bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureusNasal Colonization and Subsequent Infection in Intensive Care Unit Patients: Does Methicillin Resistance Matter?
Authors: Honda Hitoshi , Krauss Melissa J. , Coopersmith Craig M. , Kollef Marin H. , Richmond Amy M. , Fraser Victoria J. , Warren David K. 
Published: April 2010

Background.Staphylococcus aureusis an important cause of infection in intensive care unit (ICU) patients. Colonization with methicillin-resistantS. aureus(MRSA) is a risk factor for subsequentS. aureusinfection. However, MRSA-colonized patients may have more comorbidities than methicillin-susceptibleS. aureus(MSSA)-colonized or noncolonized patients and therefore may be more susceptible to infection on that basis.Objective.To determine whether MRSA-colonized patients who are admitted to medical and surgical ICUs are more likely to develop anyS. aureusinfection in the ICU, compared with patients colonized with MSSA or not colonized withS. aureus,independent of predisposing patient risk factors.Design.Prospective cohort study.Setting.A 24-bed surgical ICU and a 19-bed medical ICU of a 1,252-bed, academic hospital.Patients.A total of 9,523 patients for whom nasal swab samples were cultured forS. aureusat ICU admission during the period from December 2002 through August 2007.Methods.Patients in the ICU for more than 48 hours were examined for an ICU-acquired S.aureusinfection, defined as development ofS. aureusinfection more than 48 hours after ICU admission.Results.S. aureuscolonization was present at admission for 1,433 (27.8%) of 5,161 patients (674 [47.0%] with MRSA and 759 [53.0%] with MSSA). An ICU-acquiredS. aureusinfection developed in 113 (2.19%) patients, of whom 75 (66.4%) had an infection due to MRSA. Risk factors associated with an ICU-acquiredS. aureusinfection included MRSA colonization at admission (adjusted hazard ratio, 4.70 [95% confidence interval, 3.07-7.21]) and MSSA colonization at admission (adjusted hazard ratio, 2.47 [95% confidence interval, 1.52-4.01]).Conclusion.ICU patients colonized with S.aureuswere at greater risk of developing aS. aureusinfection in the ICU. Even after adjusting for patient-specific risk factors, MRSA-colonized patients were more likely to developS. aureusinfection, compared with MSSA-colonized or noncolonized patients.
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
Authors: Wilkerson Matthew D. , Hayes D. Neil 
Published: April 2010

Abstract
Summary: Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. These new features provide users with detailed information that enable more specific decisions in unsupervised class discovery.
Availability: ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project (http://www.bioconductor.org/).
Contact: mwilkers@med.unc.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L Pairs of Glycosyltransferase Genes Reveals Critical Contributions to Biosynthesis of the Hemicellulose Glucuronoxylan
Authors: Wu Ai-Min , Hörnblad Emma , Voxeur Aline , Gerber Lorenz , Rihouey Christophe , Lerouge Patrice , Marchant Alan 
Published: April 2010

Abstract
The hemicellulose glucuronoxylan (GX) is a major component of plant secondary cell walls. However, our understanding of GX synthesis remains limited. Here, we identify and analyze two new genes from Arabidopsis (Arabidopsis thaliana), IRREGULAR XYLEM9-LIKE (IRX9-L) and IRX14-LIKE (IRX14-L) that encode glycosyltransferase family 43 members proposed to function during xylan backbone elongation. We place IRX9-L and IRX14-L in a genetic framework with six previously described glycosyltransferase genes (IRX9, IRX10, IRX10-L, IRX14, FRAGILE FIBER8 [FRA8], and FRA8 HOMOLOG [F8H]) and investigate their function in GX synthesis. Double-mutant analysis identifies IRX9-L and IRX14-L as functional homologs of IRX9 and IRX14, respectively. Characterization of irx9 irx10 irx14 fra8 and irx9-L irx10-L irx14-L f8h quadruple mutants allows definition of a set of genes comprising IRX9, IRX10, IRX14, and FRA8 that perform the main role in GX synthesis during vegetative development. The IRX9-L, IRX10-L, IRX14-L, and F8H genes are able to partially substitute for their respective homologs and normally perform a minor function. The irx14 irx14-L double mutant virtually lacks xylan, whereas irx9 irx9-L and fra8 f8h double mutants form lowered amounts of GX displaying a greatly reduced degree of backbone polymerization. Our findings reveal two distinct sets of four genes each differentially contributing to GX biosynthesis.
Five Arabidopsis Reticulon Isoforms Share Endoplasmic Reticulum Location, Topology, and Membrane-Shaping Properties
Authors: Sparkes Imogen , Tolley Nicholas , Aller Isabel , Svozil Julia , Osterrieder Anne , Botchway Stanley , Mueller Christopher , Frigerio Lorenzo , Hawes Chris 
Published: April 2010

