. In vitro propagation of the new orchid Dendrobium trankimianum T. Yukawa

Dendrobium trankimianum T. Yukawa is a beautiful, endemic orchid of Vietnam, a new species with a first - published description in 2004. It is very rare and expected to be added to the IUCN Red List status - CR. In vitro studies of orchid D. trankimianum T. Yukawa were conducted in order to conserve and increase the genetic pool of this precious wild orchid species. The results showed that full-strength MS medium supplemented with 2.0 mg/L BA and 0.5 mg/L NAA (10.24 PLBs/explant; 90.11% explants formed PLBs) or full-strength MS medium supplemented with 1.5 mg/L TDZ and 0.5 mg/L NAA (14.11 PLBs/explant; 92.06% explants formed PLBs) were the most suitable for protocorm formation. For subculture, suitable growth of shoots were obtained on full-strength MS medium supplemented 1.5 mg/L BA (22.35 shoots/explant; shoots length of 1.96 cm) and full-strength MS medium supplemented with 60 g ripe banana per liter (25.11 shoots/explant; shoots length of 2.12 cm). The shoots in vitro were transferred to half-strength MS supplemented with different concentrations of IAA, IBA and NAA to investigate root formation. The best rooting occurred at 0,5 mg/L NAA (7.91 roots/shoot; root length of 4.01 cm; 98.51% root formation). The plantlets with uniform growth were planted on different substrate: Eco clean soil, Coconut fiber, Fern fiber, 50% Rice husk in combination with 50% Eco clean soil for research the most suitable substrate. After 60 days of transplantion and acclimatization, the result showed that Fern fiber was suitable substrate for plantlet growth in a nursery garden (8.0 roots/ explant; root length of 5.5 cm; survival rate of 93.29%)

Recommender Systems with Generative Retrieval

Modern recommender systems perform large-scale retrieval by first embedding queries and item candidates in the same unified space, followed by approximate nearest neighbor search to select top candidates given a query embedding. In this paper, we propose a novel generative retrieval approach, where the retrieval model autoregressively decodes the identifiers of the target candidates. To that end, we create semantically meaningful tuple of codewords to serve as a Semantic ID for each item. Given Semantic IDs for items in a user session, a Transformer-based sequence-to-sequence model is trained to predict the Semantic ID of the next item that the user will interact with. To the best of our knowledge, this is the first Semantic ID-based generative model for recommendation tasks. We show that recommender systems trained with the proposed paradigm significantly outperform the current SOTA models on various datasets. In addition, we show that incorporating Semantic IDs into the sequence-to-sequence model enhances its ability to generalize, as evidenced by the improved retrieval performance observed for items with no prior interaction history.Comment: Preprint versio

Cadherin clusters stabilized by a combination of specific and nonspecific cis-interactions

We demonstrate a combined experimental and computational approach for the quantitative characterization of lateral interactions between membrane-associated proteins. In particular, weak, lateral (cis) interactions between E-cadherin extracellular domains tethered to supported lipid bilayers, were studied using a combination of dynamic single-molecule F&ouml;rster Resonance Energy Transfer (FRET) and kinetic Monte Carlo (kMC) simulations. Cadherins are intercellular adhesion proteins that assemble into clusters at cell-cell contacts through cis- and trans- (adhesive) interactions. A detailed and quantitative understanding of cis-clustering has been hindered by a lack of experimental approaches capable of detecting and quantifying lateral interactions between proteins on membranes. Here single-molecule intermolecular FRET measurements of wild-type E-cadherin and cis-interaction mutants combined with simulations demonstrate that both nonspecific and specific cis-interactions contribute to lateral clustering on lipid bilayers. Moreover, the intermolecular binding and dissociation rate constants are quantitatively and independently determined, demonstrating an approach that is generalizable for other interacting proteins. </div

Effectiveness and safety of in vitro maturation of oocytes versus in vitro fertilisation in women with high antral follicle count : Study protocol for a randomised controlled trial

This work was supported by Ferring grant number 000323 and sponsored by My Duc Hospital.Peer reviewedPublisher PD

Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study

Background Meta-analysis of patients with isoniazid-resistant tuberculosis given standard first-line anti-tuberculosis treatment indicated an increased risk of multi-drug resistant tuberculosis (MDR-TB) emerging (8%), compared to drug-sensitive tuberculosis (0.3%). Here we use whole genome sequencing (WGS) to investigate whether treatment of patients with pre-existing isoniazid resistant disease with first-line anti-tuberculosis therapy risks selecting for rifampicin resistance, and hence MDR-TB. Methods Patients with isoniazid-resistant pulmonary TB were recruited and followed up for 24 months. Drug-susceptibility testing was performed by Microscopic observation drug-susceptibility assay (MODS), Mycobacterial Growth Indicator Tube (MGIT) and by WGS on isolates at first presentation and in the case of re-presentation. Where MDR-TB was diagnosed, WGS was used to determine the genomic relatedness between initial and subsequent isolates. De novo emergence of MDR-TB was assumed where the genomic distance was five or fewer single nucleotide polymorphisms (SNPs) whereas reinfection with a different MDR-TB strain was assumed where the distance was 10 or more SNPs. Results 239 patients with isoniazid-resistant pulmonary tuberculosis were recruited. Fourteen (14/239, 5.9%) patients were diagnosed with a second episode of tuberculosis that was multi-drug resistant. Six (6/239, 2.5%) were identified as having evolved MDR-TB de novo and six as having been re-infected with a different strain. In two cases the genomic distance was between 5-10 SNPs and therefore indeterminate. Conclusions In isoniazid-resistant TB, de novo emergence and reinfection of MDR-TB strains equally contributed to MDR development. Early diagnosis and optimal treatment of isoniazid resistant TB are urgently needed to avert the de novo emergence of MDR-TB during treatment

A real-time RT-PCR for detection of clade 1 and 2 H5N1 Influenza A virus using Locked Nucleic Acid (LNA) TaqMan probes

<p>Abstract</p> <p>Background</p> <p>The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants.</p> <p>Results</p> <p>We developed a single real-time RT-PCR assay for detection of both clades of H5N1 viruses, directly from clinical specimens, using locked nucleic acid TaqMan probes. Primers and probe used in this assay were designed based on a highly conserved region in the <it>HA </it>gene of H5N1 viruses. The analytical sensitivity of the assay was < 0.5 PFU and 10 - 100 ssDNA plasmid copies. A total of 106 clinical samples (58 from patients infected with clade 1, 2.1 or 2.3 H5N1 viruses and 48 from uninfected or seasonal influenza A virus-infected individuals) were tested by the assay. The assay showed 97% concordance with initial diagnostics for H5 influenza virus infection with a specificity of 100%.</p> <p>Conclusions</p> <p>This assay is a useful tool for diagnosis of H5N1 virus infections in regions where different genetic clades are co-circulating.</p

FTKHUIM: A fast and efficient method for mining top-k high-utility itemsets

High-utility itemset mining (HUIM) is an important task in the field of knowledge data discovery. The large search space and huge number of HUIs are the consequences of applying HUIM algorithms with an inappropriate user-defined minimum utility threshold value. Determining a suitable threshold value to obtain the expected results is not a simple task and requires spending a lot of time. For common users, it is difficult to define a minimum threshold utility for exploring the right number of HUIs. On the one hand, if the threshold is set too high then the number of HUIs would not be enough. On the other hand, if the threshold is set too low, too many HUIs will be mined, thus wasting both time and memory. The top-k HUIs mining problem was proposed to solve this issue, and many effective algorithms have since been introduced by researchers. In this research, a novel approach, namely FTKHUIM (Fast top k HUI Mining), is introduced to explore the top-k HUIs. One new threshold-raising strategy called RTU, a transaction utility (TU)-based threshold-raising strategy, has also been shown to rapidly increase the speed of top-k HUIM. The study also proposes a global structure to store utility values in the process of applying raising-threshold strategies to optimize these strategies. The results of experiments on various datasets prove that the FTKHUIM algorithm achieves better results with regard to both the time and search space needed.Web of Science1110480510478

