bluuebunny/crossref_metadata_2025_split huggingface dataset:
SHEA's Initiative for Confronting the Cost-Quality Conundrum
Authors: Massanari R. Michael , Simmons Bryan ,   The Society for Hospital Epidemiology of America
Published: September 2009

The US healthcare system is being buffeted by winds of change. Once viewed as a model of excellence, economic and social disequilibrium have uncovered a multitude of frailties within the system. Spiraling healthcare costs in an otherwise stagnant economy have given rise to skepticism regarding the motivations of healthcare providers. What are the issues that confront the healthcare system? What new demands do these issues place on the delivery system? How should an organization such as SHEA position itself to meet these new demands?Three major issues will confront the healthcare system during the next decade. First, 10% to 14% of the US population have limited or no access to healthcare. Steps must be taken through the political process to assure that every person living in the United States has access to a reasonable standard of medical care. Second, despite implicit rationing, the costs of healthcare continue to consume an ever-increasing proportion of society's resources. In response, a potpourri of strategies have been implemented to contain increasing costs. Third, as society learns more about processes and outcomes of medical care, concern for quality intensifies. Efforts to constrain costs are juxtaposed with demands to assure excellence and quality in medical care. During the decade of the 90s the critical questions will be how much medical care should be provided to whom and at what level of quality? If society insists that medical care should be provided to all who live in the United States but refuses to increase present resources, difficult decisions will have to be made regarding how to reallocate those resources and how to minimize the impact of reallocation on quality of care.
Nonincreased Risk of Nosocomial Infection During a 22-Day Housekeeping Personnel Strike in a Tertiary Hospital
Authors: Delgado-Rodríquez Miguel , Ramos-Cuadra Amalia , Bueno-Cavanillas Aurora , Jimenez-Romano Elena , Guillen-Solvas Jose , Galvez-Vargas Ramon 
Published: September 2009

AbstractBackground:From April 2-23, 1992, the housekeeping staff of the University of Granada Hospital was on strike. Measures were implemented to minimize the effects of the strike on patients' health and especially to diminish the risk of hospital infection.Objective:To assess the risk of nosocomial infection during the housekeeping personnel strike.Setting:An 800-bed, tertiary care hospital.Methods:A case-cohort approach was used. One hundred forty-eight infected patients (with 184 hospital infections) were detected prospectively from March 1, 1992, to May 31, 1992. A sample of 459 of the base population (patients admitted during the same period) was selected. Information on relevant risk factors for hospital infection was abstracted from patients' clinical charts after hospital discharge. Crude odds ratios and adjusted (by proportional hazards model) relative risks (RRs) for the strike period were estimated.Results:Risk of nosocomial infection did not increase during the strike period (multiple-risk factor adjusted RR= 0.99, 0.96 to 1.01/day of strike). Similar results were observed for major sites of infection (especially surgical wound) and major areas of the hospital (including gynecology, surgery, and intensive care).Conclusion:We concluded that there was no increase in the risk of nosocomial infection during the housekeeping strike.
Molecular Markers for Differentiation of Multiresistant Klebsiella Pneumoniae Isolates in a Pediatric Hospital
Authors: Lhopital Sylvie , Bonacorsi Stephane , Meis Daniele , Brahimi Naima , Mathy Stephanie , Navarro Jean , Aigrain Yves , Bingen Edouard 
Published: September 2009

