Pub Date : 2008-12-08DOI: 10.1109/BIBE.2008.4696646
Thanasis Fokas
The language of mind is electrical signaling. In this sense, Electroencephalography (EEG) and Magnetoencephalography (MEG) allow us to record in real time brain conversations. For this reason the combined use of EEG and MEG has important application both in clinical medicine as well as in the search for consciousness. Recent developments in the mathematical formalism of EEG and MEG would be presented.
{"title":"\"An effective approach to Magnetoencephalography\"","authors":"Thanasis Fokas","doi":"10.1109/BIBE.2008.4696646","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696646","url":null,"abstract":"The language of mind is electrical signaling. In this sense, Electroencephalography (EEG) and Magnetoencephalography (MEG) allow us to record in real time brain conversations. For this reason the combined use of EEG and MEG has important application both in clinical medicine as well as in the search for consciousness. Recent developments in the mathematical formalism of EEG and MEG would be presented.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126143707","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}
Pub Date : 2008-12-08DOI: 10.1109/BIBE.2008.4696643
N. Thakor
Neuroengineering is one of the fastest growing disciplines in the Biomedical Engineering community, especially in societies such as IEEE Engineering in Medicine in Biology and Medicine. I will begin my presentation with the overview of the field of Neuroengineering, spanning the cellular to brain, and from basic bench research to clinical applications. Progress in the field is covered by the journals such as the IEEE Transactions on Neural Systems and Rehabilitation Engineering that I am Editor in Chief of, covers this field. Within the field of Neuroengineering, and the journal, the ldquohot topicrdquo is brain machine interface, particularly the development of neural prostheses. I will present the basic ideas behind building the brain machine interface and expand to our recent work on the development of a dexterous arm and neural control of this dexterous arm prosthesis. The talk will present the technology, signal processing methods, the neuroscience foundations, and our work on controlling dexterous finger motions from neural signals. I will conclude the talk with some thoughts on the technological challenges faced in building the interfaces to brain and potential applications of tapping into the powers of the mind.
{"title":"\"Frontiers of Neuroengineering with focus on brain machine interface and neural prostheses\"","authors":"N. Thakor","doi":"10.1109/BIBE.2008.4696643","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696643","url":null,"abstract":"Neuroengineering is one of the fastest growing disciplines in the Biomedical Engineering community, especially in societies such as IEEE Engineering in Medicine in Biology and Medicine. I will begin my presentation with the overview of the field of Neuroengineering, spanning the cellular to brain, and from basic bench research to clinical applications. Progress in the field is covered by the journals such as the IEEE Transactions on Neural Systems and Rehabilitation Engineering that I am Editor in Chief of, covers this field. Within the field of Neuroengineering, and the journal, the ldquohot topicrdquo is brain machine interface, particularly the development of neural prostheses. I will present the basic ideas behind building the brain machine interface and expand to our recent work on the development of a dexterous arm and neural control of this dexterous arm prosthesis. The talk will present the technology, signal processing methods, the neuroscience foundations, and our work on controlling dexterous finger motions from neural signals. I will conclude the talk with some thoughts on the technological challenges faced in building the interfaces to brain and potential applications of tapping into the powers of the mind.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129410772","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}
Pub Date : 2008-12-08DOI: 10.1109/BIBE.2008.4696638
G. Chrousos
Life exists through maintenance of a complex dynamic equilibrium, or homeostasis, that is constantly challenged by intrinsic or extrinsic adverse forces, or stressors. Stress is the state of threatened or perceived as threatened homeostasis re-established by a complex repertoire of physiologic and behavioral adaptive responses. Neuroendocrine hormones play crucial roles in the coordination of both basal and threatened homeostasis and mediate the pathogenesis of dyshomeostatic or cacostatic disease states. The stress response is subserved by the stress system, located both in the central nervous system and periphery. The principal central effectors are highly interlinked, and include the hypothalamic corticotropin-releasing hormone, arginine vasopressin, and proopiomelanocortin-derived peptides, and the brainstem locus caeruleus and central autonomic norepinephrine centers. The targets of these effectors are the brain, including the executive/cognitive, reward, and fear systems and the wake/sleep centers, the growth, thyroid and reproductive axes, as well as the gastrointestinal, cardiorespiratory, metabolic, and immune systems. Appropriate basal activity and responsiveness of the stress system to stressors is a crucial prerequisite for a sense of wellbeing, successful performance of tasks, and positive social interactions. By contrast, inappropriate basal activity and responsiveness of this system may impair growth, development and body composition, and account for many neurobehavioral, endocrine, metabolic, cardiovascular, autoimmune, and allergic disorders.
