Pub Date : 2010-05-20DOI: 10.1109/EIT.2010.5612188
S. Ababneh, M. Gurcan
To effectively diagnose and monitor the treatment of diseases such as osteoarthritis, the segmentation, processing and analysis of mass volumes of medical images is gaining high importance. In this paper, a new fully automated content-based segmentation framework is proposed. The framework is designed to be compatible with a wide variety of segmentation techniques. To this end, a novel content-based two-pass block discovery mechanism is proposed to provide full automation for image segmentation. The proposed framework uses both training and local image data and disjoint block-wise image scanning to achieve ROI and background block discovery. The detected object and background blocks are then used to initialize and support the segmentation process. The effectiveness of the proposed framework is demonstrated by performing automatic segmentation of the femur and tibia bones in knee osteoarthritis MR images with 96% accuracy. Experimental results are provided which show the effectiveness of the proposed framework.
{"title":"An automated content-based segmentation framework: Application to MR images of knee for osteoarthritis research","authors":"S. Ababneh, M. Gurcan","doi":"10.1109/EIT.2010.5612188","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612188","url":null,"abstract":"To effectively diagnose and monitor the treatment of diseases such as osteoarthritis, the segmentation, processing and analysis of mass volumes of medical images is gaining high importance. In this paper, a new fully automated content-based segmentation framework is proposed. The framework is designed to be compatible with a wide variety of segmentation techniques. To this end, a novel content-based two-pass block discovery mechanism is proposed to provide full automation for image segmentation. The proposed framework uses both training and local image data and disjoint block-wise image scanning to achieve ROI and background block discovery. The detected object and background blocks are then used to initialize and support the segmentation process. The effectiveness of the proposed framework is demonstrated by performing automatic segmentation of the femur and tibia bones in knee osteoarthritis MR images with 96% accuracy. Experimental results are provided which show the effectiveness of the proposed framework.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114469792","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612126
H. Todd
The biggest cyber threat today is insecure applications. Do you write rugged hacker resistant software? If you don't you should! You should know about the threats and how to "bake" security in during each phase of the Software Development Life Cycle (SDLC).
{"title":"Secure applications — Hack-proofing your app","authors":"H. Todd","doi":"10.1109/EIT.2010.5612126","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612126","url":null,"abstract":"The biggest cyber threat today is insecure applications. Do you write rugged hacker resistant software? If you don't you should! You should know about the threats and how to \"bake\" security in during each phase of the Software Development Life Cycle (SDLC).","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114541557","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612193
I. Zyout, I. Abdel-Qader
Segmentation of microcalcifications (MCs) significantly influences the performance of shape-based method for the diagnosis of MCs, which continues to be a challenge as it tends to have high false positive results. Texture based characterization of MCs represents a possible alternative that does not require prior segmentation of MCs and may improve the positive predictive value of automated diagnosis of MCs. This paper presents a new approach to extracting textural features, specifically spectral measures, of mammographie MCs using multiscale Hessian filtering (or equivalently second derivative of Gaussian). Extracted features were individually ranked using Fisher-score criterion, which demonstrated the superior predictive ability of the normalized entropy. A set of mammographie regions (20 malignant and 13 benign cases) from the MIAS database were used to evaluate the classification performance of the proposed spectral features. Utilizing k-nearest neighbor classifier and ROC performance measure, the proposed Hessian based extracted features produced ROC curves with performance index Az = 0.83, which demonstrated the effectiveness of the proposed characterization scheme.
{"title":"Characterization of clustered microcalcifications using multiscale Hessian based feature extraction","authors":"I. Zyout, I. Abdel-Qader","doi":"10.1109/EIT.2010.5612193","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612193","url":null,"abstract":"Segmentation of microcalcifications (MCs) significantly influences the performance of shape-based method for the diagnosis of MCs, which continues to be a challenge as it tends to have high false positive results. Texture based characterization of MCs represents a possible alternative that does not require prior segmentation of MCs and may improve the positive predictive value of automated diagnosis of MCs. This paper presents a new approach to extracting textural features, specifically spectral measures, of mammographie MCs using multiscale Hessian filtering (or equivalently second derivative of Gaussian). Extracted features were individually ranked using Fisher-score criterion, which demonstrated the superior predictive ability of the normalized entropy. A set of mammographie regions (20 malignant and 13 benign cases) from the MIAS database were used to evaluate the classification performance of the proposed spectral features. Utilizing k-nearest neighbor classifier and ROC performance measure, the proposed Hessian based extracted features produced ROC curves with performance index Az = 0.83, which demonstrated the effectiveness of the proposed characterization scheme.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114769262","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612143
R. Hashemian
A new port modeling technique is presented for biasing of analog circuits. The technique uses fixator-norator pairs to pair the biasing design criteria with the power sources — locations and magnitudes — required for the biasing. Because of the operating points (OPs) being specified the technique allows the designer to linearized the circuit not only for the performance (AC) design but also for the large signal biasing design. It is shown that the fixators — nullators plus sources — keep the biasing criteria fixed during the analysis; whereas, the norators act as the place holders for the DC supplies or for the power conducting components. The rules to engage in circuit analysis with fixator-norator pairs are discussed and numerous pitfalls in this category are specified. Finally, two design examples are worked out that clearly demonstrate the capability and power of the proposed technique for biasing of any analog circuit.