Abstract
The cortical endoplasmic reticulum (ER) in tobacco (Nicotiana tabacum) epidermal cells is a network of tubules and cisternae undergoing dramatic rearrangements. Reticulons are integral membrane proteins involved in shaping ER tubules. Here, we characterized the localization, topology, effect, and interactions of five Arabidopsis thaliana reticulons (RTNs), isoforms 1-4 and 13, in the cortical ER. Our results indicate that RTNLB13 and RTNLB1-4 colocate to and constrict the tubular ER membrane. All five RTNs preferentially accumulate on ER tubules and are excluded from ER cisternae. All isoforms share the same transmembrane topology, with N and C termini facing the cytosol and four transmembrane domains. We show by Förster resonance energy transfer and fluorescence lifetime imaging microscopy that several RTNs have the capacity to interact with themselves and each other, and we suggest that oligomerization is responsible for their residence in the ER membrane. We also show that a complete reticulon homology domain is required for both RTN residence in high-curvature ER membranes and ER tubule constriction, yet it is not necessary for homotypic interactions.
Drug‐related behaviors independently associated with syphilis infection among female sex workers in two Mexico–US border cities
Authors: Loza Oralia , Patterson Thomas L. , Rusch Melanie , Martínez Gustavo A. , Lozada Remedios , Staines‐Orozco Hugo , Magis‐Rodríguez Carlos , Strathdee Steffanie A. 
Published: April 2010

ABSTRACTAims  To identify correlates of active syphilis infection among female sex workers (FSWs) in Tijuana and Ciudad Juarez.Design  Cross‐sectional analyses of baseline interview data. Correlates of active syphilis (antibody titers >1 : 8) were identified by logistic regression.Setting  Tijuana and Ciudad Juarez, two Mexican cities on the US border that are situated on major drug trafficking routes and where prostitution is quasi‐legal.Participants  A total of 914 FSWs aged ≥18 years without known human immunodeficiency virus (HIV) infection who had had recent unprotected sex with clients.Measurements  Baseline interviews and testing for syphilis antibody using Treponema pallidum particle agglutination (TPPA) and rapid plasma reagin (RPR) tests.Findings  Median age and duration in sex work were 32 and 4 years, respectively. Overall, 18.0% had ever injected drugs, 14.2% often or always used illegal drugs before or during sex in the past month, 31.4% had clients in the last 6 months who injected drugs, and 68.6% reported having clients from the United States. Prevalence of HIV and active syphilis were 5.9% and 10.3%, respectively. Factors independently associated with active syphilis included injecting drugs (AOR: 2.39; 95% CI: 1.40, 4.08), using illegal drugs before or during sex (AOR: 2.06; 95% CI: 1.16, 3.65) and having any US clients (AOR: 2.85; 95% CI: 1.43, 5.70).Conclusions  Among female sex workers in Tijuana and Ciudad Juarez, drug‐using behaviors were associated more closely with active syphilis than were sexual behaviors, suggesting the possibility of parenteral transmission of T. pallidum. Syphilis eradication programs should consider distributing sterile syringes to drug injectors and assisting FSWs with safer‐sex negotiation in the context of drug use.
Comparison of transcript profiles in late blight‐challenged Solanum cajamarquense and B3C1 potato clones
Authors: LINDQVIST‐KREUZE HANNELE , CARBAJULCA DORIS , GONZALEZ‐ESCOBEDO GEOFFREY , PÉREZ WILLMER , BONIERBALE MERIDETH 
Published: April 2010

