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1.  Community-Level Income Inequality and HIV Prevalence among Persons Who Inject Drugs in Thai Nguyen, Vietnam 
PLoS ONE  2014;9(3):e90723.
Socioeconomic status has a robust positive relationship with several health outcomes at the individual and population levels, but in the case of HIV prevalence, income inequality may be a better predictor than absolute level of income. Most studies showing a relationship between income inequality and HIV have used entire countries as the unit of analysis. In this study, we examine the association between income inequality at the community level and HIV prevalence in a sample of persons who inject drugs (PWID) in a concentrated epidemic setting. We recruited PWID and non-PWID community participants in Thai Nguyen, Vietnam, and administered a cross-sectional questionnaire; PWID were tested for HIV. We used ecologic regression to model HIV burden in our PWID study population on GINI indices of inequality calculated from total reported incomes of non-PWID community members in each commune. We also modeled HIV burden on interaction terms between GINI index and median commune income, and finally used a multi-level model to control for community level inequality and individual level income. HIV burden among PWID was significantly correlated with the commune GINI coefficient (r = 0.53, p = 0.002). HIV burden was also associated with GINI coefficient (β = 0.082, p = 0.008) and with median commune income (β = −0.018, p = 0.023) in ecological regression. In the multi-level model, higher GINI coefficient at the community level was associated with higher odds of individual HIV infection in PWID (OR = 1.46 per 0.01, p = 0.003) while higher personal income was associated with reduced odds of infection (OR = 0.98 per $10, p = 0.022). This study demonstrates a context where income inequality is associated with HIV prevalence at the community level in a concentrated epidemic. It further suggests that community level socioeconomic factors, both contextual and compositional, could be indirect determinants of HIV infection in PWID.
doi:10.1371/journal.pone.0090723
PMCID: PMC3949692  PMID: 24618892
2.  The ‘Densitometric Image Analysis Software’ and Its Application to Determine Stepwise Equilibrium Constants from Electrophoretic Mobility Shift Assays 
PLoS ONE  2014;9(1):e85146.
Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad) and the Intelligent or Advanced Quantifier (Bio Image) do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the ‘Densitometric Image Analysis Software’ has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs). For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub.ac.be.
doi:10.1371/journal.pone.0085146
PMCID: PMC3897411  PMID: 24465496
3.  Individual-level socioeconomic status and community-level inequality as determinants of stigma towards persons living with HIV who inject drugs in Thai Nguyen, Vietnam 
Journal of the International AIDS Society  2013;16(3Suppl 2):18637.
Introduction
HIV infection may be affected by multiple complex socioeconomic status (SES) factors, especially individual socioeconomic disadvantage and community-level inequality. At the same time, stigma towards HIV and marginalized groups has exacerbated persistent concentrated epidemics among key populations, such as persons who inject drugs (PWID) in Vietnam. Stigma researchers argue that stigma fundamentally depends on the existence of economic power differences in a community. In rapidly growing economies like Vietnam, the increasing gap in income and education levels, as well as an individual's absolute income and education, may create social conditions that facilitate stigma related to injecting drug use and HIV.
Methods
A cross-sectional baseline survey assessing different types of stigma and key socioeconomic characteristics was administered to 1674 PWID and 1349 community members living in physical proximity throughout the 32 communes in Thai Nguyen province, Vietnam. We created four stigma scales, including HIV-related and drug-related stigma reported by both PWID and community members. We then used ecologic Spearman's correlation, ordinary least-squares regression and multi-level generalized estimating equations to examine community-level inequality associations, individual-level SES associations and multi-level SES associations with different types of stigma, respectively.
Results
There was little urban–rural difference in stigma among communes. Higher income inequality was marginally associated with drug-related stigma reported by community members (p=0.087), and higher education inequality was significantly associated with higher HIV-related stigma reported by both PWID and community members (p<0.05). For individuals, higher education was significantly associated with lower stigma (HIV and drug related) reported by both PWID and community members. Part-time employed PWID reported more experiences and perceptions of drug-related stigma, while conversely unemployed community members reported enacting lower drug-related stigma. Multi-level analysis revealed that the relationship between education inequality and HIV-related stigma is superseded by the effect of individual-level education.
