bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Recurrent Outbreak of Nosocomial Legionnaires' Disease Detected by Urinary Antigen Testing: Evidence for Long-Term Colonization of a Hospital Plumbing System
Authors: Lepine Lisa A. , Jernigan Daniel B. , Butler Jay C. , Pruckler Janet M. , Benson Robert F. , Kim Grace , Hadler James L. , Cartter Matthew L. , Fields Barry S. 
Published: September 2009

AbstractBackground:In 1994, a hospital reported an increase in nosocomial legionnaires' disease after implementing use of a rapid urinary antigen test for Legionella pneumophila serogroup 1 (Lp-1). This hospital was the site of a previous nosocomial legionnaires' disease outbreak during 1980 to 1982.Methods:Infection control records were reviewed to compare rates of nosocomial pneumonia and the proportion of cases attributable to legionnaires' disease during the 1994 outbreak period with those during the same period in 1993. Water samples were collected for Legionella culture from the hospital's potable water system and cooling towers, and isolates were subtyped by monoclonal antibody (MAb) testing and arbitrarily primed polymerase chain reaction (AP-PCR).Results:Nosocomial pneumonia rates were similar from April through October 1993 and April through October 1994: 5.9 and 6.6 per 1,000 admissions, respectively (rate ratio [RR], 1.1; P=.56); however, 3.2% of nosocomial pneumonias were diagnosed as legionnaires' disease in 1993, compared with 23.9% in 1994 (RR, 9.4; P<.001). In 1994, most legionnaires' disease cases were detected by the urinary antigen testing alone. MAb testing and AP-PCR demonstrated identical patterns among Lp-1 isolates recovered from a patient's respiratory secretions, the hospital potable water system, and stored potable water isolates from the 1980 to 1982 outbreak.Conclusions:There may have been persistent transmission of nosocomial legionnaires' disease at this hospital that went undiscovered for many years because there was no active surveillance for legionnaires' disease. Introduction of a rapid urinary antigen test improved case ascertainment. Legionella species can be established in colonized plumbing systems and may pose a risk for infection over prolonged periods.
Controlling Legionella in Hospital Water Systems: Experience With the Superheat-and-Flush Method and Copper-Silver Ionization
Authors: Stout Janet E. , Lin Yu-Sen E. , Goetz Angella M. , Muder Robert R. 
Published: September 2009

AbstractObjective:To evaluate the effect of copper-silver ionization on Legionella colonization and nosocomial legionnaires' disease and to compare the efficacy of metal ions versus the super-heat-and-flush method of disinfection.Design:Prospective determination over a 36-month period of copper and silver ion concentrations in the recirculating hot-water system, Legionella colonization of the hospital water distribution system, and cases of nosocomial legionnaires' disease. Retrospective comparison of results with the previous 13 years, during which the superheat-and-flush method was used.Setting:The Pittsburgh Veterans' Affairs Health Care System (University Drive Division) acut-care hospital.Intervention:Three copper-silver ionization systems were installed on the hot-water distribution system in November 1994.Results:The average number of cases of legionnaires‘ disease per year and the percentage of distal sites positive for Legionella pneumophila for the superheat-and-flush method versus the copper-silver ionization method was six cases with 15% positivity versus two cases with 4% positivity, respectively. The reduction in Legionella colonization after copper-silver ionization was significant (P<.05) compared to the superheat and flush. Mean copper and silver ion concentrations (mg/L) were 0.29 and 0.054 from hot-water tanks, and 0.17 and 0.04 from distal outlets, respectively.Conclusions:We conclude that a properly maintained and monitored copper-silver ionization system was more effective than the superheat-and-flush method for reducing the recovery of Legionella from the hospital water distribution system.
Tuberculosis, Hepatitis B, Rubella, Rubeola, and Varicella Infection and Immunity Among Medical School Employees
Authors: L'Ecuyer Paul B. , Miller Marilyn , Winters Karen , Fraser Victoria J. 
Published: September 2009