SUMMARYTwo Solanum genotypes, a wild relative of cultivated potato S. cajamarquense (Cjm) and an advanced tetraploid clone B3C1 (B3), were inoculated with two Phytophthora infestans isolates and leaves were sampled at 72 and 96 h after inoculation. Gene expression in the inoculated versus noninoculated samples was monitored using the Institute of Genomic Research (TIGR) 10K potato array and real‐time reverse transcriptase‐polymerase chain reaction (RT‐PCR). The current experiment is study number 83 of the TIGR expression profiling service project, and all data are publicly available in the Solanaceae Gene Expression Database (SGED) at ftp://ftp.tigr.org/pub/data/s_tuberosum/SGED. Differentially regulated cDNA clones were selected separately for each isolate–time point interaction by significant analysis of microarray (SAM), and differentially regulated clones were classified into functional categories by MapMan. The results show that the genes activated in B3 and Cjm have largely the same biological functions and are commonly activated when plants respond to pathogen attack. The genes activated within biological function categories were considerably different between the genotypes studied, suggesting that the defence pathways activated in B3 and Cjm during the tested conditions may involve unique genes. However, as indicated by real‐time RT‐PCR, some of the genes thought to be genotype specific may be activated across genotypes at other time points during disease development.
Cutting to cope – a modern adolescent phenomenon
Authors: Hall B. , Place M. 
Published: April 2010

AbstractBackground  The frequency of young people cutting themselves appears to be increasing, with one review estimating the current prevalence across the UK to be between 1 in 12 and 1 in 15.Aim  To identify factors that are associated with self‐harm by cutting, and more especially coping strategies that if encouraged might reduce such behaviour.Method  Multivariate and exploratory factor analysis were used to analyse the results from a survey of the pupils attending four large comprehensive schools in the North of England where the frequency of cutting behaviour was causing concern.Results  Three factors were identified from the analysis – Social & Active Coping, Seeking External Solutions and Non‐Productive Coping. The Social & Active Coping was the only factor that significantly correlated with non‐cutting behaviour.Conclusions  The fostering of the elements that make up Social & Active Coping – namely working successfully and feeling a sense of achievement, together with positive friendship networks and positive diversions, including physical recreation, will help to minimize young people's sense of needing to cope by cutting themselves.
Clinical applicability of T-cell interferon-α release assay for tumour necrosis factor-α inhibitor therapy in severe psoriasis
Authors: Chiang Y. Z. , Panting K. , Dever B. , Parslew R. A. G. 
Published: April 2010

Summary
Many studies have found that screening and treatment of latent tuberculosis (TB) before starting treatment with tumour necrosis factor (TNF)-α inhibitors reduces associated TB infections. The new T-cell interferon-α release assay (TIGRA), is more specific and sensitive for detection of latent TB compared with the tuberculin skin test (TST). We report results of TIGRA in our first 63 patients commencing TNF-α inhibitors for severe psoriasis. Of the 63 patients, 5 (7.9%) had a positive TIGRA result and were started on treatment for latent TB. We found that the only risk factor for TB associated with a positive TIGRA was a history of travel to countries with high TB incidence. To our knowledge, this is the first study to identify the background risk (7.9%) of latent TB in an endemic UK population. This result emphasizes the importance of TIGRA testing to reduce the risk of TB in patients treated with TNF-α inhibitor.
Identifying refugia from climate change
Authors: Ashcroft Michael B. 
Published: April 2010

