Codon usage bias in UL53 gene of DEV was analyzed in this paper, the results indicated that it had strong bias towards to the synonymous codons with A or T at the third codon position. The codon usage bias of DEV UL53 gene and 26 reference herpesviruses were analyzed by EMBOSS program and RSCU. In addition, Phylogenetic tree indicated DEV was evolutionarily closer to CaHV-2, CaHV-3, MeHV-1. The ENC-GC3S plot revealed that the genetic heterogeneity in UL53 gene of herpesviruses was constrained by G+C content at the third codon position. Conclusions: The extent of codon usage bias in the DEV UL53 gene was highly correlated with the gene composition. Analysis of correspondence through the SAS statistics software showed the yeast expression system might be more suitable for the expression of DEV genes.
{"title":"Characterization of Codon Usage Bias in the Newly Identified DEV UL53 Gene","authors":"Shunchuan Zhang, A. Cheng, Mingshu Wang","doi":"10.1117/12.913536","DOIUrl":"https://doi.org/10.1117/12.913536","url":null,"abstract":"Codon usage bias in UL53 gene of DEV was analyzed in this paper, the results indicated that it had strong bias towards to the synonymous codons with A or T at the third codon position. The codon usage bias of DEV UL53 gene and 26 reference herpesviruses were analyzed by EMBOSS program and RSCU. In addition, Phylogenetic tree indicated DEV was evolutionarily closer to CaHV-2, CaHV-3, MeHV-1. The ENC-GC3S plot revealed that the genetic heterogeneity in UL53 gene of herpesviruses was constrained by G+C content at the third codon position. Conclusions: The extent of codon usage bias in the DEV UL53 gene was highly correlated with the gene composition. Analysis of correspondence through the SAS statistics software showed the yeast expression system might be more suitable for the expression of DEV genes.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"50 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2011-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84723601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5515126
W. Cai, Danjun Wang, Xiaodong Wen, Xubo Yu
An assessment of thermal environment and indoor air quality (IAQ) in a lagre art gallery, which is mechannically ventilated, is presented. Measurements of indoor environmental parameters, CO2, formaldehyde, NH3, Randon, and TVOC concentrations were performed, while the comprehensive air quality evaluation index was calculated to describe the employees's feeling of discomfort and indoor air classification. Results show that pollution levels of the exhibition hall classifed as Class II, and indoor air environment is in accordance with personal demand. It is revealed that the indoor air environment largely depents on the numbers of occupants and the indoor soureces owing to various human activities. This work can be used to help define the ideal or optimum exhibition environment.
{"title":"Indoor Air Quality Assessment in an Art Gallery with an HVAC System","authors":"W. Cai, Danjun Wang, Xiaodong Wen, Xubo Yu","doi":"10.1109/ICBBE.2010.5515126","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5515126","url":null,"abstract":"An assessment of thermal environment and indoor air quality (IAQ) in a lagre art gallery, which is mechannically ventilated, is presented. Measurements of indoor environmental parameters, CO2, formaldehyde, NH3, Randon, and TVOC concentrations were performed, while the comprehensive air quality evaluation index was calculated to describe the employees's feeling of discomfort and indoor air classification. Results show that pollution levels of the exhibition hall classifed as Class II, and indoor air environment is in accordance with personal demand. It is revealed that the indoor air environment largely depents on the numbers of occupants and the indoor soureces owing to various human activities. This work can be used to help define the ideal or optimum exhibition environment.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"46 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73810574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5516702
Chuan-sheng Zhang, Liying Geng, Jin Zhang, Wen-jin Zhu, L. Du
