{"title":"Atlas based segmentation of brain structures in 3D MR images","authors":"S. Ali, Muhammad Faisal Khan","doi":"10.1109/BMEI.2011.6098254","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098254","url":null,"abstract":"In this paper, we propose a robust atlas-based automatic scheme for segmentation of subcortical region and cerebellum. Two separate schemes are presented, each for registration of subcortical structures and cerebellum respectively. Registration between atlas and subject MR image is performed using thin plate spline as non-rigid transformation, normalized mutual information as image similarity measure and powell's method as optimization technique. The final transformation of subcortical structures and cerebellum is used to map the segmentation data-set from atlas to subject image. Results obtained through automatic segmentation are validated for seven structures in ten subjects using sensitivity, positive predictive value and dice coefficient. These structures include left and right ventricles, caudate nuclei, putamena and cerebellum. The values of sensitivity, positive predictive value and dice coefficient range from 0.84 to 0.98, 0.82 to 0.99 and 0.87 to 0.96 respectively.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128218927","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}
{"title":"A de novo assembly method for metagenomic DNA reads with mate pairs","authors":"Binbin Lai, Ruogu Ding, Huaiqiu Zhu","doi":"10.1109/BMEI.2011.6098547","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098547","url":null,"abstract":"A high quality assembly of reads, which are short fragments generated from shotgun sequencing, is a substantial part of the metagenome projects. Although traditional assemblers have been employed in initial analysis of the metagenomes, they cannot surmount the challenges created by the features of metagenomic data. We present a de novo assembly algorithm for metagenomes with mate pairs. Our method uses mate pair information to guide contig construction. More specifically, we developed an efficient algorithm to find the best mate pair threading paths from the overlap graph to construct contigs. Tests on simulated metagenome data show that our method produced more accurate assembly than Celera Assembler and Phrap when assembling contigs at a same level.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115478173","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}
{"title":"Ventilation distribution on different body positions measured by electrical impedance tomography","authors":"M. Volk, C. Schmid, Zhanqi Zhao, K. Möller","doi":"10.1109/BMEI.2011.6098354","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098354","url":null,"abstract":"Objective: It has been confirmed that gravitation influences ventilation distribution. The aim of the study was to validate the ability of electrical impedance tomography (EIT) in detecting ventilation inhomogeneity caused by gravitation. Methods: Ten healthy volunteers were included for this prospective study. They were asked to breathe spontaneously in four different body positions, namely supine, prone, left lateral and right lateral positions. Functional EIT images were calculated and divided into four quadrants. Results: No significant difference of air distribution was found between gravity-dependent lung regions and nondependent lung regions in both supine and prone position, while significant difference was found in both lateral positions (left lateral, left and right lung respectively: 57.6±7.2%, 42.4±7.2%, p<0.01; right lateral, left and right lung respectively:, 35.3±6.7%, 64.7±6.7%, p<0.01). Conclusion: The results indicate that the influence of gravitation on ventilation distribution depends on body positions and EIT is able to detect the ventilation inhomogeneity.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123040746","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}
J. N. Tehrani, Chenyu Wang, C. Jin, A. McEwan, O. Gibbs, E. Shanehsaz, M. Barry, A. Thiagalingam