{"title":"\"Science and technology: Genes, brain, stress and evolution\"","authors":"G. Chrousos","doi":"10.1109/BIBE.2008.4696638","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696638","url":null,"abstract":"Life exists through maintenance of a complex dynamic equilibrium, or homeostasis, that is constantly challenged by intrinsic or extrinsic adverse forces, or stressors. Stress is the state of threatened or perceived as threatened homeostasis re-established by a complex repertoire of physiologic and behavioral adaptive responses. Neuroendocrine hormones play crucial roles in the coordination of both basal and threatened homeostasis and mediate the pathogenesis of dyshomeostatic or cacostatic disease states. The stress response is subserved by the stress system, located both in the central nervous system and periphery. The principal central effectors are highly interlinked, and include the hypothalamic corticotropin-releasing hormone, arginine vasopressin, and proopiomelanocortin-derived peptides, and the brainstem locus caeruleus and central autonomic norepinephrine centers. The targets of these effectors are the brain, including the executive/cognitive, reward, and fear systems and the wake/sleep centers, the growth, thyroid and reproductive axes, as well as the gastrointestinal, cardiorespiratory, metabolic, and immune systems. Appropriate basal activity and responsiveness of the stress system to stressors is a crucial prerequisite for a sense of wellbeing, successful performance of tasks, and positive social interactions. By contrast, inappropriate basal activity and responsiveness of this system may impair growth, development and body composition, and account for many neurobehavioral, endocrine, metabolic, cardiovascular, autoimmune, and allergic disorders.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"434 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115934776","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}
Pub Date : 2008-12-08DOI: 10.1109/BIBE.2008.4696645
G. Dassios
The existing mathematical models for tumour growth, to a large extent, are new and not well established as of today. This is mainly due to the fact that there are many known and unknown factors that enter the process of malignant tumour development, and no convincing arguments about their relative importance are generally established. As a consequence of this search for a credible model, almost every tumour model that has been investigated so far refers to the highly symmetric case of the spherical geometry, where the curvature is a global invariant over its outer surface. Hence, no information about the effects of the local curvature upon the shape of the exterior proliferating boundary is available. In this presentation, we discuss first the standard Greenspan model for a spherical tumour, where the basic ideas are presented, and then we extend the model to that of triaxial ellipsoidal geometry. In this way, we elevate fundamental qualitative characteristics of the growth process that are invisible in spherical geometry. One such thing is the effect of the local mean curvature on the development of the outer boundary of the tumour, as it is governed by the Young-Laplace law, which controls the interface between two non-mixing fluids. A second advantage of the ellipsoidal model is due to the way the confocal system is generated. Indeed, in contrast to the spherical system which springs out of a central point, the confocal ellipsoidal system starts out as an inflated focal ellipse which, if it is interpreted as a biological membrane, provides a much more realistic candidate for tumour genesis. Nevertheless, the investigation of the ellipsoidal model of a tumour growth is by no means completed, and a lot of further study needs to be done before final conclusions on the effects of curvature variations are drawn.
{"title":"\"On growth of ellipsoidal tumours\"","authors":"G. Dassios","doi":"10.1109/BIBE.2008.4696645","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696645","url":null,"abstract":"The existing mathematical models for tumour growth, to a large extent, are new and not well established as of today. This is mainly due to the fact that there are many known and unknown factors that enter the process of malignant tumour development, and no convincing arguments about their relative importance are generally established. As a consequence of this search for a credible model, almost every tumour model that has been investigated so far refers to the highly symmetric case of the spherical geometry, where the curvature is a global invariant over its outer surface. Hence, no information about the effects of the local curvature upon the shape of the exterior proliferating boundary is available. In this presentation, we discuss first the standard Greenspan model for a spherical tumour, where the basic ideas are presented, and then we extend the model to that of triaxial ellipsoidal geometry. In this way, we elevate fundamental qualitative characteristics of the growth process that are invisible in spherical geometry. One such thing is the effect of the local mean curvature on the development of the outer boundary of the tumour, as it is governed by the Young-Laplace law, which controls the interface between two non-mixing fluids. A second advantage of the ellipsoidal model is due to the way the confocal system is generated. Indeed, in contrast to the spherical system which springs out of a central point, the confocal ellipsoidal system starts out as an inflated focal ellipse which, if it is interpreted as a biological membrane, provides a much more realistic candidate for tumour genesis. Nevertheless, the investigation of the ellipsoidal model of a tumour growth is by no means completed, and a lot of further study needs to be done before final conclusions on the effects of curvature variations are drawn.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133112953","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}
Pub Date : 2008-12-08DOI: 10.1109/BIBE.2008.4696641
J. Duncan
The development of methods to accurately and reproducibly recover useful quantitative information from medical images is often hampered by uncertainties in handling the data related to: image acquisition parameters, the variability of normal human anatomy and physiology, the presence of disease or other abnormal conditions, and a variety of other factors. This talk will review image analysis strategies that make use of models based on geometrical and physical/biomechanical information to help constrain the range of possible solutions in the presence of such uncertainty. The discussion will be focused by looking primarily at several problem areas in the realms of neuroanatomical structure analysis and cardiac function analysis, along with some work in cellular image analysis, with an emphasis on image segmentation and motion/deformation tracking. The presentation will include a description of the problem areas and visual examples of the image datasets being used, an overview of the mathematical techniques involved and a presentation of results obtained when analyzing actual patient image data using these methods. Emphasis will be placed on how image-derived information and appropriate modeling can be used together to address the image analysis and processing problems noted above.
