Pursuing Authenticity From Process to Outcome in a Community-Based Participatory Research Study of Intimate Partner Violence and HIV Vulnerability in North Karnataka, India.

Community-based participatory research has been seen to hold great promise by researchers aiming to bridge research and action in global health programs and practice. However, there is still much debate around whether achieving authenticity in terms of in-depth collaboration between community and academic partners is possible while pursuing academic expectations for quality. This article describes the community-based methodology for a qualitative study to explore intimate partner violence and HIV/AIDS among women in sex work, or female sex workers, and their male partners in Karnataka, South India. Developed through collaborative processes, the study methodology followed an interpretive approach to qualitative inquiry, with three key components including long-term partnerships, knowledge exchange, and orientation toward action. We then discuss lessons learned on how to pursue authenticity in terms of truly collaborative processes with inherent value that also contribute to, rather than hinder, the instrumental goal of enhancing the quality and relevance of the research outcomes

A community-based qualitative study on the experience and understandings of intimate partner violence and HIV vulnerability from the perspectives of female sex workers and male intimate partners in North Karnataka state, India.

BACKGROUND: Research has increasingly documented the important role that violence by clients and the police play in exacerbating HIV vulnerability for women in sex work. However few studies have examined violence in the intimate relationships of women in sex work, or drawn on community partnerships to explore the social dynamics involved. A community-based participatory research study was undertaken by community and academic partners leading intimate partner violence (IPV) and HIV prevention programs in Bagalkot district, Karnataka state, India. The purpose was to explore the experience and understandings of intimate partner violence and HIV/AIDS among women in sex work and their intimate partners in Bagalkot that would inform both theory and practice. METHODS: A community-based, interpretive qualitative methodology was used. Data was collected between July and October 2014 through in-depth interviews with 38 participants, including 10 couples, 13 individual female sex workers, and 5 individual male intimate partners. Purposive sampling was done to maximize variation on socio-demographic characteristics. Thematic content analysis was conducted through coding and categorization for each interview question in NVivo 10.0, followed by collaborative analysis to answer the research questions. RESULTS: The results showed that an array of interrelated, multi-level factors underlay the widespread acceptance and perpetuation of violence and lack of condom use in participants' intimate relationships. These included individual expectations that justified violence and reflected societal gender norms, compounded by stigma, legal and economic constraints relating to sex work. The results demonstrate that structural vulnerability to IPV and HIV must be addressed not only on the individual and relationship levels to resolve relevant triggers of violence and lack of condom use, but also the societal-level to address gender norms and socio-economic constraints among women in sex work and their partners. CONCLUSION: The study contributes to a better understanding on the interplay of individual agency and structural forces at a time when researchers and program planners are increasingly pondering how best to address complex and intersecting social and health issues. Ongoing research should assess the generalizability of the results and the effectiveness of structural interventions aiming to reduce IPV and HIV vulnerability in other contexts

Performance of Genotype Imputation for Rare Variants Identified in Exons and Flanking Regions of Genes

Genotype imputation has the potential to assess human genetic variation at a lower cost than assaying the variants using laboratory techniques. The performance of imputation for rare variants has not been comprehensively studied. We utilized 8865 human samples with high depth resequencing data for the exons and flanking regions of 202 genes and Genome-Wide Association Study (GWAS) data to characterize the performance of genotype imputation for rare variants. We evaluated reference sets ranging from 100 to 3713 subjects for imputing into samples typed for the Affymetrix (500K and 6.0) and Illumina 550K GWAS panels. The proportion of variants that could be well imputed (true r2>0.7) with a reference panel of 3713 individuals was: 31% (Illumina 550K) or 25% (Affymetrix 500K) with MAF (Minor Allele Frequency) less than or equal 0.001, 48% or 35% with 0.001<MAF< = 0.005, 54% or 38% with 0.005<MAF< = 0.01, 78% or 57% with 0.01<MAF< = 0.05, and 97% or 86% with MAF>0.05. The performance for common SNPs (MAF>0.05) within exons and flanking regions is comparable to imputation of more uniformly distributed SNPs. The performance for rare SNPs (0.01<MAF< = 0.05) was much more dependent on the GWAS panel and the number of reference samples. These results suggest routine use of genotype imputation for extending the assessment of common variants identified in humans via targeted exon resequencing into additional samples with GWAS data, but imputation of very rare variants (MAF< = 0.005) will require reference panels with thousands of subjects

Mixtures of Chemical Pollutants at European Legislation Safety Concentrations: How Safe Are They?

