2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)最新文献

{"title":"GPU-SD and DPD parallelization for Gromacs tools for molecular dynamics simulations","authors":"N. Goga, S. Marrink, Ruxandra Cioromela, F. Moldoveanu","doi":"10.1109/BIBE.2012.6399683","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399683","url":null,"abstract":"This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynamics systems developed by the Molecular Dynamics Group, University of Groningen, the Netherlands. One should note that molecular dynamics simulations are time-consuming simulations of systems, running time ranging from days to weeks and months. Therefore parallelization is a key issue for the well-running and use of MD software. The paper presents the main ingredients of GPU parallelization of the new algorithms and simulation results. It can be concluded that the parallelization through the use of graphical cards improves the performances of the runs as compared to the serial version of the code.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134358472","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":"Lateral resolution improvement in Optical Coherence Tomography (OCT) images","authors":"Evgenia Bousi, C. Pitris","doi":"10.1109/BIBE.2012.6399740","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399740","url":null,"abstract":"A novel method for lateral resolution improvement of Optical Coherence Tomography (OCT) images, which is independent of the focusing of the delivery optics and the depth of field, is presented. This method was inspired by radar range oversampling techniques. It is based on the lateral oversampling of the image and the estimation of the locations of the multiple scatterers which contribute to the signal. The information in the oversampled images is used to estimate the locations of multiple scatterers assuming each contributes a weighted portion to the detected signal, the weight determined by the location of the scatterer and the point spread function (PSF) of the system. A priori knowledge of the PSF is not required since optimization techniques can be employed to achieve the best possible enhancement of the image resolution. Preliminary results of such an approach on laterally oversampled OCT images have shown that it is possible to achieve a two-fold lateral resolution improvement. Moreover by performing deconvolution with the new improved PSF the lateral resolution can be further improved by another factor of two for a total of 4x improvement. Such improvement can be significant, especially in cases where the Numerical Aperture (NA) of the delivery optics is limited, such as, for example, in the case of ophthalmic imaging where the optics of the eye itself limit the lateral resolution.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"292 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131605615","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":"Predicting GPCR and enzymes function with a global approach based on LCS","authors":"L. M. Romão, J. C. Nievola","doi":"10.1109/BIBE.2012.6399665","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399665","url":null,"abstract":"The families of G-Protein Coupled Receptor (GPCR) and enzymes are among the main protein family. They represent to the scientific and medical communities, a significant target for bioactive and drug discovery programs. The model of classification of enzymes and GPCR is characterized by its hierarchical structure in format of tree and this makes more difficult its prediction. In this work we propose an adapted version of Learning Classifier Systems (LCS) data mining algorithm which tends to be more efficient than statistical methods based on homology used in tool such as PSI-BLAST. Hence, a new global model approach, called HLCS (Hierarchical Learning Classifier System) is used to predict the function of enzymes and GPCR, respecting its organizational structure of classes throughout the model development. The HLCS is expressed as a set of IF-THEN classification rules, which have the advantage of representing comprehensible knowledge to biologist users. The HLCS is evaluated with eight datasets from enzymes and GPCR, and compared with a Global Naive Bayes algorithm, named GMNB. In the tests realized the HLCS outperformed the GMNB in the databases of the GPCR proteins group type.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"47 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114097241","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 predictive control approach and interactive GUI to enhance distal environment rendering during robotized tele-echography: Interactive platform for robotized telechography","authors":"P. Vieyres, L. Josserand, Marco Chiccoli, Juan Sebastián Sandoval Arévalo, N. Morette, C. Novales, A. Fonte, Soteris Avgousti, S. Voskarides, T. Kasparis","doi":"10.1109/BIBE.2012.6399680","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399680","url":null,"abstract":"Performing a robotized telemedicine act via specific networks brings forth two issues. One is transparency in order to enable the operator, e.g. the medical ultrasound specialist, to safely and accurately perform bilateral tele-operation tasks despite the long time delays inherent to the communication link. To counter these effects, two strategies are combined to improve, at the operator site, the rendering of the interactions between the remote robotic systems with its environment (i.e. the patient), and the control of the robot's orientation. The first approach is the development of a new control architecture based on an internal model providing an anticipated value of the distant environment stiffness; it is complemented with a graphic user interface (GUI) which provides the expert with the real-time relative position of the haptic probe with the robot's end effector for a better tele-operated control. These combined strategies provide the expert with an improved interactive tool for a tele-diagnosis.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125226469","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":"Analysis of DNA methylation epidemiological data through a generic composite statistical framework","authors":"I. Valavanis, E. Sifakis, P. Georgiadis, S. Kyrtopoulos, A. Chatziioannou","doi":"10.1109/BIBE.2012.6399775","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399775","url":null,"abstract":"DNA methylation events represent epigenetic heritable modifications that regulate gene expression by affecting chromatin remodeling. They are encountered more often in CpG rich promoter regions, while they do not alter the DNA sequence itself. High-volume DNA methylation profiling methods exploit microarray technologies and provide a wealth of data. This data solicits rigorous, generic, yet ad-hoc adjusted, analytical pipelines for the meaningful systems-level analysis and interpretation. In this work, the Illumina Infinium HumanMethylation450 BeadChip platform is utilized in an epidemiological cohort from Italy in an effort to correlate interesting methylation patterns with breast cancer predisposition. The composite computational framework proposed here builds upon well established, analytical techniques, employed in mRNA analysis. For analysis purposes, the log2(ratio) of the intensities of a Methylated probe (IMeth) versus an UnMethylated probe (IUn-Meth), quoted as M-value, is used. Intensity based correction of the M-signal distribution is systematically applied, based upon Intensity-related error measures from quality controls samples incorporated in each chip. Thus, batch effects are corrected, while probe-specific, intensity-related, error measures are considered too. Robust, (based on bootstrapping) statistical measures measuring biological variation at the probe level, are derived in order to propose candidate biomarkers. To this end, coefficient variation measurements of DNA methylation between controls and cases are utilized, alleviating simultaneously the impact of technical variation, and are juxtaposed to classical statistical differential analysis measures.