bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Epidemiology of Multidrug-ResistantAcinetobacter BaumanniiDoes the Community Represent a Reservoir?
Authors: Zeana Cosmina , Larson Elaine , Sahni Jyoti , Bayuga S. J. , Wu Fann , Della-Latta Phyllis 
Published: March 2006

AbstractObjective:To explore the role of the community as a potential reservoir forAcinetobacter baumannii.Design:Antimicrobial resistance patterns and genotypes ofA. baumanniiisolates from patients in two Manhattan hospitals were compared with those ofA. baumanniiisolates from the hands of community members.Results:A total of 103 isolates from two hospitals (hospital A, 81; hospital B, 22) and 23 isolates from community residents were studied. Of the hospital isolates, 36.6% were multidrug resistant (hospital A, 68.2%; hospital B, 27.8%). In contrast, there were no multidrug-resistant isolates from the community (P< .005 between hospital and community). The prevalence ofA. baumanniion the hands of community residents was 10.4% (23 of 222). By molecular typing, 42 strains of A.baumanniiwere identified. Of the isolates from hospital A and hospital B, 55.6% (45 of 81) and 68.2% (15 of 22), respectively, were indistinguishable or closely related. In contrast, most community (83.3%) isolates were unrelated (P= .001 between hospital and community).Conclusion:Acinetobacterisolates from the community, characterized by a large variety of unrelated strains (83.3%), were distinct from the hospital isolates, of which 58.3% were closely related. The absence of multidrug-resistant strains in the community compared with 36.6% prevalence among hospital isolates suggests that the reservoir for epidemic strains resides in the hospital environment itself. To our knowledge, this is the first study to examine the community as a potential reservoir for hospital strains ofA. baumannii.
Antimicrobial Proficiency Testing of National Nosocomial Infections Surveillance System Hospital Laboratories
Authors: Hageman Jeffrey C. , Fridkin Scott K. , Mohammed Jasmine M. , Steward Christine D. , Gaynes Robert P. , Tenover Fred C. ,   National Nosocomial Infections Surveillance (NNIS) System Hospitals
Published: March 2006

AbstractObjective:The National Nosocomial Infections Surveillance (NNIS) System personnel report trends in antimicrobial-resistant pathogens. To validate select antimicrobial susceptibility testing results and to identify test methods that tend to produce errors, we conducted proficiency testing among NNIS System hospital laboratories.Setting:NNIS System hospital laboratories in the United States.Methods:Each laboratory received five organisms (ie, an imipenem-resistantSerratia marcescens,an oxacillin-resistantStaphylococcus aureus,a vancomycin-resistantEnterococcus faecalis,a vancomycin-intermediateStaphylococcus epidermidis,and an extended-spectrum beta-lactamase (ESβL)-producingKlebsiella pneumoniae).Testing results were compared with reference testing results from the Centers for Disease Control and Prevention.Results:Of 138 laboratories testing imipenem against theSerratia marcescensstrain, 110 (80%) correctly reported minimum inhibitory concentrations (MICs) or zone sizes in the resistant range. All 193 participating laboratories correctly reported theStaphylococcus aureusstrain as oxacillin resistant. Of the 193 laboratories, 169 (88%) reported correct MICs or zone sizes for the vancomycin-resistantEnterococcus faecalis.One hundred sixty-two (84%) of 193 laboratories demonstrated the ability to detect a vancomycin-intermediate strain ofStaphylococcus epidermidis;however, disk diffusion performed poorly when testing both staphylococci and enterococci with vancomycin. Although laboratory personnel correctly reported nonsusceptible extended-spectrum cephalosporins and aztreonam results forK. pneumoniae,only 98 (51%) of 193 correctly reported this organism as an ESβL producer.Conclusion:Overall, NNIS System hospital laboratory personnel detected most emerging resistance patterns. Disk diffusion continues to be unreliable for vancomycin testing of staphylococci and must be used cautiously for enterococci. Further education on the processing of ESβL-producing organisms is warranted.
Are There Regional Variations in the Diagnosis, Surveillance, and Control of Methicillin-ResistantStaphylococcus aureus?
Authors: Richet Hervé M. , Benbachir Mohamed , Brown Derek F. J. , Giamarellou Helen , Gould Ian , Gubina Marija , Heczko Piotr , Kalenic Smilja , Pana Marina , Pittet Didier , Redjeb Saida Ben , Schindler Jiri , Starling Carlos , Struelens Marc J. , Witte Wolfgang , Jarvis William R. ,   International Network for the Study and Prevention of Emerging Antimicrobial Resistance (INSPEAR)
Published: March 2006