AbstractObjective:To study the spread of extended spectrum ß-lactamase-producing, but aminoglycoside-susceptible, Klebsiella pneumoniae strains in our hospital over an 8-month period, by using two genotypic markers.Design:Ribotyping (using two endonucleases) and randomly amplified polymorphic DNA analysis (RAPD; using two different 10-mer primers) were applied to the epidemiological typing of clinical K pneumoniae isolates from stools, ileal fluid, or urine of hospitalized children.Setting and Patients:The surgical intensive care ward (S1: 9 patients, 17 isolates), surgical unit (S2: 2 patients, 2 isolates), and gastroenterology ward (GE: 1 patient, 1 isolate) of the Robert Debre Hospital of Paris, France.Results:Ribotyping of the 20 clinical isolates, the type strain of the species, and two epidemiologically unrelated isolates with EcoRI and HindlII revealed 6 and 5 different patterns, respectively. Six ribotypes were identified by using these two enzymes. RAPD generated 6 distinct patterns, in complete agreement with ribotyping. Our geno-typic results showed that 11 patients from wards Sl, S2, and GE harbored genotypically related strains, suggesting nosocomial transmission and cross-colonization between and within the three wards.Conclusions:Ribotyping and RAPD appear to be reliable methods for distinguishing K pneumoniae strains. The spread of one strain of K pneumoniae in different units of our hospital was demonstrated by both methods. However, RAPD has the advantage of simplicity and rapidity conferred by polymerase chain reaction.
Rate of Seasonal Spread of Respiratory Syncytial Virus in a Pediatric Hospital
Authors: McLaws Mary-Louise , Murphy Cathryn , Taylor Peter , Ferson Mark , Gold Julian , Donnellan Robyn , Dalton Dianne 
Published: September 2009

AbstractThe rate of nosocomial respiratory syncytial virus infection was measured in a large pediatric hospital using an incidence density method. The at-risk days for nosocomial RSV were summed during a defined winter period in which there were 54 admissions with community-acquired RSV infection giving a rate of 2.9 cases per 1,000 at-risk days (95% confidence interval, 0.3-5.4 per 1,000).
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
Authors: Sand Olivier , Thomas-Chollier Morgane , van Helden Jacques 
Published: September 2009

Abstract
Summary: The preparation of an appropriate sequence dataset is the starting point of all genomic analyses. We present retrieve-ensembl-seq, an application that considerably eases the retrieval of sequences from the Ensembl database, via our user-friendly web site or web services. The user provides Ensembl identifiers or gene names, and the program returns corresponding upstream, downstream, intronic, exonic, UTR or whole gene sequences. retrieve-ensembl-seq also offers a multiple organism mode to retrieve sequences from homologous genes at any taxonomical level. And we introduce various original filters such as the masking of coding fragments and the avoidance of sequence redundancy for genes with multiple transcripts. retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools.
Availability: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.
Contact: oly@bigre.ulb.ac.be
Comparative analysis and unification of domain–domain interaction networks
Authors: Björkholm Patrik , Sonnhammer Erik L. L. 
Published: September 2009

AbstractMotivation: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain–domain interactions, and over nine datasets are available. Our aim is to analyse the coverage and quality of the existing resources, as well as the extent of their overlap. With this knowledge, we have the opportunity to merge individual domain interaction networks to construct a comprehensive and reliable database.Results: In this article we introduce a new approach towards comparing domain–domain interaction networks. This approach is used to compare nine predicted domain and protein interaction networks. The networks were used to generate a database of unified domain interactions, UniDomInt. Each interaction in the dataset is scored according to the benchmarked reliability of the sources. The performance of UniDomInt is an improvement compared to the underlying source networks and to another composite resource, Domine.Availability: http://sonnhammer.sbc.su.se/download/UniDomInt/Contact: Erik.Sonnhammer@sbc.su.se
Age and growth of longtail tuna (Thunnus tonggol) in tropical and temperate waters of the central Indo-Pacific
Authors: Griffiths Shane P. , Fry Gary C. , Manson Fiona J. , Lou Dong C. 
Published: September 2009

