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Numerical study of electrical stimulation for neuronal cell growth on silica aerogel substrate 二氧化硅气凝胶基质上神经细胞生长的电刺激数值研究
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618484
Sakib Al Soyeb, B. Morshed, F. Sabri
{"title":"Numerical study of electrical stimulation for neuronal cell growth on silica aerogel substrate","authors":"Sakib Al Soyeb, B. Morshed, F. Sabri","doi":"10.1109/BSEC.2013.6618484","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618484","url":null,"abstract":"An aerogel-based Neuronal Printed Circuit Board (NPCB) with electrical stimulation capabilities is currently under investigation as an alternative method for repair of injury sustained to peripheral nerves. Here, we report the results of the numerical analysis of electric field distribution, fluidic motion, and temperature rise due to such superficial electrical stimuli. In this analysis, a cylindrical aerogel structure is modeled for both voltage and current stimulation using COMSOL finite element analysis software. Voltage excitation of 100 mV and current excitations of 0.1 to 1 A are applied to a pair or a single electrode of gold track with dimension of 20×2×0.2 mm3. Simulation results demonstrate that electric field lines are highly concentrated on the surface of the aerogel where the gold tracks exist. Besides, the stimulation generates fluidic motion, and the steady state temperature increase due to the stimulation is less than 1K for current stimulation of less than 0.35 A.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115304652","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: 0
Application of micro-segmentation algorithms to the healthcare market: A case study 微分割算法在医疗保健市场的应用:一个案例研究
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618489
S. Sukumar, F. Aline
{"title":"Application of micro-segmentation algorithms to the healthcare market: A case study","authors":"S. Sukumar, F. Aline","doi":"10.1109/BSEC.2013.6618489","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618489","url":null,"abstract":"We draw inspiration from the recent success of loyalty programs and targeted personalized market campaigns of retail companies such as Kroger, Netflix, etc. to understand beneficiary behaviors in the healthcare system. Our posit is that by better understanding and predicting customer behaviors we can emulate the financial success of retail companies in the healthcare market. Towards that goal, we survey current practices in market segmentation research and analyze health insurance claims data using a selected few of those algorithms. We present results and discuss insights based on the analysis.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114591981","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: 0
Benchmarking technology infrastructures for embarrassingly and non-embarrassingly parallel problems in biomedical domain 生物医学领域尴尬和非尴尬并行问题的基准技术基础设施
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618496
S. Kazmi, M. Kane, M. Krauthammer
{"title":"Benchmarking technology infrastructures for embarrassingly and non-embarrassingly parallel problems in biomedical domain","authors":"S. Kazmi, M. Kane, M. Krauthammer","doi":"10.1109/BSEC.2013.6618496","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618496","url":null,"abstract":"Having the advantage of large scale open source data available to us in multiple forms, the ultimate goal is to integrate these resources with gene sequence data to enhance our understanding and make viable inferences about the true nature of the processes that generate this data. We are investigating the use of open source subset of the National Institute of Health's National Library of Medicine (NIH/NLM) data for our analysis including text as well as image features to semantically link similar publications. Due to the sheer volume of data as well as the complexity of inference tasks, the initial problem is not in the analysis but lies in making a decision about the computational infrastructure to deploy and in data representation that will help accomplish our goals. Just like any other business process, reducing processing cost and time is of essence. This work benchmarks two open source platforms (A) Apache Hadoop with Apache Mahout, and (B) open source R using bigmemory package for performing non-embarrassingly parallel and embarrassingly parallel machine learning tasks. Singular Value Decomposition (SVD) and k-means are used to represent these two problem classes respectively and average task time is evaluated for the two architectures for a range of input data sizes. In addition, performance of these algorithms using sparse and dense matrix representation is also evaluated for clustering and feature extraction tasks. Our analysis shows that R is not able to process data larger than 2 giga-bytes, with an exponential performance degradation for data larger than 226 mega-bytes. Bigmemory package in R allowed processing of larger data but with similar degradation beyond 226 mega-bytes. As expected, Hadoop/Mahout did not perform well for SVD as compared to k-means due to the tightly coupled nature of data needed at each step and is only justified for processing of very large data sets.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130113294","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: 3
