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Engineering in Medicine and Biology Magazine, IEEE

Issue 4 • Date July-Aug. 2009

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Displaying Results 1 - 25 of 32
  • IEEE Engineering in Medicine and Biology Magazine - Front cover

    Publication Year: 2009 , Page(s): c1
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  • Table of contents

    Publication Year: 2009 , Page(s): 1 - 2
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  • On learning and discussing [From the Editor]

    Publication Year: 2009 , Page(s): 3 - 4
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  • Engineering the future of biomedicine [President's Message]

    Publication Year: 2009 , Page(s): 5
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  • Validation and verification [Letters to the Editor]

    Publication Year: 2009 , Page(s): 6 - 7
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  • Meetings and conferences [Society News]

    Publication Year: 2009 , Page(s): 8 - 9
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  • EMBC 2009 at a glance. . . [Student's Corner]

    Publication Year: 2009 , Page(s): 10 - 11
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  • The opposite of rube [Student Activities]

    Publication Year: 2009 , Page(s): 12 - 13
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  • IEEE Engineering in Medicine and Biology Magazine - Statement of Editorial Policy

    Publication Year: 2009 , Page(s): 13
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  • EMBC 2009

    Publication Year: 2009 , Page(s): 14 - 15
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  • Computational techniques and pattern recognition [Introduction to the special issue]

    Publication Year: 2009 , Page(s): 16 - 18
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  • Comparative genomic workflow

    Publication Year: 2009 , Page(s): 19 - 24
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (724 KB) |  | HTML iconHTML  

    This article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are collected from the Ensembl database. The sequences are then arranged to use for sequence alignment with basic local alignment search tool Z (BLASTZ) [10], which finds gap- free alignments of at least q% identity and I b/s in length. All the conserved noncoding regions identified are stored in a relational database. An user-friendly Web interface provides easy access to conserved regions and related information and visualization capabilities. View full abstract»

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  • Variable-length haplotype construction for geneߝgene interaction studies

    Publication Year: 2009 , Page(s): 25 - 31
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (787 KB) |  | HTML iconHTML  

    Genetic epidemiology is a research field that aims to identify genetic polymorphisms that are involved in disease susceptibility. In this article, a variable-length haplotype construction for gene-gene interaction (VarHAP) technique is proposed. The technique will involve nonparametric classification where haplotypes inferred from multiple single nucleotide polymorphism (SNP) data are the classifier inputs. View full abstract»

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  • Time-series approach to protein classification problem

    Publication Year: 2009 , Page(s): 32 - 37
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (384 KB) |  | HTML iconHTML  

    In this paper, a wavelet-based time-series approach for protein classification problem was presented. A novel feature vector based on the variation of seven physicochemical properties (hydrophobicity, electronic, isoelectric point, polarity, volume, composition, and molecular weight) of amino acids was proposed in this article. The feature vector contains the wavelet variance information of physico-chemical properties of protein sequences. The dimension of the proposed feature vector is only 35 when compared with 400-dimensional feature vector for G protein coupled receptors technique(GPCR) pred and 512-dimensional feature vector for fast Fourier transform(FFT)-based approaches. The low dimension of the feature vector will facilitate the development of computational and memory-efficient classifiers for drug discovery applications. Experiments were performed on the complete data set that is available at GPCR database(GPCRDB). Tests were also conducted on unseen or independent data sets to measure the generalization capability of the proposed classification technique. Performance comparison with GPCRpred and FFT- based approaches shows that the proposed approach performs equally well with the existing programs. The proposed approach can also be applied for prediction of protein structural classes, identification of membrane protein type, enzyme family classification, and many others. View full abstract»

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  • Structural building blocks

    Publication Year: 2009 , Page(s): 38 - 44
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1078 KB) |  | HTML iconHTML  

    The paper proposes a modified version of the mountain clustering method (MCM) to find a library of structural building blocks for the construction of three-dimensional (3-D) structures of proteins. The algorithm decides on building blocks based on a measure of local density of structural patterns. The algorithm was tested on a well-known data set and found it to successfully reconstruct a set of 71 test proteins (up to first 60 residues as done by others) with lower global-fit root mean square (RMS) errors compared to an existing method that inspired our algorithm. The constructed library of building blocks is also evaluated using some other benchmark data set for comparison. The algorithm achieved good local-fit RMS errors, indicating that these building blocks can model the nearby fragments quite accurately. In this context, two alternative ways are proposed to compare the quality of such quantization and reconstruction results, which can be used in other applications too. View full abstract»

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  • Degree of differential prioritization

    Publication Year: 2009 , Page(s): 45 - 51
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1565 KB) |  | HTML iconHTML  

    Because of the high dimensionality of the microarray data sets, feature selection (FS) has become an important challenge in molecular classification. Using the degree of differential prioritization (DDP) between relevance and antiredundancy, our proposed DDP-based FS technique is capable of achieving better accuracies than those previously reported, using a smaller predictor set. However, previously, we have neither devised nor used any method for determining the value of the DDP to be used for the data set of interest before the FS process. In this article, we propose a system for predicting the optimal value of the DDP, which costs less computationally than conventional tuning while maintaining the independence of the FS technique from the type of underlying classifier used. View full abstract»

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  • Multicellular pattern formation

    Publication Year: 2009 , Page(s): 52 - 57
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (781 KB) |  | HTML iconHTML  

