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Nguyen VK, Zimmerman S, Colacino J, Jolliet O, Patel CJ. Body dissatisfaction widens the racial disparities of Benzophenone-3, a chemical biomarker of personal care and consumer product usage. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.26.24312258. [PMID: 39252908 PMCID: PMC11383470 DOI: 10.1101/2024.08.26.24312258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Background Body dissatisfaction can drive individuals to use personal care products, exposing themselves to Benzophenone-3 (BP3). Yet, no study has examined the link between body dissatisfaction and elevated chemical exposures. Objectives Our study examines how body dissatisfaction impacts the racial differences in BP3 exposures. Methods Using NHANES 2003-2016 data for 3,072 women, we ascertained body dissatisfaction with a questionnaire on weight perception. We ran two generalized linear models with log10-transformed urinary concentrations of BP3 as the outcome variable and the following main predictors: one with race/ethnicity and another combining race/ethnicity and body dissatisfaction. We also conducted stratified analyses by race/ethnicity. We adjusted for poverty income ratio, BMI, urinary creatinine, and sunscreen usage. Results BP3 levels in Mexican American, Other Hispanic, Other Race, non-Hispanic White, and non-Hispanic Asian women were on average 59%, 56%, 33%, 16%, and 9% higher, respectively, compared to non-Hispanic Black women. Racial differences in BP3 levels are accentuated with body dissatisfaction. For example, Other Hispanic women perceiving themselves as overweight had 69% higher BP3 levels than non-Hispanic Black women (p-value = 0.01), while those perceiving themselves as at the right weight had 32% higher levels (p-value = 0.31). Moreover, minority women perceiving themselves as overweight tended to have higher BP3 levels than those who do not. For example, BP3 levels in Other Hispanic women perceiving themselves as overweight are significantly higher compared to those who do not (73%, p-value = 0.03). In contrast, such differences in the non-Hispanic White women are minimal (-0.5%, p-value = 0. 98). Discussion Minority women with body dissatisfaction show elevated BP3 exposure independent of sunscreen usage, implying that their elevated exposures may stem from using other personal care and consumer products. Further research is needed to determine if increases of exposure to potential toxicants occur among minority women with body dissatisfaction.
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Zhao B, Nguyen VK, Xu M, Colacino JA, Jolliet O. Random survival forest for predicting the combined effects of multiple physiological risk factors on all-cause mortality. Sci Rep 2024; 14:15566. [PMID: 38971926 PMCID: PMC11227534 DOI: 10.1038/s41598-024-66261-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
Understanding the combined effects of risk factors on all-cause mortality is crucial for implementing effective risk stratification and designing targeted interventions, but such combined effects are understudied. We aim to use survival-tree based machine learning models as more flexible nonparametric techniques to examine the combined effects of multiple physiological risk factors on mortality. More specifically, we (1) study the combined effects between multiple physiological factors and all-cause mortality, (2) identify the five most influential factors and visualize their combined influence on all-cause mortality, and (3) compare the mortality cut-offs with the current clinical thresholds. Data from the 1999-2014 NHANES Survey were linked to National Death Index data with follow-up through 2015 for 17,790 adults. We observed that the five most influential factors affecting mortality are the tobacco smoking biomarker cotinine, glomerular filtration rate (GFR), plasma glucose, sex, and white blood cell count. Specifically, high mortality risk is associated with being male, active smoking, low GFR, elevated plasma glucose levels, and high white blood cell count. The identified mortality-based cutoffs for these factors are mostly consistent with relevant studies and current clinical thresholds. This approach enabled us to identify important cutoffs and provide enhanced risk prediction as an important basis to inform clinical practice and develop new strategies for precision medicine.
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Nguyen VK, Middleton LYM, Huang L, Zhao N, Verly E, Kvasnicka J, Sagers L, Patel CJ, Colacino J, Jolliet O. Harmonized US National Health and Nutrition Examination Survey 1988-2018 for high throughput exposome-health discovery. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23284573. [PMID: 36798185 PMCID: PMC9934713 DOI: 10.1101/2023.02.06.23284573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The National Health and Nutrition Examination Survey (NHANES) provides data on the health and environmental exposure of the non-institutionalized US population. Such data have considerable potential to understand how the environment and behaviors impact human health. These data are also currently leveraged to answer public health questions such as prevalence of disease. However, these data need to first be processed before new insights can be derived through large-scale analyses. NHANES data are stored across hundreds of files with multiple inconsistencies. Correcting such inconsistencies takes systematic cross examination and considerable efforts but is required for accurately and reproducibly characterizing the associations between the exposome and diseases. Thus, we developed a set of curated and unified datasets and accompanied code by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-2018), totaling 134,310 participants and 4,740 variables. The variables convey 1) demographic information, 2) dietary consumption, 3) physical examination results, 4) occupation, 5) questionnaire items (e.g., physical activity, general health status, medical conditions), 6) medications, 7) mortality status linked from the National Death Index, 8) survey weights, 9) environmental exposure biomarker measurements, and 10) chemical comments that indicate which measurements are below or above the lower limit of detection. We also provide a data dictionary listing the variables and their descriptions to help researchers browse the data. We also provide R markdown files to show example codes on calculating summary statistics and running regression models to help accelerate high-throughput analysis and secular trends of the exposome. [Table: see text].