In this study, the SNPs located in the chicken pre-microRNAs were performed a genome-wide analysis. The result showed that pre-microRNA SNPs are negatively selected in respect to SNPs distribution between the pre-microRNA and their flanking regions. Interestingly, the seed regions show a higher SNP density than both the MIR and the other MIR regions excluding seed regions. Furthermore, the SNPs in the seed regions were found show fewer effects on the stability of the pre-microRNA secondary structure. The data suggest that there is a rapid evolution has occurred in the seed regions and these SNPs are tend to be more deleterious , being good candidates for causal phenotypic variability among chickens. These findings will improve our understanding of the functions, evolution of chicken pre-microRNAs
{"title":"Chicken Polymorphism at Pre-MicroRNAs Inferred from SNP Data","authors":"Chuan-sheng Zhang, Liying Geng, Jin Zhang, Wen-jin Zhu, L. Du","doi":"10.1109/ICBBE.2010.5516702","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5516702","url":null,"abstract":"In this study, the SNPs located in the chicken pre-microRNAs were performed a genome-wide analysis. The result showed that pre-microRNA SNPs are negatively selected in respect to SNPs distribution between the pre-microRNA and their flanking regions. Interestingly, the seed regions show a higher SNP density than both the MIR and the other MIR regions excluding seed regions. Furthermore, the SNPs in the seed regions were found show fewer effects on the stability of the pre-microRNA secondary structure. The data suggest that there is a rapid evolution has occurred in the seed regions and these SNPs are tend to be more deleterious , being good candidates for causal phenotypic variability among chickens. These findings will improve our understanding of the functions, evolution of chicken pre-microRNAs","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"26 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78807562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adding nutrient can accelerate diesel oil biodegradation in seawater. Response surface methodology (RSM) was employed to optimize the condition for increasing diesel oil degradation. Using a Plackett-Burman experimental design to aid in the first step of optimization, and nitrogen, phosphorus and pH were found to be significant factors affecting degradation process. To determine the optimal range of each significant variable, a central composite design was employed. Based on response surface and canonical analysis, the optimum concentrations of the nutrients were obtained as follows: nitrogen (NaNO3)0.143g, phosphorus (KH2PO4)0.022g, and the optimal pH was 7.4.
{"title":"Optimization of Nutrition Condition for Biodegradation of Diesel Oil Using Response Surface Methodology","authors":"Jincheng Li, Wenxiang Xia, Cheng-Yang Tang, Zhenxia Wang, X. Xiao, Hui Zhong, Jiuzhou Zhao","doi":"10.1109/ICBBE.2010.5516461","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5516461","url":null,"abstract":"Adding nutrient can accelerate diesel oil biodegradation in seawater. Response surface methodology (RSM) was employed to optimize the condition for increasing diesel oil degradation. Using a Plackett-Burman experimental design to aid in the first step of optimization, and nitrogen, phosphorus and pH were found to be significant factors affecting degradation process. To determine the optimal range of each significant variable, a central composite design was employed. Based on response surface and canonical analysis, the optimum concentrations of the nutrients were obtained as follows: nitrogen (NaNO3)0.143g, phosphorus (KH2PO4)0.022g, and the optimal pH was 7.4.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"329 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75904122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5517493
Lingfeng Zhu, R. Gao, Run‐tao Zhang, Li‐li Liu
Using conventional activated sludge of breweries as the inoculation sludge, stable aerobic granular sludge was fostered successfully in sequencing batch reactor, and applied to municipal sewage disposal. At room temperature, chemical oxygen demand and NH4+-N removal efficiency of aerobic granular sludge was surveyed. Results indicated that chemical oxygen demand and NH4+-N average removal efficiencies reached 80% and 82% respectively. When concentration of aerobic granular sludge changed in the range of 2700 to 3600 mg/L, aerobic granular sludge had better settling performance, and chemical oxygen demand and NH4+-N removal efficiencies were higher than the conventional activated sludge. When sludge volumetric index of granular sludge changed from 30 to 50mL/g, average particle size of granular sludge was stable in 0.5 to 1.20 mm. Simultaneous, nitrification and denitrification of aerobic granular sludge was also discussed in this research.