    Understanding the self-regulatory mechanisms controlling the spatial and temporal structure of multicellular organisms represents one of the major challenges in molecular biology. Although high-throughput data have become available with the advances in experimental technologies at a large scale, measuring gene expression levels at a high spatial resolution remains extremely difficult. As a result, the study of genetic regulatory networks in the light of spatial expression patterns still relies mainly on qualitative data. This leads to the question of how to fit the parameters of a gene regulatory network model such that a purely qualitatively defined pattern can be reproduced. This article addresses this issue and presents a general approach to generate patterns reflecting basic geometric shapes. In combination with an appropriate ordinary differential equation (ODE)-based modeling and simulation framework, a formalism to quantify qualitative patterns and integrate this concept into an evolutionary algorithm for parameter estimation is presented and tested for stripe-like patterns on two test systems. View full abstract»

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  • Data-driven approach to predict survival of cancer patients

    Publication Year: 2009 , Page(s): 58 - 66
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (2471 KB) |  | HTML iconHTML  

    We develop a novel method to identify patients 'with different disease risk level. Our method estimates the optimal partition (cutoff) of a single gene's expression level by maximizing the separation of the survival curves related to the high- and low risk of the disease behavior. We extend our approach to construct two-gene signatures, which can exhibit synergetic influence on patient survival. Using bootstrapping and statistical modeling, we evaluate the performance of our method by analyzing Affymetrix U133 data sets of two large breast cancer patient cohorts. Using 232-grade signature genes associated with different aggressiveness of breast tumor, we reveal a large number of gene pairs, which provides pronounced synergetic effect on patient's survival time and identifies patients with low- and high-risk disease subtypes. The selected survival significant genes are strongly supported by gene ontology (GO) analysis and literature data. Specifically, for the first time, we demonstrate that cyclin A2 or cyclin A and protein tyrosine phosphatase T (CCNA2- PTPRT) and megalin (LRP2)-integrin alpha-7 (ITGA7) gene pairs can provide strong clinically significant interaction effects on the survival of breast cancer patients. Our technique has the potential to be a powerful tool for classification, prediction, and prognosis of cancer and other complex diseases. View full abstract»

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  • Searching of optimal vaccination schedules

    Publication Year: 2009 , Page(s): 67 - 72
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1832 KB) |  | HTML iconHTML  

    Genetic algorithms (GAs) are a particular class of evolutionary algorithms that use techniques inspired by evolutionary biology. These are widely used in different areas of bioinformatics. In immunoinformatics, a common optimization problem is the search of optimal vaccination schedules. The problem of defining optimal schedules is particularly acute in cancer immunopreventive approaches, which requires a sequence of vaccine administrations to keep a high level of protective immunity. This paper presents a formalization of the optimization problem and show how a GA search on a model-based approach can be used to deal with the problem. View full abstract»

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  • Peptide binding to major histocompatibility complex

    Publication Year: 2009 , Page(s): 73 - 77
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (568 KB) |  | HTML iconHTML  

    Peptide binding to major histocompatibility complex (MHC) molecules is a prerequisite for initiating an immune response. This article first describes an approach to predict MHC-peptide-binding sites by using an evolutionary algorithm (EA). The predicted binders are subsequently characterized for their physicochemical properties. The details and implementation issues of the peptide-binding prediction technique are discussed, and the performance comparison with the existing methods is provided. The binding motif derived in silico is used to characterize the physicochemical properties of the experimentally determined binders. View full abstract»

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  • From Frankenstein to the pacemaker

    Publication Year: 2009 , Page(s): 78 - 84
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    This article provides an overview of the development, collections, exhibits, and programs of Bakken Museum, the world's only museum devoted to the history and science of electricity in life. View full abstract»

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  • Effect of microgravity on immune cell viability and proliferation

    Publication Year: 2009 , Page(s): 85 - 90
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (706 KB) |  | HTML iconHTML  

    Exposure to microgravity may produce changes in the performance of the immunological system at the cellular level and in the major physiological systems of the body. Weightlessness suppresses the lymphocytic functions involved in the immunity process, such as cell locomotion and expression of antigen. The present study was designed to investigate whether the proliferation and viability of lymphocytes are reduced by exposure to rotation in a three-dimensional (3-D) clinostat, which is used to simulate the microgravity of cells. The results indicate a nonsignificant decrease in the proliferation and cellular viability to the mitogen stimulation in 24 h of simulated weightlessness (P = 0.146). There was, however, a very significant (P = 0.012) decrease in proliferation and viability after 48 h of rotation in the 3-D clinostat. A comparison between 24 and 48 h of clinorotation indicates a difference between the results (P = 0.003). The present study indicates that the immunological depression associated with the spaceflight is not just related to the psychological and physiological stresses that the astronauts are subjected to, but it also seems to be caused by microgravity per se that affects the proliferation and cellular viability. View full abstract»

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  • Favorite places in the Twin Cities

    Publication Year: 2009 , Page(s): 91 - 93
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  • Medical Device Design for Six Sigma: A Road Map for Safety and Effectiveness (El-Haik, B.S. and Mekki, K.S.; 2008) [Book reviews]

    Publication Year: 2009 , Page(s): 94
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  • Biomaterials--The Intersection of Biology and Materials Science (Temenoff, J.S. et al.; 2008) [Book reviews]

    Publication Year: 2009 , Page(s): 94 - 94, 100
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Aims & Scope

IEEE Engineering in Medicine and Biology Magazine contains articles on current technologies and methods used in biomedical and clinical engineering.

 

This Magazine ceased publication in 2010. The current retitled publication is IEEE Pulse.

Full Aims & Scope