bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Hydrogen Peroxide Vapor Room Decontamination onClostridium difficileEnvironmental Contamination and Transmission in a Healthcare Setting
Authors: Boyce John M. , Havill Nancy L. , Otter Jonathan A. , McDonald L. Clifford , Adams Nicholas M. T. , Cooper Timothea , Thompson Angela , Wiggs Lois , Killgore George , Tauman Allison , Noble-Wang Judith 
Published: July 2008

Objective.To determine whether hydrogen peroxide vapor (HPV) decontamination can reduce environmental contamination with and nosocomial transmission ofClostridium difficile.Design.A prospective before-after intervention study.Setting.A hospital affected by an epidemic strain ofC. difficile.Intervention.Intensive HPV decontamination of 5 high-incidence wards followed by hospital-wide decontamination of rooms vacated by patients withC. difficile-associated disease (CDAD). The preintervention period was June 2004 through March 2005, and the intervention period was June 2005 through March 2006.Results.Eleven (25.6%) of 43 cultures of samples collected by sponge from surfaces before HPV decontamination yieldedC. difficile,compared with 0 of 37 cultures of samples obtained after HPV decontamination (P< .001). On 5 high-incidence wards, the incidence of nosocomial CDAD was significantly lower during the intervention period than during the preintervention period (1.28 vs 2.28 cases per 1,000 patient-days;P= .047). The hospital-wide CDAD incidence was lower during the intervention period than during the preintervention period (0.84 vs 1.36 cases per 1,000 patient-days;P= .26). In an analysis limited to months in which the epidemic strain was present during both the preintervention and the intervention periods, CDAD incidence was significandy lower during the intervention period than during the preintervention period (0.88 vs 1.89 cases per 1,000 patient-days;P= .047).Conclusions.HPV decontamination was efficacious in eradicating C.difficilefrom contaminated surfaces. Further studies of the impact of HPV decontamination on nosocomial transmission ofC. difficileare warranted.
BioBayes: A software package for Bayesian inference in systems biology
Authors: Vyshemirsky Vladislav , Girolami Mark 
Published: July 2008

Abstract
Motivation: There are several levels of uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree of uncertainty about the values of kinetic parameters, about the general structure of the model and about the behaviour of biochemical species which cannot be observed directly. The methods of Bayesian inference provide a consistent framework for modelling and predicting in these uncertain conditions. We present a software package for applying the Bayesian inferential methodology to problems in systems biology.
Results: Described herein is a software package, BioBayes, which provides a framework for Bayesian parameter estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package is extensible allowing additional modules to be included by developers. There are no other such packages available which provide this functionality.
Availability: http://www.dcs.gla.ac.uk/BioBayes/
Contact: vvv@dcs.gla.ac.uk
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary
Authors: Ji Shuiwang , Sun Liang , Jin Rong , Kumar Sudhir , Ye Jieping 
Published: July 2008

Abstract
Motivation: Regulation of gene expression in space and time directs its localization to a specific subset of cells during development. Systematic determination of the spatiotemporal dynamics of gene expression plays an important role in understanding the regulatory networks driving development. An atlas for the gene expression patterns of fruit fly Drosophila melanogaster has been created by whole-mount in situ hybridization, and it documents the dynamic changes of gene expression pattern during Drosophila embryogenesis. The spatial and temporal patterns of gene expression are integrated by anatomical terms from a controlled vocabulary linking together intermediate tissues developed from one another. Currently, the terms are assigned to patterns manually. However, the number of patterns generated by high-throughput in situ hybridization is rapidly increasing. It is, therefore, tempting to approach this problem by employing computational methods.
Results: In this article, we present a novel computational framework for annotating gene expression patterns using a controlled vocabulary. In the currently available high-throughput data, annotation terms are assigned to groups of patterns rather than to individual images. We propose to extract invariant features from images, and construct pyramid match kernels to measure the similarity between sets of patterns. To exploit the complementary information conveyed by different features and incorporate the correlation among patterns sharing common structures, we propose efficient convex formulations to integrate the kernels derived from various features. The proposed framework is evaluated by comparing its annotation with that of human curators, and promising performance in terms of F1 score has been reported.
Contact: jieping.ye@asu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
Authors: Masso Majid , Vaisman Iosif I. 
Published: July 2008