{"title":"Research on Aerobic Granular Sludge Disposal Municipal Sewage","authors":"Lingfeng Zhu, R. Gao, Run‐tao Zhang, Li‐li Liu","doi":"10.1109/ICBBE.2010.5517493","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5517493","url":null,"abstract":"Using conventional activated sludge of breweries as the inoculation sludge, stable aerobic granular sludge was fostered successfully in sequencing batch reactor, and applied to municipal sewage disposal. At room temperature, chemical oxygen demand and NH4+-N removal efficiency of aerobic granular sludge was surveyed. Results indicated that chemical oxygen demand and NH4+-N average removal efficiencies reached 80% and 82% respectively. When concentration of aerobic granular sludge changed in the range of 2700 to 3600 mg/L, aerobic granular sludge had better settling performance, and chemical oxygen demand and NH4+-N removal efficiencies were higher than the conventional activated sludge. When sludge volumetric index of granular sludge changed from 30 to 50mL/g, average particle size of granular sludge was stable in 0.5 to 1.20 mm. Simultaneous, nitrification and denitrification of aerobic granular sludge was also discussed in this research.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"45 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78527673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5516730
Jiang Wu, Jiehe Chen, Yanyan Zhang, Minqiang Shen, Lili Zhao, Xuyuan Yu, Lin Chai, Xin Li, Keyi Li
In this paper, the sampling methods and digestion methods during mercury test in plants were reviewed and Aqua regia-hydrofluoric acid digestion and HNO3-H2SO4-V2O5 digestion were adopted to test plant samples located at a campus. The mercury testing results with two digestion methods were compared with each other, and the corresponding conclusions have been taken out.
{"title":"Multi-Method Measurement on Mercury Concentration in Plants","authors":"Jiang Wu, Jiehe Chen, Yanyan Zhang, Minqiang Shen, Lili Zhao, Xuyuan Yu, Lin Chai, Xin Li, Keyi Li","doi":"10.1109/ICBBE.2010.5516730","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5516730","url":null,"abstract":"In this paper, the sampling methods and digestion methods during mercury test in plants were reviewed and Aqua regia-hydrofluoric acid digestion and HNO3-H2SO4-V2O5 digestion were adopted to test plant samples located at a campus. The mercury testing results with two digestion methods were compared with each other, and the corresponding conclusions have been taken out.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"22 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74191663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5517774
G. Weng, Jian Su
DNA microarrays provide a simple tool to identify and quantify the gene expression for tens of thousands of genes simultaneously. Image processing is an important step in microarrays experiments. This paper presents a novel technique for removing gene's noises based on the offset vector field and segmenting genes using the expectation maximization algorithm. Simulations show that the new technique for microarray images filtering and segmentation has better performance than most of the common ways. The results of experiments are computationally attractive, have excellent performance and can preserve spots' data while efficiently suppress noises.
{"title":"Microarray Images Processing Using the Offset Vector Field and Expectation Maximization Algorithm","authors":"G. Weng, Jian Su","doi":"10.1109/ICBBE.2010.5517774","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5517774","url":null,"abstract":"DNA microarrays provide a simple tool to identify and quantify the gene expression for tens of thousands of genes simultaneously. Image processing is an important step in microarrays experiments. This paper presents a novel technique for removing gene's noises based on the offset vector field and segmenting genes using the expectation maximization algorithm. Simulations show that the new technique for microarray images filtering and segmentation has better performance than most of the common ways. The results of experiments are computationally attractive, have excellent performance and can preserve spots' data while efficiently suppress noises.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"23 5 1","pages":"1-3"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90754052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5516323
Jiawei Dou, Weiming Zheng
In this work we investigate a problem of existence of positive periodic solutions for a class of impulsive differential equations in the plane. This describes generally the competition between normal and tumor cells in a periodically changing environment under chemotherapeutic treatment. The mathematical problem involves a coupled system of Lotka-Volterra together with periodically pulsed conditions. We use the monotone method to construct the upper and lower sequences converging to the periodic solution of the system.
