Genomic data mining for the computational prediction of small non-coding RNA genes

The objective of this research is to develop a novel computational prediction algorithm for non-coding RNA (ncRNA) genes using features computable for any genomic sequence without the need for comparative analysis. Existing comparative-based methods require the knowledge of closely related organisms in order to search for sequence and structural similarities. This approach imposes constraints on the type of ncRNAs, the organism, and the regions where the ncRNAs can be found. We have developed a novel approach for ncRNA gene prediction without the limitations of current comparative-based methods. Our work has established a ncRNA database required for subsequent feature and genomic analysis. Furthermore, we have identified significant features from folding-, structural-, and ensemble-based statistics for use in ncRNA prediction. We have also examined higher-order gene structures, namely operons, to discover potential insights into how ncRNAs are transcribed. Being able to automatically identify ncRNAs on a genome-wide scale is immensely powerful for incorporating it into a pipeline for large-scale genome annotation. This work will contribute to a more comprehensive annotation of ncRNA genes in microbial genomes to meet the demands of functional and regulatory genomic studies.Ph.D.Committee Chair: Dr. G. Tong Zhou; Committee Member: Dr. Arthur Koblasz; Committee Member: Dr. Eberhard Voit; Committee Member: Dr. Xiaoli Ma; Committee Member: Dr. Ying X

Effects of different fibre sources in pig diets on growth performance, gas emissions and slurry characteristics

The effects of different fibre sources in pig diets on growth performance, ammonia (NH3), hydrogen sulphide (H2S), greenhouse gas (GHG) emissions and slurry characteristics was studied on 20 crossbred pigs [Duroc x F1 (Landrace x Yorkshire)]. The experimental diets included one low-fibre (LF) diet without maize distiller’s dried grains with solubles (DDGS), brewer’s grain (BG) and coconut cake (CC) and 3 high-fibre (HF) diets with maize DDGS or BG or CC. The experiment was conducted according to a completely randomized design with 5 replications and lasted 62 days. In the growing period and the overall, pigs fed diets LF and HF-DDGS had higher average daily gain (ADG) compared to pigs fed diets HF-BG and HF-CC (P 0.05), while N and P excretions (g/head/day) were greater for diet HF-CC than for diet LF (P < 0.05). The CO2 emission was greater for diets HF-BG and HF-CC than for diets LF and HF-DDGS (P 0.05). In both periods, CH4 emission was lower in diet LF than in diet HF-BG and HF-CC (P < 0.05), while NH3 emission was higher for pigs fed diet LF than pigs fed HF-BG and HF-CC (P < 0.05). The H2 S emission was not affected by diets in both periods. In conclusion, different fibre sources in pig diets may be a practical method to alter growth performance, slurry characteristics and NH3, GHG emissions

Heat Stress Affects Seed Set and Grain Quality of Vietnamese Rice Cultivars during Heading and Grain Filling Period

Environmental stress trigger a variety of rice plant response, ranging from alters seed set, grain yield and grain quality during flowering and grain filling stage.&nbsp; Efforts are required to improve our understanding of the impact of heat stress on rice production, which are essential strategies in rice cultivation. This article investigated the seed set, yield components and grain yield of Vietnamese rice cultivars (Indica germplasm) under high temperature environment during the flowering and grain filling stage. Six rice cultivars, including popular cultivars and new cultivars of Cuu Long Delta Rice Research Institute, and one popular extraneous cultivar with differences in maturing time, were grown in pots at high temperature (HT) and natural temperature condition as control (CT). All rice cultivars were subjected to the high temperature starting from the heading stage to the harvest maturity, applied by greenhouse effect. The greenhouse has about 25 cm window opening on 3 sides for air ventilation. The seed set rate of the heat-sensitive rice genotypes decreased significantly under HT, leading to a significant reduction in grain yield. The lowest seed set was recorded in “OM4900” (44.3%) and “OM18” (39.9%) under high temperature environment. The lower yield in all rice cultivars at an elevated temperature resulted in a dramatic decrease of filled grains and contributed to a loss of 1000-grain weight. ‘“OM892” is a potential rice cultivar for heat tolerant breeding program due to the seed set percentage was above 80% in both HT and CT conditions. High temperature during the grain filling stage resulted in a decreased amylose and increased chalkiness for all OM cultivars

1M parameters are enough? A lightweight CNN-based model for medical image segmentation

Convolutional neural networks (CNNs) and Transformer-based models are being widely applied in medical image segmentation thanks to their ability to extract high-level features and capture important aspects of the image. However, there is often a trade-off between the need for high accuracy and the desire for low computational cost. A model with higher parameters can theoretically achieve better performance but also result in more computational complexity and higher memory usage, and thus is not practical to implement. In this paper, we look for a lightweight U-Net-based model which can remain the same or even achieve better performance, namely U-Lite. We design U-Lite based on the principle of Depthwise Separable Convolution so that the model can both leverage the strength of CNNs and reduce a remarkable number of computing parameters. Specifically, we propose Axial Depthwise Convolutions with kernels 7x7 in both the encoder and decoder to enlarge the model receptive field. To further improve the performance, we use several Axial Dilated Depthwise Convolutions with filters 3x3 for the bottleneck as one of our branches. Overall, U-Lite contains only 878K parameters, 35 times less than the traditional U-Net, and much more times less than other modern Transformer-based models. The proposed model cuts down a large amount of computational complexity while attaining an impressive performance on medical segmentation tasks compared to other state-of-the-art architectures. The code will be available at: https://github.com/duong-db/U-Lite.Comment: 6 pages, 7 figure

CDIO-based teaching at universities: A case study for students majoring in electrical and electronic engineering technology, Vietnam