Conclusions
The results of the study confirm that socioeconomic factors at both the individual level and community level affect different types of stigma in different ways. Attention should be paid to these differences when planning structural or educational interventions to reduce stigma, and additional research should investigate the mechanisms with which SES and inequality affect social relationships and, in turn, stigma.
doi:10.7448/IAS.16.3.18637
PMCID: PMC3833190  PMID: 24242257
stigma; injection drug users; persons who inject drugs; HIV; income inequality; socioeconomic status; GINI coefficient; multi-level model; social determinants of health
4.  Oseltamivir resistance among influenza viruses: surveillance in northern Viet Nam, 2009–2012 
Introduction
Antiviral resistance has been reported in seasonal influenza A viruses and avian influenza A(H5N1) viruses in Viet Nam, raising concerns about the efficacy of treatment.
Methods
We analysed specimens from two sources during the period 2009–2012: influenza-positive samples from influenza-like illness patients at sentinel clinics in northern Viet Nam and isolates from patients with confirmed A(H5N1) infections. Pyrosequencing was used to detect mutations: H275Y [for A(H1N1) and A(H5N1)], E119V [for A(H3N2)] and I117V [for A(H5N1)]. A neuraminidase inhibition assay was used to determine the Inhibitory Concentration 50 (IC50) values for all influenza A and B isolates.
Results
There were 341 influenza A positive samples identified; influenza A(H1N1)pdm09 was identified most frequently (n = 215). In 2009, oseltamivir resistance was observed in 100% (19 of 19) of seasonal A(H1N1) isolates and 1.4% (3/215) of A(H1N1)pdm09 isolates. This H275Y mutation was not found in influenza subtypes A(H5N1) or A(H3N2) isolates.
Discussion
In Viet Nam, seasonal and A(H5N1) influenza vaccines are not currently available; thus, effective treatment is required. The presence of oseltamivir-resistant viruses is therefore a concern. Active surveillance for oseltamivir resistance among influenza viruses circulating in Viet Nam should be continued.
doi:10.5365/WPSAR.2013.4.1.010
PMCID: PMC3762967  PMID: 24015368
5.  Implementation of Web-Based Respondent-Driven Sampling among Men Who Have Sex with Men in Vietnam 
PLoS ONE  2012;7(11):e49417.
Objective
Lack of representative data about hidden groups, like men who have sex with men (MSM), hinders an evidence-based response to the HIV epidemics. Respondent-driven sampling (RDS) was developed to overcome sampling challenges in studies of populations like MSM for which sampling frames are absent. Internet-based RDS (webRDS) can potentially circumvent limitations of the original RDS method. We aimed to implement and evaluate webRDS among a hidden population.
Methods and Design
This cross-sectional study took place 18 February to 12 April, 2011 among MSM in Vietnam. Inclusion criteria were men, aged 18 and above, who had ever had sex with another man and were living in Vietnam. Participants were invited by an MSM friend, logged in, and answered a survey. Participants could recruit up to four MSM friends. We evaluated the system by its success in generating sustained recruitment and the degree to which the sample compositions stabilized with increasing sample size.
Results
Twenty starting participants generated 676 participants over 24 recruitment waves. Analyses did not show evidence of bias due to ineligible participation. Estimated mean age was 22 years and 82% came from the two large metropolitan areas. 32 out of 63 provinces were represented. The median number of sexual partners during the last six months was two. The sample composition stabilized well for 16 out of 17 variables.
Conclusion
Results indicate that webRDS could be implemented at a low cost among Internet-using MSM in Vietnam. WebRDS may be a promising method for sampling of Internet-using MSM and other hidden groups.
doi:10.1371/journal.pone.0049417
PMCID: PMC3495883  PMID: 23152902
6.  Common Variation at BARD1 Results in the Expression of an Oncogenic Isoform that Influences Neuroblastoma Susceptibility and Oncogenicity 
Cancer Research  2012;72(8):2068-2078.
