bluuebunny/crossref_metadata_2025_split huggingface dataset:
Central Line-Associated Infections as Defined by the Centers for Medicare and Medicaid Services' Hospital-Acquired Condition versus Standard Infection Control Surveillance Why Hospital Compare Seems Conflicted
Authors: Moehring Rebekah W. , Staheli Russell , Miller Becky A. , Chen Luke Francis , Sexton Daniel John , Anderson Deverick John 
Published: January 2013

Objective.To evaluate the concordance of case-finding methods for central line-associated infection as defined by Centers for Medicare and Medicaid Services (CMS) hospital-acquired condition (HAC) compared with traditional infection control (IC) methods.Setting.One tertiary care and 2 community hospitals in North Carolina.Patients.Adult and pediatric hospitalized patients determined to have central line infection by either case-finding method.Methods.We performed a retrospective comparative analysis of infection detected using HAC versus standard IC central line–associated bloodstream infection surveillance from October 1, 2007, through December 31, 2009. One billing and 2 IC databases were queried and matched to determine the number and concordance of cases identified by each method. Manual review of 25 cases from each discordant category was performed. Sensitivity and positive predictive value (PPV) were calculated using IC as criterion standard.Results.A total of 1,505 cases were identified: 844 by International Classification of Diseases, Ninth Revision (ICD-9), and 798 by IC. A total of 204 cases (24%) identified by ICD-9 were deemed not present at hospital admission by coders. Only 112 cases (13%) were concordant. HAC sensitivity was 14% and PPV was 55% compared with IC. Concordance was low regardless of hospital type. Primary reasons for discordance included differences in surveillance and clinical definitions, clinical uncertainty, and poor documentation.Conclusions.The case-finding method used by CMS HAC and the methods used for traditional IC surveillance frequently do not agree. This can lead to conflicting results when these 2 measures are used as hospital quality metrics.
The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs
Authors: Levine Timothy P. , Daniels Rachel D. , Gatta Alberto T. , Wong Louise H. , Hayes Matthew J. 
Published: January 2013

AbstractMotivation: Fronto-temporal dementia (FTD) and amyotrophic lateral sclerosis (ALS, also called motor neuron disease, MND) are severe neurodegenerative diseases that show considerable overlap at the clinical and cellular level. The most common single mutation in families with FTD or ALS has recently been mapped to a non-coding repeat expansion in the uncharacterized gene C9ORF72. Although a plausible mechanism for disease is that aberrant C9ORF72 mRNA poisons splicing, it is important to determine the cellular function of C9ORF72, about which nothing is known.Results: Sensitive homology searches showed that C9ORF72 is a full-length distant homologue of proteins related to Differentially Expressed in Normal and Neoplasia (DENN), which is a GDP/GTP exchange factor (GEF) that activates Rab-GTPases. Our results suggest that C9ORF72 is likely to regulate membrane traffic in conjunction with Rab-GTPase switches, and we propose to name the gene and its product DENN-like 72 (DENNL72).Supplementary information: Supplementary data are available at Bioinformatics online.Contact: tim.levine@ucl.ac.uk
Searching for virus phylotypes
Authors: Chevenet François , Jung Matthieu , Peeters Martine , de Oliveira Tulio , Gascuel Olivier 
Published: January 2013

Abstract
Motivation: Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance.
Results: We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in low computing times, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is large, containing &gt;3000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones.
Availability: This method and companion tools are implemented in an interactive Web interface (www.phylotype.org), which provides a wide choice of graphical views and output formats, and allows for exploratory analyses of large data sets.
Contact: francois.chevenet@ird.fr, gascuel@lirmm.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Grape RNA-Seq analysis pipeline environment
Authors: Knowles David G. , Röder Maik , Merkel Angelika , Guigó Roderic 
Published: January 2013