{"title":"\"Model-based strategies for biomedical image analysis\"","authors":"J. Duncan","doi":"10.1109/BIBE.2008.4696641","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696641","url":null,"abstract":"The development of methods to accurately and reproducibly recover useful quantitative information from medical images is often hampered by uncertainties in handling the data related to: image acquisition parameters, the variability of normal human anatomy and physiology, the presence of disease or other abnormal conditions, and a variety of other factors. This talk will review image analysis strategies that make use of models based on geometrical and physical/biomechanical information to help constrain the range of possible solutions in the presence of such uncertainty. The discussion will be focused by looking primarily at several problem areas in the realms of neuroanatomical structure analysis and cardiac function analysis, along with some work in cellular image analysis, with an emphasis on image segmentation and motion/deformation tracking. The presentation will include a description of the problem areas and visual examples of the image datasets being used, an overview of the mathematical techniques involved and a presentation of results obtained when analyzing actual patient image data using these methods. Emphasis will be placed on how image-derived information and appropriate modeling can be used together to address the image analysis and processing problems noted above.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125972231","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}
Pub Date : 2008-12-08DOI: 10.1109/BIBE.2008.4696642
L. Gatzoulis
For almost two decades now, significant and systematic support has been given to research activities in the domain of ehealth through the framework Programmes of the European Commission. This investment has helped the deployment of ehealth infrastructure, tools and services like regional health networks, electronic prescriptions and electronic health records in primary care. Research activities in ehealth in Europe continue under the latest 7 th Research framework programme (FP7), with increased budgetary support. Their aim is to help healthcare delivery systems cope with the pressure and challenges which arise from several factors such as the demographic change and the prevalence of chronic diseases. Two main directions of research refer to the domains of ldquopersonal health systemsrdquo and ldquovirtual physiological humanrdquo. The speech will outline the activities in these domains and how these contribute to the vision of ldquoperson-centricrdquo care, meaning: 1. empowerment of individuals to manage their health conditions and lifestyles 2. development of personalised solutions for efficient treatment or management of chronic diseases, early diagnosis and prevention, as well as prediction of onset of diseases.
{"title":"\"Recent research activitiesin Europe: Supporting the evolution of healthcare\"","authors":"L. Gatzoulis","doi":"10.1109/BIBE.2008.4696642","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696642","url":null,"abstract":"For almost two decades now, significant and systematic support has been given to research activities in the domain of ehealth through the framework Programmes of the European Commission. This investment has helped the deployment of ehealth infrastructure, tools and services like regional health networks, electronic prescriptions and electronic health records in primary care. Research activities in ehealth in Europe continue under the latest 7 th Research framework programme (FP7), with increased budgetary support. Their aim is to help healthcare delivery systems cope with the pressure and challenges which arise from several factors such as the demographic change and the prevalence of chronic diseases. Two main directions of research refer to the domains of ldquopersonal health systemsrdquo and ldquovirtual physiological humanrdquo. The speech will outline the activities in these domains and how these contribute to the vision of ldquoperson-centricrdquo care, meaning: 1. empowerment of individuals to manage their health conditions and lifestyles 2. development of personalised solutions for efficient treatment or management of chronic diseases, early diagnosis and prevention, as well as prediction of onset of diseases.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126005705","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}
Pub Date : 2008-10-01DOI: 10.1109/BIBE.2008.4696639
Metin Akay
Recent advances in medical technology have significantly improved the human health in developed countries. However, these advances remain out of touch for much of the worldpsilas population. We still face unprecedented healthcare challenges in the 21st century. The prevalence of major diseases today, from the global AIDS pandemic to antibiotic-resistant tuberculosis, cuts across the healthcare, political, economic, social, and biomedical disciplines: These diseases will continue affecting the world unless major measures are taken to develop comprehensive prevention and treatment programs. Thus, biomedical engineers are expected to play a critical role in developing novel and affordable medical technology and drugs to solve global healthcare problems, especially in the developing countries. In this talk, we discuss the healthcare systems, financing, delivery and management in the world, recent advances in information technologies in biomedicine and their use in diagnosing, treating, and preventing diseases, using novel technologies to develop new drugs, technology regulation, and ethical issues surrounding the use of novel technologies.
