Long Triệu - Academia.edu (original) (raw)

Papers by Long Triệu

Annals of Clinical Microbiology and Antimicrobials, May 6, 2019

Background: Invasive meningococcal disease (IMD) persists in military units in Vietnam despite th... more Background: Invasive meningococcal disease (IMD) persists in military units in Vietnam despite the availability of antibiotics and vaccines. A hindrance to reducing the incidence of IMD in Vietnam is a lack of molecular data from isolates of the causative agent, Neisseria meningitidis from this country. Here, we characterized key genetic and epidemiological features of an invasive N. meningitidis isolate from a military unit in Vietnam using whole-genome sequencing. Methods: Neisseria meningitidis was isolated from a conscript admitted for meningitis and tested against seven antibiotics. DNA from the isolate was extracted and sequenced using the Illumina HiSeq platform. Denovo assembly and scaffolding were performed to construct a draft genome assembly, from which genes were predicted and functionally annotated. Genome analysis included epidemiological characterization, genomic composition and identification of antibiotic resistance genes. Results: Susceptibility testing of the isolate showed high levels of resistance to chloramphenicol and diminished susceptibility to ampicillin and rifampicin. A draft genome of ~ 2.1 Mb was assembled, containing 2451 protein coding sequences, 49 tRNAs and 3 rRNAs. Fifteen coding sequences sharing ≥ 84% identity with known antibiotic resistance genes were identified. Genome analysis revealed abundant repetitive DNAs and two prophages. Epidemiological typing revealed newly described sequence type, antigenic finetype and Bexsero ® Antigen Sequence Typing (BAST). The BAST profile showed no coverage by either Bexsero ® or Trumenba ®. Conclusions: Our results present the first genome assembly of an invasive N. meningitidis isolate from a military unit in Vietnam. This study illustrates the usefulness of whole genome sequencing (WGS) analysis for epidemiological and antibiotic resistance studies and surveillance of IMD in Vietnam.

All research results presented in this dissertation have been worked out under the supervision of... more All research results presented in this dissertation have been worked out under the supervision of Christoph Buchheim. Partial results on the active set based branch-and-bound algorithm in Chapter 5 have been published in [42]. Further extensions of this chapter were developed in a productive cooperation with Marianna

Acta Tropica, Oct 1, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

arXiv (Cornell University), Dec 8, 2015

We propose a feasible active set method for convex quadratic programming problems with non-negati... more We propose a feasible active set method for convex quadratic programming problems with non-negativity constraints. This method is specifically designed to be embedded into a branch-and-bound algorithm for convex quadratic mixed integer programming problems. The branch-and-bound algorithm generalizes the approach for unconstrained convex quadratic integer programming proposed by Buchheim, Caprara and Lodi [8] to the presence of linear constraints. The main feature of the latter approach consists in a sophisticated preprocessing phase, leading to a fast enumeration of the branch-and-bound nodes. Moreover, the feasible active set method takes advantage of this preprocessing phase and is well suited for reoptimization. Experimental results for randomly generated instances show that the new approach significantly outperforms the MIQP solver of CPLEX 12.6 for instances with a small number of constraints.

We present an exact algorithm for mean-risk optimization subject to a budget constraint, where de... more We present an exact algorithm for mean-risk optimization subject to a budget constraint, where decision variables may be continuous or integer. The risk is measured by the covariance matrix and weighted by an arbitrary monotone function, which allows to model risk-aversion in a very individual way. We address this class of convex mixed-integer minimization problems by designing a branch-and-bound algorithm, where at each node, the continuous relaxation is solved by a non-monotone Frank-Wolfe type algorithm with away-steps. Experimental results on portfolio optimization problems show that our approach can outperform the MISOCP solver of CPLEX 12.6 for instances where a linear risk-weighting function is considered.

PeerJ, Jul 21, 2020

Background. Neisseria meningitidis remains the main cause of sporadic meningitis and sepsis in mi... more Background. Neisseria meningitidis remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged N. meningitidis isolates from these units and other units in proximity. Methods. Strains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global N. meningitidis collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test. Results. Genome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero R or Trumenba R , and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel sequence types extending beyond individual camps were found from epidemiological data of 25 other isolates. Our results add to the sparse published molecular data of N. meningitidis How to cite this article Le TT, Tran TX, Trieu LP, Austin CM, Nguyen HM, Quyen DV. 2020. Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam. PeerJ 8:e9502 http://doi.org/10.7717/peerj.9502 in the military units in Vietnam, highlight their diversity, distinct genetic features and antibiotic resistance pattern, and emphasize the need for further studies on the molecular characteristics of N. meningitidis in Vietnam.