Abstract
Motivation: The avalanche of data arriving since the development of NGS technologies have prompted the need for developing fast, accurate and easily automated bioinformatic tools capable of dealing with massive datasets. Among the most productive applications of NGS technologies is the sequencing of cellular RNA, known as RNA-Seq. Although RNA-Seq provides similar or superior dynamic range than microarrays at similar or lower cost, the lack of standard and user-friendly pipelines is a bottleneck preventing RNA-Seq from becoming the standard for transcriptome analysis.
Results: In this work we present a pipeline for processing and analyzing RNA-Seq data, that we have named Grape (Grape RNA-Seq Analysis Pipeline Environment). Grape supports raw sequencing reads produced by a variety of technologies, either in FASTA or FASTQ format, or as prealigned reads in SAM/BAM format. A minimal Grape configuration consists of the file location of the raw sequencing reads, the genome of the species and the corresponding gene and transcript annotation.
Grape first runs a set of quality control steps, and then aligns the reads to the genome, a step that is omitted for prealigned read formats. Grape next estimates gene and transcript expression levels, calculates exon inclusion levels and identifies novel transcripts.
Grape can be run on a single computer or in parallel on a computer cluster. It is distributed with specific mapping and quantification tools, but given its modular design, any tool supporting popular data interchange formats can be integrated.
Availability: Grape can be obtained from the Bioinformatics and Genomics website at: http://big.crg.cat/services/grape.
Contact: david.gonzalez@crg.eu or roderic.guigo@crg.eu
SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology
Authors: Adams Richard , Clark Allan , Yamaguchi Azusa , Hanlon Neil , Tsorman Nikos , Ali Shakir , Lebedeva Galina , Goltsov Alexey , Sorokin Anatoly , Akman Ozgur E. , Troein Carl , Millar Andrew J. , Goryanin Igor , Gilmore Stephen 
Published: January 2013

Abstract
Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats.
Availability and implementation: All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.
Contact: stg@inf.ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Baseline characteristics of patients in the Reduction of Events with Darbepoetin alfa in Heart Failure trial (RED‐HF)
Authors: McMurray John J.V. , Anand Inder S. , Diaz Rafael , Maggioni Aldo P. , O'Connor Christopher , Pfeffer Marc A. , Solomon Scott D. , Tendera Michal , van Veldhuisen Dirk J. , Albizem Moetaz , Cheng Sunfa , Scarlata Debra , Swedberg Karl , Young James B. ,   on behalf of the RED‐HF Committees Investigators
Published: January 2013

AimsThis report describes the baseline characteristics of patients in the Reduction of Events with Darbepoetin alfa in Heart Failure trial (RED‐HF) which is testing the hypothesis that anaemia correction with darbepoetin alfa will reduce the composite endpoint of death from any cause or hospital admission for worsening heart failure, and improve other outcomes.Methods and resultsKey demographic, clinical, and laboratory findings, along with baseline treatment, are reported and compared with those of patients in other recent clinical trials in heart failure. Compared with other recent trials, RED‐HF enrolled more elderly [mean age 70 (SD 11.4) years], female (41%), and black (9%) patients. RED‐HF patients more often had diabetes (46%) and renal impairment (72% had an estimated glomerular filtration rate <60 mL/min/1.73 m2). Patients in RED‐HF had heart failure of longer duration [5.3 (5.4) years], worse NYHA class (35% II, 63% III, and 2% IV), and more signs of congestion. Mean EF was 30% (6.8%). RED‐HF patients were well treated at randomization, and pharmacological therapy at baseline was broadly similar to that of other recent trials, taking account of study‐specific inclusion/exclusion criteria. Median (interquartile range) haemoglobin at baseline was 112 (106–117) g/L.ConclusionThe anaemic patients enrolled in RED‐HF were older, moderately to markedly symptomatic, and had extensive co‐morbidity.
Reducing Wastage of Inhalation Anesthetics Using Real-time Decision Support to Notify of Excessive Fresh Gas Flow
Authors: Nair Bala G. , Peterson Gene N. , Neradilek Moni B. , Newman Shu Fang , Huang Elaine Y. , Schwid Howard A. 
Published: January 2013

Abstract

Background:
Reduced consumption of inhalation anesthetics can be safely achieved by reducing excess fresh gas flow (FGF). In this study the authors describe the use of a real-time decision support tool to reduce excess FGF to lower, less wasteful levels.