AbstractMotivation: Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into protein structure and function. Such models are also valuable for the design and engineering of new proteins. Previously described methods have utilized properties of protein sequence or structure to predict the free energy change of mutants due to thermal (ΔΔG) and denaturant (ΔΔGH2O) denaturations, as well as mutant thermal stability (ΔTm), through the application of either computational energy-based approaches or machine learning techniques. However, accuracy associated with applying these methods separately is frequently far from optimal.Results: We detail a computational mutagenesis technique based on a four-body, knowledge-based, statistical contact potential. For any mutation due to a single amino acid replacement in a protein, the method provides an empirical normalized measure of the ensuing environmental perturbation occurring at every residue position. A feature vector is generated for the mutant by considering perturbations at the mutated position and it's ordered six nearest neighbors in the 3-dimensional (3D) protein structure. These predictors of stability change are evaluated by applying machine learning tools to large training sets of mutants derived from diverse proteins that have been experimentally studied and described. Predictive models based on our combined approach are either comparable to, or in many cases significantly outperform, previously published results.Availability: A web server with supporting documentation is available at http://proteins.gmu.edu/automuteContact: ivaisman@gmu.edu
Heterogeneity and weak coupling may explain the synchronization characteristics of cells in the arterial wall
Authors: Jacobsen Jens Christian Brings , Aalkjaer Christian , Matchkov Vladimir V , Nilsson Holger , Freiberg Jacob J , Holstein-Rathlou Niels-Henrik 
Published: July 2008

Vascular smooth muscle cells (SMCs) exhibit different types of calcium dynamics. Static vascular tone is associated with unsynchronized calcium waves and the developed force depends on the number of recruited cells. Global calcium transients synchronized among a large number of cells cause rhythmic development of force known as vasomotion. We present experimental data showing a considerable heterogeneity in cellular calcium dynamics in the vascular wall. In stimulated vessels, some SMCs remain quiescent, whereas others display waves of variable frequency. At the onset of vasomotion, all SMCs are enrolled into synchronized oscillation.
Simulations of coupled SMCs show that the experimentally observed cellular recruitment, the presence of quiescent cells and the variation in oscillation frequency may arise if the cell population is phenotypically heterogeneous. In this case, quiescent cells can be entrained at the onset of vasomotion by the collective driving force from the synchronized oscillations in the membrane potential of the surrounding cells. Partial synchronization arises with an increase in the concentration of cyclic guanosine monophosphate, but in a heterogeneous cell population complete synchronization also requires a high-conductance pathway that provides strong coupling between the cells.
Quantitative Proteomics of a ChloroplastSRP54Sorting Mutant and Its Genetic Interactions withCLPC1in Arabidopsis
Authors: Rutschow Heidi , Ytterberg A. Jimmy , Friso Giulia , Nilsson Robert , van Wijk Klaas J. 
Published: July 2008

