of turbulence in magnetized plasma is being carried out in DC glow discharge plasma. The time series floating potential fluctuation experimental data are acquired from the plasma by Langmuir probe. Continuous wavelet transform (CWT) analysis considering db4 mother wavelet has been applied to the experimental data and self-similarity properties are detected by evaluating the Hurst exponent from the wavelet variance plotting. From the CWT spectrum, effort is made to extract a highly correlated frequency by locating the brightest spot. Accordingly, those signals are treated for finding out correlation dimension and the Liapunov exponent so that the exact frequency responsible for the chaotic behavior could be found out.
DMEAS: DNA methylation entropy analysis software
Authors: He Jianlin , Sun Xinxi , Shao Xiaojian , Liang Liji , Xie Hehuang 
Published: June 2013

Abstract
Summary: DMEAS is the first user-friendly tool dedicated to analyze the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. It supports the analysis of both locus-specific and genome-wide bisulfite sequencing data. DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It determines the DNA methylation level and calculates methylation entropy for genomic segments to enable the quantitative assessment of DNA methylation variations observed in cell populations.
Availability and implementation: DMEAS program, user guide and all the testing data are freely available from http://sourceforge.net/projects/dmeas/files/
Contact: davidxie@vt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Joint network and node selection for pathway-based genomic data analysis
Authors: Zhe Shandian , Naqvi Syed A. Z. , Yang Yifan , Qi Yuan 
Published: June 2013

AbstractMotivation: By capturing various biochemical interactions, biological pathways provide insight into underlying biological processes. Given high-dimensional microarray or RNA-sequencing data, a critical challenge is how to integrate them with rich information from pathway databases to jointly select relevant pathways and genes for phenotype prediction or disease prognosis. Addressing this challenge can help us deepen biological understanding of phenotypes and diseases from a systems perspective.Results: In this article, we propose a novel sparse Bayesian model for joint network and node selection. This model integrates information from networks (e.g. pathways) and nodes (e.g. genes) by a hybrid of conditional and generative components. For the conditional component, we propose a sparse prior based on graph Laplacian matrices, each of which encodes detailed correlation structures between network nodes. For the generative component, we use a spike and slab prior over network nodes. The integration of these two components, coupled with efficient variational inference, enables the selection of networks as well as correlated network nodes in the selected networks.Simulation results demonstrate improved predictive performance and selection accuracy of our method over alternative methods. Based on three expression datasets for cancer study and the KEGG pathway database, we selected relevant genes and pathways, many of which are supported by biological literature. In addition to pathway analysis, our method is expected to have a wide range of applications in selecting relevant groups of correlated high-dimensional biomarkers.Availability: The code can be downloaded at www.cs.purdue.edu/homes/szhe/software.html.Contact: alanqi@purdue.edu
Effect of Hemorrhage and Hypotension on Transcranial Motor-evoked Potentials in Swine
Authors: Lieberman Jeremy A. , Feiner John , Lyon Russ , Rollins Mark D. 
Published: June 2013

Abstract

Background:
Transcranial motor-evoked potentials (TcMEPs) monitor spinal cord motor tract integrity. Using a swine model, the authors studied the effects of vasodilatory hypotension, hemorrhage, and various resuscitation efforts on TcMEP responses.

Methods:
Twelve pigs were anesthetized with constant infusions of propofol, ketamine, and fentanyl. Animals were incrementally hemorrhaged, until bilateral tibialis anterior TcMEP amplitude decreased to less than 40% of baseline or until 50% of the blood volume was removed. Mean arterial pressure (MAP), cardiac output (CO), and oxygen delivery (DO2) were examined. Resuscitation with phenylephrine, epinephrine, and colloid were evaluated. In seven animals, vasodilatory hypotension was examined. Paired comparisons and multivariate analysis were performed.

Results:
Hemorrhage significantly reduced (as a percentage of baseline, mean ± SD) TcMEPs (left, 33 ± 29%; right, 26 ± 21%), MAP (60 ± 17%), CO (49 ± 12%), and DO2 (43 ± 13%), P value less than 0.001 for all. Vasodilation reduced MAP comparably, but TcMEPs, CO, and DO2, were not significantly lowered. After hemorrhage, restoration of MAP with phenylephrine did not improve TcMEPs, CO, or DO2, but similar restoration of MAP with epinephrine restored (to percentage of baseline) TcMEPs (59 ± 40%), and significantly increased CO (81 ± 17%) and DO2 (72 ± 19%) compared with both hemorrhage and phenylephrine, P value less than 0.05 for all. Resuscitation with colloid did not improve TcMEPs. Multivariate analysis revealed that changes in TcMEPs were more closely associated with changes in CO and DO2 as compared with MAP.