AbstractGriffiths, S. P., Fry, G. C., Manson, F. J., and Lou, D. C. 2010. Age and growth of longtail tuna (Thunnus tonggol) in tropical and temperate waters of the central Indo-Pacific. – ICES Journal of Marine Science, 67: 125–134. Age and growth of longtail tuna (Thunnus tonggol) were assessed by examination of annual growth increments in sectioned sagittal otoliths from 461 fish (238–1250 mm fork length, LF) sampled from tropical and temperate waters in the central Indo-Pacific between February 2003 and April 2005. Edge and microincrement analyses (presumed daily increments) suggest that longtail tuna deposit a single annual growth increment mainly between August and October. Age was, therefore, estimated for all fish by counting assumed annual growth increments. Ages ranged from 154 d to 18.7 years, with most fish being 3–9 years. Five growth models were fitted to length-at-age data, all of which indicated that the species is relatively slow-growing and long-lived. Recaptures of two tagged fish at liberty for 6.2 and 10.5 years support this notion. A bias-corrected form of Akaike's Information Criterion determined that the Schnute–Richards model provided the best fit to length-at-age data, with model parameter estimates (sexes combined) of L∞ = 135.4 cm LF, K = 22.3 year−1, t0 = 0.120 years, δ = 150.0, v = 0.019, and γ = 2.7 × 10−8. There was no significant difference in growth between sexes. The results suggest that longtail tuna grow more slowly and live longer than other tuna species of similar size. Coupled with their restricted neritic distribution, longtail tuna may be vulnerable to overexploitation by fisheries, and caution needs to be exercised in managing the species until more reliable biological and catch data are collected to assess the status of the population.
Cephalochordates (Amphioxus or Lancelets): A Model for Understanding the Evolution of Chordate Characters: Figure 1.
Authors: Yu J.K. Sky , Holland Linda Z. 
Published: September 2009

INTRODUCTIONCephalochordates, commonly called amphioxus or lancelets, are marine invertebrate chordates. They were traditionally held as the closest living relatives of vertebrates and have long occupied a key phylogenetic position in our discussions on the origin of vertebrates. However, recent molecular phylogenetic analyses have placed tunicates as the sister taxon of vertebrates and cephalochordates as the most basal chordate group. Therefore, studies on cephalochordates can also provide important insights for understanding the conserved patterning mechanisms for all chordates. Cephalochordates and vertebrates share several key chordate features, namely, the dorsal nerve cord, notochord, segmented somites, and pharyngeal gill slits. However, vertebrates have ~25% more genes than amphioxus and several features not present in cephalochordates, including a more elaborate head and forebrain, migratory neural crest, and neurogenic placodes. During the last two decades, expression patterns of important developmental genes have been used extensively to infer homologies between cephalochordate and vertebrate embryos. These studies have answered some long-standing questions concerning the evolution of vertebrates from their invertebrate ancestors and have also generated interesting hypotheses for further investigations. With the completion of a cephalochordate genome project in 2008, comparison between cephalochordate and vertebrate genomes has allowed us to postulate a picture for the genome of the last common ancestor of all chordates. Such comparisons are also providing important biological insights into the functional biology of cephalochordates and the evolutionary origin of developmental mechanisms that led to the emergence of the vertebrate body plan.
The Western Clawed Frog (Xenopus tropicalis): An Emerging Vertebrate Model for Developmental Genetics and Environmental Toxicology
Authors: Showell Chris , Conlon Frank L. 
Published: September 2009

INTRODUCTIONXenopus tropicalis, also known as Silurana tropicalis or the Western clawed frog, is a small, wholly aquatic frog that is found in the countries that lie along the west coast of equatorial Africa from Gabon to Sierra Leone. It is a diploid relative of Xenopus laevis, a frog that has found many uses in laboratories throughout the world. X. tropicalis closely resembles its relative in anatomy throughout its life cycle. It shares its advantages as a model organism for studying many aspects of vertebrate biology, particularly the genetic, biochemical, and environmental factors that influence vertebrate development from embryonic stages through adulthood. It also shares much of its biology with more distantly related species, including mammals, but unlike mammalian model organisms, routine manipulation of X. tropicalis in the laboratory can produce thousands of embryos for experimental analysis. X. tropicalis is also finding uses as an important test species for assessing the impact of environmental toxins and disease on amphibians, which are in decline in many areas of the world due to waterborne pollutants and infectious agents such as the chytrid fungus.
In Vivo Imaging of Mammalian Cells: Cell Engineering and Viability
Authors: Swedlow Jason R. , Andrews Paul D. , Platani Melpomeni 
Published: September 2009