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Nguyen VK, Colacino J, Patel CJ, Sartor M, Jolliet O. Identification of occupations susceptible to high exposure and risk associated with multiple toxicants in an observational study: National Health and Nutrition Examination Survey 1999-2014. EXPOSOME 2022; 2:osac004. [PMID: 35832257 PMCID: PMC9266352 DOI: 10.1093/exposome/osac004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 01/18/2023]
Abstract
Occupational exposures to toxicants are estimated to cause over 370 000 premature deaths annually. The risks due to multiple workplace chemical exposures and those occupations most susceptible to the resulting health effects remain poorly characterized. The aim of this study is to identify occupations with elevated toxicant biomarker concentrations and increased health risk associated with toxicant exposures in a diverse working US population. For this observational study of 51 008 participants, we used data from the 1999-2014 National Health and Nutrition Examination Survey. We characterized differences in chemical exposures by occupational group for 131 chemicals by applying a series of generalized linear models with the outcome as biomarker concentrations and the main predictor as the occupational groups, adjusting for age, sex, race/ethnicity, poverty income ratio, study period, and biomarker of tobacco use. For each occupational group, we calculated percentages of participants with chemical biomarker levels exceeding acceptable health-based guidelines. Blue-collar workers from "Construction," "Professional, Scientific, Technical Services," "Real Estate, Rental, Leasing," "Manufacturing," and "Wholesale Trade" have higher biomarker levels of toxicants such as several heavy metals, acrylamide, glycideamide, and several volatile organic compounds (VOCs) compared with their white-collar counterparts. Moreover, blue-collar workers from these industries have toxicant concentrations exceeding acceptable levels: arsenic (16%-58%), lead (1%-3%), cadmium (1%-11%), glycideamide (3%-6%), and VOCs (1%-33%). Blue-collar workers have higher toxicant levels relative to their white-collar counterparts, often exceeding acceptable levels associated with noncancer effects. Our findings identify multiple occupations to prioritize for targeted interventions and health policies to monitor and reduce toxicant exposures.
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Duda M, Sovacool KL, Farzaneh N, Nguyen VK, Haynes SE, Falk H, Furman KL, Walker LA, Diao R, Oneka M, Drotos AC, Woloshin A, Dotson GA, Kriebel A, Meng L, Thiede SN, Lapp Z, Wolford BN. Teaching Python for Data Science: Collaborative development of a modular & interactive curriculum. THE JOURNAL OF OPEN SOURCE EDUCATION 2021; 4:138. [PMID: 35187422 PMCID: PMC8851894 DOI: 10.21105/jose.00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We are bioinformatics trainees at the University of Michigan who started a local chapter of Girls Who Code to provide a fun and supportive environment for high school women to learn the power of coding. Our goal was to cover basic coding topics and data science concepts through live coding and hands-on practice. However, we could not find a resource that exactly met our needs. Therefore, over the past three years, we have developed a curriculum and instructional format using Jupyter notebooks to effectively teach introductory Python for data science. This method, inspired by The Carpentries organization, uses bite-sized lessons followed by independent practice time to reinforce coding concepts, and culminates in a data science capstone project using real-world data. We believe our open curriculum is a valuable resource to the wider education community and hope that educators will use and improve our lessons, practice problems, and teaching best practices. Anyone can contribute to our Open Educational Resources on GitHub.
