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"Nguyen, Hoang"
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Business process crowdsourcing : concept, ontology and decision support
This book conceptualises and develops crowdsourcing as an organisational business process. It argues that although for many organisations crowdsourcing still implies an immature one-off endeavour, when developed to a more repeatable business process it can harness innovation and agility. The book offers a process model to guide organisations towards the establishment of business process crowdsourcing (BPC), and empirically showcases and evaluates the model using two current major crowdsourcing projects. In order to consolidate the domain knowledge, the BPC model is turned into a heavyweight ontology capturing the concepts, hierarchical relationships and decision-making relationships necessary to establish crowdsourcing as a business process in an organisation. Lastly, based on the ontology it presents a decision tool that provides advice on making informed decisions about the performance of business process crowdsourcing activities.
Book
Dichotomous engagement of HDAC3 activity governs inflammatory responses
The histone deacetylases (HDACs) are a superfamily of chromatin-modifying enzymes that silence transcription through the modification of histones. Among them, HDAC3 is unique in that interaction with nuclear receptor corepressors 1 and 2 (NCoR1/2) is required to engage its catalytic activity
1
–
3
. However, global loss of HDAC3 also results in the repression of transcription, the mechanism of which is currently unclear
4
–
8
. Here we report that, during the activation of macrophages by lipopolysaccharides, HDAC3 is recruited to activating transcription factor 2 (ATF2)-bound sites without NCoR1/2 and activates the expression of inflammatory genes through a non-canonical mechanism. By contrast, the deacetylase activity of HDAC3 is selectively engaged at ATF3-bound sites that suppress Toll-like receptor signalling. Loss of HDAC3 in macrophages safeguards mice from lethal exposure to lipopolysaccharides, but this protection is not conferred upon genetic or pharmacological abolition of the catalytic activity of HDAC3. Our findings show that HDAC3 is a dichotomous transcriptional activator and repressor, with a non-canonical deacetylase-independent function that is vital for the innate immune system.
During the activation of mouse macrophages by lipopolysaccharides, histone deacetylase 3 controls inflammatory responses by both repressing and activating gene transcription depending on its differential association with transcription factors.
Journal Article
Synthesis of Silica-Coated Magnetic Nanoparticles and Application in the Detection of Pathogenic Viruses
Magnetic Fe3O4 nanoparticles were prepared by coprecipitation and then coated with silica. These Fe3O4/SiO2 nanoparticles consisted of a 10–15 nm magnetic core and a silica shell of 2–5 nm thickness. The superparamagnetic property of the Fe3O4/SiO2 particles with the magnetization of 42.5 emu/g was confirmed by vibrating sample magnetometer (VSM). We further optimized buffers with these Fe3O4/SiO2 nanoparticles to isolate genomic DNA of hepatitis virus type B (HBV) and of Epstein-Barr virus (EBV) for detection of the viruses based on polymerase chain reaction (PCR) amplification of a 434 bp fragment of S gene specific for HBV and 250 bp fragment of nuclear antigen encoding gene specific for EBV. The purification efficiency of DNA of both HBV and EBV using obtained Fe3O4/SiO2 nanoparticles was superior to that obtained with commercialized Fe3O4/SiO2 microparticles, as indicated by (i) brighter PCR-amplified bands for both HBV and EBV and (ii) higher sensitivity in PCR-based detection of EBV load (copies/mL). The time required for DNA isolation using Fe3O4/SiO2 nanoparticles was significantly reduced as the particles were attracted to magnets more quickly (15–20 s) than the commercialized microparticles (2-3 min).
Journal Article
Waste Management System Using IoT-Based Machine Learning in University
Along with the development of the Internet of Things (IoT), waste management has appeared as a serious issue. Waste management is a daily task in urban areas, which requires a large amount of labour resources and affects natural, budgetary, efficiency, and social aspects. Many approaches have been proposed to optimize waste management, such as using the nearest neighbour search, colony optimization, genetic algorithm, and particle swarm optimization methods. However, the results are still too vague and cannot be applied in real systems, such as in universities or cities. Recently, there has been a trend of combining optimal waste management strategies with low-cost IoT architectures. In this paper, we propose a novel method that vigorously and efficiently achieves waste management by predicting the probability of the waste level in trash bins. By using machine learning and graph theory, the system can optimize the collection of waste with the shortest path. This article presents an investigation case implemented at the real campus of Ton Duc Thang University (Vietnam) to evaluate the performance and practicability of the system’s implementation. We examine data transfer on the LoRa module and demonstrate the advantages of the proposed system, which is implemented through a simple circuit designed with low cost, ease of use, and replace ability. Our system saves time by finding the best route in the management of waste collection.
Journal Article
iPromoter-Seqvec: identifying promoters using bidirectional long short-term memory and sequence-embedded features
Background
Promoters, non-coding DNA sequences located at upstream regions of the transcription start site of genes/gene clusters, are essential regulatory elements for the initiation and regulation of transcriptional processes. Furthermore, identifying promoters in DNA sequences and genomes significantly contributes to discovering entire structures of genes of interest. Therefore, exploration of promoter regions is one of the most imperative topics in molecular genetics and biology. Besides experimental techniques, computational methods have been developed to predict promoters. In this study, we propose iPromoter-Seqvec – an efficient computational model to predict TATA and non-TATA promoters in human and mouse genomes using bidirectional long short-term memory neural networks in combination with sequence-embedded features extracted from input sequences. The promoter and non-promoter sequences were retrieved from the Eukaryotic Promoter database and then were refined to create four benchmark datasets.