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121160418","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":"Biological interaction networks based on sparse temporal expansion of graphical models","authors":"K. Kalantzaki, E. Bei, M. Garofalakis, M. Zervakis","doi":"10.1109/BIBE.2012.6399721","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399721","url":null,"abstract":"Biological networks are often described as probabilistic graphs in the context of gene and protein sequence analysis in molecular biology. Microarrays and proteomics technology allow the monitoring of expression levels over thousands of biological units over time. In experimental efforts we are interested in unveiling pairwise interactions. Many graphical models have been introduced in order to discover associations from the expression data analysis. However, the small size of samples compared to the number of observed genes/proteins makes the inference of the network structure quite challenging. In this study we generate gene-protein networks from sparse experimental data using two methods, partial correlations and Kernel Density Estimation, in order to capture genetic interactions. Dynamic Gaussian analysis is used to match special characteristics to genes and proteins at different time stages utilizing the KDE method for expressing Gaussian associations with non-linear parameters.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121340843","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":"Strengths and weaknesses of the European concept of informed consent: Theoretical issues and practical examples","authors":"N. Forgó, M. Góralczyk, C. Rex","doi":"10.1109/BIBE.2012.6399776","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399776","url":null,"abstract":"A general overview of the legal requirements for consent in health in European Union is presented and a comparison between three different usage of consent is being offered: consent for care; consent for clinical trial participation and consent for data processing. On a second stage a practical example of the strengths and weaknesses of the European concept of informed consent, the research project Linked2Safety is presented. Particular attention is being paid to the involved patients in the project, the different types of consent and the phases of the project as well as the data within the project.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121382746","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":"Development of a Knowledge Base for smart screening of language disorders in primary care","authors":"María Luisa Martín Ruiz, Miguel Valero, Iván Pau, M. Lucas, Maria Peñafiel Puerto","doi":"10.1109/BIBE.2012.6399660","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399660","url":null,"abstract":"Monitoring of neuro-evolutive development from birth until the age of six is a decisive factor in a child's quality of life. Early detection of development disorders in early childhood can facilitate necessary diagnosis and/or treatment. Primary-care pediatricians play a key role in early detection of development alterations as they can undertake the preventive and therapeutic actions necessary in the interest of a child's optimal development. The focus of this research paper is the construction of a Knowledge Base for smart screening aimed to assist pediatricians in processes of early referral in language disorders. The proposed model provides health professionals with a decision-making tool that supports referral processes. In this way, essential diagnostic and/or therapeutic actions are triggered for a comprehensive individual development. The resulting system was developed on the basis of an analysis and verification of 21 cases of children with language disorders.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126862720","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 theoretical mathematical modeling of Parkinson's disease using Fuzzy Cognitive Maps","authors":"P. Groumpos, Antigoni P. Anninou","doi":"10.1109/BIBE.2012.6399748","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399748","url":null,"abstract":"The mathematical model of medical problems is considered. The aim of this paper is to present a new approach in modeling the disease of Parkinson using Fuzzy Cognitive Maps (FCM). Basic theories of FCMs are reviewed and presented. Decision Support Systems (DSS) for Medical problems are considered. The disease of Parkinson is mathematically modeled using Fuzzy Cognitive Maps and three (3) experts. Linguistic variables are proposed and used to describe the correlation among concepts of the FCM. Simulations are performed and very interesting results are obtained and discussed.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"123 13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126887214","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":"Evaluation of wound healing process based on texture analysis","authors":"C. Loizou, T. Kasparis, Orthodoxia Mitsi, Michalis Polyviou","doi":"10.1109/BIBE.2012.6399754","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399754","url":null,"abstract":"Wound healing rate, remains an interesting and important issue, in which modern imaging techniques have not yet given a definitive answer. In order to guide better therapeutic interventions, a better understanding of the fundamental mechanisms driving tissue repair are required. The wound healing rate is primarily quantified by the rate of change of the wound's surface area. The objective of this study was to establish a standardised and objective technique to asses the progress of wound healing in foot by means of texture analysis. The methods of image pre-processing, segmentation and texture analysis together with visual expert's evaluation were used to assess the wound healing process. A total of 40 digital images from ten different subjects with food wounds were taken every third day, for 12 days, by an inexpensive digital camera under variable lighting conditions. The images were intensity normalized, and wounds were automatic segmented using a snake's segmentation system. From the segmented wounds 15 different texture characteristics and 4 different geometrical features were extracted in order to identify features that quantify the rate of wound healing. We found texture characteristics that may indicate the progression of wound healing process. More specifically, some texture features increase (mean, contrast), while some other texture features decrease (entropy, sum of squares variance, sum average, sum variance) with the progression of the wound healing process. Some of these features were found to be significantly different in a specific time point and this could be used to indicate the rate of wound healing. No significant differences were found for all geometrical measures. The results of this study suggest that some texture features might be used to monitor the wound healing process, thus reducing the workload of experts, provide standardization, reduce costs, and improve the quality for patients. The simplicity of the method also suggests that it may be a valuable tool in clinical wound evaluation. Future work will incorporate additional texture and geometrical features for assessing the wound healing process in order to be used in the real clinical praxis.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"177 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115306581","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}