The Sudden Dominance of blaCTX–M Harbouring Plasmids in Shigella spp. Circulating in Southern Vietnam

Shigellosis is a disease caused by bacteria belonging to Shigella spp. and is a leading cause of bacterial gastrointestinal infections in infants in unindustrialized countries. The Shigellae are dynamic and capable of rapid change when placed under selective pressure in a human population. Extended spectrum beta lactamases (ESBLs) are enzymes capable of degrading cephalosporins (a group of antimicrobial agents) and the genes that encode them are common in pathogenic E. coli and other related organisms in industrialized countries. In southern Vietnam, we have isolated multiple cephalosporin-resistant Shigella that express ESBLs. Furthermore, over two years these strains have replaced strains isolated from patients with shigellosis that cannot express ESBLs. Our work describes the genes responsible for this characteristic and we investigate one of the elements carrying one of these genes. These finding have implications for treatment of shigellosis and support the growing necessity for vaccine development. Our findings also may be pertinent for other countries undergoing a similar economic transition to Vietnam's and the corresponding effect on bacterial populations

A Multi-Center Randomized Trial to Assess the Efficacy of Gatifloxacin versus Ciprofloxacin for the Treatment of Shigellosis in Vietnamese Children

The bacterial genus Shigella is the most common cause of dysentery (diarrhea containing blood and/or mucus) and the disease is common in developing countries with limitations in sanitation. Children are most at risk of infection and frequently require hospitalization and antimicrobial therapy. The WHO currently recommends the fluoroquinolone, ciprofloxacin, for the treatment of childhood Shigella infections. In recent years there has been a sharp increase in the number of organisms that exhibit resistance to nalidixic acid (an antimicrobial related to ciprofloxacin), corresponding with reduced susceptibility to ciprofloxacin. We hypothesized that infections with Shigella strains that demonstrate resistance to nalidixic acid may prevent effective treatment with ciprofloxacin. We performed a randomized controlled trial to compare 3 day ciprofloxacin therapy with 3 days of gatifloxacin, a newer generation fluoroquinolone with greater activity than ciprofloxacin. We measured treatment failure and time to the cessation of individual disease symptoms in 249 children with dysentery treated with gatifloxacin and 245 treated with ciprofloxacin. We could identify no significant differences in treatment failure between the two groups or in time to the cessation of individual symptoms. We conclude that, in Vietnam, ciprofloxacin and gatifloxacin are similarly effective for the treatment of acute dysentery

A randomised controlled trial of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDITOF-MS) versus conventional microbiological methods for identifying pathogens: Impact on optimal antimicrobial therapy of invasive bacterial and fungal infections in Vietnam.

OBJECTIVES: We assessed the impact of MALDITOF-MS on the timeliness of optimal antimicrobial therapy through a parallel-arm randomised controlled trial in two hospitals in Vietnam. METHODS: We recruited patients with a pathogen (bacterial or fungal) cultured from a normally sterile sample. Samples were randomly assigned (1:1) to identification by MALDITOF-MS or conventional diagnostics. The primary outcome was the proportion on optimal antimicrobial therapy within 24 h of positive culture, determined by a blinded independent review committee. Trial registered at ClinicalTrials.gov (NCT02306330). RESULTS: Among 1005 randomised patients, pathogens were isolated from 628 (326 intervention, 302 control), with 377 excluded as likely contaminants or discharged/died before positive culture. Most isolates were cultured from blood (421/628, 67.0%). The proportion receiving optimal antimicrobial therapy within 24 h (the primary outcome) or 48 h of growth was not significantly different between MALDITOF-MS and control arms (135/326, 41.4% vs 120/302, 39.7%; Adjusted Odds ration (AOR) 1.17, p = 0.40 and 151/326, 46.3% vs 141/302, 46.7%; AOR 1.05 p = 0.79, respectively). CONCLUSIONS: MALDITOF-MS, in the absence of an antimicrobial stewardship programme, did not improve the proportion on optimal antimicrobial therapy at 24 or 48 h after first growth in a lower-middle income setting with high rates of antibiotic resistance