The risk posed by complex chemical mixtures in the environment to wildlife and humans is increasingly debated, but has been rarely tested under environmentally relevant scenarios. To address this issue, two mixtures of 14 or 19 substances of concern (pesticides, pharmaceuticals, heavy metals, polyaromatic hydrocarbons, a surfactant, and a plasticizer), each present at its safety limit concentration imposed by the European legislation, were prepared and tested for their toxic effects. The effects of the mixtures were assessed in 35 bioassays, based on 11 organisms representing different trophic levels. A consortium of 16 laboratories was involved in performing the bioassays. The mixtures elicited quantifiable toxic effects on some of the test systems employed, including i) changes in marine microbial composition, ii) microalgae toxicity, iii) immobilization in the crustacean Daphnia magna, iv) fish embryo toxicity, v) impaired frog embryo development, and vi) increased expression on oxidative stress-linked reporter genes. Estrogenic activity close to regulatory safety limit concentrations was uncovered by receptor-binding assays. The results highlight the need of precautionary actions on the assessment of chemical mixtures even in cases where individual toxicants are present at seemingly harmless concentration

Mixtures of chemical pollutants at European legislation safety concentrations: how safe are they?

The risk posed by complex chemical mixtures in the environment to wildlife and humans is increasingly debated, but has been rarely tested under environmentally relevant scenarios. To address this issue, two mixtures of 14 or 19 substances of concern (pesticides, pharmaceuticals, heavy metals, polyaromatic hydrocarbons, a surfactant, and a plasticizer), each present at its safety limit concentration imposed by the European legislation, were prepared and tested for their toxic effects. The effects of the mixtures were assessed in 35 bioassays, based on 11 organisms representing different trophic levels. A consortium of 16 laboratories was involved in performing the bioassays. The mixtures elicited quantifiable toxic effects on some of the test systems employed, including i) changes in marine microbial composition, ii) microalgae toxicity, iii) immobilization in the crustacean Daphnia magna, iv) fish embryo toxicity, v) impaired frog embryo development, and vi) increased expression on oxidative stress-linked reporter genes. Estrogenic activity close to regulatory safety limit concentrations was uncovered by receptor-binding assays. The results highlight the need of precautionary actions on the assessment of chemical mixtures even in cases where individual toxicants are present at seemingly harmless concentrations

Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage

<p>Abstract</p> <p>Background</p> <p>HIV-1 targets human cells expressing both the CD4 receptor, which binds the viral envelope glycoprotein gp120, as well as either the CCR5 (R5) or CXCR4 (X4) co-receptors, which interact primarily with the third hypervariable loop (V3 loop) of gp120. Determination of HIV-1 affinity for either the R5 or X4 co-receptor on host cells facilitates the inclusion of co-receptor antagonists as a part of patient treatment strategies. A dataset of 1193 distinct gp120 V3 loop peptide sequences (989 R5-utilizing, 204 X4-capable) is utilized to train predictive classifiers based on implementations of random forest, support vector machine, boosted decision tree, and neural network machine learning algorithms. An <it>in silico </it>mutagenesis procedure employing multibody statistical potentials, computational geometry, and threading of variant V3 sequences onto an experimental structure, is used to generate a feature vector representation for each variant whose components measure environmental perturbations at corresponding structural positions.</p> <p>Results</p> <p>Classifier performance is evaluated based on stratified 10-fold cross-validation, stratified dataset splits (2/3 training, 1/3 validation), and leave-one-out cross-validation. Best reported values of sensitivity (85%), specificity (100%), and precision (98%) for predicting X4-capable HIV-1 virus, overall accuracy (97%), Matthew's correlation coefficient (89%), balanced error rate (0.08), and ROC area (0.97) all reach critical thresholds, suggesting that the models outperform six other state-of-the-art methods and come closer to competing with phenotype assays.</p> <p>Conclusions</p> <p>The trained classifiers provide instantaneous and reliable predictions regarding HIV-1 co-receptor usage, requiring only translated V3 loop genotypes as input. Furthermore, the novelty of these computational mutagenesis based predictor attributes distinguishes the models as orthogonal and complementary to previous methods that utilize sequence, structure, and/or evolutionary information. The classifiers are available online at <url>http://proteins.gmu.edu/automute</url>.</p

Porous zinc and cobalt 2-nitroimidazolate frameworks with six-membered ring windows and a layered cobalt 2-nitroimidazolate polymorph