{"title":"Edge enhancement for retinal vasculature caliber evaluation in prediction of cardiovascular disease","authors":"J. N. Tehrani, Chenyu Wang, C. Jin, A. McEwan, O. Gibbs, E. Shanehsaz, M. Barry, A. Thiagalingam","doi":"10.1109/BMEI.2011.6098251","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098251","url":null,"abstract":"At the moment, the gold standard in detection of coronary disease is coronary angiography. Recent studies show that retinal arteriolar and venular caliber change is associated with many cardiovascular risk factors. Thus, investigating blood column diameters inside retinal vessels during cardiac cycle (ECG gating) could help cardiologists in the prediction of cardiovascular disease. In this paper, we demonstrated an improved image preprocessing step for computer aided diagnosis algorithms that could be useful in measuring the width of the blood column. The algorithm consists of three main steps. First, higher resolution images at 21 megapixels were captured along with an inbuilt 570nm red-free filter to maximize the blood signal. Second, the image was decomposed using a Gabor filter at four different directions (0, 45, 90 and 135 degree) and maximum responses were obtained over the four directions. Finally, the size of vessels is calculated by performing the sliding linear regression filter (SLRF) on vessels slices. The results suggest the use of edge enhancement with SLRF decrease the variability by 2-3 times and might lead to more deterministic vessel widths with less variation.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116656642","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}
X. Jiang, D. Gao, Chunfang Wang, Lei Liu, Yanhong Dong, Xiaoai Zhu, Hong-xia Ma, Bingjie Li, Chengbo Xu, Tao Hu, Y. Zheng
{"title":"Prokaryotic expression and analysis on the ag85b-mpb64 fusion gene of Mycobacterium bovis","authors":"X. Jiang, D. Gao, Chunfang Wang, Lei Liu, Yanhong Dong, Xiaoai Zhu, Hong-xia Ma, Bingjie Li, Chengbo Xu, Tao Hu, Y. Zheng","doi":"10.1109/BMEI.2011.6098706","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098706","url":null,"abstract":"For raising the antigenicity of Mycobacterium bovis single antigen, fusion protein of two genes was acquired. The DNA fragments of ag85b and mpb64 were fused by splicing by overlapping extension (SOE) polymerase chain reaction(PCR), and the fusion gene ag85b-mpb64 were cloned into pMD-18-T vector, then we got the recombinant plasmid pMD-85b-64. pMD-85b-64 and pET28a(+) were digested by BamH I and EcoR I double enzymes. The purified pMD-85b-64 fusion gene was subcloned into the expression vector pET28a(+), and the prokaryotic expression vector pET-85b-64 was constructed. Plasmid containing pET-85b-64 was transformed into competence Escherichia coli BL21 (DE3). The bacterium was induced by isopropyl-β-D-thiogalactopyranoside(IPTG) and its lysates were loaded directly onto sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), approximately 58 ku exogenous protein was observed on the SDS-PAGE. The protein was analyzed by using Western blotting, the results indicated that the protein was of antigenic activity of Mycobacterium bovis. These results could serve as a basis for further studies on the usefulness of the fusion gene and its expression product in the development of subunit vaccine and DNA vaccine against bovine tuberculosis.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"114 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116674483","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}
Wei Wang, Lintao Hu, Yun Deng, Na Wang, Jian Sun, Wu Wang
{"title":"Studies on wave field of extracorporeal focused shock wave therapy system","authors":"Wei Wang, Lintao Hu, Yun Deng, Na Wang, Jian Sun, Wu Wang","doi":"10.1109/BMEI.2011.6098439","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098439","url":null,"abstract":"The extracorporeal Focused Shock Wave Therapy (EFSWT), is used to treat human tissue disease as a non-invasive technology. Wave field of EFSWT is very complex without standard analysis and modeling method. It is worthy to study the field of ESWT and has significance. According to ultrasonic theory, the parameters of the ultrasound pressure field in core frequency and the transducer are measured, and a model based on the ultrasound field theory has been developed and simulated with measured data. The results suggest the model has good performances to analyze and model EFSWT, and is helpful to design acoustic field, transducer parameters, and model them to estimate effect in tissue treatment. The simulation results using LabVIEW show that it can promote the effect and safety of the medical device.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116863682","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}