INTRODUCTIONThere are a number of instances in which the use of live cell imaging has provided critical insight into cellular and tissue function. It has therefore become a requisite analytical tool for use in cell biology, neurobiology, and developmental biology, as well as a routine method practiced in many biomedical research laboratories. The technical requirements for performing live cell imaging include a capacity to engineer appropriate cells for the imaging experiment and access to a digital image acquisition system. The availability of fluorescent protein (FP) technology allows the molecular specificity of fluorescent markers to be used in a genetically encoded manner. In this article, we describe techniques for the generation and maintenance of fluorescently labeled cells and their use in live cell imaging experiments.
In Vivo Dimethyl Sulfate (DMS) Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR): Figure 1.
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T. 
Published: September 2009

INTRODUCTIONLigation-mediated polymerase chain reaction (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. LM-PCR can be coupled to a number of DNA modification and cleavage reagents. Coupling to dimethyl sulfate (DMS) modification, described here, results in assays that are analogous to in vitro DNase I footprinting or methylation protection. In this method, DMS is added directly to intact cells. After quenching the modification reaction, genomic DNA is purified, and cleavage adjacent to modified bases is induced by piperidine treatment. LM-PCR is then performed on the cleaved genomic DNA.
Chromatin Immunoprecipitation (ChIP)
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T. 
Published: September 2009

INTRODUCTIONChromatin immunoprecipitation (ChIP) is an invaluable method for studying interactions between specific proteins or modified forms of proteins and a genomic DNA region. ChIP can be used to determine whether a transcription factor interacts with a candidate target gene and is used with equal frequency to monitor the presence of histones with post-translational modifications at specific genomic locations. In early ChIP studies, UV light from a transilluminator was used to cross-link proteins to DNA irreversibly. The cross-linked chromatin was then either sonicated or cleaved with restriction enzymes to generate smaller DNA fragments, followed by immunoprecipitation with the desired antibodies. The precipitated protein-DNA adducts were then purified, treated with a protease, and analyzed by dot blot or Southern blot using a radiolabeled probe derived from the cloned DNA fragment of interest. The use of formaldehyde as a reversible protein-DNA and protein-protein cross-linking agent for ChIP and the use of polymerase chain reaction (PCR) to detect precipitated DNA fragments were later added as components of the modern ChIP procedure. The protocol below represents a standard ChIP procedure for use in mammalian cells. Cross-linking is performed by adding formaldehyde to growing cells, and chromatin is prepared, sheared by sonication, and precleared to reduce nonspecific immunoprecipitation. Immunoprecipitation is performed with a specific antibody. After elution of the protein-DNA complexes from protein A- or protein G-agarose resin, the samples are heated to reverse the covalent cross-links. The DNA fragments are purified and analyzed by PCR or real-time PCR.
Position-Based Clustering of Microarray Expression Data
Authors: Faulk Christopher , Kim Joomyeong 
Published: September 2009

INTRODUCTIONMicroarray expression analysis has traditionally focused only on genes with the highest expression level changes, ignoring the majority of genes with lower fold changes. To address this problem, we provide a simple method that can derive additional useful biological information from the rest of the genes included on an array. Chromosomal position information combined with expression data, either raw or in expression-level changes, gives a regional overview of expression from an array. This protocol is tailored to Affymetrix data, but can be used for other types of microarray results. The procedure is illustrated by the reanalysis of a data set, GSE5230, previously deposited in the Gene Expression Omnibus (GEO). Using this procedure, we identified several classes of chromosomal regions where expression levels were affected in concert. Linking expression data to chromosomal position also allowed us to identify several genomic regions displaying low but steady fold change, which were missed by traditional approaches. Overall, this method is useful in detecting regional regulatory changes. It should allow for greater use of the large quantity of previously overlooked microarray data.
Induction of Spawning in the Starlet Sea Anemone Nematostella vectensis, In Vitro Fertilization of Gametes, and Dejellying of Zygotes
Authors: Genikhovich Grigory , Technau Ulrich 
Published: September 2009

