First record of Cantharellus minor from Vietnam with identification support from a combination of nrLSU and nrSSU phylogenetic analysis

Background: A previously identified sample XC02, which was collected from a pine forest (Pinus kesiya Royle ex Gordon), in Xuan Tho Commune, Da Lat, Lam Dong Province, Vietnam, was identified as Cantharellus minor based on morphology and nrLSU phylogeny analysis. Sequence analysis of multiple genes are becoming more and more common for phylogenetic analysis of mushrooms.Method: Total DNA was isolated from sample XC02. The primer NS1, NS4 were applied to amplify the target gene the nuclear ribosomal small subunit DNA (nrSSU). For phylogenetic analysis, individual and concatenated datasets (nrSSU and nrLSU-nrSSU) were constructed. Phylogenetic tree was constructed with MEGA 6.0 with a 1000 replicate bootstrap based on the neighbor joining, maximum likelihood, maximum parsimony method.  Results: A concatenated dataset containing a total of 14 sequences from Cantharellus, Craterellus (Cantharellaceae, Canthraellales) and Hydnum (Hydnaceae, Cantharellales) were constructed. For the specimen XC02, the phylogenies based on the first, second, and third datasets (nrLSU, nrSSU, and nrLSU-nrSSU) and the morphological analysis, reported in our previous study, strongly confirmed the identity of XC02 as Cantharellus minor.Conclusion: The combination between the morphological analysis and phylogenetic analysis is confirmed as the best approach for the identification of Cantharellus and other mushroom species that we collected in the Central Highlands, Vietnam.Keywords: nrLSU; Cantharellus, Cantharellus minor; nrSSU; nrLSU; phylogeny analysis; Vietna

Applied bioinformatics tools for analysis of Microrna-214 expression and prediction of its potential targets genes in Nasopharyngeal carcinoma

miRNA (microRNA) are short RNA molecules in length from 20 to 24 nucleotides that have been shown to play an important role in regulating gene expression in many different types of human cancer. Meanwhile, miRNA-214 is one of the known miRNAs involved in the formation of nasopharyngeal carcinoma (NPC) through overexpression that promotes proliferation and development of cancer cells. However, in Vietnam, the study of miR-214 related to NPC has not been conducted yet. With the aims to develop the further studies of miR-214 on NPC in Vietnamese patients, in this initial study, we conducted the analysis of miR-214 expression in previous publications, as well as the prediction of miR-214 potential target genes, which involved in many cellular pathways. Here we applied bioinformatics tools to predict miRNAs and their targets, and discuss the role of miR-214 in the context of human cancers. As the results, miR-214 acted as the oncogenic roles in NPC, relevanted to many pathways, such as cell proliferation, apoptosis, metastasis and invasion through the its target genes LTF, Bim, Bax, LINC0086, etc. In conclusion, the use of computional approaches facilitate the further experimental validation of miRNAs in general, particularly miR-214, in Vietnamese NPC patients

HIV-Associated TB in An Giang Province, Vietnam, 2001–2004: Epidemiology and TB Treatment Outcomes

BACKGROUND: Mortality is high in HIV-infected TB patients, but few studies from Southeast Asia have documented the benefits of interventions, such as co-trimoxazole (CTX), in reducing mortality during TB treatment. To help guide policy in Vietnam, we studied the epidemiology of HIV-associated TB in one province and examined factors associated with outcomes, including the impact of CTX use. METHODOLOGY/PRINCIPAL FINDINGS: We retrospectively abstracted data for all HIV-infected persons diagnosed with TB from 2001-2004 in An Giang, a province in southern Vietnam in which TB patients receive HIV counseling and testing. We used standard WHO definitions to classify TB treatment outcomes. We conducted multivariate analysis to identify risk factors for the composite outcome of death, default, or treatment failure during TB treatment. From 2001-2004, 637 HIV-infected TB patients were diagnosed in An Giang. Of these, 501 (79%) were male, 321 (50%) were aged 25-34 years, and the most common self-reported HIV risk factor was sex with a commercial sex worker in 221 (35%). TB was classified as smear-positive in 531 (83%). During TB treatment, 167 (26%) patients died, 9 (1%) defaulted, and 6 (1%) failed treatment. Of 454 patients who took CTX, 116 (26%) had an unsuccessful outcome compared with 33 (70%) of 47 patients who did not take CTX (relative risk, 0.4; 95% confidence interval [CI], 0.3-0.5). Adjusting for male sex, rural residence, TB smear status and disease location, and the occurrence of adverse events during TB treatment in multivariate analysis, the benefit of CTX persisted (adjusted odds ratio for unsuccessful outcome 0.1; CI, 0.1-0.3). CONCLUSIONS/SIGNIFICANCE: In An Giang, Vietnam, HIV-associated TB was associated with poor TB treatment outcomes. Outcomes were significantly better in those taking CTX. This finding suggests that Vietnam should consider applying WHO recommendations to prescribe CTX to all HIV-infected TB patients

Identification of diagnostic serum protein profiles of glioblastoma patients

Diagnosis of a glioblastoma (GBM) is triggered by the onset of symptoms and is based on cerebral imaging and histological examination. Serum-based biomarkers may support detection of GBM. Here, we explored serum protein concentrations of GBM patients and used data mining to explore profiles of biomarkers and determine whether these are associated with the clinical status of the patients. Gene and protein expression data for astrocytoma and GBM were used to identify secreted proteins differently expressed in tumors and in normal brain tissues. Tumor expression and serum concentrations of 14 candidate proteins were analyzed for 23 GBM patients and nine healthy subjects. Data-mining methods involving all 14 proteins were used as an initial evaluation step to find clinically informative profiles. Data mining identified a serum protein profile formed by BMP2, HSP70, and CXCL10 that enabled correct assignment to the GBM group with specificity and sensitivity of 89 and 96%, respectively (p < 0.0001, Fischer’s exact test). Survival for more than 15 months after tumor resection was associated with a profile formed by TSP1, HSP70, and IGFBP3, enabling correct assignment in all cases (p < 0.0001, Fischer’s exact test). No correlation was found with tumor size or age of the patient. This study shows that robust serum profiles for GBM may be identified by data mining on the basis of a relatively small study cohort. Profiles of more than one biomarker enable more specific assignment to the GBM and survival group than those based on single proteins, confirming earlier attempts to correlate single markers with cancer. These conceptual findings will be a basis for validation in a larger sample size

Numerical modeling of prefabricated vertical drain with vacuum consolidation technique

This paper addresses the issue of the latest analytical method when tackling a vacuum consolidation problem in a ground improvement project using prefabricated vertical drains (PVD) and the necessity of using numerical simulation. This paper aims to introduce a matching scheme to derive appropriate soil and drain properties in analytical solution and numerical modeling (axisymmetric and plane strain conditions). The scheme started with the analytical solution with a trial process of matching the predicted and measured settlements. The derived parameters are then adopted in the numerical modeling. Depending on the scenarios considered including axisymmetric and plane strain conditions, some parameters such as permeability need to be adjusted to have the best fit in the settlement estimation. In situ monitoring data from a case history of a road construction project in Vietnam was adopted in the back-analysis to demonstrate the application of the proposed matching scheme. In addition, the effectiveness of soft ground treatment by prefabricated vertical drain is evaluated in numerical modeling and field measurement. Very good agreement in settlement behavior and the effective stress variation between numerical simulation and field measurement have illustrated the proposed matching scheme’s appropriateness

Clinical characteristics of HIV-infected TB patients (n = 637) – An Giang, Vietnam, 2001 – 2004.

1<p>29 missing data</p>2<p>188 missing data</p>3<p>288 missing data</p