{"title":"Hardware implementation in DGPS accuracy improvement by using RSCMAC","authors":"Ching-Tsan Chiang, J. Hsu, Sheng Yang","doi":"10.1109/BMEI.2011.6098782","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098782","url":null,"abstract":"The purpose of this research is to develop and apply the “Recurrent S_CMAC_GBF (RSCMAC) [2] to enhance the accuracy of Global Positioning System (GPS). The performance is implemented and tested by a FPGA chip. In the research, the previous work has accomplished outstanding performance by using RSCMAC to predict GPS receiver static error to improve the error of the Differential-GPS. The simulation result shows 10 times accuracy is improved — GPS error is improved from larger than **** 20M to less than **** 2M. This paper employs previous research result to whole area prediction (non single fixed position), and then implements the performance by a FPGA chip. The key point is to commercialize the prototype design and its development. The most advantage of this project is to improve inexpensive GPS receiver positioning errors to increase the economic benefit of higher accuracy.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127143701","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}
{"title":"Particle swarm optimization-based support vector regression and Bayesian networks applied to the toxicity of organic compounds to tadpoles (Rana japonica)","authors":"Q. Su, W. Lu, X. Liu, T. Gu, B. Niu","doi":"10.1109/BMEI.2011.6098692","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098692","url":null,"abstract":"Particle swarm optimization (PSO) is a new optimization method with strong global search capability. In present work, PSO-support vector regression (SVR) model was proposed to predict the toxicity of organic compounds to tadpoles (Rana japonica), in which PSO was used to determine free parameters of SVR. These results showed that the prediction accuracy of PSO-SVR model is higher than those mode of MLR and PLS. Moreover, Bayesian networks (BNs) was adopted to describe the relationship between toxicity associated with molecular descriptors in this work. The result of BNs was considered to be reasonable.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"74 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127169520","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}
{"title":"Estimation of pulse transit time using time delay estimation techniques","authors":"S. T. Veerabhadrappa, A. Vyas, S. Anand","doi":"10.1109/BMEI.2011.6098490","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098490","url":null,"abstract":"The pulse wave propagation is the important electromechanical characteristics of biomedical signals. Conventionally the pulse propagation features are extracted by estimating the propagation time delay between two points called pulse transit time(PTT). The PTT estimation is based on the phase analysis of the cross power spectrum and bispectrum between the ECG and pulse signal. In this paper, The generalized cross correlation and bispectrum methods are discussed. The PTT is estimated from ECG and pulse waveform by measuring time between R peak of ECG to systolic peak of pulse signal. Simulation using MITBIH polysomnographic database and carried out to compare the two approches. It is shown that the bispectral modified phase transform provides the better estimates of pulse transit time.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124890315","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}
Yanqun Wang, Xianjun Meng, Bin Li, Xiyun Sun, Qi Zhang
{"title":"Effect of ultrasonic-assisted extraction on antioxidant activity and molecular weight distribution of polysaccharides from Schisandra Chinensis (Turcz.) baill","authors":"Yanqun Wang, Xianjun Meng, Bin Li, Xiyun Sun, Qi Zhang","doi":"10.1109/BMEI.2011.6098603","DOIUrl":"https://doi.org/10.1109/BMEI.2011.6098603","url":null,"abstract":"The molecular weight distribution and antioxidant activity of polysaccharides from Schisandra chinensis (SCP) extracted by hot-water and ultrasonic pretreatment assisted were investigated, including scavenging activities against hydroxyl radical, 1,1-diphenyl-2-picrylhydrazyl (DPPH) and superoxide anion. Obvious differences in molecular weight distribution and antioxidant activity between the hot-water extracts and ultrasonic pretreatment assisted extracts were observed. The SCP with ultrasonic pretreatment was degraded causing an increase of fractions. Both of SCP showed a noticeable scavenging activity against hydroxyl radical and DPPH, and the antioxidant activity of SCP, with ultrasonic pretreatment, was higher. However, superoxide anion scavenging activity of SCP was hardly observed.","PeriodicalId":102860,"journal":{"name":"2011 4th International Conference on Biomedical Engineering and Informatics (BMEI)","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125820892","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}