Conclusions:
Hypotension from hemorrhage, but not vasodilation, is associated with a decrease in TcMEP amplitude. After hemorrhage, restoration of TcMEPs with epinephrine but not phenylephrine indicates that CO and DO2 affect TcMEPs more than MAP. Monitoring CO may be beneficial in major spine surgery when using TcMEP monitoring.
Real-time Closed-loop Control in a Rodent Model of Medically Induced Coma Using Burst Suppression
Authors: Ching ShiNung , Liberman Max Y. , Chemali Jessica J. , Westover M. Brandon , Kenny Jonathan D. , Solt Ken , Purdon Patrick L. , Brown Emery N. 
Published: June 2013

Abstract

Background:
A medically induced coma is an anesthetic state of profound brain inactivation created to treat status epilepticus and to provide cerebral protection after traumatic brain injuries. The authors hypothesized that a closed-loop anesthetic delivery system could automatically and precisely control the electroencephalogram state of burst suppression and efficiently maintain a medically induced coma.

Methods:
In six rats, the authors implemented a closed-loop anesthetic delivery system for propofol consisting of: a computer-controlled pump infusion, a two-compartment pharmacokinetics model defining propofol’s electroencephalogram effects, the burst-suppression probability algorithm to compute in real time from the electroencephalogram the brain’s burst-suppression state, an online parameter-estimation procedure and a proportional-integral controller. In the control experiment each rat was randomly assigned to one of the six burst-suppression probability target trajectories constructed by permuting the burst-suppression probability levels of 0.4, 0.65, and 0.9 with linear transitions between levels.

Results:
In each animal the controller maintained approximately 60 min of tight, real-time control of burst suppression by tracking each burst-suppression probability target level for 15 min and two between-level transitions for 5–10 min. The posterior probability that the closed-loop anesthetic delivery system was reliable across all levels was 0.94 (95% CI, 0.77–1.00; n = 18) and that the system was accurate across all levels was 1.00 (95% CI, 0.84–1.00; n = 18).

Conclusion:
The findings of this study establish the feasibility of using a closed-loop anesthetic delivery systems to achieve in real time reliable and accurate control of burst suppression in rodents and suggest a paradigm to precisely control medically induced coma in patients.
Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor
Authors: Bertaccini Edward J. , Yoluk Ozge , Lindahl Erik R. , Trudell James R. 
Published: June 2013

Abstract

Background:
Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). Although its molecular structure remains unknown, significant progress has been made toward understanding its interactions with anesthetics via molecular modeling.

Methods:
The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH-sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50s.

Results:
Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between α and β subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50.

Conclusion:
Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed a correlation of ligand docking scores with experimentally measured GABAaR potentiation.
RootNav: Navigating Images of Complex Root Architectures
Authors: Pound Michael P. , French Andrew P. , Atkinson Jonathan A. , Wells Darren M. , Bennett Malcolm J. , Pridmore Tony 
Published: June 2013

AbstractWe present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. The automatic component of RootNav takes a top-down approach, utilizing the powerful expectation maximization classification algorithm to examine regions of the input image, calculating the likelihood that given pixels correspond to roots. This information is used as the basis for an optimization approach to root detection and quantification, which effectively fits a root model to the image data. The resulting user experience is akin to defining routes on a motorist’s satellite navigation system: RootNav makes an initial optimized estimate of paths from the seed point to root apices, and the user is able to easily and intuitively refine the results using a visual approach. The proposed method is evaluated on winter wheat (Triticum aestivum) images (and demonstrated on Arabidopsis [Arabidopsis thaliana], Brassica napus, and rice [Oryza sativa]), and results are compared with manual analysis. Four exemplar traits are calculated and show clear illustrative differences between some of the wheat accessions. RootNav, however, provides the structural information needed to support extraction of a wider variety of biologically relevant measures. A separate viewer tool is provided to recover a rich set of architectural traits from RootNav’s core representation.