{"title":"New port modeling for analog circuit biasing design","authors":"R. Hashemian","doi":"10.1109/EIT.2010.5612143","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612143","url":null,"abstract":"A new port modeling technique is presented for biasing of analog circuits. The technique uses fixator-norator pairs to pair the biasing design criteria with the power sources — locations and magnitudes — required for the biasing. Because of the operating points (OPs) being specified the technique allows the designer to linearized the circuit not only for the performance (AC) design but also for the large signal biasing design. It is shown that the fixators — nullators plus sources — keep the biasing criteria fixed during the analysis; whereas, the norators act as the place holders for the DC supplies or for the power conducting components. The rules to engage in circuit analysis with fixator-norator pairs are discussed and numerous pitfalls in this category are specified. Finally, two design examples are worked out that clearly demonstrate the capability and power of the proposed technique for biasing of any analog circuit.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130248949","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612182
R. Aldunate
Real time situational awareness has the potential to improve the response and management of intelligent transportation system (ITS) components in critical situations. In the event of sudden or potentially dangerous situations, such as hazardous material spills or reckless driving, every second counts to reduce the overall impact of the event. Currently, assessing surface deterioration and identifying unsafe conditions can be costly and timely to a monitoring agency, and often requires traffic control and other delays to the users of a highway system. Utilizing vehicles as probes to sense and collect these data would give traffic and agency planners a continuously updated view of the network. This article introduces a model to analyze the feasibility of achieving near-real-time situational awareness for highway systems by Vehicle Ad-hoc Networks (VANETs). Each vehicle acts as a data collection probe, gathering information such as surface friction and distress, and is enabled with short-range wireless technology, allowing condition awareness broadcasts to be propagated to other vehicles. The analysis suggests it would be possible to provide awareness up to several kilometers away from the location of the issue in a near-real-time manner, provided adequate traffic density. This approach is envisioned to be particularly suitable for critical traffic monitoring, such as in emergency management and homeland security applications related to transportation systems.
{"title":"Understanding the capabilities of a vehicle Ad-hoc Network for highway systems","authors":"R. Aldunate","doi":"10.1109/EIT.2010.5612182","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612182","url":null,"abstract":"Real time situational awareness has the potential to improve the response and management of intelligent transportation system (ITS) components in critical situations. In the event of sudden or potentially dangerous situations, such as hazardous material spills or reckless driving, every second counts to reduce the overall impact of the event. Currently, assessing surface deterioration and identifying unsafe conditions can be costly and timely to a monitoring agency, and often requires traffic control and other delays to the users of a highway system. Utilizing vehicles as probes to sense and collect these data would give traffic and agency planners a continuously updated view of the network. This article introduces a model to analyze the feasibility of achieving near-real-time situational awareness for highway systems by Vehicle Ad-hoc Networks (VANETs). Each vehicle acts as a data collection probe, gathering information such as surface friction and distress, and is enabled with short-range wireless technology, allowing condition awareness broadcasts to be propagated to other vehicles. The analysis suggests it would be possible to provide awareness up to several kilometers away from the location of the issue in a near-real-time manner, provided adequate traffic density. This approach is envisioned to be particularly suitable for critical traffic monitoring, such as in emergency management and homeland security applications related to transportation systems.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117055079","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612169
Yu Cai
People in rural areas are less likely to obtain broadband Internet access due to a combination of economic disadvantage, technical difficulties, and lack of service providers. There is a great need to develop robust, low-cost and easy-to-maintain network management platform for Wireless Internet Service Providers (WISP) in rural areas. The goal of this project is to partner with a small local start-up WISP and relieves some serious management & security problems the company encountered by the provision of an open source network management & monitoring system as well as a robust core router. To achieve the goal, an internal test bed consisting of a Wireless Router Application Platform (WRAP) was setup in a lab environment. Various open-source network applications such as Nagios, Snort, MRTG and Open VPN were customized and integrated. Several business management applications were also developed, including Request Tracker System, MySQL-based customer database, and database-driven web application for management interface. All these systems integrated together will allow a network management team to diagnose and solve network connectivity and security issues accurately and promptly. The survey shows that the proposed solution significantly reduce the company's operation cost and improve the customers' satisfaction.