AbstractThis article highlights how the loose definition of the term ‘refugia’ has led to discrepancies in methods used to assess the vulnerability of species to the current trend of rising global temperatures. The term ‘refugia’ is commonly used without distinguishing between macrorefugia and microrefugia, ex situ refugia and in situ refugia, glacial and interglacial refugia or refugia based on habitat stability and refugia based on climatic stability. It is not always clear which definition is being used, and this makes it difficult to assess the appropriateness of the methods employed. For example, it is crucial to develop accurate fine‐scale climate grids when identifying microrefugia, but coarse‐scale macroclimate might be adequate for determining macrorefugia. Similarly, identifying in situ refugia might be more appropriate for species with poor dispersal ability but this may overestimate the extinction risk for good dispersers. More care needs to be taken to properly define the context when referring to refugia from climate change so that the validity of methods and the conservation significance of refugia can be assessed.
Little shrimp left on the shelf: the roles that sea‐level change, ocean currents and continental shelf width play in the genetic connectivity of a seagrass‐associated species
Authors: Haig Jodie A. , Connolly Rod M. , Hughes Jane M. 
Published: April 2010

AbstractAim  Caridean shrimp are diverse and abundant inhabitants of seagrass beds. Anthropogenic disturbances have already reduced and fragmented seagrass habitat, and the rate of change is likely to increase in the future. It is therefore becoming increasingly important to build a basis of understanding of connectivity among populations of seagrass‐associated fauna. Phycomenes zostericola is closely associated with seagrass and makes an ideal study species with which to explore patterns of connectivity and the influence of biogeographic boundaries and historical sea‐level changes on seagrass‐associated species. We hypothesized that strong currents and the high potential of P. zostericola for dispersal and adult movement would result, for the most part, in panmixia. We also hypothesized that if structure was evident, it would occur close to known biogeographic boundaries in Queensland.Location  Phycomenes zostericola is an abundant shrimp species distributed throughout Queensland’s seagrass habitats. Nineteen seagrass sites from the Torres Strait Islands and Queensland coastlines were sampled.Methods  Molecular sequence data for a 590 base pair fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) was analysed for 279 specimens of P. zostericola. Phylogeographic patterns were analysed using nested clade phylogeographic analysis (NCPA); an isolation‐by‐distance effect was tested using a Mantel test; the effect of biogeographic boundaries was tested using an analysis of molecular variance (AMOVA), and also a spatial analysis of molecular variance (SAMOVA); demographic expansions were tested for using Tajima’s D, Fu’s FS and timing estimated using mismatch analysis; the timing of vicariant events was estimated using coalescent analysis (im program).Results  Contrary to our original hypothesis, the strong marine currents are not a connective influence among populations of P. zostericola. Regional genetic structure and an isolation‐by‐distance effect are enhanced by existing coastal biogeographic boundaries. Population genetic structure and demographic history are intricately linked to the effects of a tumultuous Pleistocene sea‐level history on the Queensland continental shelf.Main conclusions  Connectivity diminishes among populations of P. zostericola over scales larger than a few hundred kilometres. As seagrass habitats world‐wide become increasingly fragmented, low levels of connectivity will result in an isolated future for P. zostericola and other species reliant on seagrass as habitat.
Multiple periglacial refugia in the Patagonian steppe and post‐glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza
Authors: Cosacov Andrea , Sérsic Alicia N. , Sosa Victoria , Johnson Leigh A. , Cocucci Andrea A. 
Published: April 2010