AbstractObjective:To assess baseline health status of a medical school employee population and to assess this population's acceptance of vaccination and other interventions to reduce risk of disease transmission.Design:A retrospective review of an employee health records database for a 4-year period.Setting:A large, urban university hospital.Participants:5,007 employees screened by employee health for immunity to vaccine-preventable illnesses and tuberculosis.Results:9.4% of the employees had positive tuberculin skin tests, with a conversion rate of 6.4% for those who had negative tests within the previous 2 years. Two individuals were identified who had active pulmonary tuberculosis. Fewer than 10% of the individuals for whom isoniazid chemoprophylaxis was recommended completed the 6 months of therapy. Most clinical employees (96.1%) did not have a history of prior hepatitis B virus (HBV) infection or immunization, but 77% of them subsequently completed the vaccination series. Most employees with a negative history for infection with or immunization against rubella, rubeola, and varicella had serological evidence of immunity (90.2%, 97.9%, and 87.2%, respectively).Conclusions:Review of aggregate employee health databases may assist individuals who must establish strategies for prevention of occupational illness and disease transmission in this specialized setting. While many employees at risk for HBV complete the vaccination series, strategies for improving this rate could be helpful. Substantial work is needed to analyze reasons why so few individuals for whom isoniazid chemoprophylaxis is recommended complete the therapy, and strategies tailored to the impediments identified should be implemented.
Detection of Bordetella pertussis and Respiratory Syncytial Virus in Air Samples From Hospital Rooms
Authors: Aintablian Nectar , Walpita Pramila , Sawyer Mark H. 
Published: September 2009

AbstractObjective:To evaluate the distribution of Bordetella pertussis and respiratory syncytial virus (RSV) in the hospital setting.Design:Air samples were collected using filters in the hospital rooms of 12 children with pertussis and 27 children with RSV infection. Material eluted from these filters was subjected to RSV- and B pertussis-specific polymerase chain reaction (PCR) amplification.Setting:Patients were hospitalized in private rooms in one of two referral centers, a university teaching hospital and a university-affiliated private children's hospital.Patients:12 children (16 days-3 years of age) with documented pertussis infection and 27 patients (10 days-7 years of age) with documented RSV infection.Results:B pertussis DNA was detected in 7 (58%) of 12 rooms housing pertussis patients and in 16 (25%) of 63 total samples. B pertussis DNA was detected as far as 4 m away from the patient's bedside. The detection of B pertussis DNA in air samples did not change over the short duration of hospitalization. RSV RNA was detected in 17 (63%) of 27 rooms housing RSV-infected patients and in 32 (22%) of 143 total samples. RSV RNA was detected at distances as far as 7 m from the patient's bedside and for up to 7 days of hospitalization.Conclusions:Using PCR-based detection methods, B pertussis DNA and RSV RNA both can be detected in air samples from the hospital rooms of infected patients. Both can be detected at large distances from a patient's bedside in a minority of cases. These detection methods are suitable for further studies of control measures used to contain nosocomial infections caused by both B pertussis and RSV.
Epidemiological Analysis Defining Concurrent Outbreaks of Serratia marcescens and Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive-Care Unit
Authors: Campbell Judith R. , Zaccaria Elena , Mason Edward O. , Baker Carol J. 
Published: September 2009

AbstractObjective:To describe the epidemiology, interventions, and molecular typing methods used during the investigation and control of concurrent outbreaks of Serratia marcescens and methicillin-resistant Staphylococcus aureus (MRSA) infections in a neonatal intensive-care unit (NICU).Setting:A 206-bed women's and infants' hospital with a 48-bed NICU.Design:A 22-week, prospective, descriptive study of all NICU infants with S marcescens or MRSA infection or colonization. Repetitive polymerase chain reaction (rep PCR) and pulsed-field gel electrophoresis (PFGE), respectively, were applied to the typing of S marcescens and MRSA isolates.Interventions:Infants with S marcescens or MRSA infection or colonization were placed in isolation; all other infants were cohorted. A multidisciplinary task force implemented education for all hospital and medical staff regarding policies essential for outbreak control. Changes in physical setting and patient contact procedure were required to promote adherence to existing policies.Results:Two premature infants had S marcescens infection, and five were colonized; rep PCR verified that both invasive and three of five colonizing isolates were related genotypically. Five bacteremic and 10 MRSA-colonized infants were identified; PFGE confirmed that 12 of the isolates had similar electrophoretic patterns. S marcescens infection was eliminated from the NICU 3 weeks after interventions were initiated. MRSA infections also were eliminated, and MRSA colonization fell to below pre-outbreak rates within 8 weeks. Despite a 100% increase in NICU patient days per month during the subsequent 2 years, no further clusters of S marcescens or MRSA infection have occurred.Conclusions:Concurrent outbreaks of S marcescens and MRSA in an NICU were confirmed by genotyping of strains. Control was achieved by isolation and cohorting of patients and strict adherence to NICU policies and procedures.
Identification of genes involved in the same pathways using a Hidden Markov Model-based approach
Authors: Senf Alexander , Chen Xue-wen 
Published: September 2009