AbstractObjective:To assess the way healthcare facilities (HCFs) diagnose, survey, and control methicillin-resistantStaphylococcus aureus(MRSA).Design:Questionnaire.Setting:Ninety HCFs in 30 countries.Results:Evaluation of susceptibility testing methods showed that 8 laboratories (9%) used oxacillin disks with antimicrobial content different from the one recommended, 12 (13%) did not determine MRSA susceptibility to vancomycin, and 4 (4.5%) reported instances of isolation of vancomycin-resistantS. aureusbut neither confirmed this resistance nor alerted public health authorities. A MRSA control program was reported by 55 (61.1%) of the HCFs. The following isolation precautions were routinely used: hospitalization in a private room (34.4%), wearing of gloves (62.2%), wearing of gowns (44.4%), hand washing by healthcare workers (53.3%), use of an isolation sign on the patient's door (43%), or all four. When the characteristics of HCFs with low incidence rates (< 0.4 per 1,000 patient-days) were compared with those of HCFs with high incidence rates (P= 0.4 per 1,000 patient-days), having a higher mean number of beds per infection control nurse was the only factor significantly associated with HCFs with high incidence rates (834 vs 318 beds;P= .02).Conclusion:Our results emphasize the urgent need to strengthen the microbiologic and epidemiologic capacities of HCFs worldwide to prevent MRSA transmission and to prepare them to address the possible emergence of vancomycin-resistantS. aureus.
Predictive Value and Cost-Effectiveness Analysis of a Rapid Polymerase Chain Reaction for Preoperative Detection of Nasal Carriage ofStaphylococcus aureus
Authors: Shrestha Nabin K. , Shermock Kenneth M. , Gordon Steven M. , Tuohy Marion J. , Wilson Deborah A. , Cwynar Roberta E. , Banbury Michael K. , Longworth David L. , Isada Carlos M. , Mawhorter Steven D. , Procop Gary W. 
Published: March 2006

AbstractObjective:To determine the accuracy and cost-effectiveness of a polymerase chain reaction (PCR) for detecting nasal carriage ofStaphylococcus aureusdirectly from clinical specimens.Cross-Sectional Study:This occurred in a tertiary-care hospital in Cleveland, Ohio, and included 239 consecutive patients who were scheduled for a cardiothoracic surgical procedure. Conventional cultures and a PCR for S.aureusfrom nasal swabs were used as measurements.Cost-Effectiveness Analysis:Data sources were market prices and Bureau of Labor Statistics. The time horizon was the maximum period for availability of culture results (3 days). Interventions included universal mupirocin therapy without testing; initial therapy, with termination if PCR negative (treat-PCR); initial therapy, with termination if culture negative (treat-culture); treat PCR-positive carriers (PCR-guided treatment); and treat culture-positive carriers (culture-guided treatment). The perspective was institutional and costs and the length of time to treatment were outcome measures.Results:Sixty-seven (28%) of the 239 swabs grewS. aureus.Rapid PCR was 97.0% sensitive and 97.1% specific for the detection of S.aureus.For populations with prevalences of nasalS. aureuscarriage of up to 50%, the PCR assay had negative predictive values of greater than 97%. PCR-guided treatment had the lowest incremental cost-effectiveness ratio ($1.93 per additional day compared with the culture strategy). Among immediate treatment strategies, treat-PCR was most cost-effective. The universal therapy strategy cost $38.19 more per additional day gained with carrier identification compared with the PCR strategy.Conclusion:Rapid real-time PCR is an accurate, rapid, and cost-effective method for identifyingS. aureuscarriers for preoperative intervention.
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
Authors: Machné Rainer , Finney Andrew , Müller Stefan , Lu James , Widder Stefanie , Flamm Christoph 
Published: March 2006

Abstract
The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of ordinary differential equations, their Jacobian matrix and other derivatives. SUNDIALS' CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a rough overview on the behavior of different tools and are discussed in the Supplementary Material. The native application program interface provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBML and non SBML data sources. Optional modules based on XMGrace and Graphviz allow quick inspection of structure and dynamics.
Availability:
Contact: xtof@tbi.univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
A generalization of the PST algorithm: modeling the sparse nature of protein sequences
Authors: Leonardi Florencia G. 
Published: March 2006