AbstractAim  We perform a phylogeographical study of an endemic Patagonian herbaceous plant to assess whether geographical patterns of genetic variation correspond to in situ Pleistocene survival or to glacial retreat and post‐glacial expansion. We also seek to determine the locations of potential glacial refugia and post‐glacial colonization routes.Location  Southern Andes and Patagonian steppe.Methods  We used Calceolaria polyrhiza, a widely distributed Patagonian herbaceous plant that occurs mainly in the understorey of Nothofagus rain forests and in the arid Patagonian steppe, as our model system. The chloroplast intergenic spacer trnH–psbA was sequenced for 590 individuals from 68 populations. Sequence data were analysed using phylogenetic (maximum parsimony, maximum likelihood and Bayesian inference) and population genetic (spatial analyses of molecular variance, mismatch distributions and neutrality tests) methods. Nested clade phylogeographic analyses, and divergence time estimates using a calibrated molecular clock, were also conducted.Results  A total of 27 haplotypes identified in the present study clustered into four primary genealogical lineages, revealing three significant latitudinal phylogeographical breaks. The two high Andean lineages probably split first, during the late Miocene, and the Patagonian lineage split around 4 Ma, coincident with the establishment of the Patagonian steppe. Within each haplogroup, major diversification occurred in the Pleistocene. The Patagonian groups show a pattern consistent with a rapid post‐glacial expansion and colonization of the Andean flanks, achieved independently by four lineages. The highest haplotype diversity was found along a longitudinal transect that is remarkably congruent with the limit of the ice‐sheet extension during the Greatest Patagonian Glaciation. A north‐east expansion is evident, which is probably associated with the ‘Arid Diagonal’ fluctuations.Main conclusions  Glacial climate fluctuations had a substantial impact on the diversification, distribution and demography of the study species. A scenario of multiple periglacial Pleistocene refugia and subsequent multiple recolonization routes, from eastern Patagonia to the Andean flanks, may explain the phylogeographical patterns observed. However, current genetic structure also preserves the imprints of older events that probably occurred in the Miocene and Pliocene, providing evidence that multiple processes, operating at different spatial and temporal scales, have moulded biodiversity in Patagonia.
Gender differences in the effect of fish oil on appetite, inflammation and nutritional status in haemodialysis patients
Authors: Zabel R. , Ash S. , King N. , Naslund E. , Bauer J. 
Published: April 2010

AbstractBackground:  Haemodialysis patients show signs of chronic inflammation and reduced appetite, which is associated with a worse clinical status and an increased mortality risk. Fish oil has anti‐inflammatory properties and may be useful as a therapeutic treatment. There is limited evidence to indicate the feasibility and efficacy of this intervention in dialysis patients. The present study aimed to compare the effect of 12 weeks of supplementation with fish oil on markers of appetite and inflammation in male and female haemodialysis patients.Methods:  The study was conducted in 28 haemodialysis patients. All patients were prescribed 3 g of fish oil per day for 12 weeks. Changes in appetite, plasma fatty acid profiles and inflammatory markers were measured at baseline and at 12 weeks.Results:  The mean (SD) increase in percent plasma eicosapentaenoic acid was statistically significant [1.1 (0.8) to 4.1 (2.2), P < 0.001], which was a strong indicator of good adherence. There were trends towards reductions in peptide YY (−9%; P = 0.078) and an increase in subjective sensations of hunger (+12%; P = 0.406), which reflects an increase in motivation to eat. Males (n = 13) experienced a more marked increase in hunger compared to females (+23% versus −6%), which was associated with maintenance in C‐reactive protein and interleukin‐6, and a reduction in soluble intercellular adhesion molecule‐1.Conclusions:  The results obtained demonstrate meaningful trends towards improvements in subjective appetite and certain inflammatory markers (although no change in dietary intake) and this effect was more pronounced in males. However, the levels of some inflammatory markers increased in females and this requires further study. The high level of adherence achieved indicates that an intervention requiring patients to consume four fish oil capsules per day is achievable. This was a short‐term study and the effects need to be confirmed in a randomised controlled trial.
Staying in the here‐and‐now: A pilot study on the use of dialectical behaviour therapy group skills training for forensic clients with intellectual disability
Authors: Sakdalan J. A. , Shaw J. , Collier V. 
Published: April 2010

AbstractBackground  Dialectic behaviour therapy (DBT) has been widely used with individuals diagnosed with borderline personality disorder who exhibit severe emotional and behavioural dysregulation. There is a paucity of research in assessing the effectiveness of DBT with forensic clients with intellectual disability (ID).Methods  This pilot study aims to evaluate the effectiveness of the DBT group skills training programme adapted particularly for offenders with ID. Six participants completed the 13‐week adapted DBT group skills training programme. All participants exhibited challenging behaviours and have a history of prior charges or convictions for violent crimes. The study conducted pre‐ and post‐tests using instruments that measured dynamic risks, relative strengths, coping skills and global functioning.Results  The study result showed improvement across all measures. A decrease in the level of risks, increase in relative strengths and general improvement in overall functioning were found significant. The results were promising particularly as a stand‐alone adapted DBT group skills training programme for this client group.