arXiv (Cornell University), Jul 21, 2015

Solar RRL, Jun 23, 2017

The article demonstrates the fabrication of a-Si:H thin films in a N 2-filled glove box via atmos... more The article demonstrates the fabrication of a-Si:H thin films in a N 2-filled glove box via atmospheric pressure chemical vapor deposition (APCVD) using a vaporized silicon hydride polymer/silicon nanoparticle composite ink prepared from trisilane (Si 3 H 8). It is shown via Raman spectroscopy that the films exhibit good short and mid-range atomic order. Fourier transform infrared spectroscopy reveals a fairly compact microstructure and a hydrogen concentration of 13-18 at.%. Photothermal deflection spectroscopy demonstrates a sub band gap absorption only a factor of $6 higher than that of solar-grade plasma-enhanced CVD (PECVD) material. As a demonstration of the utility of our ink, c-Si wafer surface passivation layers are deposited resulting in effective minority charge carrier lifetimes exceeding 400 ms. These lifetimes constitute the as of yet the highest reported values achieved using liquid precursors for bifacial coating without subsequent hydrogen radical treatment. The high electronic quality of the layers is shown via the fabrication of a n-i-p thin-film solar cell with an APCVD intrinsic absorber layer exhibiting an efficiency of 3.4% and hence, placing its photovoltaic performance among the highest reported for cells processed from the liquid phase and without a back reflector.

Infection and Drug Resistance

Despite strict surveillance, Neisseria meningitidis still causes life-threatening invasive mening... more Despite strict surveillance, Neisseria meningitidis still causes life-threatening invasive meningococcal disease (IMD). The study aimed to describe the prevalence, clinical and subclinical features, and treatment outcomes of IMD among young soldiers of the Vietnam People's Army. Methods: A prospective, population-based surveillance study was conducted in all Vietnamese military hospitals from January 2014 to June 2021. The presence of Neisseria meningitidis was confirmed by PCR or culture from blood or/and CSF. Epidemiological indices (incidence, serogroups, and distribution of cases by length of service), medical history, clinical and subclinical features, and treatment outcomes were documented and analyzed. Results: There were 69 IMD cases (91% serogroup B) documented, mainly in conscripts (91%). The highest annual incidence was 3.33/100,000 soldiers per year. Of these cases, 44% were meningitis (n=30), 19% septicemia (n=13), and 38% meningococcemia (n=26). The most common clinical symptoms were neck stiffness (61 cases, 88%), petechial rash (51%), and shock (20 cases, 29%). Laboratory findings showed leukocytosis in 96% of IMD cases, PCT >0.05 (ng/mL) in 100%, elevated leukocyte count (>1,000/mm3) in 71%, and high protein >1 g/L in 70%. The overall mortality rate was 9%. Two cases were found to be resistant to ceftriaxone. Prognostic factors of severity included petechial rash (OR = 9.82, p < 0.001), septicemia (OR = 5.83, p < 0.001), meningococcemia (OR = 6.22, p < 0.001), low platelet count, prolonged prothrombin time; high PCT (AUC = 0.84, p < 0.001), and increased creatinine (AUC = 0.86, p < 0.001). Conclusion: IMD remains a health threat in the armed forces in Vietnam, especially among new recruits. To the best of our knowledge, this is the first study in Vietnam describing ceftriaxone resistance in Neisseria meningitidis and suggests the need to reconsider standard empiric therapy for IMD.

PLOS ONE, 2020

Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low-and middle... more Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low-and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017-2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2-3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7-22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.

SIAM Journal on Optimization, 2016

Lecture Notes in Computer Science, 2013

We present a quadratic outer approximation scheme for solving general convex integer programs, wh... more We present a quadratic outer approximation scheme for solving general convex integer programs, where suitable quadratic approximations are used to underestimate the objective function instead of classical linear approximations. As a resulting surrogate problem we consider the problem of minimizing a function given as the maximum of finitely many convex quadratic functions having the same Hessian matrix. A fast algorithm for minimizing such functions over integer variables is presented. Our algorithm is based on a fast branch-and-bound approach for convex quadratic integer programming proposed by Buchheim, Caprara and Lodi [5]. The main feature of the latter approach consists in a fast incremental computation of continuous global minima, which are used as lower bounds. We generalize this idea to the case of k convex quadratic functions, implicitly reducing the problem to 2 k − 1 convex quadratic integer programs. Each node of the branch-and-bound algorithm can be processed in O(2 k n) time. Experimental results for a class of convex integer problems with exponential objective functions are presented. Compared with Bonmin's outer approximation algorithm BOA and branch-and-bound algorithm B-BB, running times for both ternary and unbounded instances turn out to be very competitive.

Lecture Notes in Computer Science, 2014

We present a fast branch-and-bound algorithm for solving convex quadratic integer programs with f... more We present a fast branch-and-bound algorithm for solving convex quadratic integer programs with few linear constraints. In each node, we solve the dual problem of the continuous relaxation using an infeasible active set method proposed by Kunisch and Rendl [11] to get a lower bound; this active set algorithm is well suited for reoptimization. Our algorithm generalizes a branch-and-bound approach for unconstrained convex quadratic integer programming proposed by Buchheim, Caprara and Lodi [5] to the presence of linear constraints. The main feature of the latter approach consists in a sophisticated preprocessing phase, leading to a fast enumeration of the branch-and-bound nodes. Experimental results for randomly generated instances are presented. The new approach significantly outperforms the MIQP solver of CPLEX 12.4 for instances with a small number of constraints.

Springer eBooks, 2014

Journal of Global Optimization, 2017