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Nguyen VK, Colacino J, Chung MK, Goallec AL, Jolliet O, Patel CJ. Characterising the relationships between physiological indicators and all-cause mortality (NHANES): a population-based cohort study. THE LANCET. HEALTHY LONGEVITY 2021; 2:e651-e662. [PMID: 34825242 PMCID: PMC8612451 DOI: 10.1016/s2666-7568(21)00212-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Mortality risk stratification based on dichotomising a physiological indicator with a cutoff point might not adequately capture increased mortality risk and might not account for non-linear associations. We aimed to characterise the linear and non-linear relationships of 27 physiological indicators with all-cause mortality to evaluate whether the current clinical thresholds are suitable in distinguishing patients at high risk for mortality from those at low risk. METHODS For this observational cohort study of the US non-institutionalised population, we used data from adults (≥18 years) included in the 1999-2014 National Health and Nutrition Examination Survey (NHANES) linked with National Death Index mortality data collected from Jan 1, 1999, up until Dec 31, 2015. We used Cox proportional hazards regression models adjusted for age, sex, and race or ethnicity to assess associations of physiological indicators with all-cause mortality. We assessed non-linear associations by discretising the physiological indicator into nine quantiles (termed novemtiles) and by using a weighted sum of cubic polynomials (spline). We used ten-fold cross validation to select the most appropriate model using the concordance index, Nagelkerke R2, and Akaike Information Criterion. We identified the level of each physiological indicator that led to a 10% increase in mortality risk to define our cutoffs used to compare with the current clinical thresholds. FINDINGS We included 47 266 adults of 82 091 assessed for eligibility. 25 (93%) of 27 indicators showed non-linear associations with substantial increases compared with linear models in mortality risk (1·5-2·5-times increase). Height and 60 s pulse were the only physiological indicators to show linear associations. For example, participants with an estimated glomerular filtration rate (GFR) of less than 65 mL/min per 1·73 m2 or between 90-116 mL/min per 1·73 m2 are at moderate (hazard ratio 1-2) mortality risk. Those with a GFR greater than 117 mL/min per 1·73 m2 show substantial (hazard ratio ≥2) mortality risk. Both lower and higher values of cholesterol are associated with increased mortality risk. The current clinical thresholds do not align with our mortality-based cutoffs for fat deposition indices, 60 s pulse, triglycerides, cholesterol-related indicators, alkaline phosphatase, glycohaemoglobin, homoeostatic model assessment of insulin resistance, and GFR. For these indicators, the misalignment suggests the need to consider an additional bound when only one is provided. INTERPRETATION Most clinical indicators were shown to have non-linear associations with all-cause mortality. Furthermore, considering these non-linear associations can help derive reliable cutoffs to complement risk stratification and help inform clinical care delivery. Given the poor alignment with our proposed cutoffs, the current clinical thresholds might not adequately capture mortality risk.
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Chung MK, Rappaport SM, Wheelock CE, Nguyen VK, van der Meer TP, Miller GW, Vermeulen R, Patel CJ. Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:85001. [PMID: 34435882 PMCID: PMC8388254 DOI: 10.1289/ehp8327] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/28/2021] [Accepted: 07/13/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Recent developments in technologies have offered opportunities to measure the exposome with unprecedented accuracy and scale. However, because most investigations have targeted only a few exposures at a time, it is hypothesized that the majority of the environmental determinants of chronic diseases remain unknown. OBJECTIVES We describe a functional exposome concept and explain how it can leverage existing bioassays and high-resolution mass spectrometry for exploratory study. We discuss how such an approach can address well-known barriers to interpret exposures and present a vision of next-generation exposomics. DISCUSSION The exposome is vast. Instead of trying to capture all exposures, we can reduce the complexity by measuring the functional exposome-the totality of the biologically active exposures relevant to disease development-through coupling biochemical receptor-binding assays with affinity purification-mass spectrometry. We claim the idea of capturing exposures with functional biomolecules opens new opportunities to solve critical problems in exposomics, including low-dose detection, unknown annotations, and complex mixtures of exposures. Although novel, biology-based measurement can make use of the existing data processing and bioinformatics pipelines. The functional exposome concept also complements conventional targeted and untargeted approaches for understanding exposure-disease relationships. CONCLUSIONS Although measurement technology has advanced, critical technological, analytical, and inferential barriers impede the detection of many environmental exposures relevant to chronic-disease etiology. Through biology-driven exposomics, it is possible to simultaneously scale up discovery of these causal environmental factors. https://doi.org/10.1289/EHP8327.
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Nguyen VK, Kahana A, Heidt J, Polemi K, Kvasnicka J, Jolliet O, Colacino JA. A comprehensive analysis of racial disparities in chemical biomarker concentrations in United States women, 1999-2014. ENVIRONMENT INTERNATIONAL 2020; 137:105496. [PMID: 32113086 PMCID: PMC7137529 DOI: 10.1016/j.envint.2020.105496] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Stark racial disparities in disease incidence among American women remain a persistent public health challenge. These disparities likely result from complex interactions between genetic, social, lifestyle, and environmental risk factors. The influence of environmental risk factors, such as chemical exposure, however, may be substantial and is poorly understood. OBJECTIVES We quantitatively evaluated chemical-exposure disparities by race/ethnicity, life stage, and time in United States (US) women (n = 38,080) by using biomarker data for 143 chemicals from the National Health and Nutrition Examination Survey (NHANES) 1999-2014. METHODS We applied a series of survey-weighted, generalized linear models using data from the entire NHANES women population along with cycle and age-group stratified subpopulations. The outcome was chemical biomarker concentration, and the main predictor was race/ethnicity with adjustment for age, socioeconomic status, smoking habits, and NHANES cycle. RESULTS Compared to non-Hispanic White women, the highest disparities were observed for non-Hispanic Black, Mexican American, Other Hispanic, and Other Race/Multi-Racial women with higher levels of pesticides and their metabolites, including 2,5-dichlorophenol, o,p'-DDE, beta-hexachlorocyclohexane, and 2,4-dichlorophenol, along with personal care and consumer product compounds, including parabens and monoethyl phthalate, as well as several metals, such as mercury and arsenic. Moreover, for Mexican American, Other Hispanic, and non-Hispanic black women, there were several exposure disparities that persisted across age groups, such as higher 2,4- and 2,5-dichlorophenol concentrations. Exposure levels for methyl and propyl parabens, however, were the highest in non-Hispanic black compared to non-Hispanic white children with average differences exceeding 4-fold. Exposure disparities for methyl and propyl parabens are increasing over time in Other Race/Multi-Racial women while fluctuating for non-Hispanic Black, Mexican American, and Other Hispanic. Cotinine levels are among the highest in Non-Hispanic White women compared to Mexican American and Other Hispanic women with disparities plateauing and increasing, respectively. DISCUSSION We systematically evaluated differences in chemical exposures across women of various race/ethnic groups and across age groups and time. Our findings could help inform chemical prioritization in designing epidemiological and toxicological studies. In addition, they could help guide public health interventions to reduce environmental and health disparities across populations.
