Koun-Tem Sun

Genotyping of Hepatitis B Virus – Genotypes A to G by Multiplex Polymerase Chain Reaction

Objectives: Eight genotypes (A–H) of hepatitis B virus (HBV) are known with variations in nucleotide sequences greater than 8%. Several recent publications found that the clinical course and outcome of antiviral therapy depended on the genotype of the infecting HBV strain. Large epidemiological studies will require the availability of a system which is rapid, reliable and can be performed on a large number of samples. Methods: To establish a simple and accurate genotyping method, the study collected 369 HBV complete genomic sequences from the GenBank database. Type-specific primers were also designed that separated HBV genotypes A to G by multiplex polymerase chain reaction. Results: By comparison with the traditional restriction fragment length polymorphism method, over 93% of 441 samples were accurately genotyped by current assay, with a higher detection rate and sensitivity to detect mixed HBV infections. Conclusions: This methodology can be applied only to areas prevalent with HBV genotypes A to G. However, it provides an efficient alternative for clinical diagnosis and large-scale studies.

Creating IRT-Based Parallel Test Forms Using the Genetic Algorithm Method

In educational measurement, the construction of parallel test forms is often a combinatorial optimization problem that involves the time-consuming selection of items to construct tests having approximately the same test information functions (TIFs) and constraints. This article proposes a novel method, genetic algorithm (GA), to construct parallel test forms effectively. The sum of squared errors of the generated TIFs produced by GA were compared with those of the Swanson and Stocking method, and the Wang and Ackerman method. Experimental results show that tests constructed using GA yielded lower error, and an average improvement ratio above 90%.

ART2-based genetic watermarking

A genetic watermarking approach based on ART2 neural network is proposed in the paper. This approach uses an ART2 neural network to classify 8/spl times/8 DCT blocks of images in training sets. For each cluster, genetic algorithm (GA) is then performed to find out the optimal coefficients for watermark embedding. All the results are recorded in a table, called optimal position table (OPT). According to the OPT table, the coefficients for watermark embedding can be decided straightforward. Two features of the proposed approach make itself a suitable enhancement for genetic watermarking. First, it has the ability to keep and refine the results obtained from genetic watermarking. Second, the proposed method greatly increases the speed of genetic watermarking so that genetic watermarking can be used in practice. The experimental results shows that the watermarked images are perceptually equal to the originals, and that the watermarks are still detectable after low pass filtering, high pass filtering and JPEG compression.

Design of Chinese Spelling System Based on ERP

This paper presented a brain-computer Chinese Spelling System, which allow the users to spell out Chinese words via his/her brain signals. This system analyzed brain signals by ERPs to find out the subject¡¦s demand. To detect subject¡¦s demand, the flashing phonetic symbols, or Chinese words, were showed in a matrix for subject. The system would totally collected brain signals while matrix flashing, and then analyzed the collected signals by ERPs. Based on analyzed ERPs, the P300 achieved a significant difference between two events, target and non-target, in statistics. Based on the significant difference, the system could detect the subject¡¦s demands and showed the detected phonetic symbols in the monitor. When all the symbols had been selected, the system would automatically spell Chinese words. According to experiment, the accuracy of this system was up to 90 percent. The development of this system provides severe motor disabilities a tool to communicate with external environment.

Reactions of Brain in English Reading Tests

The purpose of this research is to analyze the event-related potentials (ERPs) of brain waves while engaged in reading in English. The brain wave responses of participants in choosing correct and incorrect answers on English reading tests were studied. Three English reading tests at differing levels of difficulty were used in the experiment and twelve participants (non-native English learners), six males and six females whose ages ranged from 20 to 24, voluntarily participated in the experiment. Experimental results were analyzed by independent t-tests on the EEG potentials of participants having different levels of English proficiency. A significant difference was observed at the frontal lobe under differing conditions. Subjects who chose incorrect answers on the tests elicited a higher N600, a finding similar to that of previous literature. In addition, an interesting result was found: for males, the significant area was located in the right hemisphere, whereas for females, it was in the left hemisphere. This seems to imply that males and females employ different areas of the brain to comprehend the meaning of difficult statements.

Brainwave Technology Gives Internet Access to the Physically Disabled

It is impossible for severely disabled people to browse or learn through the Internet due to the mere lack of independent control of the mouse. This paper proposes a brain computer interface (BCI) to aid severely disabled individuals, such as people disabled by amyotrophic lateral sclerosis (ALS), in browsing or learning on the Internet. By analyzing specific components of event-related potentials (ERPs), cursor control can be achieved. The cursor can be controlled by brain waves in a user-friendly manner to move or click on the web page. The major contributions of this research include: (1) designing a BCI for disabled people, (2) embedding the BCIs cursor controller into a web page, (3) conducting clinical experiments, (4) analysing the experimental results, system accuracy, and effectiveness, and (5) evaluating the systems practicability and giving suggestions for future work. There are two innovative technologies proposed in this research: (1) a specific component of ERPs located at O1, the N2P3 (the difference between the peak and trough of N200 and P300), was used to differentiate targeted from non-targeted (non-selected) signals, (2) instead of a fixed position style BCI, a movable watermark style BCI which follows the cursor was designed. The novel technique supported by a user-friendly interface helps the disabled have contact with the outside world resulting in positive emotions.