AbstractMotivation: The sequencing of whole genomes from various species has provided us with a wealth of genetic information. To make use of the vast amounts of data available today it is necessary to devise computer-based analysis techniques.Results: We propose a Hidden Markov Model (HMM) based algorithm to detect groups of genes functionally similar to a set of input genes from microarray expression data. A subset of experiments from a microarray is selected based on a set of related input genes. HMMs are trained from the input genes and a group of random gene input sets to provide significance estimates. Every gene in the microarray is scored using all HMMs and significant matches with the input genes are retained. We ran this algorithm on the life cycle of Drosophila microarray data set with KEGG pathways for cell cycle and translation factors as input data sets. Results show high functional similarity in resulting gene sets, increasing our biological insight into gene pathways and KEGG annotations. The algorithm performed very well compared to the Signature Algorithm and a purely correlation-based approach.Availability: Java source codes and data sets are available at http://www.ittc.ku.edu/∼xwchen/software.htmContact: xwchen@ittc.ku.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Why compare marine ecosystems?
Authors: Murawski Steven A. , Steele John H. , Taylor Phillip , Fogarty Michael J. , Sissenwine Michael P. , Ford Michael , Suchman Cynthia 
Published: September 2009

Abstract
Murawski, S. A., Steele, J. H., Taylor, P., Fogarty, M. J., Sissenwine, M. P., Ford, M., and Suchman, C. 2010. Why compare marine ecosystems? – ICES Journal of Marine Science, 67: 1–9. Effective marine ecosystem-based management (EBM) requires understanding the key processes and relationships controlling the aspects of biodiversity, productivity, and resilience to perturbations. Unfortunately, the scales, complexity, and non-linear dynamics that characterize marine ecosystems often confound managing for these properties. Nevertheless, scientifically derived decision-support tools (DSTs) are needed to account for impacts resulting from a variety of simultaneous human activities. Three possible methodologies for revealing mechanisms necessary to develop DSTs for EBM are: (i) controlled experimentation, (ii) iterative programmes of observation and modelling (“learning by doing”), and (iii) comparative ecosystem analysis. We have seen that controlled experiments are limited in capturing the complexity necessary to develop models of marine ecosystem dynamics with sufficient realism at appropriate scales. Iterative programmes of observation, model building, and assessment are useful for specific ecosystem issues but rarely lead to generally transferable products. Comparative ecosystem analyses may be the most effective, building on the first two by inferring ecosystem processes based on comparisons and contrasts of ecosystem response to human-induced factors. We propose a hierarchical system of ecosystem comparisons to include within-ecosystem comparisons (utilizing temporal and spatial changes in relation to human activities), within-ecosystem-type comparisons (e.g. coral reefs, temperate continental shelves, upwelling areas), and cross-ecosystem-type comparisons (e.g. coral reefs vs. boreal, terrestrial vs. marine ecosystems). Such a hierarchical comparative approach should lead to better understanding of the processes controlling biodiversity, productivity, and the resilience of marine ecosystems. In turn, better understanding of these processes will lead to the development of increasingly general laws, hypotheses, functional forms, governing equations, and broad interpretations of ecosystem responses to human activities, ultimately improving DSTs in support of EBM.
The Starlet Sea Anemone Nematostella vectensis: An Anthozoan Model Organism for Studies in Comparative Genomics and Functional Evolutionary Developmental Biology
Authors: Genikhovich Grigory , Technau Ulrich 
Published: September 2009