AbstractcpSRP54 (for chloroplast SIGNAL RECOGNITION PARTICLE54) is involved in cotranslational and posttranslational sorting of thylakoid proteins. The Arabidopsis (Arabidopsis thaliana) cpSRP54 null mutant, ffc1-2, is pale green with delayed development. Western-blot analysis of individual leaves showed that the SRP sorting pathway, but not the SecY/E translocon, was strongly down-regulated with progressive leaf development in both wild-type and ffc1-2 plants. To further understand the impact of cpSRP54 deletion, a quantitative comparison of ffc2-1 was carried out for total leaf proteomes of young seedlings and for chloroplast proteomes of fully developed leaves using stable isotope labeling (isobaric stable isotope labeling and isotope-coded affinity tags) and two-dimensional gels. This showed that cpSRP54 deletion led to a change in light-harvesting complex composition, an increase of PsbS, and a decreased photosystem I/II ratio. Moreover, the cpSRP54 deletion led in young leaves to up-regulation of thylakoid proteases and stromal chaperones, including ClpC. In contrast, the stromal protein homeostasis machinery returned to wild-type levels in mature leaves, consistent with the developmental down-regulation of the SRP pathway. A differential response between young and mature leaves was also found in carbon metabolism, with an up-regulation of the Calvin cycle and the photorespiratory pathway in peroxisomes and mitochondria in young leaves but not in old leaves. The Calvin cycle was down-regulated in mature leaves to adjust to the reduced capacity of the light reaction, while reactive oxygen species defense proteins were up-regulated. The significance of ClpC up-regulation was confirmed through the generation of an ffc2-1 clpc1 double mutant. This mutant was seedling lethal under autotrophic conditions but could be partially rescued under heterotrophic conditions.
Minimum and optimum light requirements for laryngoscopy in paediatric anaesthesia: a manikin study*
Authors: Malan C. A. , Scholz A. , Wilkes A. R. , Hampson M. A. , Hall J. E. 
Published: July 2008

SummaryDirect laryngoscopy is performed regularly in paediatric anaesthetic practice for the purpose of intubating a patient's trachea. A minimum illumination of 700 lux at a distance of 20 mm has been suggested in a draft standard for laryngoscopes from the International Organization for Standardization. We investigated the minimum and optimum illumination required by anaesthetists during laryngoscopy. Fifty anaesthetists were recruited to perform laryngoscopy on a child manikin with a selection of laryngoscope blades and bulbs attached to a variable voltage supply. There was a large variation in the illumination range of different bulb and blade combinations. We demonstrated a large interindividual variability between anaesthetists for illumination requirements during laryngoscopy. Anaesthetists can see the larynx at very low light levels, but optimum illumination was significantly greater than minimum illumination. Two of the six combinations could produce more than 700 lux. In all, 78% and 54% of anaesthetists considered 700 lux too bright with a halogen and xenon bulb, respectively. Our study suggests that the proposed standard of 700 lux may possibly be too bright.
Therapeutic hypothermia in comatose patients after out‐of‐hospital cardiac arrest*
Authors: Hay A. W. , Swann D. G. , Bell K. , Walsh T. S. , Cook B. 
Published: July 2008

SummaryOur intensive care unit has been treating comatose patients, following an out‐of‐hospital cardiac arrest, with therapeutic hypothermia since 2002. In all, 139 out‐of‐hospital cardiac arrest patients were admitted in the 4‐year period 2002–5. Of these, 27% had a favourable outcome (discharged home or to rehabilitation). Forty‐one per cent of patients presenting with ventricular fibrillation (VF) and 7% of non‐VF patients had a favourable outcome. No patient with an estimated time from collapse to first attempt at cardiopulmonary resuscitation over 12 min survived to hospital discharge. Twenty‐two per cent of patients over 70 years were discharged home, suggesting age was not a barrier to surviving out‐of‐hospital cardiac arrest. The introduction of a therapeutic hypothermia clinical pathway, at the end of 2003 improved the efficiency of cooling. The percentage of patients cooled to below 34 °C within 4 h increased from 15 to 51% and those cooled for more than 12 h increased from 30 to 83%.
Dexmedetomidine and cardiac protection for non‐cardiac surgery: a meta‐analysis of randomised controlled trials
Authors: Biccard B. M. , Goga S. , De Beurs J. 
Published: July 2008