Method:
The authors applied a decision support tool called the Smart Anesthesia Manager™ (University of Washington, Seattle, WA) that analyzes real-time data from an Anesthesia Information Management System to notify the anesthesia team if FGF exceeds 1 l/min. If sevoflurane consumption reached 2 minimum alveolar concentration-hour under low flow anesthesia (FGF < 2 l/min), a second message was generated to increase FGF to 2 l/min, to comply with Food and Drug Administration guidelines. To evaluate the tool, mean FGF between surgical incision and the end of procedure was compared in four phases: (1) a baseline period before instituting decision rules, (2) Intervention-1 when decision support to reduce FGF was applied, (3) Intervention-2 when the decision rule to reduce flow was deliberately inactivated, and (4) Intervention-3 when decision rules were reactivated.

Results:
The mean ± SD FGF reduced from 2.10 ± 1.12 l/min (n = 1,714) during baseline to 1.60 ± 1.01 l/min (n = 2,232) when decision rules were instituted (P < 0.001). When the decision rule to reduce flow was inactivated, mean FGF increased to 1.87 ± 1.15 l/min (n = 1,732) (P < 0.001), with an increasing trend in FGF of 0.1 l/min/month (P = 0.02). On reactivating the decision rules, the mean FGF came down to 1.59 ± 1.02 l/min (n = 1,845). Through the Smart Anesthesia Messenger™ system, the authors saved 9.5 l of sevoflurane, 6.0 l of desflurane, and 0.8 l isoflurane per month, translating to an annual savings of $104,916.

Conclusions:
Real-time notification is an effective way to reduce inhalation agent usage through decreased excess FGFs.
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
Authors: Shakya Migun , Quince Christopher , Campbell James H. , Yang Zamin K. , Schadt Christopher W. , Podar Mircea 
Published: January 2013

SummaryNext‐generation sequencing has dramatically changed the landscape of microbial ecology, large‐scale and in‐depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon‐specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine‐tuning experimental and computational parameters used to characterize natural communities.
High temporal variability in commensal Escherichia coli strain communities of a herbivorous marsupial
Authors: Blyton Michaela D. J. , Banks Sam C. , Peakall Rod , Gordon David M. 
Published: January 2013

SummaryAlthough Escherichia coli is an important model organism for bacterial research, few studies have explored the nature of temporal variation in E. coli strains within the intestinal tracts of host individuals. In this study the E. coli strains of 54 mountain brushtail possums were sampled on four occasions during a year. This allowed temporal changes to be quantified both at the host population level and within individuals. Escherichia coli strains were identified using a combination of rep‐PCR profiles from two primers (CGG and ERIC) and phylogenetic group assigned by quadruplex PCR. The study revealed considerable changes in community structure within individuals among all time periods. In fact, temporal variation within individuals accounted for more of the variation in E. coli community structure than differences between animals. In contrast to the within‐host dynamics, there were no significant differences among the time periods at the host population level. It was also found that there was no effect of host age or sex on strain community structure within host individuals. These findings highlight the importance of temporal variation in the ecology of E. coli, while the methods applied in this study may serve as a foundation for further work in this area.
Randomised trial of cervical cerclage, with and without occlusion, for the prevention of preterm birth in women suspected for cervical insufficiency
Authors: Brix N , Secher NJ , McCormack CD , Helmig RB , Hein M , Weber T , Mittal S , Kurdi W , Palacio M , Henriksen TB ,   the CERVO group
Published: January 2013

ObjectiveTo evaluate the effect of cerclage, with and without cervical occlusion.DesignMulticentre, stratified, randomised controlled trial.SettingHospital‐based multicentre study with 18 tertiary centres from nine countries.PopulationWomen with a history of cervical insufficiency (prophylactic trial) and women with a short cervix (therapeutic trial) were recruited from August 2006 to August 2011.MethodsA centralised telephone randomisation service with a computer system was used to randomise women to cervical cerclage with or without cervical occlusion. Only the analyst performing the interim analyses was blinded.Main outcome measuresThe take‐home baby rate (number of infants discharged alive from the hospital), gestational age at delivery, and the number of days in the neonatal intensive care unit (NICU).ResultsWomen (n = 309) were stratified into the prophylactic trial (n = 213) or the therapeutic trial (n = 96). The trial stopped early due to slow recruitment and an interim analysis showing no benefit of occlusion. Final analysis comprised 197 women in the prophylactic trial and 87 women in the therapeutic trial. No added effect of cervical occlusion was found in terms of the take‐home baby rate in the prophylactic trial (92 versus 90%, RR 1.03, 95% CI 0.94–1.12) or in the therapeutic trial (81 versus 85%, RR 0.96, 95% CI 0.79–1.16). No effect of cervical occlusion was found in terms of gestational age at delivery and number of days the neonate spent in the NICU. Cervical occlusion was associated with no harm.ConclusionsCervical occlusion with cerclage had no significant additional effect.
Do Farmers Internalise Environmental Spillovers of Pesticides in Production?
Authors: Skevas Theodoros , Stefanou Spiro E. , Lansink Alfons Oude 
Published: January 2013