The Study of Using Sure Stream to Construct Ubiquitous Learning Environment

Over the recent years, with the rapid development of science and technology, the Internet has become a necessary part of human life and is used for communication, transmission of files and remote login, etc. However, most mobile learning platforms on the market face a common problem: the traditional multipoint communication technique is limited by the bandwidth of the network, and therefore, users cannot obtain the best learning scenery. In this study, we adopted the theory of context- aware learning and introduced novel communication techniques, and proposed a technique using Sure Stream Streaming Service, with the aim of ensuring the smoothness and stability of media communication. We, based on the characteristics of HSDPA mobile communication, established an environment for ubiquitous learning, creating good conditions for E- learning. In this study, we also tested various types of wireless communication media on the market, and generated corresponding test reports as reference materials for related researches.

Hepatocellular carcinoma-associated single-nucleotide variants and deletions identified by the use of genome-wide high-throughput analysis of hepatitis B virus

This study investigated hepatitis B virus (HBV) single‐nucleotide variants (SNVs) and deletion mutations linked with hepatocellular carcinoma (HCC). Ninety‐three HCC patients and 108 non‐HCC patients were enrolled for HBV genome‐wide next‐generation sequencing (NGS) analysis. A systematic literature review and a meta‐analysis were performed to validate NGS‐defined HCC‐associated SNVs and deletions. The experimental results identified 60 NGS‐defined HCC‐associated SNVs, including 41 novel SNVs, and their pathogenic frequencies. Each SNV was specific for either genotype B (n = 24) or genotype C (n = 34), except for nt53C, which was present in both genotypes. The pathogenic frequencies of these HCC‐associated SNVs showed a distinct U‐shaped distribution pattern. According to the meta‐analysis and literature review, 167 HBV variants from 109 publications were categorized into four levels (A–D) of supporting evidence that they are associated with HCC. The proportion of NGS‐defined HCC‐associated SNVs among these HBV variants declined significantly from 75% of 12 HCC‐associated variants by meta‐analysis (Level A) to 0% of 10 HCC‐unassociated variants by meta‐analysis (Level D) (P < 0.0001). PreS deletions were significantly associated with HCC, in terms of deletion index, for both genotypes B (P = 0.030) and C (P = 0.049). For genotype C, preS deletions involving a specific fragment (nt2977–3013) were significantly associated with HCC (HCC versus non‐HCC, 6/34 versus 0/32, P = 0.025). Meta‐analysis of preS deletions showed significant association with HCC (summary odds ratio 3.0; 95% confidence interval 2.3–3.9). Transfection of Huh7 cells showed that all of the five novel NGS‐defined HCC‐associated SNVs in the small surface region influenced hepatocarcinogenesis pathways, including endoplasmic reticulum‐stress and DNA repair systems, as shown by microarray, real‐time polymerase chain reaction and western blot analysis. Their carcinogenic mechanisms are worthy of further research. Copyright

HCC-Associated Single Nucleotide Variants and Deletions Identified Using Genome-Wide High Throughput Analysis of HBV

This study investigated hepatitis B virus (HBV) single‐nucleotide variants (SNVs) and deletion mutations linked with hepatocellular carcinoma (HCC). Ninety‐three HCC patients and 108 non‐HCC patients were enrolled for HBV genome‐wide next‐generation sequencing (NGS) analysis. A systematic literature review and a meta‐analysis were performed to validate NGS‐defined HCC‐associated SNVs and deletions. The experimental results identified 60 NGS‐defined HCC‐associated SNVs, including 41 novel SNVs, and their pathogenic frequencies. Each SNV was specific for either genotype B (n = 24) or genotype C (n = 34), except for nt53C, which was present in both genotypes. The pathogenic frequencies of these HCC‐associated SNVs showed a distinct U‐shaped distribution pattern. According to the meta‐analysis and literature review, 167 HBV variants from 109 publications were categorized into four levels (A–D) of supporting evidence that they are associated with HCC. The proportion of NGS‐defined HCC‐associated SNVs among these HBV variants declined significantly from 75% of 12 HCC‐associated variants by meta‐analysis (Level A) to 0% of 10 HCC‐unassociated variants by meta‐analysis (Level D) (P < 0.0001). PreS deletions were significantly associated with HCC, in terms of deletion index, for both genotypes B (P = 0.030) and C (P = 0.049). For genotype C, preS deletions involving a specific fragment (nt2977–3013) were significantly associated with HCC (HCC versus non‐HCC, 6/34 versus 0/32, P = 0.025). Meta‐analysis of preS deletions showed significant association with HCC (summary odds ratio 3.0; 95% confidence interval 2.3–3.9). Transfection of Huh7 cells showed that all of the five novel NGS‐defined HCC‐associated SNVs in the small surface region influenced hepatocarcinogenesis pathways, including endoplasmic reticulum‐stress and DNA repair systems, as shown by microarray, real‐time polymerase chain reaction and western blot analysis. Their carcinogenic mechanisms are worthy of further research. Copyright

Comparisons between the Hybrid Taguchi-Genetic Algorithm and Genetic Algorithm

Hybrid Taguchi genetic algorithm can be used to solve the global continuous optimization problems. Aside from the global search capability of traditional genetic algorithm, it further combines Taguchi experimental method to explore the optimal feasibility ...