SummaryWe conducted a systematic review of the effects of dexmedetomidine on cardiac outcomes following non‐cardiac surgery. We included prospective, randomised peri‐operative studies of dexmedetomidine that reported mortality, cardiac morbidity or adverse drug events. A PubMed Central and EMBASE search was conducted up to July 2007. The reference lists of identified papers were examined for further trials. Of 425 studies identified, 20 were included in the meta‐analysis (840 patients). Dexmedetomidine was associated with a trend towards improved cardiac outcomes; all‐cause mortality (OR 0.27, 95% CI 0.01–7.13, p = 0.44), non‐fatal myocardial infarction (OR 0.26, 95% CI 0.04–1.60, p = 0.14), and myocardial ischaemia (OR 0.65, 95% CI 0.26–1.63, p = 0.36). Peri‐operative hypotension (26%, OR 3.80, 95% CI 1.91–7.54, p = 0.0001) and bradycardia (17%, OR 5.45, 95% CI 2.98–9.95, p < 0.00001) were significantly increased. An anticholinergic did not reduce the incidence of bradycardia (p = 0.43). A randomised placebo‐controlled trial of dexmedetomidine is warranted.
Impacts of climatic stability on the structural and functional aspects of macroinvertebrate communities after severe drought
Authors: GRISWOLD MARCUS W. , BERZINIS REBECCA W. , CRISMAN THOMAS L. , GOLLADAY STEPHEN W. 
Published: July 2008

Summary1. Unpredictable, extreme climatic events (e.g. droughts) can potentially destabilize aquatic communities. From 1998 to 2002, southwestern Georgia, U.S.A., experienced the third worst drought of the last 100 years, leading to loss of surface flow in many small streams. We sampled macroinvertebrates, flow and water chemistry in small headwater streams from 2001 to 2007 in two adjacent coastal plain streams of contrasting headwater type (wetland and groundwater‐fed seep) following resumption of flow.2. Decreasing water temperature, conductivity and nutrient concentrations within the first 2 years of the study indicated flushing of the streambed associated with increased discharge. Invertebrate community composition became less variable over time and during wetter years, reflecting water chemistry, hydrological and climate conditions.3. A core set of species appeared immediately following breaking of the drought in both streams, reflecting a shared species pool. These species exhibited resilience traits, including short life cycles and resistance to desiccation, which allowed for rapid recovery from disturbance. Such species, which were small‐bodied, sclerotized and abundant in the drift, were then replaced as flows increased by those that were larger, soft‐bodied and rare in drift, suggesting a more stable and less ephemeral habitat.4. Hydrologic regime and long‐term precipitation indices were strongly correlated with invertebrate community and trait structure. Long‐term data allowed for better interpretation of the effects of infrequent disturbances on aquatic ecosystems. Additionally, long‐term precipitation indices (i.e. 48‐month standardized precipitation index) can indicate the likelihood of a return to drought, allowing for the collection of pre‐disturbance data.
Comparison of three research models of portal hypertension in mice: macroscopic, histological and portal pressure evaluation
Authors: Geerts Anja M. , Vanheule Eline , Praet Marleen , Van Vlierberghe Hans , De Vos Martine , Colle Isabelle 
Published: July 2008