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Nguyen VK, Colacino JA, Arnot JA, Kvasnicka J, Jolliet O. Characterization of age-based trends to identify chemical biomarkers of higher levels in children. ENVIRONMENT INTERNATIONAL 2019; 122:117-129. [PMID: 30528102 PMCID: PMC6903703 DOI: 10.1016/j.envint.2018.10.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/01/2018] [Accepted: 10/21/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Chemical biomarker concentrations are driven by complex interactions between chemical use patterns, exposure pathways, and toxicokinetic parameters such as biological half-lives. Criteria to differentiate legacy from current exposures are helpful for interpreting variation in age-based and time trends of chemical exposure and identifying chemicals to which children are highly exposed. A systematic approach is needed to study temporal trends for a wide range of chemicals in the US population. OBJECTIVES Using National Health and Nutrition Examination Survey (NHANES) data on measured biomarker concentrations for 141 chemicals from 1999 to 2014, we aim to 1) understand the influence of temporal determinants, in particular time trends, biological half-lives, and restriction dates on age-based trends, 2) systematically define an age-based pattern to identify chemicals with ongoing and high exposure in children, and 3) characterize how age-based trends for six Per- and Polyfluoroalkyl Substances (PFASs) are changing over time. METHODS We performed an integrated analysis of biological half-lives and restriction dates, compared distributions of chemical biomarker concentrations by age group, and then applied a series of regression models to evaluate the linear (βage) and nonlinear (βage2) relationships between age and chemical biomarker levels. RESULTS For restricted chemicals, a minimum persistence of 1 year in the human body is needed to observe substantial differences between the less exposed young population and historically exposed adults. We define a metric ( [Formula: see text] ) that identifies several phthalates, brominated flame retardants, pesticides, and metals such as lead and tungsten as elevated and ongoing exposures in children. While a substantial reduction in children's exposures was reflected in PFOS and PFOA, levels of PFNA and PFHxS in children were higher in 2013-2014 compared to those in 1999-2000. CONCLUSIONS Integrating a series of regression models with systemized stratified analyses by age group enabled us to define an age-based pattern to identify chemicals that are of higher levels in children.
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Aboubacrine SA, Niamba P, Boileau C, Zunzunegui MV, Machouf N, Nguyen VK, Rashed S. Inadequate adherence to antiretroviral treatment and prevention in hospital and community sites in Burkina Faso and Mali: a study by the ATARAO group. Int J STD AIDS 2016; 18:741-7. [DOI: 10.1258/095646207782212243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Our objective was to determine the prevalence and identify the factors that influence antiretroviral therapy (ART) adherence among patients in Bamako and Ouagadougou. A cross-sectional study was conducted among 94 men and 176 women receiving ART. Data were collected through questionnaires and chart reviews. Logistic regressions were performed to isolate determinants of adherence. Overall, 58% of the patients were adherent, but there were differences in the levels of adherence according to country and treatment site. Sociodemographic factors were not associated with adherence. However, social characteristics such as having children, in Ouagadougou, or being a housewife and not planning to have a child in the next year, in Bamako were associated with adherence. Time on ART was negatively associated with adherence in both countries with decline occurring later in Bamako. Levels of adherence are inadequate particularly among more experienced patients. Further adherence research and monitoring using longitudinal designs are warranted to assess the extent to which adherence is declining with time on treatment.