Abstract
Motivation: A central problem in genomics is to determine the function of a protein using the information contained in its amino acid sequence. Variable length Markov chains (VLMC) are a promising class of models that can effectively classify proteins into families and they can be estimated in linear time and space.
Results: We introduce a new algorithm, called Sparse Probabilistic Suffix Trees (SPST), that identifies equivalences between the contexts of a VLMC. We show that, in many cases, the identification of these equivalences can improve the classification rate of the classical Probabilistic Suffix Trees (PST) algorithm. We also show that better classification can be achieved by identifying representative fingerprints in the amino acid chains, and this variation in the SPST algorithm is called F-SPST.
Availability: The SPST algorithm can be freely downloaded from the site
Contact: leonardi@ime.usp.br
Supplementary information: Supplementary data are available at Bioinformatics online.
‘The times, are they a‐changing?’ As the world enters a new millennium are we as paediatricians keeping up with the changing needs of children?
Authors: Heussler H. S. , Polnay Leon , Katz Manuel 
Published: March 2006

This paper describes changes that are occurring in paediatric practice in a variety of settings. The ‘new morbidity’ demands focused training of paediatricians of the twenty‐first century. Areas that include advocacy, public health, adolescence, chronic illness, health promotion, behavioural issues, parenting and family dynamics, social influences, health and social inequalities, managerial decision making and technological advances should be a part of paediatric training. These factors assume different importance in developing nations where priorities may be more focused on public health, nutrition and health promotion.Partnership with others who have children's interests at heart, for example mental health services, public health, social sciences, education and social services is imperative in planning service development informed by good information systems incorporating measures of mortality and morbidity. Copyright © 2000 John Wiley & Sons, Ltd.
Auditing Risk Management: Fine in Theory but who can do it in Practice?
Authors: Crawford Margaret , Stein William 
Published: March 2006

This paper investigates risk management structures in organisations and how these comply with best practice in corporate governance. We carried out an exploratory study (in 2001) of four large public and private sector organisations in the United Kingdom. Interviews were conducted with risk managers and internal auditors to ascertain the extent to which emerging structures complied with the Turnbull Guidance to the Combined Code.We found that structures are in place to deliver a sound system of internal control including risk management. Internal auditors and risk managers are both involved but their respective roles are often not sufficiently well defined to avoid overlaps and gaps. We also found that several of the organisations studied rely on external auditors to conduct the required annual review of risk management.
The Impact of Accounting Standards on Audit Firm Switch Rates
Authors: Atkinson Keith E. , Taylor Charles W. , Flesher Dale L. , Stocks Morris H. 
Published: March 2006

ABSTRACT: Researchers have conjectured that accounting standards decrease the rate at which clients change auditors. They argue that conflict caused by disagreements over accounting standards is reduced because there are fewer acceptable accounting principles. Surprisingly, there is little empirical evidence that investigates the impact of accounting standards on audit firm switch rates.This study investigates the relationship between accounting standards and audit firm switch rates. The paper presents surprising evidence that in the year of enactment, accounting standards cause clients to change auditors at a faster rate. This finding supports the idea that conflict is created over the implementation of the standard which results in a client changing auditors. The paper also supports traditional thought by presenting evidence that in years following the issuance of an accounting standard clients change auditors at slower rates. This finding supports the idea that conflict will be reduced in future years because there are fewer acceptable accounting principles on which an auditor and a client can disagree.Data Availability: Data are available from sources identified in the text.
Financial Statement Transparency and Auditor Responsibility: Enron and Andersen
Authors: Wu Ben Koon Hong , Roebuck Peter , Summers Suzanne 
Published: March 2006

‘Business risk’ is a concept that has emerged from the recent development in new audit methodologies. This paper investigates auditor perceptions of business risk factors in the planning stage of an audit. Auditors were asked to classify risk factors as to whether the factors are primarily business risk or inherent risk. We also examine how auditors modify their audit strategies based upon the categorisation of risks, and the impact on their ability to detect risk of fraud from the consideration of those risk factors.Results indicate that auditors perceive business risk as a distinct risk factor. There is however some overlapping of business risk and inherent risk factors, and some risk factors previously considered as inherent risk now appear to be included as business risk. Results indicate a weak articulation between business risk and audit strategy. To the extent that auditors do adjust audit strategy for business risk, auditors increase analytical procedures rather than detailed substantive testing. Auditors did not view business risk factors as impacting their ability to detect risk of fraud.
Regional occupancy in unicellular eukaryotes: a reflection of niche breadth, habitat availability or size‐related dispersal capacity?
Authors: HEINO JANI , SOININEN JANNE 
Published: March 2006