SummaryThe characterization of mice models of portal hypertension (PHT) is lacking in the literature. Therefore, the aim of the present study was to make a histological approach during development of PHT in two models of cirrhosis with PHT compared with one model of isolated PHT. The model of isolated PHT was developed by partial portal vein ligation (PPVL). Two portal hypertensive cirrhotic mice models were developed either by common bile duct ligation (CBDL) or administration of carbon tetrachloride (CCl4) subcutaneously (twice weekly, 1 ml/kg). These models represent, respectively, a secondary biliary cirrhosis and alcoholic cirrhosis. Mice were killed at several time points to evaluate liver changes by histological and ultrastructural methods. A correlation was made with portal pressure measurements. Histology revealed the absence of fibrosis or cirrhosis in PPVL mice. They developed an isolated portal hypertension. After CBDL induction, the mice developed the characteristics of cirrhosis after 6 weeks, with simultaneous increase in portal pressures. Fifty percent of the mice had ascites at that time point. Sixteen weeks after administration of CCl4, a micronodular cirrhotic aspect of the liver was seen associated with signs of portal hypertension. This is the first descriptive study of three widely used animal models in mice, allowing the study of pathophysiological changes in cirrhosis and portal hypertension. The PPVL in mice leads to a model of isolated portal hypertension. Secondary biliary cirrhosis developed after 6 weeks of common bile duct ligation in 50% of the mice that developed ascites. Subcutaneous injection of CCl4 for 16 weeks induces cirrhosis and poral hypertension, without ascites. Moreover, the present study is the first description of a cirrhotic model in mice developed by subcutaneous injections of CCl4. Well‐described mice models will facilitate use of knock‐out or transgenic mice and lead to a better understanding of the underlying molecular pathways in the field of portal hypertension and cirrhosis.
Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery
Authors: BARR KELLY R. , LINDSAY DENISE L. , ATHREY GIRI , LANCE RICHARD F. , HAYDEN TIMOTHY J. , TWEDDALE SCOTT A. , LEBERG PAUL L. 
Published: July 2008

AbstractBlack‐capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (FST = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black‐capped vireos are capable of large‐scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.
Do outbreaks affect genetic population structure? A worldwide survey inLocusta migratoria, a pest plagued by microsatellite null alleles
Authors: CHAPUIS M‐P. , LECOQ M. , MICHALAKIS Y. , LOISEAU A. , SWORD G. A. , PIRY S. , ESTOUP A. 
Published: July 2008

AbstractAn understanding of the role of factors intrinsic to a species’ life history in structuring contemporary genetic variation is a fundamental, but understudied, aspect of evolutionary biology. Here, we assessed the influence of the propensity to outbreak in shaping worldwide genetic variation inLocusta migratoria, a cosmopolitan pest well known for its expression of density‐dependent phase polyphenism. We scored 14 microsatellites in nine subspecies from 25 populations distributed over most of the species’ range in regions that vary in the historical frequency and extent of their outbreaks. We rejected the hypothesis thatL. migratoriaconsists of two genetically distinct clusters adapted to habitats either rarely (nonoutbreaking) or cyclically (outbreaking) favourable to increases in population density. We also invalidated the current subspecific taxonomic classification based on morphometrics. Bayesian inferences indicated evidence of a homogenizing effect of outbreaks onL. migratoriapopulation structure. Geographical and ecological barriers to gene flow in conjunction with historical events can also explain the observed patterns. By systematically assessing the effects of null alleles using computer simulations, we also provide a template for the analysis of microsatellite data sets characterized by a high prevalence of null alleles.
Delayed reproduction in Arabidopsis thaliana improves fitness in soil with suboptimal phosphorus availability
Authors: NORD ERIC A. , LYNCH JONATHAN P. 
Published: July 2008

ABSTRACTLow phosphorus availability (low P) often delays flowering and maturity in annual plants, while abiotic stress generally accelerates flowering and maturity. The utility of this response is unknown. We hypothesize that phenological delay in low P is beneficial by permitting more time for phosphorus acquisition and utilization. We grew seven genotypes of Arabidopsis thaliana with contrasting phenology in high and low P. Low P delayed bolting and maturity in all genotypes. Low P decreased root length, but not root‐length duration (the integral of root length over time), because phenological delay allowed low‐P plants to compensate for shorter root length. Root‐length duration was correlated with phosphorus accumulation. Leaf phosphorus duration (the integral of leaf phosphorus over time) was correlated with reproductive biomass, indicating the utility of increased phosphorus utilization. Phenological delays accounted for up to 30% of biomass production when low‐P plants were compared to models of plants with no delays. These results support the hypothesis that phenological delay in low P is adaptive and leads to increased phosphorus acquisition and utilization. Because low P conditions are prevalent, understanding the utility of this response could be useful in crop breeding and in predicting plant responses to global climate change.