AbstractPesticides are used in agriculture to protect crops from pests and diseases, with indiscriminate pesticide use having several adverse effects on the environment and human health. An important question is whether the environmental spillovers of pesticides also affect the farmers’ production environment. We use a model of optimal pesticide use that explicitly incorporates the symmetric and asymmetric effect of pesticides’ environmental spillovers on crop production. The application focuses on panel data from Dutch cash crop producers. We show that pesticides have a positive direct impact on output and a negative indirect impact through their effects on the production environment.
Occurrence and diversity of entomopathogenic fungi in cultivated and uncultivated soils in Pakistan
Authors: Wakil Waqas , Ghazanfar M. Usman , Riasat Tahira , Kwon Young Jung , Qayyum Mirza Abdul , Yasin Muhammad 
Published: January 2013

AbstractThe distribution of entomopathogenic fungi in various geographical areas of Punjab, Pakistan, is poorly understood. The present study was planned to explore the occurrence and diversity of entomopathogenic fungi from soils collected from cultivated and non‐cultivated habitats. The detailed survey of different habitats (crop fields, fruits, vegetables, forests) was conducted to collect soil samples and the associated fungi were isolated using Galleria bait method. Among 210 soil samples, 168 fungal isolates were recovered and identified, with 98 from forests, 32 from vegetables, 30 from field crops and 8 from fruits. The major entomopathogenic fungi recovered from these samples were Beauveria bassiana, Metarhizium anisopliae, Paecilomyces lilacinus, B. brongniartii, P. chlamydosporia and Lecanicillium attenuatum. The diversity of entomopathogenic fungi was greater in soil samples from forests compared to crop fields, vegetables and fruits, respectively. The geographical attributes (altitude, longitude, latitude) greatly influenced the occurrence of entomopathogenic fungi with the highest number of isolates found from >600 m altitude, 33°–34′N latitude, and 73°74′E longitude from soil samples. The results of the surveys clearly indicated that the entomopathogenic fungi are distributed in the soils which may be used in successful IPM programs in future.
Insecticidal activity of the chitinase from the Spodoptera litura nucleopolyhedrovirus
Authors: Wang Yong , Choi Jae Young , Roh Jong Yul , Tao Xue Ying , Liu Qin , Lee Joo Hyun , Kim Jae Su , Kim Woo Jin , Je Yeon Ho 
Published: January 2013

AbstractBaculovirus chitinase gene (chiA) is a late gene essential for liquefying the host insect at a late stage of infection for its hydrolyzing chitin function. In a previous report, baculovirus ChiA has been shown to offer many interesting new opportunities for pest control. Recently, a putative chiA gene was identified in the Korean isolate of the Spodoptera litura nucleopolyhedorvirus (SpliMNPV‐K1) genome. The open reading frame (ORF) contains 1692 nucelotides and encodes a protein of 563 amino acids with a predicted molecular weight of about 62.6 kDa. To study the insecticidal activity of ChiA from SpliMNPV‐K1, we constructed a recombinant AcMNPV, Ap‐SlChiA, which is designed to express the ChiA under the control of a polyhedrin promoter. Western blot analysis indicated that ChiA was successfully expressed by this recombinant virus. Chitinase assay revealed that the chitobiosidase and endochitinase activity of the recombinant virus was 2.5‐ and 3.9‐flods higher than those of wild‐type AcMNPV, respectively. In addition, the recombinant virus showed higher evident insecticidal activity against 3rd instar larvae of Spodotera exigua than that of the AcMNPV. These results suggest that the chiA gene from SpliMNPV‐K1 could be successfully applied to improve pathogenicity of baculoviruses.