The mechanisms underlying genetic susceptibility at loci discovered by genome-wide association study (GWAS) approaches in human cancer remain largely undefined. In this study we characterized the high-risk neuroblastoma association at the BRCA1-related locus, BARD1, showing that disease-associated variations correlate with increased expression of the oncogenically activated isoform, BARD1β. In neuroblastoma cells, silencing of BARD1β showed genotype-specific cytotoxic effects, including decreased substrate-adherent, anchorage-independent, and foci growth. In established murine fibroblasts, overexpression of BARD1β was sufficient for neoplastic transformation. BARD1β stabilized the Aurora family of kinases in neuroblastoma cells, suggesting both a mechanism for the observed effect and a potential therapeutic strategy. Together, our findings identify BARD1β as an oncogenic driver of high-risk neuroblastoma tumorigenesis, and more generally, they illustrate how robust GWAS signals offer genomic landmarks to identify molecular mechanisms involved in both tumor initiation and malignant progression. The interaction of BARD1β with the Aurora family of kinases lends strong support to the ongoing work to develop Aurora kinase inhibitors for clinically aggressive neuroblastoma.
doi:10.1158/0008-5472.CAN-11-3703
PMCID: PMC3328617  PMID: 22350409
genome-wide association; neuroblastoma; BARD1; cancer susceptibility genes; functional genomics; oncogenes; genotype-phenotype correlations
7.  Water Level Flux in Household Containers in Vietnam - A Key Determinant of Aedes aegypti Population Dynamics 
PLoS ONE  2012;7(7):e39067.
We examined changes in the abundance of immature Aedes aegypti at the household and water storage container level during the dry-season (June-July, 2008) in Tri Nguyen village, central Vietnam. We conducted quantitative immature mosquito surveys of 171 containers in the same 41 households, with replacement of samples, every two days during a 29-day period. We developed multi-level mixed effects regression models to investigate container and household variability in pupal abundance. The percentage of houses that were positive for I/II instars, III/IV instars and pupae during any one survey ranged from 19.5–43.9%, 48.8–75.6% and 17.1–53.7%, respectively. The mean numbers of Ae. aegypti pupae per house ranged between 1.9–12.6 over the study period. Estimates of absolute pupal abundance were highly variable over the 29-day period despite relatively stable weather conditions. Most variability in pupal abundance occurred at the container rather than the household level. A key determinant of Ae. aegypti production was the frequent filling of the containers with water, which caused asynchronous hatching of Ae. aegypti eggs and development of cohorts of immatures. We calculated the probability of the water volume of a large container (>500L) increasing or decreasing by ≥20% to be 0.05 and 0.07 per day, respectively, and for small containers (<500L) to be 0.11 and 0.13 per day, respectively. These human water-management behaviors are important determinants of Ae. aegypti production during the dry season. This has implications for choosing a suitable Wolbachia strain for release as it appears that prolonged egg desiccation does not occur in this village.
doi:10.1371/journal.pone.0039067
PMCID: PMC3404066  PMID: 22911683
8.  Integrative genomics identifies LMO1 as a neuroblastoma oncogene 
Nature  2010;469(7329):216-220.
Neuroblastoma is a childhood cancer of the sympathetic nervous system that accounts for approximately 10% of all paediatric oncology deaths1,2. To identify genetic risk factors for neuroblastoma, we performed a genome-wide association study (GWAS) on 2,251 patients and 6,097 control subjects of European ancestry from four case series. Here we report a significant association within LIM domain only 1 (LMO1) at 11p15.4 (rs110419, combined P = 5.2 × 10−16, odds ratio of risk allele = 1.34 (95% confidence interval 1.25–1.44)). The signal was enriched in the subset of patients with the most aggressive form of the disease. LMO1 encodes a cysteine-rich transcriptional regulator, and its paralogues (LMO2, LMO3 and LMO4) have each been previously implicated in cancer. In parallel, we analysed genome-wide DNA copy number alterations in 701 primary tumours. We found that the LMO1 locus was aberrant in 12.4% through a duplication event, and that this event was associated with more advanced disease (P < 0.0001) and survival (P = 0.041). The germline single nucleotide polymorphism (SNP) risk alleles and somatic copy number gains were associated with increased LMO1 expression in neuroblastoma cell lines and primary tumours, consistent with a gain-of-function role in tumorigenesis. Short hairpin RNA (shRNA)-mediated depletion of LMO1 inhibited growth of neuroblastoma cells with high LMO1 expression, whereas forced expression of LMO1 in neuroblastoma cells with low LMO1 expression enhanced proliferation. These data show that common polymorphisms at the LMO1 locus are strongly associated with susceptibility to developing neuroblastoma, but also may influence the likelihood of further somatic alterations at this locus, leading to malignant progression.
doi:10.1038/nature09609
PMCID: PMC3320515  PMID: 21124317
9.  Gender relations and sexual communication among female students in the Mekong River Delta of Vietnam 
Culture, health & sexuality  2010;12(6):591-601.