Multiscale modeling of RNA 3D structures RNA三维结构的多尺度建模
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618482
David R. Bell, Z. Xia, Pengyu Y. Ren
{"title":"Multiscale modeling of RNA 3D structures","authors":"David R. Bell, Z. Xia, Pengyu Y. Ren","doi":"10.1109/BSEC.2013.6618482","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618482","url":null,"abstract":"Balancing accuracy and computational efficiency while studying biomolecular structures and dynamics necessitates scalable modeling techniques. We have been developing a coarse-grained model for RNA that uses pseudoatoms in place of all-atom representation. By reducing the number of interactions and mean-field representation of environmental effects, significant improvement in computational efficiency is achieved in a comparison to all-atom based physical modeling approaches. A five bead coarse-grained model utilized for RNA 3D structure prediction is presented. Unique features of this framework include the direct mapping between all atom and coarse-grained models, incorporation of electrostatic interactions, continuous and analytical energy function that can be used in molecular dynamics simulations, and statistical derived parameters. Here we present the basic framework of our model and recent applications to RNA folding.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122651459","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: 0
A biomechanical model of Pacinian Corpuscle & Skin 太平洋小体与皮肤的生物力学模型
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618485
A. Biswas, M. Manivannan, M. Srinivasan
{"title":"A biomechanical model of Pacinian Corpuscle & Skin","authors":"A. Biswas, M. Manivannan, M. Srinivasan","doi":"10.1109/BSEC.2013.6618485","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618485","url":null,"abstract":"This paper describes a wide band biomechanical model of Pacinian Corpuscle (PC) embedded in skin and its response against the trapezoidal and sinusoidal stimuli in order to study human vibrotactile (VT) sensitivity near the VT Sensitivity Threshold (VTST) covering few 10s of Hz to few kHz. The overall model includes mechanical signal conditioning in both skin layers and PC lamellae. The developed model describes the mechanical signal processing of the PC lamellar structure in a recursive transfer function and its response is validated against the data from literature.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"53 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120904209","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: 11
A bioinformatics pipeline for sequence to structure: A case study with a Cml patient undergoing treatment with imatinib 从序列到结构的生物信息学管道:一个接受伊马替尼治疗的Cml患者的案例研究
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618499
A. Chacko, Shankarrao Patil, A. Upadhayay, A. Nagrajan, R. Khatri, D. Arya, S. Krishna, Ramanathan Sowdhamini, C. Ross
{"title":"A bioinformatics pipeline for sequence to structure: A case study with a Cml patient undergoing treatment with imatinib","authors":"A. Chacko, Shankarrao Patil, A. Upadhayay, A. Nagrajan, R. Khatri, D. Arya, S. Krishna, Ramanathan Sowdhamini, C. Ross","doi":"10.1109/BSEC.2013.6618499","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618499","url":null,"abstract":"Chronic Myeloid Leukaemia (CML) is a resultant of the 9:22 translocation event leading to the constitutive kinase activity of BCR-ABL. Imatinib is the drug used as the first line therapy in CML. We report a longitudinal case study for a CML patient under treatment with imatinib. The bone marrow aspirate of this CML patient was used for exome sequencing. Single nucleotide variants (SNVs) unique to the exome sequencing sample datasets were analysed with an emphasis on kinases. These mutations were mapped to the structure to further understand the significance of the SNVs in the context of its stability and kinase-drug interaction. Here we present a data filtering pipeline with examples for sequence to structure approach. This strategy can be used to filter kinases from next generation sequencing data relevant to cancers.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126553533","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: 0
