HIV Testing among Patients with Presumptive Tuberculosis: How Do We Implement in a Routine Programmatic Setting? Results of a Large Operational Research from India.

BACKGROUND: In March 2012, World Health Organization recommended that HIV testing should be offered to all patients with presumptive TB (previously called TB suspects). How this is best implemented and monitored in routine health care settings in India was not known. An operational research was conducted in Karnataka State (South India, population 64 million, accounts for 10% of India's HIV burden), to test processes and learn results and challenges of screening presumptive TB patients for HIV within routine health care settings. METHODS: In this cross-sectional study conducted between January-March 2012, all presumptive TB patients attending public sector sputum microscopy centres state-wide were offered HIV testing by the laboratory technician, and referred to the nearest public sector HIV counselling and testing services, usually within the same facility. The HIV status of the patients was recorded in the routine TB laboratory form and TB laboratory register. The laboratory register was compiled to obtain the number of presumptive TB patients whose HIV status was ascertained, and the number found HIV positive. Aggregate data on reasons for non-testing were compiled at district level. RESULTS: Overall, 115,308 patients with presumptive TB were examined for sputum smear microscopy at 645 microscopy centres state-wide. Of these, HIV status was ascertained for 62,847(55%) among whom 7,559(12%) were HIV-positive, and of these, 3,034(40%) were newly diagnosed. Reasons for non-testing were reported for 37,700(72%) of the 52,461 patients without HIV testing; non-availability of testing services at site of sputum collection was cited by health staff in 54% of respondents. Only 4% of patients opted out of HIV testing. CONCLUSION: Offering HIV testing routinely to presumptive TB patients detected large numbers of previously-undetected instances of HIV infection. Several operational challenges were noted which provide useful lessons for improving uptake of HIV testing in this important group

Molecular characterization of Vibrio cholerae outbreak strains with altered El Tor biotype from southern India

Forty-four Vibrio cholerae isolates collected over a 7-month period in Chennai, India in 2004 were characterized for gene traits, antimicrobial susceptibility and genomic fingerprints. All 44 isolates were identified as O1 El Tor Ogawa, positive for various toxigenic and pathogenic genes viz. ace, ctxB, hlyA, ompU, ompW, rfbO1, rtx, tcpA, toxR and zot. Nucleotide sequencing revealed the presence of cholera toxin B of classical biotype in all the El Tor isolates, suggesting infection of isolates by classical CTXΦ. Antibiogram analysis showed a broad-spectrum antibiotic resistance that was also confirmed by the presence of resistant genes in the genomes. All isolates contained a class 1 integron and an SXT constin. However, isolates were sensitive to chloramphenicol and tested negative for the chloramphenicol resistant gene suggesting a deletion in SXT constin. Fingerprinting analysis of isolates by ERIC- and Box PCR revealed similar DNA patterns indicating the clonal dissemination of a single predominant V. cholerae O1 strain throughout the 2004 outbreak in Chennai

Heat Stress and Goat Welfare: Adaptation and Production Considerations

This review attempted to collate and synthesize information on goat welfare and production constraints during heat stress exposure. Among the farm animals, goats arguably are considered the best-suited animals to survive in tropical climates. Heat stress was found to negatively influence growth, milk and meat production and compromised the immune response, thereby significantly reducing goats’ welfare under extensive conditions and transportation. Although considered extremely adapted to tropical climates, their production can be compromised to cope with heat stress. Therefore, information on goat adaptation and production performance during heat exposure could help assess their welfare. Such information would be valuable as the farming communities are often struggling in their efforts to assess animal welfare, especially in tropical regions. Broadly three aspects must be considered to ensure appropriate welfare in goats, and these include (i) housing and environment; (ii) breeding and genetics and (iii) handling and transport. Apart from these, there are a few other negative welfare factors in goat rearing, which differ across the production system being followed. Such negative practices are predominant in extensive systems and include nutritional stress, limited supply of good quality water, climatic extremes, parasitic infestation and lameness, culminating in low production, reproduction and high mortality rates. Broadly two types of methodologies are available to assess welfare in goats in these systems: (i) animal-based measures include behavioral measurements, health and production records and disease symptoms; (ii) resources based and management-based measures include stocking density, manpower, housing conditions and health plans. Goat welfare could be assessed based on several indicators covering behavioral, physical, physiological and productive responses. The important indicators of goat welfare include agonistic behavior, vocalization, skin temperature, body condition score (BCS), hair coat conditions, rectal temperature, respiration rate, heart rate, sweating, reduced growth, reduced milk production and reduced reproductive efficiency. There are also different approaches available by which the welfare of goats could be assessed, such as naturalistic, functional and subjective approaches. Thus, assessing welfare in goats at every production stage is a prerequisite for ensuring appropriate production in this all-important species to guarantee optimum returns to the marginal and subsistence farmers

