Time for a culture change? Suboptimal compliance with blood culture standards at a district hospital in Cape Town

Background. The benchmark for contaminated blood cultures (BCs) is 3%. The South African (SA)  guideline aims to optimise BC yield and reduce contamination. Data on BC collection practices in SA  since the publication of the 2010 SA guideline are lacking.Objective. To evaluate compliance with the national guideline for the optimal use of BCs and determine  the BC contamination rate at a local district hospital.Method. An audit of compliance with 22 BC standards was conducted at a district hospital in Cape Town, SA. Standards were evaluated by reviewing clinical and laboratory data and by a clinician questionnaire.Results. Of the 425 BCs reviewed, 12.5% had positive growth, and 4.5% grew contaminants. Only 33% of BC bottles contained the recommended fill volume of 8 - 10 mL, and 96.9% of patients had a single BC within a 24-hour period. Of all the BCs, only 7.8% had a combined blood volume of at least 20 mL. The yield of pathogens in BCs collected after antibiotic exposure was 4.9% compared with 7.5% for those cultures with no prior antibiotic exposure (p=0.3). The overall median needle-to-incubator transport time was 11 hours 25 minutes.Conclusion. The BC contamination rate was high and compliance with most standards was variable or not met. The findings may not be generalisable to other hospitals, and we recommend that each institution reviews its own BC practices. Recommendations made to hospital staff included a re-audit following  implementation of these recommendations

Comparative study of single and multislice computed tomography for assessment of the mandibular canal

OBJECTIVE: The purpose of this study was to evaluate the accuracy of relative measurements from the roof of the mandibular canal to the alveolar crest in multislice (multidetector) computed tomography (MDCT) and single-slice computed tomography (SSCT). MATERIAL AND METHODS: The sample consisted of 26 printed CT films (7 SSCT and 19 MDCT) from the files of the LABI-3D (3D Imaging Laboratory) of the School of Dentistry of the University of São Paulo (FOUSP), which had been acquired using different protocols. Two observers analyzed in a randomized and independent order a series of 22 oblique CT reconstructions of each patient. Each observer analyzed the CT scans twice. The length of the mandibular canal and the distance between the mandibular canal roof and the crest of the alveolar ridge were obtained. Dahlberg test was used for statistical analysis. RESULTS: The mean error found for the mandibular canal length measurements obtained from SSCT was 0.53 mm in the interobserver analysis, and 0.38 mm for both observers. On MDCT images, the mean error was 0.0 mm in the interobserver analysis, and 0.0 and 0.23 mm in the intraobserver analysis. Regarding the distance between the mandibular canal roof and the alveolar bone crest, the SSCT images showed a mean error of 1.16 mm in the interobserver analysis and 0.66 and 0.59 mm in the intraobserver analysis. In the MDCT images, the mean error was 0.72 mm in the interobserver analysis and 0.50 and 0.54 mm in the intraobserver analysis. CONCLUSION: Multislice CT was demonstrated a more accurate method and demonstrated high reproducibility in the analysis of important anatomical landmarks for planning of mandibular dental implants, namely the mandibular canal pathway and alveolar crest height

Holographic Conductivity in Disordered Systems

The main purpose of this paper is to holographically study the behavior of conductivity in 2+1 dimensional disordered systems. We analyze probe D-brane systems in AdS/CFT with random closed string and open string background fields. We give a prescription of calculating the DC conductivity holographically in disordered systems. In particular, we find an analytical formula of the conductivity in the presence of codimension one randomness. We also systematically study the AC conductivity in various probe brane setups without disorder and find analogues of Mott insulators.Comment: 43 pages, 28 figures, latex, references added, minor correction

Isolated and dynamical horizons and their applications

Over the past three decades, black holes have played an important role in quantum gravity, mathematical physics, numerical relativity and gravitational wave phenomenology. However, conceptual settings and mathematical models used to discuss them have varied considerably from one area to another. Over the last five years a new, quasi-local framework was introduced to analyze diverse facets of black holes in a unified manner. In this framework, evolving black holes are modeled by dynamical horizons and black holes in equilibrium by isolated horizons. We review basic properties of these horizons and summarize applications to mathematical physics, numerical relativity and quantum gravity. This paradigm has led to significant generalizations of several results in black hole physics. Specifically, it has introduced a more physical setting for black hole thermodynamics and for black hole entropy calculations in quantum gravity; suggested a phenomenological model for hairy black holes; provided novel techniques to extract physics from numerical simulations; and led to new laws governing the dynamics of black holes in exact general relativity.Comment: 77 pages, 12 figures. Typos and references correcte

