2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献_第10页

A new reconstruction algorithm for photoacoustic imaging based on geometric information of ROI 一种基于感兴趣区域几何信息的光声成像重建算法

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367692

W. Ham, Kyumann Im, Sanghun Park, Kangsan Lee, Chulgyu Song

引用次数: 1

Thermo-mechanical numerical analysis of stent unit cell 支架单元胞热-力学数值分析

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367641

V. Dunić, N. Busarac, V. Slavkovic, R. Slavkovic

引用次数: 0

Amyloid beta plaque reduction with antibodies crossing the blood brain barrier opened with focused ultrasound in a rabbit model 在兔模型中，通过聚焦超声打开抗体穿过血脑屏障减少淀粉样蛋白斑块

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367707

M. Yiannakou, C. Damianou

引用次数: 0

Computational simulation of blood flow in a DeBakey type I aortic dissection DeBakey I型主动脉夹层血流的计算模拟

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367656

S. Djorovic, N. Filipovic, V. Stojić, L. Velicki

{"title":"Computational simulation of blood flow in a DeBakey type I aortic dissection","authors":"S. Djorovic, N. Filipovic, V. Stojić, L. Velicki","doi":"10.1109/BIBE.2015.7367656","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367656","url":null,"abstract":"The main purpose of this study is to examine how flow field in aortic dissection is affected by its geometry and flow condition. Two models of DeBakey type I aortic dissection, which involves the entire aorta, were analyzed. Patient-specific geometries were reconstructed, based on Computed tomography (CT) scan images, in order to obtain 3D finite element meshes. Computational fluid dynamics (CFD), which uses numeric methods and algorithms for the simulation of blood flow by solving the Navier-Stokes equations on computational meshes, enhances the understanding of disease progression. For that purpose, the major fluid dynamic parameters and indicators of disease progression, such as velocity field, pressure and shear stress, were computed and analyzed. The computed results showed higher velocities in the ascending aorta, the inlet and outlet tears and the iliac arteries, in case of both models. The pressure distribution showed high zones in the ascending aorta, while the shear stress distribution showed low zones in the aneurysm part, in case of both models. In summary, the presented study can be extended to a larger patient group in a longitudinal study with the goal to determine the potential value of CFD simulations in prediction of aneurysmal growth and rupture.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129752637","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}

引用次数: 1

A micro emboli vs non-emboli classification system based on the directional dual tree rational dilation wavelet transform 基于定向对偶树有理扩张小波变换的微栓子与非栓子分类系统

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367735

Gorkem Serbes, Betul Erdogdu Sakar, N. Aydin

{"title":"A micro emboli vs non-emboli classification system based on the directional dual tree rational dilation wavelet transform","authors":"Gorkem Serbes, Betul Erdogdu Sakar, N. Aydin","doi":"10.1109/BIBE.2015.7367735","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367735","url":null,"abstract":"Transcranial Doppler (TCD) is a widely used, non-invasive, rapid and reproducible monitoring method for observing the condition of middle cerebral artery. Micro embolic signals, which appear in various clinical scenarios such as; carotid stenosis, aortic arch plaques, atrial fibrillation, myocardial infarction, patent foramen ovale and valvular stenosis, can be detected by the analysis of TCD signals. Discrete wavelet transform based methods were frequently used in literature for micro embolic signal detection. However, in all the previously used complex/non-complex discrete wavelet transform based methods, low Q-factor wavelets were employed for feature extraction. Low Q-factor wavelets have been successfully used for processing piecewise smooth signals but for the embolic signals, a discrete wavelet transform with better frequency resolution is needed. Therefore in this study, a novel Directional Dual Tree Rational Dilation Wavelet Transform (DDT-RADWT), in which the Q-factor of the analysis and synthesis filters can be adjusted due to the properties of signal of interest, is used as the feature extractor. DDT-RADWT is applied to a dataset consisting of 130 micro embolic signals and 130 non-embolic signals (65 artifacts and 65 Doppler speckles) and the obtained coefficients are used as features. In the proposed method, in order to utilize from the different frequency characteristics of micro embolic, artifact and Doppler speckle signals, the DDT-RADWT is applied with high Q-factor filters. The extracted coefficients are given to k-NN and SVM classifiers with the aim of discriminating two classes of micro embolic signals and non-embolic signals. The results show that higher general accuracy and micro embolic signal detection accuracies are obtained with high Q-factor wavelet analysis.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130230730","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}

引用次数: 2

Application of active contours method in assessment of optimal approach trajectory to brain tumor 活动轮廓法在评估脑肿瘤最佳入路轨迹中的应用