This work was supported by the European Community Seventh Framework Program (FP7/2007-2013) [grant agreement number 608490] (project M4CO2). A.O. would like to acknowledge the SCI for awarding a scholarship for her PhD research. G.M. thanks Institut Universitaire de France for its support. S.S. would like to thank the EPSRC for support EP/M506631/1. S.E.A would like to thank the Royal Society and Wolfson Foundation for a merit award.Polymorphs of Zn(2-nIm)2 (compound 1 ) and Co(2-nIm)2 (compounds 2 and 3 ) (2-nIm = 2-nitroimidazole) have been prepared by two routes: solvothermal synthesis and recrystallisation of ZIF-65(Zn/Co). Compounds 1 and 2 are isostructural, with a tetrahedrally-connected framework topology related to, but different from, that of tridymite (lonsdaleite). Single crystal X-ray diffraction analysis showed that in compound 1 (Pccn, Z = 8; a = 8.462(8) Å, b = 14.549(15) Å, c = 18.799(18) Å, V = 2314(4) Å3) there is rotational disorder for two of the three crystallographically-distinct linker types, which has been investigated computationally and by solid-state NMR spectroscopy. Detailed adsorption studies on a sample of 1 prepared by recrystallisation show 1.1 mmol g-1 uptake of CO2 at 0.1 bar (25 °C) with high affinity for CO2 over CH4 and N2 (adsorption enthalpies of 39.5, 26.0 and 18.5 kJ mol-1, respectively). A cobalt analogue (compound 2 ) with improved water stability (but lower porosity) has also been prepared. Changing the conditions of synthesis and recrystallisation gives rise to a cobalt 2-nitroimidazolate (Co(2-nIm)2, compound 3 ), which has a layered structure (I41/amd, a = 6.025(18) Å, c = 26.95(8) Å, V = 978.3(5) Å3) containing sheets of tetrahedrally-connected Co2+ cations composed of four membered rings, without porosity.PostprintPostprintPeer reviewe

FOXP3 Expression Is Upregulated in CD4+T Cells in Progressive HIV-1 Infection and Is a Marker of Disease Severity

Understanding the role of different classes of T cells during HIV infection is critical to determining which responses correlate with protective immunity. To date, it is unclear whether alterations in regulatory T cell (Treg) function are contributory to progression of HIV infection.FOXP3 expression was measured by both qRT-PCR and by flow cytometry in HIV-infected individuals and uninfected controls together with expression of CD25, GITR and CTLA-4. Cultured peripheral blood mononuclear cells were stimulated with anti-CD3 and cell proliferation was assessed by CFSE dilution.HIV infected individuals had significantly higher frequencies of CD4(+)FOXP3(+) T cells (median of 8.11%; range 1.33%-26.27%) than healthy controls (median 3.72%; range 1.3-7.5%; P = 0.002), despite having lower absolute counts of CD4(+)FOXP3(+) T cells. There was a significant positive correlation between the frequency of CD4(+)FOXP3(+) T cells and viral load (rho = 0.593 P = 0.003) and a significant negative correlation with CD4 count (rho = -0.423 P = 0.044). 48% of our patients had CD4 counts below 200 cells/microl and these patients showed a marked elevation of FOXP3 percentage (median 10% range 4.07%-26.27%). Assessing the mechanism of increased FOXP3 frequency, we found that the high FOXP3 levels noted in HIV infected individuals dropped rapidly in unstimulated culture conditions but could be restimulated by T cell receptor stimulation. This suggests that the high FOXP3 expression in HIV infected patients is likely due to FOXP3 upregulation by individual CD4(+) T cells following antigenic or other stimulation.FOXP3 expression in the CD4(+) T cell population is a marker of severity of HIV infection and a potential prognostic marker of disease progression

Early Antibiotic Exposure Is Not Detrimental to Therapeutic Effect from Immunotherapy in Hepatocellular Carcinoma

BACKGROUND AND RATIONALE: Immune checkpoint inhibitor (ICI) therapy is an expanding therapeutic option for hepatocellular carcinoma (HCC). Antibiotics (ATB) taken prior to or early during ICI therapy can impact immunotherapy efficacy across indications; however, the effect of ATB is undefined in HCC. METHODS: In a large international cohort of 450 ICI recipients from Europe, North America, and Asia, we categorized patients according to timing of ATB focusing on exposure within −30 to +30 days from ICI (early immunotherapy period [EIOP]). EIOP was evaluated in association with overall survival (OS), progression-free survival (PFS), and best radiologic response using RECIST 1.1 criteria. RESULTS: Our study comprised mostly cirrhotic (329, 73.3%) males (355, 79.1%) with a Child-Turcotte Pugh class of A (332, 73.9%), receiving ICI after 1 therapy line (251, 55.9%) for HCC of Barcelona clinic liver cancer stage C (325, 72.4%). EIOP (n = 170, 37.9%) was independent of baseline clinicopathologic features of HCC and correlated with longer PFS (6.1 vs. 3.7 months, log-rank p = 0.0135). EIOP+ patients had similar OS, overall response, and disease control rates (DCRs) compared to EIOP. The effect of EIOP persisted in landmark time analyses and in multivariable models, confirming the independent predictive role of EIOP in influencing PFS following adjustment for covariates reflective of tumor burden, liver function, and ICI regimen administered. In patients receiving programmed cell death-1 receptor/ligand inhibitors monotherapy, EIOP was also associated with higher DCRs (61.4% vs. 50.9%, p = 0.0494). CONCLUSIONS: Unlike other oncological indications, ATB in the 30 days before or after ICI initiation is associated with improved benefit from immunotherapy, independent of disease and treatment-related features. Evaluation of the immune microbiologic determinants of response to ICI in HCC warrants further investigation