INTRODUCTIONNematostella vectensis is a brackish water sea anemone of the family Edwardsiidae. The polyps can be reared with a full life cycle in laboratories with direct access to seawater or in inland laboratories. Robust protocols for the induction of gametogenesis have been established, which can yield thousands of embryos every day and allow for fairly synchronized development of individual batches. Embryos develop into primary polyps within 7-9 d and sexual maturity is reached after 3-6 mo. Zygotes are accessible for most modern molecular and developmental techniques, including gene knockdown by morpholino injection, generation of transgenics, in situ hybridization, and antibody staining. Various cDNA libraries and a bacterial artificial chromosome (BAC) library are available and the genome has been sequenced at ~6.5X coverage. The diploid set of chromosomes is 30 and, based on the sequence assembly, the genome size is 450 Mbp. Expressed sequence tag (EST) and genome analyses have emphasized the striking degree of sequence conservation and complexity in terms of gene content between Nematostella and vertebrates. This indicates that many ancestral traits have been preserved in Nematostella. Taken together with its experimental tractability, this makes Nematostella a very attractive model system among the representatives of basal metazoan lineages.
In Vivo Imaging of Mammalian Cells: Image Acquisition and Analysis: Figure 1.
Authors: Swedlow Jason R. , Andrews Paul D. , Platani Melpomeni 
Published: September 2009

INTRODUCTIONLive cell imaging provides a powerful technique for the analysis of molecular dynamics within cells. Advances in imaging technology and probe design have established this approach as an important tool in modern biology. It is now possible to obtain commercial turnkey systems for digital imaging using a number of different imaging modalities. Nevertheless, it still requires considerable technical care and expertise to conduct a successful experiment. To perform a successful imaging experiment, it is important to maximize the signal-to-noise ratio (S:N) while minimizing damage to the cells. In this article, we focus on the use of fluorescence microscopy in live cell imaging, although most of the points discussed are relevant to any type of imaging. We describe many of the methods and considerations that are required for performing a successful imaging experiment in living cells. However, we do not provide a single recipe for success: The approach is much too empirical and depends on careful observation of the particular cells under investigation.
In Vivo DNase I, MNase, and Restriction Enzyme Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR): Figure 1.
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T. 
Published: September 2009

INTRODUCTIONGenomic footprinting and related methods can reveal important protein-DNA interactions not detected using other methods. This protocol presents procedures for DNase I genomic footprinting, micrococcal nuclease (MNase) mapping of nucleosome positioning, and monitoring nucleosome remodeling via restriction enzyme accessibility. These procedures rely on a technique known as ligation-mediated polymerase chain reaction (LM-PCR), which can be used in concert with a variety of agents that cleave or modify genomic DNA within an intact cell or nucleus, with each agent providing unique insight into the regulation of a gene. LM-PCR is a powerful technique for detecting DNA strand breaks within a complex sample because of its extreme sensitivity and specificity. This general method has proven to be invaluable for several purposes, in particular, in analysis of the properties of an endogenous DNA locus. Coupling LM-PCR to DNase I digestion results in assays that are analogous to in vitro DNase I footprinting or methylation protection. Coupling to MNase digestion allows for the high-resolution analysis of nucleosome positioning. Coupling to restriction enzyme digestion in isolated nuclei provides evidence of nucleosome remodeling. For each of these methods, nuclei must first be isolated by lysis of the cells with a non-ionic detergent, followed by centrifugation. The isolated nuclei are then treated with the appropriate nuclease, followed by purification of the genomic DNA. LM-PCR is then performed on the cleaved genomic DNA.
In Situ Hybridization of Starlet Sea Anemone (Nematostella vectensis) Embryos, Larvae, and Polyps
Authors: Genikhovich Grigory , Technau Ulrich 
Published: September 2009

INTRODUCTIONWhole-mount in situ hybridization is used to reveal the spatiotemporal expression pattern of a gene in tissue samples without sectioning the tissue. This protocol describes procedures for fixing starlet sea anemone (Nematostella vectensis) embryos, larvae, and polyps, hybridizing with a digoxigenin (DIG)-labeled RNA probe, and detecting the bound probe.
Extraction of DNA from Adult Amphioxus Tissue
Authors: Yu J.K. Sky , Holland Linda Z. 
Published: September 2009