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Haidara A, Chamberland A, Sylla M, Aboubacrine SA, Cissé M, Traore HA, Maiga MY, Tounkara A, Nguyen VK, Tremblay C. High level of primary drug resistance in Mali. HIV Med 2010; 11:404-11. [PMID: 20146734 DOI: 10.1111/j.1468-1293.2009.00806.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND As access to antiretroviral drugs increases in developing countries, it will become increasingly important to monitor the emergence of resistance and to define the molecular pathways involved to identify optimal therapeutic regimens. METHODS We performed genotypic resistance testing on plasma obtained from 101 HIV-infected treatment-naïve individuals from Mali. Genotyping was carried out using the Virco protocols and HXB2 was used as the reference strain. RESULTS CRF02_AG was the most common subtype, present in 71.3% of our patient population. Other subtypes included B, C, G, CRF06_CPX, CRF09_CPX, CRF01_AE, A2/CRF16_A2D, A1 and CRF13_CPX. A total of 9.9% [95% confidence interval (CI) 6.9-12.9%] of patients had at least one resistance mutation. The prevalences of mutations conferring resistance to nucleoside reverse transcriptase inhibitors (NRTIs), nonnucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were 5% (95% CI 0.7-9.2%), 6% (95% CI 1.3-10.6%) and 0%, respectively. The most frequent mutations were T215A/Y for NRTIs and K103N/T for NNRTIs. One patient harboured three NRTI resistance mutations and one NNRTI mutation. This is the first reported case of multi-drug-resistant viral transmission in Mali. Polymorphisms at protease codons 10I/V and 33F potentially associated with resistance were observed in 18.8% and 1% of patients, respectively. Several polymorphisms in the C-terminal domain of reverse transcriptase were observed: A371V (in 63.4% of patients), G335D (76.2%), E399D (10.9%) and G333E (1%). CONCLUSION Primary resistance was seen in 9.9% of subjects, which is higher than previously reported in Mali. Taking into consideration other polymorphisms in protease such as L10I/V and 33F, primary resistance could reach 28.7% (95% CI 19.9-37.5%). Our study reflects the need to monitor the evolution of resistance on a regular basis and trends of transmitted resistance.
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Schou TW, Labouriau R, Permin A, Christensen JP, Sørensen P, Cu HP, Nguyen VK, Juul-Madsen HR. MHC haplotype and susceptibility to experimental infections (Salmonella Enteritidis, Pasteurella multocida or Ascaridia galli) in a commercial and an indigenous chicken breed. Vet Immunol Immunopathol 2009; 135:52-63. [PMID: 19945754 DOI: 10.1016/j.vetimm.2009.10.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 10/26/2009] [Accepted: 10/27/2009] [Indexed: 10/20/2022]
Abstract
In three independent experimental infection studies, the susceptibility and course of infection of three pathogens considered of importance in most poultry production systems, Ascaridia galli, Salmonella Enteritidis and Pasteurella multocida were compared in two chicken breeds, the indigenous Vietnamese Ri and the commercial Luong Phuong. Furthermore, the association of the Major Histocompatibility Complex (MHC) with disease-related parameters was evaluated, using alleles of the LEI0258 microsatellite as markers for MHC haplotypes. The Ri chickens were found to be more resistant to A. galli and S. Enteritidis than commercial Luong Phuong chickens. In contrast, the Ri chickens were more susceptible to P. multocida, although production parameters were more affected in the Luong Phuong chickens. Furthermore, it was shown that the individual variations observed in response to the infections were influenced by the MHC. Using marker alleles of the microsatellite LEI0258, which is located within the MHC region, several MHC haplotypes were identified as being associated with infection intensity of A. galli. An association of the MHC with the specific antibody response to S. Enteritidis was also found where four MHC haplotypes were shown to be associated with high specific antibody response. Finally, one MHC haplotype was identified as being associated with pathological lesions and mortality in the P. multocida experiment. Although not statistically significant, our analysis suggested that this haplotype might be associated with resistance. These results demonstrate the presence of local genetic resources in Vietnamese chickens, which could be utilized in breeding programmes aiming at improving disease resistance.
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Nguyen VK. Government-by-exception: Enrolment and experimentality in mass HIV treatment programmes in Africa. SOCIAL THEORY & HEALTH 2009. [DOI: 10.1057/sth.2009.12] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Muyldermans S, Baral TN, Retamozzo VC, De Baetselier P, De Genst E, Kinne J, Leonhardt H, Magez S, Nguyen VK, Revets H, Rothbauer U, Stijlemans B, Tillib S, Wernery U, Wyns L, Hassanzadeh-Ghassabeh G, Saerens D. Camelid immunoglobulins and nanobody technology. Vet Immunol Immunopathol 2008; 128:178-83. [PMID: 19026455 DOI: 10.1016/j.vetimm.2008.10.299] [Citation(s) in RCA: 362] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
It is well established that all camelids have unique antibodies circulating in their blood. Unlike antibodies from other species, these special antibodies are devoid of light chains and are composed of a heavy-chain homodimer. These so-called heavy-chain antibodies (HCAbs) are expressed after a V-D-J rearrangement and require dedicated constant gamma-genes. An immune response is raised in these so-called heavy-chain antibodies following classical immunization protocols. These HCAbs are easily purified from serum, and the antigen-binding fragment interacts with parts of the target that are less antigenic to conventional antibodies. Since the antigen-binding site of the dromedary HCAb is comprised in one single domain, referred to as variable domain of heavy chain of HCAb (VHH) or nanobody (Nb), we designed a strategy to clone the Nb repertoire of an immunized dromedary and to select the Nbs with specificity for our target antigens. The monoclonal Nbs are well produced in bacteria, are very stable and highly soluble, and bind their cognate antigen with high affinity and specificity. We have successfully developed recombinant Nbs for research purposes, as probe in biosensors, to diagnose infections, and to treat diseases like cancer or trypanosomosis.