{"title":"\"Biomedical engineering for global healthcare\"","authors":"Metin Akay","doi":"10.1109/BIBE.2008.4696639","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696639","url":null,"abstract":"Recent advances in medical technology have significantly improved the human health in developed countries. However, these advances remain out of touch for much of the worldpsilas population. We still face unprecedented healthcare challenges in the 21st century. The prevalence of major diseases today, from the global AIDS pandemic to antibiotic-resistant tuberculosis, cuts across the healthcare, political, economic, social, and biomedical disciplines: These diseases will continue affecting the world unless major measures are taken to develop comprehensive prevention and treatment programs. Thus, biomedical engineers are expected to play a critical role in developing novel and affordable medical technology and drugs to solve global healthcare problems, especially in the developing countries. In this talk, we discuss the healthcare systems, financing, delivery and management in the world, recent advances in information technologies in biomedicine and their use in diagnosing, treating, and preventing diseases, using novel technologies to develop new drugs, technology regulation, and ethical issues surrounding the use of novel technologies.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125647838","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}
Pub Date : 2008-10-01DOI: 10.1109/BIBE.2008.4696647
E. Bongcam-Rudloff
For future European biobanks and genetic epidemiology projects it is essential to produce standards operating procedures (SOP) for efficient handling of the quality-control and data merging issues from different data sets. Along with databases detailing sample collections it is also necessary to ensure early access to important new research tools, and that state-of-the-art techniques are readily available. I will during this talk present some background information and I will then speak more in detail about a database that we propose can be used to complements the databases focused on the collection of samples of human and animal origin from well-characterized populations. MolMeth (Molecular Methods database) is a database system that catalogs laboratory protocols and methods for the life sciences. It is of particular value for large-scale applications in biobanks and systems biology, but also provides value in scientific communication about molecular procedures in general. It is designed to meet a growing need for structure in protocol specifications while offering convenience for contributors and easy access for end users. Structured protocols offer several advantages over current "flat file" protocol databases, such as allowing protocol presentation be adapted for different purposes. It also provides a foundation for automated reasoning regarding protocols.
{"title":"\"Biobanks, biomolecular resources and bioinformatics for health care and medical research in Europe\"","authors":"E. Bongcam-Rudloff","doi":"10.1109/BIBE.2008.4696647","DOIUrl":"https://doi.org/10.1109/BIBE.2008.4696647","url":null,"abstract":"For future European biobanks and genetic epidemiology projects it is essential to produce standards operating procedures (SOP) for efficient handling of the quality-control and data merging issues from different data sets. Along with databases detailing sample collections it is also necessary to ensure early access to important new research tools, and that state-of-the-art techniques are readily available. I will during this talk present some background information and I will then speak more in detail about a database that we propose can be used to complements the databases focused on the collection of samples of human and animal origin from well-characterized populations. MolMeth (Molecular Methods database) is a database system that catalogs laboratory protocols and methods for the life sciences. It is of particular value for large-scale applications in biobanks and systems biology, but also provides value in scientific communication about molecular procedures in general. It is designed to meet a growing need for structure in protocol specifications while offering convenience for contributors and easy access for end users. Structured protocols offer several advantages over current \"flat file\" protocol databases, such as allowing protocol presentation be adapted for different purposes. It also provides a foundation for automated reasoning regarding protocols.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131020804","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}
Pub Date : 2007-11-05DOI: 10.1109/BIBE.2007.4375529
A. Dunker, C. Oldfield, Jingwei Meng, P. Romero, Jack Y. Yang, Z. Obradovic, V. Uversky
About 10 years ago we published our first predictor of intrinsically disordered protein residues in another IEEE journal, the Proceedings of the IEEE International Conference on Neural Networks. Others call such proteins "natively unfolded" and "intrinsically unstructured." Since then, we and others have substantially improved the prediction of intrinsically disordered residues. The prediction of protein intrinsic disorder is similar to the prediction of secondary structure in terms of methodology, but, at the structural level, secondary structure (especially random coil) and intrinsic disorder differ completely in their dynamic motion. First, we will briefly describe the prediction of protein disorder, show the progress from ~ 70 % to ~ 85 % per residue prediction accuracy, and show that intrinsically disordered proteins are common over the three domains of life, but are especially common among the eukaryotes. Next we will discuss our methods for deducing functions that are associated with disordered rather than structured proteins. In brief, structured proteins have advantages for catalysis while disordered proteins and regions have advantages for the reversible, weak binding often observed in signaling, control, and regulation. After that we will discuss how disorder facilitates binding diversity in protein-protein interaction networks, both for single disordered regions binding to many partners and for many disordered regions with different sequences binding to a common site on the surface of one structured protein. Part three presents data indicating that alternative splicing is more prevalent in regions of RNA that code for disorder than those that code for structure, thus providing a means for evolving tissue-specific signaling networks. Finally, we will present a novel approach to drug discovery based on disordered protein.