Summary1. The distribution patterns of unicellular and multicellular organisms have recently been shown to differ profoundly, with the former probably being mostly cosmopolitan, whereas the latter are mostly restricted to certain regions. However, the within‐region distribution patterns of these two organism groups may be rather similar.2. We predicted that the degree of regional occupancy in unicellular eukaryotes would be related to niche characteristics, dispersal ability and size, as has been found previously for multicellular organisms. The niche characteristics we considered were niche position, that measures marginality in species habitat distribution, and niche breadth, that measures amplitude in species habitat distribution. Niche characteristics were determined using Outlying Mean Index (OMI) analysis.3. We found that the regional occupancy in our model group of unicellular eukaryotes, stream diatoms, was primarily a reflection of the niche position of a species or, more generally, habitat availability. Thus, non‐marginal species (i.e. species that occupied common habitat conditions across the region) tended to be more widely distributed than marginal species (i.e. species that were restricted to a limited range of rare habitat conditions). This finding was further supported by the general linear model, with niche position, niche breadth, maximum size and attachment mode as explanatory variables: niche position was by far the most important variable accounting for variability in regional occupancy, with significant amounts of additional variation related to niche breadth and maximum size of diatoms.4. Thus, the degree of regional occupancy among unicellular eukaryotes may be primarily governed by habitat availability, supporting former findings for multicellular organisms.
Effects of pH on electron transport system (ETS) activity and oxygen consumption in Gammarus fossarum, Asellus aquaticus and Niphargus sphagnicolus
Authors: SIMČIČ TATJANA , BRANCELJ ANTON 
Published: March 2006

Summary1. Electron transport system (ETS) activity and oxygen consumption were measured in three crustacean species (Gammarus fossarum, Asellus aquaticus and Niphargus sphagnicolus) that differ in their pH tolerance. Measurements were made under four different pH regimes: strongly acid (pH 4.5–5.0), weakly acid (5.5–6.0), ‘neutral’ (7.0–7.8) and alkaline (8.5–9.0).2. The significantly lower ETS activity/respiration (ETS/R) ratios observed in strongly acid water than in neutral and alkaline water indicate an effect of acidity on metabolism of the organisms. The main reason for the lower ratios is not increased oxygen consumption (except for G. fossarum in strongly acid water) but decreased ETS activity. Metabolic potential was lower in strongly and weakly acid water than in neutral water. Therefore, efficient exploitation of metabolic potential (i.e. of relatively large production of ATP with the existing enzyme machinery) probably enables N. sphagnicolus and A. aquaticus to survive in an acid environment.3. Increased oxygen consumption of G. fossarum in strongly acid water indicates an acid stress that leads to the collapse of metabolism and, consequent death of the animals.4. Although N. sphagnicolus is found exclusively in permanently acid water, no negative effect of alkaline water on metabolism was observed. This species can, therefore, be best considered as an acid‐resistant species, not an acidobiont.
Size‐dependent effects of an invasive herbivorous snail (Pomacea canaliculata) on macrophytes and periphyton in Asian wetlands
Authors: CARLSSON NILS O. L. , BRÖNMARK CHRISTER 
Published: March 2006

Summary1. The invasive golden apple snail (Pomacea canaliculata), native to South America, is a serious pest on rice seedlings in south‐east Asia and has also been shown to consume large amounts of macrophytes in natural wetlands, with large effects on ecosystem functioning. Earlier studies suggest that the snail undergoes an ontogenetic diet shift, feeding on algae and detritus as juveniles and shifting to aquatic macrophytes as adults.2. Here, we study the effects of snail populations with a size‐structure typical of either populations at an invasive front or the size‐structure of established populations. In an enclosure experiment performed in a wetland in Laos, we compared treatments with small snails only (3 mm; invasive treatment) to treatments with small, medium sized (10 mm) and adult (>25 mm) snails (established treatment). The effects of snail grazing on three aquatic macrophyte species and periphytic algae were quantified.3. We found that snails of all sizes had a strong negative effect on the biomass of all macrophyte species and periphytic algae. There was no evidence of an ontogenetic diet change, i.e. snails in both the invasive and established treatments affected macrophyte biomass. Foraging was size‐dependent in that small snails had higher relative foraging capacity (g plant consumed per g of snail) compared with medium and adult snails. Small snails, therefore, depressed growth of medium snails at increasing densities through exploitative competition for preferred resources, while adult snails did not grow at all in the presence of small snails.4. Density dependence is common in freshwater invertebrates, including gastropod populations, but differences in size dependent foraging‐ and competitive‐ability have rarely been demonstrated in this group of organisms. Knowledge about intra‐specific differences in ecological performance may, however, both deepen our understanding of the processes that underlie population dynamics in invertebrates such as gastropods, and help develop control strategies for invasive golden apple snails.