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- Tran, Ngoc Hieu, et al.
(author)
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Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data
- 2020
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Journal article (peer-reviewed)abstract
- The under-representation of several ethnic groups in existing genetic databases and studies have undermined our understanding of the genetic variations and associated traits or diseases in many populations. Cost and technology limitations remain the challenges in performing large-scale genome sequencing projects in many developing countries, including Vietnam. As one of the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an alternative untapped resource for genetic studies. Here we performed a large-scale genomic analysis of 2683 pregnant Vietnamese women using their NIPT data and identified a comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency distribution of disease-associated genetic variants between the Vietnamese and other populations, thus highlighting a need for genome-wide association studies dedicated to the Vietnamese population. The resulted database of Vietnamese genetic variants, their allele frequency distribution, and their associated diseases presents a valuable resource for future genetic studies.
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| 2. |
- Dao, Trong Tuan, et al.
(author)
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Resveratrol suppressed lps-induced cox-2 VIA miR-146a-5p inhibition in raw246.7 cells
- 2017
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In: Farmacia. - 0014-8237. ; 65:2, s. 214-218
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Journal article (peer-reviewed)abstract
- Trans-resveratrol (Res) is a well-known natural stilbene frequently found in grapes which have been reported to possess antioxidant, anti-cancer activities and inhibited COX-2 expression. MicroRNAs (miRNAs) are short endogenous non-coding RNAs involved in the regulation of mRNA stability and protein synthesis. In our research, resveratrol isolated from Vitis heyneana Roem. & Schult Vitis heyneana was observed to suppress lipopolysaccharides (LPS)-induced COX-2 expression in Raw264.7 cells in a dose dependent manner. Using qPCR it was revealed that LPS induced the expression of miR-25, miR- 125a, miR-125b, miR-146a-5p, miR-146a-3p and miR-455. However, we only observed miR-146a-5p expression significantly decreased in resveratrol compared to untreated-control group. In addition, resveratrol abrogated the effect of miR-146a-5p mimic induced-COX-2 expression in Raw264.7 cells. Taken together, this study demonstrated for the first time the involvement of miR-146a-5p in resveratrol inhibited LPS-induced COX-2 expression in Raw264.7 cells.
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| 4. |
- Luu, Chinh, et al.
(author)
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Framework of Spatial Flood Risk Assessment for a Case Study in Quang Binh Province, Vietnam
- 2020
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In: Sustainability. - Switzerland : MDPI. - 2071-1050. ; 12:7, s. 1-17
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Journal article (peer-reviewed)abstract
- Vietnam has been extensively affected by floods, suffering heavy losses in human life andproperty. While the Vietnamese government has focused on structural measures of flood defence such as levees and early warning systems, the country still lacks flood risk assessment methodologies and frameworks at local and national levels. In response to this gap, this study developed a flood risk assessment framework that uses historical flood mark data and a high- resolution digital elevation model to create an inundation map, then combined this map with exposure and vulnerability data to develop a holistic flood risk assessment map. The case study is the October 2010 flood event in Quang Binh province, which caused 74 deaths, 210 injuries, 188,628 flooded properties, 9019 ha of submerged and damaged agricultural land, and widespread damages to canals, levees, and roads. The final flood risk map showed a total inundation area of 64348 ha, in which 8.3% area of low risk, 16.3% area of medium risk, 12.0% area of high risk, 37.1% area of very high risk, and 26.2% area of extremely high risk. The holistic flood risk assessment map of QuangBinh province is a valuable tool and source for flood preparedness activities at the local scale.
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| 6. |
- Phu, Vu Dinh, et al.