In vivo imaging to initialize a biophysical model of tumor growth: Preliminary results 体内成像初始化肿瘤生长的生物物理模型:初步结果
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618487
D. Hormuth, T. Yankeelov
{"title":"In vivo imaging to initialize a biophysical model of tumor growth: Preliminary results","authors":"D. Hormuth, T. Yankeelov","doi":"10.1109/BSEC.2013.6618487","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618487","url":null,"abstract":"Recent advances in MRI and PET have increased the availability of noninvasive measurements of the molecular, cellular, and physiological characteristics of tumors. It may be possible to incorporate these measurables into realistic biophysical models that can then be used to predict tumor growth and therapy response on an individual basis. Here we incorporate quantitative imaging data acquired during the course of a tumor development in rat model of glioma. Early measurements are used to initialize and constrain a biophysical model to predict tumor status at later time points. The initial results show a promising ability to use early time point data to predict later time point tumor size, cellularity, and distribution.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125195797","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: 0
Energy-based architecture for classification of publication figures 出版物数字分类的基于能量的体系结构
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 2013-05-21 DOI: 10.1109/BSEC.2013.6618492
P. Barbano, M. Nagy, M. Krauthammer
{"title":"Energy-based architecture for classification of publication figures","authors":"P. Barbano, M. Nagy, M. Krauthammer","doi":"10.1109/BSEC.2013.6618492","DOIUrl":"https://doi.org/10.1109/BSEC.2013.6618492","url":null,"abstract":"We present an implementation of the experimental and theoretical results obtained in the analysis of text and image content of biomedical publications. Particularly, we propose a novel optical recognition system using an adaptive algorithm for the classification and analysis of highly heterogeneous images in research papers. When compared with conventional algorithms, our technology substantially increases the probability of detection and classification of images buried in text or obscured by other images. We report successful testing of the new architecture using PubMed publications.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129929786","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: 3
BSEC 2013: A note from the Conference Chairs BSEC 2013:会议主席的说明
2013 Biomedical Sciences and Engineering Conference (BSEC) Pub Date : 1900-01-01 DOI: 10.1109/bsec.2011.5872331
{"title":"BSEC 2013: A note from the Conference Chairs","authors":"","doi":"10.1109/bsec.2011.5872331","DOIUrl":"https://doi.org/10.1109/bsec.2011.5872331","url":null,"abstract":"The Biomedical Science and Engineering Center (BSEC) at Oak Ridge National Laboratory (ORNL) held its Fourth annual conference in Oak Ridge May 21–23, 2013. BSEC was established in 2003 as an umbrella organization to provide a platform for biomedical translation of ORNL scientific and technical innovations. The strategic mission of the Biomedical Science and Engineering Center (BSEC) is to catalyze interdisciplinary biomedical research on national medical challenges that is synergistic with the DOE mission and ORNL capabilities. Supporting DOE's strategic goal for improved US economic competitiveness and quality of life through innovations in science and technology, the center brings together scientists to solve challenging biomedical problems that can benefit from the unique ORNL resources: (i) broad spectrum of core expertise in physics, chemistry, mathematics, biology, engineering, and computer science; (ii) leading high performance computing infrastructure, specialized equipment, and sophisticated instrumentation; (iii) proven platform for productive multidisciplinary collaborations with academia, industry, medical centers, and federal agencies; and (iv) experienced technology transfer for commercialization and licensing. The center pursues a broad biomedical research agenda in: ▪ knowledge discovery technologies for transforming the fields of biology and medicine; ▪ advances in materials, devices, and technologies to reduce the burdens of disease and disability and improve health care quality; ▪ customized solutions for health problems impacting civilian, military, and veteran populations; and ▪ Infrastructure development and support tools for large scale biomedical research and health care delivery initiatives.","PeriodicalId":431045,"journal":{"name":"2013 Biomedical Sciences and Engineering Conference (BSEC)","volume":"74 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127376969","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: 0
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