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Ndiaye C, Boileau C, Zunzunegui MV, Koala S, Aboubacrine SA, Niamba P, Nguyen VK, Rashed S. Gender-related factors influencing HIV serostatus disclosure in patients receiving HAART in West Africa. WORLD HEALTH & POPULATION 2008; 10:43-54. [PMID: 19369822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Disclosure of HIV serostatus remains an important tool for the prevention of new infections and early initiation of treatment for HIV-positive individuals' regular sexual partners. Our aim is to identify factors associated with disclosure to partner in patients taking antiretroviral treatment, with a gender- and sex-based approach. In this study conducted in Mali and Burkina Faso, men (154) and women (164) who reported being in a marital or cohabitating relationship were included. Sex-specific bivariate analyses and multivariate logistic regression were performed to identify determinants of disclosure. Disclosure to partner was 72.1% in men and 79.9% in women. Results of bivariate and multivariate analyses indicated that cohabiting with partner was strongly associated with disclosure in both men and women. In men only, older age, literacy and having good communication with the treating doctor were significantly associated with disclosure. Among women, disclosure was associated with having children and high self-reported importance of religion. Future research and interventions promoting disclosure should take into account these differences reflecting the social construction of gender roles in these settings.
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Jones SL, Nguyen VK, Nguyen TMP, Athan E. Prevalence of multiresistant Gram-negative organisms in a surgical hospital in Ho Chi Minh Cit, Vietnam. Trop Med Int Health 2006; 11:1725-30. [PMID: 17054753 DOI: 10.1111/j.1365-3156.2006.01731.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
OBJECTIVE To determine resistance patterns of multiresistant Gram-negative organisms at a surgical hospital in Ho Chi Minh City, Vietnam, in order to guide appropriate antibiotic prescribing and improve infection control procedures. METHOD All samples sent in for microbiological analysis over a 3-month period were included. A resource neutral double disc-diffusion test was introduced to detect the presence of extended-spectrum beta-lactamase (ESBL) production. RESULTS We obtained 350 bacterial isolates from clinical specimens; 87.4% were Gram-negative bacteria (GNB). Of these, 88.9% were Enterobacteriaceae, of which 14.7% produced ESBL. Fifteen (37.5%) of these were isolated within 48 h of admission. Resistance to gentamicin and ciprofloxacin occurred in 70.0% and 72.5% of those organisms that produced ESBL and in 39.5% and 38.7% of those that did not. Resistance to third-generation cephalosporins was common: 36.7% of all GNB were resistant to ceftriaxone, 34.0% to cefotaxime, 19.6% to ceftazidime and 36.7% to cefoperazone. CONCLUSION Multiresistant Gram-negative organisms are common and pose a challenge to antibiotic therapy. Successful implementation of a simple test to detect ESBL production allowed reporting of these organisms, appropriate antibiotic prescribing and infection control interventions. Development of antibiotic-prescribing guidelines must take into account these resistance patterns.
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Suzuki K, Kanameda M, Inui K, Ogawa T, Nguyen VK, Dang TTS, Pfeiffer DU. A longitudinal study to identify constraints to dairy cattle health and production in rural smallholder communities in Northern Vietnam. Res Vet Sci 2006; 81:177-84. [PMID: 16481015 DOI: 10.1016/j.rvsc.2005.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 11/30/2005] [Accepted: 12/07/2005] [Indexed: 10/25/2022]
Abstract
The objective of the study was to investigate constraints to dairy cattle health and production in rural smallholder communities in northern Vietnam, one of the target areas of the Vietnam government's dairy development programme. A total of 99 dairy farms (11 per commune) were recruited from 9 of 32 communes in Ba Vi District, using random two-stage cluster sampling. After the initial questionnaire interviews were conducted, farms were visited at three monthly intervals over a period of 1 year. Information on several health and production parameters relating to the study cattle was collected. Using multiple indicator modelling, it was found that Fasciola infestation, farmers who had been involved in dairying for longer (not indicative of better management skills), larger herd size, and cattle being kept in a shed were linked to reduced reproductive performances.