Results
The area under the receiver operating characteristic curve (AUCROC) and the area under the precision-recall curve (AUCPR) were used as two key metrics to evaluate model performance. Results on independent test sets showed that iPromoter-Seqvec outperformed other state-of-the-art methods with AUCROC values ranging from 0.85 to 0.99 and AUCPR values ranging from 0.86 to 0.99. Models predicting TATA promoters in both species had slightly higher predictive power compared to those predicting non-TATA promoters. With a novel idea of constructing artificial non-promoter sequences based on promoter sequences, our models were able to learn highly specific characteristics discriminating promoters from non-promoters to improve predictive efficiency.
Conclusions
iPromoter-Seqvec is a stable and robust model for predicting both TATA and non-TATA promoters in human and mouse genomes. Our proposed method was also deployed as an online web server with a user-friendly interface to support research communities. Links to our source codes and web server are available at
https://github.com/mldlproject/2022-iPromoter-Seqvec
.
Journal Article
Expression of 42 kDa chitinase of Trichoderma asperellum (Ta-CHI42) from a synthetic gene in Escherichia coli
Abstract
Chitinases are enzymes that catalyze the degradation of chitin, a major component of the cell walls of pathogenic fungi and cuticles of insects, gaining increasing attention for the control of fungal pathogens and insect pests. Production of recombinant chitinase in a suitable host can result in a more pure product with less processing time and a significantly larger yield than that produced by native microorganisms. The present study aimed to express the synthetic chi42 gene (syncodChi42), which was optimized from the chi42 gene of Trichoderma asperellum SH16, in Escherichia coli to produce 42 kDa chitinase (Ta-CHI42); then determined the activity of this enzyme, characterizations and in vitro antifungal activity as well as its immunogenicity in mice. The results showed that Ta-CHI42 was overexpressed in E. coli. Analysis of the colloidal chitin hydrolytic activity of purified Ta-CHI42 on an agar plate revealed that this enzyme was in a highly active form. This is a neutral chitinase with pH stability in a range of 6–8 and has an optimum temperature of 45°C with thermal stability in a range of 25–35°C. The chitinolytic activity of Ta-CHI42 was almost completely abolished by 5 mM Zn2+ or 1% SDS, whereas it remained about haft under the effect of 1 M urea, 1% Triton X-100 or 5 mM Cu2+. Except for ions such as Mn2+ and Ca2+ at 5 mM that have enhanced chitinolytic activity; 5 mM of Na+, Fe2+ or Mg2+ ions or 1 mM EDTA negatively impacted the enzyme. Ta-CHI42 at 60 U/mL concentration strongly inhibited the growth of the pathogenic fungus Aspergillus niger. Analysis of western blot indicated that the polyclonal antibody against Ta-CHI42 was greatly produced in mice. It can be used to analyze the expression of the syncodChi42 gene in transgenic plants, through immunoblotting assays, for resistance to pathogenic fungi.
This study aims to express the synthetic chi42 gene encodes 42 kDa chitinase of T. asperellum in E. coli, determine the enzyme characterizations, antifungal activity and its immunogenesis in the mouse.
Journal Article
Hypothalamic REV-ERB nuclear receptors control diurnal food intake and leptin sensitivity in diet-induced obese mice
Obesity occurs when energy expenditure is outweighed by energy intake. Tuberal hypothalamic nuclei, including the arcuate nucleus (ARC), ventromedial nucleus (VMH), and dorsomedial nucleus (DMH), control food intake and energy expenditure. Here we report that, in contrast with females, male mice lacking circadian nuclear receptors REV-ERBα and -β in the tuberal hypothalamus (HDKO mice) gained excessive weight on an obesogenic high-fat diet due to both decreased energy expenditure and increased food intake during the light phase. Moreover, rebound food intake after fasting was markedly increased in HDKO mice. Integrative transcriptomic and cistromic analyses revealed that such disruption in feeding behavior was due to perturbed REV-ERB-dependent leptin signaling in the ARC. Indeed, in vivo leptin sensitivity was impaired in HDKO mice on an obesogenic diet in a diurnal manner. Thus, REV-ERBs play a crucial role in hypothalamic control of food intake and diurnal leptin sensitivity in diet-induced obesity.
Journal Article
Assessment of peak bone mineral density and its associated factors in Vietnamese adults: A cross-sectional study
Osteoporosis is a growing public health concern in Vietnam, yet population-specific reference data for peak bone mineral density (PBD) remain limited. This study aimed to establish a standard PBD dataset and identify factors associated with bone mineral density (BMD) in Vietnamese adults.
A cross-sectional study included 1,378 participants (410 men, 968 women) in Hue City, Vietnam. BMD was measured at the lumbar spine (LS), femoral neck (FN), and total hip (TH) using dual-energy X-ray absorptiometry (DXA). A cubic polynomial regression models were performed to identify peak bone density (PBD). Age-standardized prevalence of osteoporosis was calculated using the 2024 Vietnamese population structure.
Men exhibited higher BMD than women across all skeletal sites. The estimated age of PBD attainment was 20-29 years in men and approximately 30 years in women. Age was the strongest negative predictor of BMD, while body weight and height showed positive correlations. The age-standardized prevalence of osteoporosis was highest at the LS (33.58%), followed by the TH (12.77%) and FN (2.69%). Women showed a markedly higher prevalence than men, with a sharp increase observed after menopause.
This study provides an updated reference dataset for PBD in the Vietnamese population, notably revealing that men attain peak bone density earlier than women. Furthermore, the findings underscore the high prevalence of osteoporosis at the lumbar spine, suggesting a need for early screening strategies targeting high-risk groups.
Journal Article