(author)
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Burden of Hospital Acquired Infections and Antimicrobial Use in Vietnamese Adult Intensive Care Units
- 2016
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In: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 11:1
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Journal article (peer-reviewed)abstract
- Background Vietnam is a lower middle-income country with no national surveillance system for hospital-acquired infections (HAIs). We assessed the prevalence of hospital-acquired infections and antimicrobial use in adult intensive care units (ICUs) across Vietnam. Methods Monthly repeated point prevalence surveys were systematically conducted to assess HAI prevalence and antimicrobial use in 15 adult ICUs across Vietnam. Adults admitted to participating ICUs before 08: 00 a.m. on the survey day were included. Results Among 3287 patients enrolled, the HAI prevalence was 29.5% (965/3266 patients, 21 missing). Pneumonia accounted for 79.4% (804/1012) of HAIs Most HAIs (84.5% [855/1012]) were acquired in the survey hospital with 42.5% (363/855) acquired prior to ICU admission and 57.5% (492/855) developed during ICU admission. In multivariate analysis, the strongest risk factors for HAI acquired in ICU were: intubation (OR 2.76), urinary catheter (OR 2.12), no involvement of a family member in patient care (OR 1.94), and surgery after admission (OR 1.66). 726 bacterial isolates were cultured from 622/1012 HAIs, most frequently Acinetobacter baumannii (177/726 [24.4%]), Pseudomonas aeruginosa (100/726 [13.8%]), and Klebsiella pneumoniae (84/726 [11.6%]), with carbapenem resistance rates of 89.2%, 55.7%, and 14.9% respectively. Antimicrobials were prescribed for 84.8% (2787/ 3287) patients, with 73.7% of patients receiving two or more. The most common antimicrobial groups were third generation cephalosporins, fluoroquinolones, and carbapenems (20.1%, 19.4%, and 14.1% of total antimicrobials, respectively). Conclusion A high prevalence of HAIs was observed, mainly caused by Gram-negative bacteria with high carbapenem resistance rates. This in combination with a high rate of antimicrobial use illustrates the urgent need to improve rational antimicrobial use and infection control efforts.
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| 7. |
- Sushko, Iurii, et al.
(author)
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Applicability Domains for Classification Problems : Benchmarking of Distance to Models for Ames Mutagenicity Set.
- 2010
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In: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 50:12, s. 2094-2111
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Journal article (peer-reviewed)abstract
- The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed parameter of "distance to model" (DM) is defined as a metric of similarity between the training and test set compounds that have been subjected to QSAR/QSPR modeling. In our previous work, we demonstrated the utility and optimal performance of DM metrics that have been based on the standard deviation within an ensemble of QSAR models. The current study applies such analysis to 30 QSAR models for the Ames mutagenicity data set that were previously reported within the 2009 QSAR challenge. We demonstrate that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs. The presented approach identifies 30-60% of compounds having an accuracy of prediction similar to the interlaboratory accuracy of the Ames test, which is estimated to be 90%. Thus, the in silico predictions can be used to halve the cost of experimental measurements by providing a similar prediction accuracy. The developed model has been made publicly available at http://ochem.eu/models/1 .
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| 10. |
- Zhu, Hao, et al.
(author)
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Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis
- 2008
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In: Journal of chemical information and modeling. - : American Chemical Society. - 1549-9596 .- 1549-960X. ; 48:4, s. 766-784
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Journal article (peer-reviewed)abstract
- Selecting most rigorous quantitative structure-activity relationship (QSAR) approaches is of great importance in the development of robust and predictive models of chemical toxicity. To address this issue in a systematic way, we have formed an international virtual collaboratory consisting of six independent groups with shared interests in computational chemical toxicology. We have compiled an aqueous toxicity data set containing 983 unique compounds tested in the same laboratory over a decade against Tetrahymena pyriformis. A modeling set including 644 compounds was selected randomly from the original set and distributed to all groups that used their own QSAR tools for model development. The remaining 339 compounds in the original set (external set I) as well as 110 additional compounds (external set II) published recently by the same laboratory (after this computational study was already in progress) were used as two independent validation sets to assess the external predictive power of individual models. In total, our virtual collaboratory has developed 15 different types of QSAR models of aquatic toxicity for the training set. The internal prediction accuracy for the modeling set ranged from 0.76 to 0.93 as measured by the leave-one-out cross-validation correlation coefficient ( Q abs2). The prediction accuracy for the external validation sets I and II ranged from 0.71 to 0.85 (linear regression coefficient R absI2) and from 0.38 to 0.83 (linear regression coefficient R absII2), respectively. The use of an applicability domain threshold implemented in most models generally improved the external prediction accuracy but at the same time led to a decrease in chemical space coverage. Finally, several consensus models were developed by averaging the predicted aquatic toxicity for every compound using all 15 models, with or without taking into account their respective applicability domains. We find that consensus models afford higher prediction accuracy for the external validation data sets with the highest space coverage as compared to individual constituent models. Our studies prove the power of a collaborative and consensual approach to QSAR model development. The best validated models of aquatic toxicity developed by our collaboratory (both individual and consensus) can be used as reliable computational predictors of aquatic toxicity and are available from any of the participating laboratories.
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