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Somers R, Dorny P, Nguyen VK, Dang TCT, Goddeeris B, Craig PS, Vercruysse J. Taenia solium taeniasis and cysticercosis in three communities in north Vietnam. Trop Med Int Health 2006; 11:65-72. [PMID: 16398757 DOI: 10.1111/j.1365-3156.2005.01537.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES (1) To investigate the response to a serum antigen-detecting ELISA for cysticercosis and a stool coproantigen test for taeniasis in two rural communities (mountainous and coastal areas) and one group of (peri-)urban factory workers; and (2) to examine clinical features of human cysticercosis in northern Vietnam. METHODS Villagers and factory workers and their families were informed and invited to participate in the study. Blood and faecal samples were collected from the participants and a simple questionnaire on taeniasis/cysticercosis completed. Serum was examined for the presence of circulating cysticercus antigen by a monoclonal-based sandwich ELISA. Ag-ELISA positive persons underwent a clinical examination and a computed tomography (CT) scan. Stool samples were examined microscopically for the presence of Taenia eggs and for copro-antigens. Tapeworms were identified following therapeutic expulsion using morphology and PCR-RFLP. RESULTS Circulating cysticercus antigens, suggesting active infection, were detected in 5.3% (16/303), 0.6% (1/175) and 0.0% (0/229) of the sampled individuals from the mountainous, coastal and urban regions, respectively. Clinical examination and CT scan of the cysticercus antigen positive persons showed that active cysticercosis did not cause severe disease in most cases. Taenia copro-antigens were found in 0.3% (1/297), 1.8% (3/166) and 0.0% (0/228) of the stool samples from the mountainous, coastal and urban communities, respectively. Three tapeworms were expelled after treatment: two Taenia solium and one Taenia saginata. CONCLUSION This survey points to a focal distribution of taeniasis/cysticercosis and suggests that human cysticercosis is rather acquired due to close contact with a T. solium carrier and self-infection, than through infection from the environment.
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Machouf N, Thomas R, Nguyen VK, Trottier B, Boulassel MR, Wainberg MA, Routy JP. Effects of drug resistance on viral load in patients failing antiretroviral therapy. J Med Virol 2006; 78:608-13. [PMID: 16555280 DOI: 10.1002/jmv.20582] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Previous studies on patients who develop drug resistant HIV-1 variants have shown that continued use of failing regimens might provide clinical benefit. However, the effect of long-term exposure to drug resistant variants may lead to emergence of compensatory mutations that may jeopardize this effect. In this study, we assess associations among type and number of drug resistant mutations, viral load and disease progression in patients with long-term follow up. Patients with genotypic testing performed at the time of treatment failure were enrolled. Comparison of viral load and CD4 cell count between different resistance groups was performed using analysis of variance. Multiple linear regression analysis was performed to assess the simultaneous effects of the presence of particular mutations and their accumulation on viral load. Data from 475 patients who were followed for a median of 43 months from October 1999 to July 2005 were studied. A "V shape" relationship was observed between the number of mutations and viral load. Specifically, in patients harboring up to five mutations, viral load was reduced by 0.8 log/copies when compared to wild-type variants. However, with more than six mutations viral load progressively increased. Certain reverse transcriptase mutations such as M184V/I, K70R, V108I, and protease mutations such as L33FIV, M84V, and M36I were associated with reduced viral load. Together, these findings suggest that long-term maintenance of a sub-optimal antiretroviral regimen may have deleterious consequences for the patient.
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Conrath KE, Wernery U, Muyldermans S, Nguyen VK. Emergence and evolution of functional heavy-chain antibodies in Camelidae. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2003; 27:87-103. [PMID: 12543123 DOI: 10.1016/s0145-305x(02)00071-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antibodies of jawed-vertebrates are composed of paired heavy (H) and light (L) polypeptide chains. Surprisingly, the sera of camelids, nurse shark and wobbegong shark, and possibly ratfish contain antibodies that lack L-chains. In camelids, these Heavy-chain antibodies (HCAbs) are gamma-isotypes, and are functional in antigen binding. In this review we focus on the dedicated immunoglobulin (Ig) genes that encode the HCAb in Camelidae (camels, dromedaries and llamas), about their origin, and how these camel immunoglobulins evolved and acquire a large and diverse repertoire of antigen binding sites in absence of the H-L combinatorial diversity.