Kin5 Knockdown in Tetrahymena thermophila Using RNAi Blocks Cargo Transport of Gef1

A critical process that builds and maintains the eukaryotic cilium is intraflagellar transport (IFT). This process utilizes members of the kinesin-2 superfamily to transport cargo into the cilium (anterograde transport) and a dynein motor for the retrograde traffic. Using a novel RNAi knockdown method, we have analyzed the function of the homodimeric IFT kinesin-2, Kin5, in Tetrahymena ciliary transport. In RNAi transformants, Kin5 was severely downregulated and disappeared from the cilia, but cilia did not resorb, although tip structure was affected. After deciliation of the knockdown cell, cilia regrew and cells swam, which suggested that Kin5 is not responsible for the trafficking of axonemal precursors to build the cilium, but could be transporting molecules that act in ciliary signal transduction, such as guanine nucleotide exchange proteins (GEFs). Gef1 is a Tetrahymena ciliary protein, and current coimmunoprecipitation and immunofluorescence studies showed that it is absent in regrowing cilia of the knockdown cells lacking ciliary Kin5. We suggest that one important cargo of Kin5 is Gef1 and knockdown of Kin5 results in cell lethality

The Scottish Bladder Cancer Quality Performance Indicators Influencing Outcomes, Prognosis, and Surveillance (Scot BC Quality OPS) Clinical Project

The aim of the Scot BC Quality OPS clinical project is to create a reliable prospective data set for evaluating real-world effectiveness and efficiency consequent to standardisation and monitoring of bladder cancer treatment (through the national Quality Performance Indicator programme) and streamlined surveillance in Scotland. Several work packages have been created, reflecting wide clinical and research collaboration

Structural bases for the interaction of frataxin with the central components of iron–sulphur cluster assembly

Reduced levels of frataxin, an essential protein of as yet unknown function, are responsible for causing the neurodegenerative pathology Friedreich's ataxia. Independent reports have linked frataxin to iron–sulphur cluster assembly through interactions with the two central components of this machinery: desulphurase Nfs1/IscS and the scaffold protein Isu/IscU. In this study, we use a combination of biophysical methods to define the structural bases of the interaction of CyaY (the bacterial orthologue of frataxin) with the IscS/IscU complex. We show that CyaY binds IscS as a monomer in a pocket between the active site and the IscS dimer interface. Recognition does not require iron and occurs through electrostatic interactions of complementary charged residues. Mutations at the complex interface affect the rates of enzymatic cluster formation. CyaY binding strengthens the affinity of the IscS/IscU complex. Our data suggest a new paradigm for understanding the role of frataxin as a regulator of IscS functions

Actin binding to WH2 domains regulates nuclear import of the multifunctional actin regulator JMY