{"title":"The Periodic Solutions of Impulsive Competition System on Tumor-Normal Cell Interaction","authors":"Jiawei Dou, Weiming Zheng","doi":"10.1109/ICBBE.2010.5516323","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5516323","url":null,"abstract":"In this work we investigate a problem of existence of positive periodic solutions for a class of impulsive differential equations in the plane. This describes generally the competition between normal and tumor cells in a periodically changing environment under chemotherapeutic treatment. The mathematical problem involves a coupled system of Lotka-Volterra together with periodically pulsed conditions. We use the monotone method to construct the upper and lower sequences converging to the periodic solution of the system.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"62 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78080666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5516328
Hui Peng, D. Liu
We first designed two chirp-coded excitation/ compression schemes which were applied to ultrasound elasticity imaging in simulation method using Field II. The simulation results demonstrate that in low echo-signal-to-noise ratio (eSNR) conditions, the performance of chirp-coded pulse for elasticity imaging is much better than the conventional short pulse, and indicate that elastographic signal-to-noise ratio (SNRe) of strain images for chirp-coded pulse is a function of attenuation, electronic noise, applied strain, pulse length, compression filter and depth. Comparing the effects of two chirp-coded excitation/compression schemes on strain imaging, we demonstrate that under the conditions of low eSNR, the first scheme, the combination of chirp excitation pulse with window and matched compression filter, is suitable to be used in low attenuation situations, and the second scheme, the combination of chirp excitation pulse without window and mismatched compression filter, is fit to be used in high attenuation situations. Finally, we applied the second chirp-coded scheme to a real-time freehand ultrasound strain imaging system and phantom experimental results are consistent with that in simulation method.
{"title":"Chirp-Coded Pulse Excitation for Ultrasound Elasticity Imaging","authors":"Hui Peng, D. Liu","doi":"10.1109/ICBBE.2010.5516328","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5516328","url":null,"abstract":"We first designed two chirp-coded excitation/ compression schemes which were applied to ultrasound elasticity imaging in simulation method using Field II. The simulation results demonstrate that in low echo-signal-to-noise ratio (eSNR) conditions, the performance of chirp-coded pulse for elasticity imaging is much better than the conventional short pulse, and indicate that elastographic signal-to-noise ratio (SNRe) of strain images for chirp-coded pulse is a function of attenuation, electronic noise, applied strain, pulse length, compression filter and depth. Comparing the effects of two chirp-coded excitation/compression schemes on strain imaging, we demonstrate that under the conditions of low eSNR, the first scheme, the combination of chirp excitation pulse with window and matched compression filter, is suitable to be used in low attenuation situations, and the second scheme, the combination of chirp excitation pulse without window and mismatched compression filter, is fit to be used in high attenuation situations. Finally, we applied the second chirp-coded scheme to a real-time freehand ultrasound strain imaging system and phantom experimental results are consistent with that in simulation method.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"10 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84595253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2010-07-23DOI: 10.1109/ICBBE.2010.5516946
L. Hao, S. Shen, J. Gao, Jing’ai Wang
Non-point source pollution is one of the major problems caused by agricultural activities especially from planting cultivation. This paper describes the application of the Soil and Water Assessment Tool (SWAT) model in agricultural non-point source pollution of the Laohahe River watershed, located in northeast China. This initial hydrologic modeling analysis will facilitate future applications of SWAT to this area for various watershed analyses, including water quality.
{"title":"Application of SWAT in Non-Point Source Pollution of Upper Xiliaohe Basin, China","authors":"L. Hao, S. Shen, J. Gao, Jing’ai Wang","doi":"10.1109/ICBBE.2010.5516946","DOIUrl":"https://doi.org/10.1109/ICBBE.2010.5516946","url":null,"abstract":"Non-point source pollution is one of the major problems caused by agricultural activities especially from planting cultivation. This paper describes the application of the Soil and Water Assessment Tool (SWAT) model in agricultural non-point source pollution of the Laohahe River watershed, located in northeast China. This initial hydrologic modeling analysis will facilitate future applications of SWAT to this area for various watershed analyses, including water quality.","PeriodicalId":6396,"journal":{"name":"2010 4th International Conference on Bioinformatics and Biomedical Engineering","volume":"5 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2010-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76128563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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