In the 1980s of the twentieth century, universities in developed countries began to realize the growing gap between the capabilities of new graduate engineers and the actual requirements of engineering branches. The strong progress of technology requires engineers to have the intellectual abilities and necessary job-specific skills to master that progress. This paper focuses on Conceive, Design, Implement and Operate (CDIO) approach-based teaching for students majoring in electrical and electronic engineering technology at engineering universities in Vietnam to demonstrate the feasibility of the teaching model. The experimental method of synthesizing qualitative and quantitative results for 90 students in control and experimental classes was used. The experimental and control classes both had 45 students. SPSS software version&nbsp;22 was used to gather data and evaluate the learning results of the two experimental and control groups. According to the findings of the T-test analysis of the independent variables for the two groups, the experimental class performed better in academics and had students in the experimental group who were more satisfied with their post-test scores. This result contributes to confirm that the use of the CDIO-based teaching model in Vietnam is effective for students majoring in electrical and electronic engineering technology

VIETNAMESE STUDENT RESEARCHERS’ EXPECTATIONS OF THEIR SUPERVISOR AND SUPERVISION PROCESS

In Vietnam, scientific research is no longer just the work of scientists, graduate students, scholars, or lecturers; tertiary students are also encouraged to conduct scientific research. Therefore, the scientific research work of students receives more attention from educators. The research on carrying out scientific research of students is also therefore increasing. However, researchers do not seem to have paid enough attention to the role of supervisors during the supervision process. The evidence is that there are few studies on supervisors in Vietnam. Therefore, this study was conducted to learn about the role of supervisors from the student's perspective and expectations. Specifically, this study was conducted quantitatively with the use of a questionnaire consisting of 49 questions with a 5-point Likert scale. A total of 100 English-major students at a university in Southwest Vietnam participated in this study by answering the questionnaire. The results from the questionnaire show that students had high expectations from their supervisors. Specifically, students expect their supervisor to be someone who respects their opinions, has good scientific research knowledge, can give constructive comments, and is always willing to help them when needed. Based on research findings, supervisors are encouraged to participate in professional development training related to scientific research to improve their research knowledge and skills. Along with that, supervisors need to be aware of their role during the process of guiding students to do scientific research.  Article visualizations

Isolation an agar degradation Bacillus sp. AT6 and preliminary application for seaweed saccharification

Background: Agar is a common polysaccharide found in nature. However, agar is strongly resisted to the degradation processing, leading to limitation of its application in various areas. Thus, finding an effective solution for agar saccharification significantly improves the economically effects of agar based substrates.Methods: Soil samples were collected from TienPhong Forestry Ltd. Company, ThuyXuan District, ThuaThien Hue province, Vietnam. Potential agar degrading bacteria were screened on a mineral salt agar medium. The isolate was identified based on 16S rRNA nucleotide sequence, morphological, physiological, and biochemical characteristics. Agarase production was evaluated by modification culture conditions including incubation time, shaking speed, and initial inoculum size. Molecular mass of extracellular agarase was determined by native SDS-PAGE. The effect of pH, temperature, metal ions, and organic solvents were conducted for enzyme characterization. Application of enzyme was investigated on seaweed saccharification.Result: An agar degrading bacterial strain was isolated from soils and identified as Bacillus sp. AT6. Maximal agarase accumulation obtained in the culture containing an inoculum size of 10% (v/v), shaking speed of 210 rpm, and 96 hours incubation. The agarase revealed a single band on zymogram analysis with an apparent molecular weight of 180 kDa. The optimal temperature and pH were 40°C and pH 8.0, respectively. All tested metal ions and organic solvents partially decreased enzyme activity. Treatment seaweed by agarase resulted in reducing sugars release present in the reaction, indicating the saccharification of seaweed was succeeded.Conclusion: Bacillus sp. AT6 is a new report of agarolytic bacteria that produces extracellular agarase enzymes. The present results promise strain AT6 is a great candidate for agar saccharification for industrial application

Factors Affecting Successful Quality Assurance Implementation in Vietnamese Higher Education: A Qualitative Study

Quality assurance and accreditation was officially introduced into the higher education system in Vietnam over ten years ago. It is evident that quality assurance has resulted in positive impacts on university management, teaching, learning and research activities. This paper aims to explore factors that aid the successful implementation of higher education quality assurance and accreditation in Vietnam. Through semi-structured interviews with 32 participants, this study identified a number of factors that contributed to quality assurance processes, including awareness of the importance of quality assurance, better institutional manager leadership, support of university lecturers, staff, and students, and the vital responsibility of internal quality assurance staff. These confirm that internal stakeholders play an important role in undertaking quality assurance programmes and activities

DETERMINATION THE PRIORITY OF FACTORS INFLUENCING OVERSEAS INVESTMENT DESTINATIONS OF BUSINESSES USING AN ANALYTIC HIERARCHY PROCESS METHOD

Because of the great benefits overseas investment brings, countries and businesses are increasingly concerned with the question of an ideal investment destination. Many studies have shown that, factors of the consumption market, the infrastructure and resources, economic and political environment have a significant impact on the decision to choose an investment location, however the priority order of these factors are different for various research spaces. By studying the specific case of Viettel Group - one of the largest telecommunications groups in Vietnam that is having many international investment activities in recent years, the study has been verified the priority order of factors influencing the decision to choose an overseas investment location of this corporation. The research outcomes show that the group of factors that have the most influence on investment decisions is the group "Consumption market", more specifically, the sub-factor "Market Size" is considered more than the others.    Keywords: Investment Destinations, Foreign Investment Decision, Analytic Hierarchy Process