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology of the Cell 23 (2012): 853-863, doi:10.1091/mbc.E11-12-0992.Junction-mediating and regulatory protein (JMY) is a regulator of both transcription and actin filament assembly. In response to DNA damage, JMY accumulates in the nucleus and promotes p53-dependent apoptosis. JMY's actin-regulatory activity relies on a cluster of three actin-binding Wiskott–Aldrich syndrome protein homology 2 (WH2) domains that nucleate filaments directly and also promote nucleation activity of the Arp2/3 complex. In addition to these activities, we find that the WH2 cluster overlaps an atypical, bipartite nuclear localization sequence (NLS) and controls JMY's subcellular localization. Actin monomers bound to the WH2 domains block binding of importins to the NLS and prevent nuclear import of JMY. Mutations that impair actin binding, or cellular perturbations that induce actin filament assembly and decrease the concentration of monomeric actin in the cytoplasm, cause JMY to accumulate in the nucleus. DNA damage induces both cytoplasmic actin polymerization and nuclear import of JMY, and we find that damage-induced nuclear localization of JMY requires both the WH2/NLS region and importin β. On the basis of our results, we propose that actin assembly regulates nuclear import of JMY in response to DNA damage.This work was supported by grants from the National Institutes of Health, an American Heart Association Predoctoral Fellowship (J.B.Z.), the Robert Day Allen Fellowship Fund (J.B.Z.), and a National Science Foundation Predoctoral Fellowship (B.B.)

Deep residual networks for quantification of muscle fiber orientation and curvature from ultrasound images

This paper concerns fully automatic and objective measurement of human skeletal muscle fiber orientation directly from standard b-mode ultrasound images using deep residual (ResNet) and convolutional neural networks (CNN). Fiber orientation and length is related with active and passive states of force production within muscle. There is currently no non-invasive way to measure force directly from muscle. Measurement of forces and other contractile parameters like muscle length change, thickness, and tendon length is not only important for understanding healthy muscle, but such information has contributed to understanding, diagnosis, monitoring, targeting and treatment of diseases ranging from myositis to stroke and motor neurone disease (MND). We applied well established deep learning methods to ultrasound data recorded from 19 healthy participants (5 female, ages: 30 ± 7.7) and achieved state of the art accuracy in predicting fiber orientation directly from ultrasound images of the calf muscles. First we used a previously developed segmentation technique to extract a region of interest within the gastrocnemius muscle. Then we asked an expert to annotate the main line of fiber orientation in 4 × 4 partitions of 400 normalized images. A linear model was then applied to the annotations to regulate and recover the orientation field for each image. Then we applied a CNN and a ResNet to predict the fiber orientation in each image. With leave one participant out cross-validation and dropout as a regulariser, we were able to demonstrate state of the art performance, recovering the fiber orientation with an average error of just 2°

Host sequence motifs shared by HIV predict response to antiretroviral therapy

<p>Abstract</p> <p>Background</p> <p>The HIV viral genome mutates at a high rate and poses a significant long term health risk even in the presence of combination antiretroviral therapy. Current methods for predicting a patient's response to therapy rely on site-directed mutagenesis experiments and <it>in vitro </it>resistance assays. In this bioinformatics study we treat response to antiretroviral therapy as a two-body problem: response to therapy is considered to be a function of both the host and pathogen proteomes. We set out to identify potential responders based on the presence or absence of host protein and DNA motifs on the HIV proteome.</p> <p>Results</p> <p>An alignment of thousands of HIV-1 sequences attested to extensive variation in nucleotide sequence but also showed conservation of eukaryotic short linear motifs on the protein coding regions. The reduction in viral load of patients in the Stanford HIV Drug Resistance Database exhibited a bimodal distribution after 24 weeks of antiretroviral therapy, with 2,000 copies/ml cutoff. Similarly, patients allocated into responder/non-responder categories based on consistent viral load reduction during a 24 week period showed clear separation. In both cases of phenotype identification, a set of features composed of short linear motifs in the reverse transcriptase region of HIV sequence accurately predicted a patient's response to therapy. Motifs that overlap resistance sites were highly predictive of responder identification in single drug regimens but these features lost importance in defining responders in multi-drug therapies.</p> <p>Conclusion</p> <p>HIV sequence mutates in a way that preferentially preserves peptide sequence motifs that are also found in the human proteome. The presence and absence of such motifs at specific regions of the HIV sequence is highly predictive of response to therapy. Some of these predictive motifs overlap with known HIV-1 resistance sites. These motifs are well established in bioinformatics databases and hence do not require identification via <it>in vitro </it>mutation experiments.</p