INTRODUCTIONThis protocol describes a reliable method for inducing spawning in the starlet sea anemone Nematostella vectensis under laboratory conditions. Spawning occurs at ~13±3 h after the onset of the inductive cues, which are a particular combination of light and temperature. This method has been used successfully on a daily basis with rotating cultures, yielding thousands of embryos every day. Each given female or male can be induced once per week. For long-term health, an induction once every 10-14 d is less exhausting to the animals. The protocol also describes the dejellying of the zygotes for further manipulation of the embryos.
Anti-acetylated Tubulin Antibody Staining and Phalloidin Staining in the Starlet Sea Anemone Nematostella vectensis
Authors: Genikhovich Grigory , Technau Ulrich 
Published: September 2009

INTRODUCTIONThis protocol describes anti-acetylated tubulin antibody staining in the starlet sea anemone Nematostella vectensis. The antibody against acetylated tubulin mainly recognizes cilia in N. vectensis. In planula larvae, it not only stains the cilia covering the ectoderm, but also is a good marker for the apical tuft at the aboral pole. Variations of this protocol can be used for staining with other antibodies (Marlow et al. 2009). However, not all antigens are preserved by fixation in paraformaldehyde; thus, alternative fixation methods are also described. In addition, an optional step of phalloidin staining of fibrillar actin is included.
Amphioxus (Branchiostoma floridae) Spawning and Embryo Collection
Authors: Yu J.K. Sky , Holland Linda Z. 
Published: September 2009

INTRODUCTIONThis protocol describes how to obtain and collect embryos from the amphioxus Branchiostoma floridae. Currently, it is only possible to obtain fertilizable gametes from this species on the days in summer when ripe animals would normally spawn in the field once about every 2 wk. Sexes are separate, and in the natural environment, mature oocytes undergo meiotic maturation and arrest at the second meiotic metaphase in the early afternoon, while sperm gain the ability to become motile upon exposure to seawater. In the evening, animals with mature gametes emerge from the sand to spawn ~30 min after sunset, that is, ~9:00 p.m. Animals collected in the afternoon of the day of spawning can be brought into the laboratory and prevented from spawning by the normal room light in the laboratory, allowing the investigator to obtain freshly spawned eggs and sperm throughout the night either by placing adults in the dark or by applying a mild electric shock (50 V DC). Unfortunately, toward dawn of the next day, the quality of gametes begins to drop, and the animals stop spawning. Therefore, investigators need to work during the night to fertilize eggs and perform experiments on early embryos.
Amphioxus Whole-Mount In Situ Hybridization
Authors: Yu J.K. Sky , Holland Linda Z. 
Published: September 2009

INTRODUCTIONThe in situ hybridization (ISH) technique is one of the basic methods of developmental biology. It allows the distributions of specific transcripts to be detected in fixed cells or embryos during development. This protocol describes ISH of digoxigenin (DIG)-labeled antisense RNA probes to whole-mount amphioxus embryos and larvae. Embryos are fixed and permeabilized before being hybridized with the DIG-labeled antisense RNA probes. Following hybridization, transcripts are detected immunohistochemically with an anti-DIG antibody conjugated to alkaline phosphatase. The gene expression patterns are visualized in the embryos with colorimeric substrates of alkaline phosphatase. Labeled embryos are photographed as whole mounts, after which they can be embedded in Spurr’s resin and sectioned if desired. To facilitate the handling of small amphioxus embryos during whole-mount ISH, we developed a method of solution exchange using homemade mesh-bottom baskets and multiwell plates. This method speeds up time-consuming aspiration and decanting of buffers and avoids accidental loss of precious embryos during these steps. Because ISH conditions are the same for most of the probes tested, this design allows high-throughput analysis of gene expression during embryogenesis to be carried out.