Young women’s ability to pursue a safer-sex life in line with their wishes is crucial to their sexual health. Although some previous observations have suggested that young women’s lack of ability to negotiate safer sex is due to gender power imbalances in the culture of Vietnam, studies that have tested this hypothesis explicitly and quantitatively are few and far between. The present study aimed to test the association between perceived gender relations and perceived self-efficacy in communicating sexual matters among undergraduate female students in the Mekong River Delta of Vietnam. The analysis involved secondary data from 260 subjects from a larger survey regarding gender equity. Structural equation modeling was used to examine the study’s hypothesis. Results showed that adherence to traditional gender roles and norms was significantly associated with female students’ reduced self-efficacy to communicate on safer-sex matters, such as refusing unwanted sex or requesting condom use. This association remained invariant in the cross-validation process between partnered and unpartnered groups. Programmes that aim to promote safer-sex negotiation and practices for this population may need to address the influence of gender relations and power.
doi:10.1080/13691050902968769
PMCID: PMC3099437  PMID: 19499393
gender relations; sexuality; self-efficacy; young women; Vietnam
10.  The protein–DNA contacts in RutR·carAB operator complexes 
Nucleic Acids Research  2010;38(18):6286-6300.
Pyrimidine-specific regulation of the upstream carP1 promoter of the carbamoylphosphate synthase operon of Escherichia coli requires numerous trans-acting factors: the allosteric transcription regulator RutR, the nucleoid-associated protein integration host factor, and the trigger enzymes aminopeptidase A and PyrH (UMP-kinase). RutR, a TetR family member, binds far upstream of carP1. Here, we establish a high-resolution contact map of RutR•carP1 complexes for backbone and base-specific contacts, analyze DNA bending, determine the DNA sequence specificity of RutR binding by saturation mutagenesis, demonstrate that uracil but not thymine is the physiologically relevant ligand that inhibits the DNA binding capacity of RutR and build a model of the RutR·operator DNA complex based on the crystal structures of RutR and of the DNA-bound family member QacR. Finally, we test the validity of this model with site-directed mutagenesis of the helix–turn–helix DNA binding motif and in vitro binding studies with the cognate purified mutant RutR proteins.
doi:10.1093/nar/gkq385
PMCID: PMC2952853  PMID: 20472642
11.  Insights into the architecture and stoichiometry of Escherichia coli PepA•DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy 
Nucleic Acids Research  2009;37(5):1463-1476.
Multifunctional Aminopeptidase A (PepA) from Escherichia coli is involved in the control of two distinct DNA transaction processes: transcriptional repression of the carAB operon, encoding carbamoyl phosphate synthase and site-specific resolution of ColE1-type plasmid multimers. Both processes require communication at a distance along a DNA molecule and PepA is the major structural component of the nucleoprotein complexes that underlie this communication. Atomic Force Microscopy was used to analyze the architecture of PepA·carAB and PepA·cer site complexes. Contour length measurements, bending angle analyses and volume determinations demonstrate that the carP1 operator is foreshortened by ∼235 bp through wrapping around one PepA hexamer. The highly deformed part of the operator extends from slightly upstream of the –35 hexamer of the carP1 promoter to just downstream of the IHF-binding site, and comprises the binding sites for the PurR and RutR transcriptional regulators. This extreme remodeling of the carP1 control region provides a straightforward explanation for the strict requirement of PepA in the establishment of pyrimidine and purine-specific repression of carAB transcription. We further provide a direct physical proof that PepA is able to synapse two cer sites in direct repeat in a large interwrapped nucleoprotein complex, likely comprising two PepA hexamers.
doi:10.1093/nar/gkn1078
PMCID: PMC2655662  PMID: 19136463

Results 1-11 (11)