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Nguyen VK, Hamers R, Wyns L, Muyldermans S. Camel heavy-chain antibodies: diverse germline V(H)H and specific mechanisms enlarge the antigen-binding repertoire. EMBO J 2000; 19:921-30. [PMID: 10698934 PMCID: PMC305632 DOI: 10.1093/emboj/19.5.921] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The antigen-binding site of the camel heavy-chain antibodies devoid of light chain consists of a single variable domain (V(H)H) that obviously lacks the V(H)-V(L) combinatorial diversity. To evaluate the extent of the V(H)H antigen-binding repertoire, a germline database was constructed from PCR-amplified V(H)H/V(H) segments of a single specimen of Camelus dromedarius. A total of 33 V(H)H and 39 V()H unique sequences were identified, encoded by 42 and 50 different genes, respectively. Sequence comparison indicates that the V(H)Hs evolved within the V(H) subgroup III. Nevertheless, the V(H)H germline segments are highly diverse, leading to a broad structural repertoire of the antigen-binding loops. Seven V(H)H subfamilies were recognized, of which five were confirmed to be expressed in vivo. Comparison of germline and cDNA sequences demonstrates that the rearranged V(H)Hs are extensively diversified by somatic mutation processes, leading to an additional hypervariable region and a high incidence of nucleotide insertions or deletions. These diversification processes are driven by hypermutation and recombination hotspots embedded in the V(H)H germline genes at the regions affecting the structure of the antigen-binding loops.
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Nguyen VK, Leclerc N, Wolff CM, Kennel P, Fonteneau P, Deyes R, Warter JM, Poindron P. Protection of immunoreactivity of dry immobilized proteins on microtitration plates in ELISA: application for detection of autoantibodies in myasthenia gravis. J Biotechnol 1999; 72:115-25. [PMID: 10406102 DOI: 10.1016/s0168-1656(99)00099-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We show the ability of the BSA-trehalose film to convert normally fragile proteins such as mouse monoclonal antibody to the Alzheimer precursor protein A4 (APP695) and cell line TE671 acetylcholine receptor (AChRTE671) into a stable reagent, after its immobilization on microtitration plates. The remarkable property of the dry immobilized proteins are their stability under prolonged exposure to temperatures as high as 50 degrees C. Using the AChRTE671, the proposed method was applied for the measurement of anti-AChR autoantibodies in Myasthenia gravis by means of an enzyme-linked immunosorbent assay (ELISA). The test was shown to be specific and able to detect anti-AChR autoantibodies at concentrations as low as 3 nM. Using the same AchRTE671 as antigen, the results of examination of 34 serum samples for detection of anti-AChR autoantibodies by ELISA were compared with those of the conventional radioimmunoprecipitation assay (RIA). It was concluded that ELISA is another useful method for the diagnosis of M. gravis. The ELISA method offers a rapid, simple, safe and inexpensive means for mass screening of M. gravis.
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Nguyen VK, Jacquiet P, Duranton C, Bergeaud JP, Prevot F, Dorchies P. [Reactions of cells of nasal and sinusoidal mucosa of goats and sheep naturally infected by Oestrus ovis Linné 1758 (Diptera: Oestridae)]. Parasite 1999; 6:141-9. [PMID: 10416188 DOI: 10.1051/parasite/1999062141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OEstrosis is a very common myiasis of sheep and goats in mediterranean and tropical countries. Goats are suitable hosts for OEstrus ovis but the parasitic burden remain lower than in sheep. Cellular responses (mucous and serous mast cells, eosinophis and globules leucocytes) were measured in 30 infected and 30 non infected sheep and in 23 infected and 24 non infected goats. The presence of OEstrus ovis larvae led to an important inflammatory response in sheep and in goats as well. Furthermore, the intensity of the cellular response correlated with the larva burden, specially with globules leucocytes and eosinophils. Nevertheless, huge differences occurred between sheep and goats responses even in similar larval burden range. Infected sheep showed larger counts of mucous mast cells than goats, the differences were smaller in serous mast cells and eosinophils and no difference was detected in globules leucocytes (intraepithelial mast cells) counts between the two hosts species. These results were compared with those obtained in gastro-intestinal strongyles infections.
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Nguyen VK, Hamers R, Wyns L, Muyldermans S. Loss of splice consensus signal is responsible for the removal of the entire C(H)1 domain of the functional camel IGG2A heavy-chain antibodies. Mol Immunol 1999; 36:515-24. [PMID: 10475606 DOI: 10.1016/s0161-5890(99)00067-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular basis for the absence of the C(H)1 domain in naturally occurring heavy-chain antibodies of the camelids was assessed by determining the entire Camelus dromedarius gamma2a heavy-chain constant gene. The organization of the camel gamma2a constant heavy-chain gene obtained from a liver genomic library appears to be typical of all other mammalian gamma genes sequenced to date. It contains the switch, CH1, hinge, CH2, CH3, M1 and M2 exons. In contrast to the case in mouse and human heavy chain diseases, the camel gamma2a gene shows no major structural defect, and its equivalent CHI exon is intact. However, sequence analysis has revealed that the splicing site, immediately after the CH1 exon, is defective due to point mutations, especially the G(+1) to A(+1) transversion seems to be detrimental. It is concluded that the loss of the splice consensus signal is responsible for the removal of the entire CH1 domain in camel gamma2a heavy-chain immunoglobulins. Additionally, a closer analysis of the hinge exon suggests the possible involvement of transposons in the genetic variation of mammalian Cgamma hinges.
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