{"title":"Development of an open source network management & monitoring platform for wireless broadband service provider in rural areas","authors":"Yu Cai","doi":"10.1109/EIT.2010.5612169","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612169","url":null,"abstract":"People in rural areas are less likely to obtain broadband Internet access due to a combination of economic disadvantage, technical difficulties, and lack of service providers. There is a great need to develop robust, low-cost and easy-to-maintain network management platform for Wireless Internet Service Providers (WISP) in rural areas. The goal of this project is to partner with a small local start-up WISP and relieves some serious management & security problems the company encountered by the provision of an open source network management & monitoring system as well as a robust core router. To achieve the goal, an internal test bed consisting of a Wireless Router Application Platform (WRAP) was setup in a lab environment. Various open-source network applications such as Nagios, Snort, MRTG and Open VPN were customized and integrated. Several business management applications were also developed, including Request Tracker System, MySQL-based customer database, and database-driven web application for management interface. All these systems integrated together will allow a network management team to diagnose and solve network connectivity and security issues accurately and promptly. The survey shows that the proposed solution significantly reduce the company's operation cost and improve the customers' satisfaction.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"57 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126562773","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612176
D. Amarandei, M. El-Said
Current Analog Telephone Adaptors (ATA) which are commonly used by small business and home offices to implement Internet telephony applications are designed to work with an audio bandwidth of 300 Hz to 3.4 KHz, a holdover from the one hundred year history of telephone companies trying to accommodate a high volume of calls over copper. Recent network improvements in the last decade allow for a wider bandwidth. However, existing work in wideband audio for telephony has been mainly focused either on mobile telephony or high end teleconferencing equipment but not on ATA devices. This paper proposes improvements to ATA devices that allow an audio bandwidth of 50 Hz to 7 KHz. An implementation is discussed where a minimal upgrade to an open source ATA based on GPL licensed hardware is modified to support wideband, and a middleware layer software is modified to also handle the wider bandwidth. Moreover, promising results when using the modified hardware and software were obtained. The results indicated that with slight CPU overloading, the modified hardware and software can be used for wideband telephony.
{"title":"Implementation of wideband VoIP middleware using embedded systems","authors":"D. Amarandei, M. El-Said","doi":"10.1109/EIT.2010.5612176","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612176","url":null,"abstract":"Current Analog Telephone Adaptors (ATA) which are commonly used by small business and home offices to implement Internet telephony applications are designed to work with an audio bandwidth of 300 Hz to 3.4 KHz, a holdover from the one hundred year history of telephone companies trying to accommodate a high volume of calls over copper. Recent network improvements in the last decade allow for a wider bandwidth. However, existing work in wideband audio for telephony has been mainly focused either on mobile telephony or high end teleconferencing equipment but not on ATA devices. This paper proposes improvements to ATA devices that allow an audio bandwidth of 50 Hz to 7 KHz. An implementation is discussed where a minimal upgrade to an open source ATA based on GPL licensed hardware is modified to support wideband, and a middleware layer software is modified to also handle the wider bandwidth. Moreover, promising results when using the modified hardware and software were obtained. The results indicated that with slight CPU overloading, the modified hardware and software can be used for wideband telephony.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116130760","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612094
J. Kaylor, Konstantin Laufer, G. Thiruvathukal
We present a novel form of intra-volume directory layering with hierarchical, inheritance-like namespace unification. While each layer of an OLFS volume constitutes a subvolume that can be mounted separately in a fan-in configuration, the entire hierarchy is always accessible (online) and fully navigable through any mounted layer. OLFS uses a relational database to store its layering metadata and either a relational database or any (virtual) host file system as its backing store, along with metadata and block caching for improved performance. Because OLFS runs as a virtual file system in user-space, its capabilities are available to all existing software without modification or special privileges. We have developed a reference implementation of OLFS for FUSE based on MySQL and XFS, and conducted performance benchmarking against XFS by itself. We explore several applications of OLFS, such as enhanced server synchronization, transactional file operations, and versioning.