INTRODUCTIONThis protocol describes the extraction of DNA from adult amphioxus (Branchiostoma floridae). Generally, we use adult B. floridae animals for extracting genomic DNA because the embryos are more precious and are only available during the summer breeding season. Whole adult amphioxus or dissected tissues are rapidly frozen and crushed to produce readily digestible pieces. The processed tissue is incubated in a buffer with proteinase K and sodium dodecyl sulfate (SDS) until most of the cellular protein is degraded. After removing protein from the samples by successive organic extractions, genomic DNA is recovered by ethanol precipitation. The resulting DNA can be used for Southern blotting, polymerase chain reaction (PCR), or other applications.
Construction of Gene-Targeting Vectors by Recombineering
Authors: Lee Song-Choon , Liu Pentao 
Published: September 2009

INTRODUCTIONThe critical step in generating a knockout mouse is gene-targeting vector construction. Recombineering technology has greatly streamlined the vector construction process. This protocol describes a method for making conditional knockout (cko) targeting vectors using the pSim18 plasmid. This plasmid carries the three λ phage Red genes (Gam, Bet, and Exo) under the control of the pL promoter, which is in turn regulated by the temperature-sensitive CI857 repressor. Hence, the heat-inducible recombineering functions can be easily delivered to bacterial artificial chromosomes (BACs) using a simple plasmid transformation, allowing one to manipulate any cloned mouse genomic region in Escherichia coli for cko vector construction. The conditional targeting vectors described in this protocol generate a flexible reporter/null/conditional allele in the mouse.
Egg Collection and In Vitro Fertilization of the Western Clawed Frog Xenopus tropicalis
Authors: Showell Chris , Conlon Frank L. 
Published: September 2009

INTRODUCTIONThe eggs of Xenopus laevis have been widely used in studies investigating a variety of aspects of biology, such as control of the cell cycle, RNA processing, and the cytoskeleton. The Western clawed frog Xenopus tropicalis is likely to prove useful for such studies in the future, because of the potential to combine traditional experimental approaches with genetic analysis and the available genome sequence. The eggs of X. tropicalis are also a key starting material for transgenesis. Here, we describe a method for the routine collection of eggs from X. tropicalis, together with a method for in vitro fertilization. Very large numbers of eggs, often more than 2000, can be obtained from a single X. tropicalis female. In vitro fertilization is a valuable alternative to natural mating for generating embryos. It is particularly useful for microinjection experiments and when collecting embryos at a series of defined developmental stages (e.g., for studies of gene expression), because it produces embryos that develop synchronously during early embryonic development. The typical yield of embryos ranges from several hundred to more than 1000 per fertilization.
Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora)
Authors: Wolsan Mieczyslaw , Sato Jun J. 
Published: September 2009

AbstractMissing data are commonly thought to impede a resolved or accurate reconstruction of phylogenetic relationships, and probabilistic analysis techniques are increasingly viewed as less vulnerable to the negative effects of data incompleteness than parsimony analyses. We test both assumptions empirically by conducting parsimony and Bayesian analyses on an approximately 1.5 × 106‐cell (27 965 characters × 52 species) mustelid–procyonid molecular supermatrix with 62.7% missing entries. Contrary to the first assumption, phylogenetic relationships inferred from our analyses are fully (Bayesian) or almost fully (parsimony) resolved topologically with mostly strong support and also largely in accord with prior molecular estimations of mustelid and procyonid phylogeny derived with parsimony, Bayesian, and other probabilistic analysis techniques from smaller but complete or nearly complete data sets. Contrary to the second assumption, we found no compelling evidence in support of a relationship between the inferior performance of parsimony and taxon incompleteness (i.e. the proportion of missing character data for a taxon), although we found evidence for a connection between the inferior performance of parsimony and character incompleteness (i.e. no overlap in character data between some taxa). The relatively good performance of our analyses may be related to the large number of sampled characters, so that most taxa (even highly incomplete ones) are represented by a sufficient number of characters allowing both approaches to resolve their relationships.© The Willi Hennig Society 2009.