Modeling electromagnetic form factors of light and heavy pseudoscalar mesons

The electromagnetic form factors of light and heavy pseudoscalar mesons are calculated within two covariant constituent-quark models, a light-front and a dispersion relation approach. We investigate the details and physical origins of the model dependence of various hadronic observables: the weak decay constant, the charge radius and the elastic electromagnetic form factor.Comment: 6 pages, 4 figures, use revtex4. Figure 2 and references are corrected. Acknoledgments are adde

Animal model integration to AutDB, a genetic database for autism

<p>Abstract</p> <p>Background</p> <p>In the post-genomic era, multi-faceted research on complex disorders such as autism has generated diverse types of molecular information related to its pathogenesis. The rapid accumulation of putative candidate genes/loci for Autism Spectrum Disorders (ASD) and ASD-related animal models poses a major challenge for systematic analysis of their content. We previously created the Autism Database (AutDB) to provide a publicly available web portal for ongoing collection, manual annotation, and visualization of genes linked to ASD. Here, we describe the design, development, and integration of a new module within AutDB for ongoing collection and comprehensive cataloguing of ASD-related animal models.</p> <p>Description</p> <p>As with the original AutDB, all data is extracted from published, peer-reviewed scientific literature. Animal models are annotated with a new standardized vocabulary of phenotypic terms developed by our researchers which is designed to reflect the diverse clinical manifestations of ASD. The new Animal Model module is seamlessly integrated to AutDB for dissemination of diverse information related to ASD. Animal model entries within the new module are linked to corresponding candidate genes in the original "Human Gene" module of the resource, thereby allowing for cross-modal navigation between gene models and human gene studies. Although the current release of the Animal Model module is restricted to mouse models, it was designed with an expandable framework which can easily incorporate additional species and non-genetic etiological models of autism in the future.</p> <p>Conclusions</p> <p>Importantly, this modular ASD database provides a platform from which data mining, bioinformatics, and/or computational biology strategies may be adopted to develop predictive disease models that may offer further insights into the molecular underpinnings of this disorder. It also serves as a general model for disease-driven databases curating phenotypic characteristics of corresponding animal models.</p

Expression Profiling of Autism Candidate Genes during Human Brain Development Implicates Central Immune Signaling Pathways

The Autism Spectrum Disorders (ASD) represent a clinically heterogeneous set of conditions with strong hereditary components. Despite substantial efforts to uncover the genetic basis of ASD, the genomic etiology appears complex and a clear understanding of the molecular mechanisms underlying Autism remains elusive. We hypothesized that focusing gene interaction networks on ASD-implicated genes that are highly expressed in the developing brain may reveal core mechanisms that are otherwise obscured by the genomic heterogeneity of the disorder. Here we report an in silico study of the gene expression profile from ASD-implicated genes in the unaffected developing human brain. By implementing a biologically relevant approach, we identified a subset of highly expressed ASD-candidate genes from which interactome networks were derived. Strikingly, immune signaling through NFκB, Tnf, and Jnk was central to ASD networks at multiple levels of our analysis, and cell-type specific expression suggested glia—in addition to neurons—deserve consideration. This work provides integrated genomic evidence that ASD-implicated genes may converge on central cytokine signaling pathways

Limited Neutralizing Antibody Specificities Drive Neutralization Escape in Early HIV-1 Subtype C Infection

We previously showed that HIV-1 subtype C viruses elicit potent but highly type-specific neutralizing antibodies (nAb) within the first year of infection. In order to determine the specificity and evolution of these autologous nAbs, we examined neutralization escape in four individuals whose responses against the earliest envelope differed in magnitude and potency. Neutralization escape occurred in all participants, with later viruses showing decreased sensitivity to contemporaneous sera, although they retained sensitivity to new nAb responses. Early nAb responses were very restricted, occurring sequentially and targeting only two regions of the envelope. In V1V2, limited amino acid changes often involving indels or glycans, mediated partial or complete escape, with nAbs targeting the V1V2 region directly in 2 cases. The alpha-2 helix of C3 was also a nAb target, with neutralization escape associated with changes to positively charged residues. In one individual, relatively high titers of anti-C3 nAbs were required to drive genetic escape, taking up to 7 weeks for the resistant variant to predominate. Thereafter titers waned but were still measurable. Development of this single anti-C3 nAb specificity was associated with a 7-fold drop in HIV-1 viral load and a 4-fold rebound as the escape mutation emerged. Overall, our data suggest the development of a very limited number of neutralizing antibody specificities during the early stages of HIV-1 subtype C infection, with temporal fluctuations in specificities as escape occurs. While the mechanism of neutralization escape appears to vary between individuals, the involvement of limited regions suggests there might be common vulnerabilities in the HIV-1 subtype C transmitted envelope