{"title":"Online Layered File System (OLFS): A layered and versioned filesystem and performance analysis","authors":"J. Kaylor, Konstantin Laufer, G. Thiruvathukal","doi":"10.1109/EIT.2010.5612094","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612094","url":null,"abstract":"We present a novel form of intra-volume directory layering with hierarchical, inheritance-like namespace unification. While each layer of an OLFS volume constitutes a subvolume that can be mounted separately in a fan-in configuration, the entire hierarchy is always accessible (online) and fully navigable through any mounted layer. OLFS uses a relational database to store its layering metadata and either a relational database or any (virtual) host file system as its backing store, along with metadata and block caching for improved performance. Because OLFS runs as a virtual file system in user-space, its capabilities are available to all existing software without modification or special privileges. We have developed a reference implementation of OLFS for FUSE based on MySQL and XFS, and conducted performance benchmarking against XFS by itself. We explore several applications of OLFS, such as enhanced server synchronization, transactional file operations, and versioning.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128499113","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612113
J. Renner, H. Zollner, T. Bohnke, Burkart Vos
This paper analyzes the effects of multipath propagation for localization of non-cooperative mobile phones (GMSK modulation) in indoor environments with reinforced concrete walls and metal objects. For localization based on Time Difference of Arrival (TDOA) calculation, cross-correlation of signals received by different sensors yields accurate propagation delays under dominant direct-path conditions. However, parameters like varying transmitter positions and frequency hopping influence the wireless channel causing systematic overestimation of calculated delays, especially under dense multipath conditions. By comparing the results of channel sounding and actual sensor data we try to characterize the non-coherent wireless channel and its multipath propagation effects with respect to TDOA correlation methods.
{"title":"Characterization of dense multipath effects for non-coherent GMSK wireless channels in indoor environments","authors":"J. Renner, H. Zollner, T. Bohnke, Burkart Vos","doi":"10.1109/EIT.2010.5612113","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612113","url":null,"abstract":"This paper analyzes the effects of multipath propagation for localization of non-cooperative mobile phones (GMSK modulation) in indoor environments with reinforced concrete walls and metal objects. For localization based on Time Difference of Arrival (TDOA) calculation, cross-correlation of signals received by different sensors yields accurate propagation delays under dominant direct-path conditions. However, parameters like varying transmitter positions and frequency hopping influence the wireless channel causing systematic overestimation of calculated delays, especially under dense multipath conditions. By comparing the results of channel sounding and actual sensor data we try to characterize the non-coherent wireless channel and its multipath propagation effects with respect to TDOA correlation methods.","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"126 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128029275","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 : 2010-05-20DOI: 10.1109/EIT.2010.5612184
M. Bataineh, Lun Huang, Alicia Fuente Acedo, G. Atkin, N. Menhart
Informational analysis of genetic sequences has revealed the existence of significant analogies between the genetic process and information processing systems used in the field of communications engineering. By analyzing key elements involved in the process of gene expression, we have developed several communications and coding theory based models for the process of translation [1–5]. A previous research investigated the use of coding theory based models that quantitatively describe the behavior of the ribosome during translation initiation in prokaryotic organisms [1]. In this paper we have investigated an augmented block code model with modified criteria and assumptions. We have also employed several minimum distance decoders to verify the proposed modified model based on the free energies involved in the binding between the ribosome and the mRNA sequence. The key biological elements considered in forming the investigated model are: the last 13 bases of the 3' end of the 16S rRNA molecule, the common features of bacterial ribosomal binding sites (such as the existence and location of the Shine-Dalgarno sequence), the energies involved in the rRNA-mRNA interaction, and RNA/DNA base-pairing principles. The model was tested on five different E. coli bacterial genomes. The obtained results prove the validity and significance of the model in clearly distinguishing four different test groups of gene predictions. Two of them are based on well known gene finder softwares (e.g. GeneMark [2] and Glimmer [3]).
{"title":"An augmented block code model for protein translation using free energy based distance decoders","authors":"M. Bataineh, Lun Huang, Alicia Fuente Acedo, G. Atkin, N. Menhart","doi":"10.1109/EIT.2010.5612184","DOIUrl":"https://doi.org/10.1109/EIT.2010.5612184","url":null,"abstract":"Informational analysis of genetic sequences has revealed the existence of significant analogies between the genetic process and information processing systems used in the field of communications engineering. By analyzing key elements involved in the process of gene expression, we have developed several communications and coding theory based models for the process of translation [1–5]. A previous research investigated the use of coding theory based models that quantitatively describe the behavior of the ribosome during translation initiation in prokaryotic organisms [1]. In this paper we have investigated an augmented block code model with modified criteria and assumptions. We have also employed several minimum distance decoders to verify the proposed modified model based on the free energies involved in the binding between the ribosome and the mRNA sequence. The key biological elements considered in forming the investigated model are: the last 13 bases of the 3' end of the 16S rRNA molecule, the common features of bacterial ribosomal binding sites (such as the existence and location of the Shine-Dalgarno sequence), the energies involved in the rRNA-mRNA interaction, and RNA/DNA base-pairing principles. The model was tested on five different E. coli bacterial genomes. The obtained results prove the validity and significance of the model in clearly distinguishing four different test groups of gene predictions. Two of them are based on well known gene finder softwares (e.g. GeneMark [2] and Glimmer [3]).","PeriodicalId":305049,"journal":{"name":"2010 IEEE International Conference on Electro/Information Technology","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132464756","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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