{"title":"Intrinsically Disordered Proteins: Predictions and Applications","authors":"A. Dunker, C. Oldfield, Jingwei Meng, P. Romero, Jack Y. Yang, Z. Obradovic, V. Uversky","doi":"10.1109/BIBE.2007.4375529","DOIUrl":"https://doi.org/10.1109/BIBE.2007.4375529","url":null,"abstract":"About 10 years ago we published our first predictor of intrinsically disordered protein residues in another IEEE journal, the Proceedings of the IEEE International Conference on Neural Networks. Others call such proteins \"natively unfolded\" and \"intrinsically unstructured.\" Since then, we and others have substantially improved the prediction of intrinsically disordered residues. The prediction of protein intrinsic disorder is similar to the prediction of secondary structure in terms of methodology, but, at the structural level, secondary structure (especially random coil) and intrinsic disorder differ completely in their dynamic motion. First, we will briefly describe the prediction of protein disorder, show the progress from ~ 70 % to ~ 85 % per residue prediction accuracy, and show that intrinsically disordered proteins are common over the three domains of life, but are especially common among the eukaryotes. Next we will discuss our methods for deducing functions that are associated with disordered rather than structured proteins. In brief, structured proteins have advantages for catalysis while disordered proteins and regions have advantages for the reversible, weak binding often observed in signaling, control, and regulation. After that we will discuss how disorder facilitates binding diversity in protein-protein interaction networks, both for single disordered regions binding to many partners and for many disordered regions with different sequences binding to a common site on the surface of one structured protein. Part three presents data indicating that alternative splicing is more prevalent in regions of RNA that code for disorder than those that code for structure, thus providing a means for evolving tissue-specific signaling networks. Finally, we will present a novel approach to drug discovery based on disordered protein.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"7 4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115467454","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}
Pub Date : 2007-10-01DOI: 10.1109/BIBE.2007.4375716
A. E. D. L. Serna
Systolic implementations of dynamic programming solutions that utilize a similarity matrix can achieve appreciable performance with both course-and fine-grain parallelization. A limitation of systolic array design is that score routing between array elements, array I/O bandwidth, and score memory capacity are dependent upon the length of the sequence that can be processed. A novel approach of differential scoring is presented that exploits adjacency and decouples the complexity of score routing and systolic array bandwidth to sequence length. Instead, these design parameters become a function of algorithm sensitivity. As a consequence, the Simile implementation of differential scoring for sequence alignment has reduced score routing, I/O bandwidth, and score storage by 82% for sequences of length 10 and has significantly improved gate count, clock rate, and power utilization per systolic processing element.
{"title":"Differential Scoring for Systolic Sequence Alignment","authors":"A. E. D. L. Serna","doi":"10.1109/BIBE.2007.4375716","DOIUrl":"https://doi.org/10.1109/BIBE.2007.4375716","url":null,"abstract":"Systolic implementations of dynamic programming solutions that utilize a similarity matrix can achieve appreciable performance with both course-and fine-grain parallelization. A limitation of systolic array design is that score routing between array elements, array I/O bandwidth, and score memory capacity are dependent upon the length of the sequence that can be processed. A novel approach of differential scoring is presented that exploits adjacency and decouples the complexity of score routing and systolic array bandwidth to sequence length. Instead, these design parameters become a function of algorithm sensitivity. As a consequence, the Simile implementation of differential scoring for sequence alignment has reduced score routing, I/O bandwidth, and score storage by 82% for sequences of length 10 and has significantly improved gate count, clock rate, and power utilization per systolic processing element.","PeriodicalId":147263,"journal":{"name":"International Conferences on Biological Information and Biomedical Engineering","volume":"142 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123422382","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}
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