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367661

T. Šušteršič, Miodrag Peulić, N. Filipovic, A. Peulić

引用次数: 0

Making sense of the biological complexity through the platform-driven unification of the analytical and visualization tasks 通过平台驱动的分析和可视化任务的统一来理解生物复杂性

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367724

Theodoras Koutsandreas, E. Pilalis, E. Vlachavas, D. Koczan, S. Klippel, A. Dimitrakopoulou-Strauss, I. Valavanis, A. Chatziioannou

{"title":"Making sense of the biological complexity through the platform-driven unification of the analytical and visualization tasks","authors":"Theodoras Koutsandreas, E. Pilalis, E. Vlachavas, D. Koczan, S. Klippel, A. Dimitrakopoulou-Strauss, I. Valavanis, A. Chatziioannou","doi":"10.1109/BIBE.2015.7367724","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367724","url":null,"abstract":"The development of several biomedical ontologies and databases for structuring and categorizing knowledge in life sciences, and particularly the ones which refer to the functions and interactions of biomolecules, have contributed to the rapid inflation of the semantic information universe that describes cellular complexity, at different scales. Together with the ever-growing number of high-throughput molecular data, generated by DNA microarray or NGS experiments, they stress the need for powerful, intuitive data representation methods, which manage to make sense out of the myriads of interactions and pinpoint those with a causal contribution to the phenotypes studied. In this paper, we present a web application, which overall combines computational methodologies and data visualization techniques, in order to deliver comprehensible illustrations of cellular complexity, for voluminous, molecular datasets, linking the individual genes, with the relevant biological processes, in which they participate, while it manages to prioritize those processes according to their involvement in the cellular phenotype studied. The application highlights molecular information (functions, processes, cellular compartments) according several criteria (enrichment score, expression, etc) sorts out regulatory hub genes, with a pivotal role in the phenotype studied, while, most importantly, novel visualization modules provide an efficient, intuitive illustration that aids easy systems' level interpretation. The pipeline is showcased here using a colon cancer dataset.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128581946","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}

引用次数: 4

Optimization of data-intensive next generation sequencing in high performance computing 高性能计算中数据密集型下一代排序的优化

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367654

N. Kathiresan, Rashid J. Al-Ali, P. Jithesh, Tariq AbuZaid, Ramzi Temanni, A. Ptitsyn

{"title":"Optimization of data-intensive next generation sequencing in high performance computing","authors":"N. Kathiresan, Rashid J. Al-Ali, P. Jithesh, Tariq AbuZaid, Ramzi Temanni, A. Ptitsyn","doi":"10.1109/BIBE.2015.7367654","DOIUrl":"https://doi.org/10.1109/BIBE.2015.7367654","url":null,"abstract":"Advancement in Next Generation Sequencing (NGS) technology are associated with ever-increasing volume of genomic data every year. These genomic data are efficiently processed by empirical parallelism using High Performance Computing (HPC). The processed data can be used for genome-wide association studies, genetics, personalized medicine and many other areas. There are different kind of algorithms and implementations used in different phases of genome processing. In this paper, we used BWAKIT and GATK based software for processing larger volume of genomic data that are referred as \"NGS workflow at SIDRA\". We used BWAKIT for genome alignment and GATK for variant discovery in the NGS workflow that required larger computation and huge memory requirement respectively. We observed, the CPU utilization is not more than 45% during variant discovery and hence, it is necessary to understand the optimal selection (in terms of number of threads or cores) of the resources during the NGS workflow automation. We analyzed the performance bottleneck and application optimization in terms of \"scalability\" (use maximum available CPUs and memory) and \"multiple instances of NGS workflow with different genome data within a node\" (process more volume of genome data concurrently with limited set of CPUs and memory). We observed that, 40%, 65%, 71% and 76% improvement in performance while processing 2, 4, 8 and 16 samples concurrently using our own scheduling heuristics. As a result, our proposed NGS workflow automation will improve the performance upto 76% compared to application scalability based workflows.","PeriodicalId":422807,"journal":{"name":"2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"166 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127581707","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}

引用次数: 4

A robust data scaling algorithm for gene expression classification 一种用于基因表达分类的稳健数据缩放算法

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367734

X. Cao, Z. Obradovic

引用次数: 8

Pathway enrichment analysis of Chuan-wu for rheumatoid arthritis 川武治疗类风湿关节炎的途径富集分析

2015 IEEE 15th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2015-11-02 DOI: 10.1109/BIBE.2015.7367644

Hongtao Guo, Lingru Wang, Rong Li, Ting Hao, Guang Zheng

引用次数: 0