Biomedical subjects

Cheng-Hong Yang

Publications and source records attributed to Cheng-Hong Yang.

6 recordsLinked to original sources

PubMed2006

V-MitoSNP: visualization of human mitochondrial SNPs.

BACKGROUND: Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs) is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved. DESCRIPTION: V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1) color-coded visual input by selecting genes of interest on the genome graph, (2) keyword search by locus, disease and mtSNP rs# ID, (3) visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4) sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs) flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP. CONCLUSION: V-MitoSNP is a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies.

Base Sequence↗

PubMed2006

Fuzzy support vector machines for adaptive Morse code recognition.

Morse code is now being harnessed for use in rehabilitation applications of augmentative-alternative communication and assistive technology, facilitating mobility, environmental control and adapted worksite access. In this paper, Morse code is selected as a communication adaptive device for persons who suffer from muscle atrophy, cerebral palsy or other severe handicaps. A stable typing rate is strictly required for Morse code to be effective as a communication tool. Therefore, an adaptive automatic recognition method with a high recognition rate is needed. The proposed system uses both fuzzy support vector machines and the variable-degree variable-step-size least-mean-square algorithm to achieve these objectives. We apply fuzzy memberships to each point, and provide different contributions to the decision learning function for support vector machines. Statistical analyses demonstrated that the proposed method elicited a higher recognition rate than other algorithms in the literature.

Algorithms↗

PubMed2006

SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

BACKGROUND: The restriction fragment length polymorphism (RFLP) is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs). Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. RESULTS: Three user-friendly inputs are included: 1) NCBI dbSNP "rs" or "ss" IDs; 2) NCBI Entrez gene ID and HUGO gene name; 3) any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes. CONCLUSION: This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at http://bio.kuas.edu.tw/snp-rflp/.

Animals↗

PubMed2006

Development of an enhanced leg muscle rehabilitation system.

This paper aims to develop an enhanced rehabilitation and assessment system for people with impaired leg muscles, and for people who need to improve their leg muscle function. Through interactive design and real time evaluation, medical staff can totally control the training situation for patients and therefore provide a better training program, so that overall a better treatment performance can be achieved. The system consists of four major parts. Sensory and signal conversion circuits convert the lever arm lengths and muscle strengths of the leg into a proper electronic signal and then deliver this to the computer. Then, the intelligent and interactive interface design lets a trainee complete the training process independently without the involvement of medical staff. In addition, the trainee can see the training results at the end of the training process on the computer screen. The training protection and evaluation mechanism effectively monitors the training situation, based on the individual status settings by the medical staff, and thus any further impairment can be avoided. The database management system is developed to store related personal data, system settings and training results, which can then be retrieved for control and assessment. In comparison to similar equipment the proposed system demonstrates a much better performance, particularly in system functions, accuracy, operation and costs.

Equipment Design↗

PubMed2004

Counter-propagation network with variable degree variable step size LMS for single switch typing recognition.

Morse code is now being harnessed for use in rehabilitation applications of augmentative-alternative communication and assistive technology, including mobility, environmental control and adapted worksite access. In this paper, Morse code is selected as a communication adaptive device for disabled persons who suffer from muscle atrophy, cerebral palsy or other severe handicaps. A stable typing rate is strictly required for Morse code to be effective as a communication tool. This restriction is a major hindrance. Therefore, a switch adaptive automatic recognition method with a high recognition rate is needed. The proposed system combines counter-propagation networks with a variable degree variable step size LMS algorithm. It is divided into five stages: space recognition, tone recognition, learning process, adaptive processing, and character recognition. Statistical analyses demonstrated that the proposed method elicited a better recognition rate in comparison to alternative methods in the literature.

Adult↗

PubMed2003

Morse code application for wireless environmental control systems for severely disabled individuals.

Some physically-disabled people with neuromuscular diseases such as amyotrophic lateral sclerosis, multiple sclerosis, muscular dystrophy, or other conditions that hinder their ability to write, type, and speak, require an assistive tool for purposes of augmentative and alternative communication in their daily lives. In this paper, we designed and implemented a wireless environmental control system using Morse code as an adapted access communication tool. The proposed system includes four parts: input-control module; recognition module; wireless-control module; and electronic-equipment-control module. The signals are transmitted using adopted radio frequencies, which permits long distance transmission without space limitation. Experimental results revealed that three participants with physical handicaps were able to gain access to electronic facilities after two months' practice with the new system.

Activities of Daily Living↗