{"title":"Efficient alignment of next generation sequencing data using MapReduce on the cloud","authors":"Rawan AlSaad, Q. Malluhi, M. Abouelhoda","doi":"10.1109/CIBEC.2012.6473312","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473312","url":null,"abstract":"This paper presents a methodology for running NGS read mapping tools in the cloud environment based on the MapReduce programming paradigm. As a demonstration, the recently developed and robust sequence alignment tool, BFAST, is used within our methodology to handle massive datasets. The results of our experiments show that the transformation of existing read mapping tools to run within the MapReduce framework dramatically reduces the total execution time and enables the user to utilize the resources provided by the cloud.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"2012 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121580980","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":"Pectoral muscle identification in mammograms for Computer Aided Diagnosis of breast cancer","authors":"S. A. Hassan, M. Sayed, F. Farag, G. Gouhar","doi":"10.1109/CIBEC.2012.6473337","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473337","url":null,"abstract":"In Computer Aided Diagnosis (CAD) systems of breast cancer, extraction of the breast region and delineation of the breast contour with the pectoral muscle being removed is an essential preprocessing step. Primarily it allows the search for abnormalities to be limited to the region of the breast without undue effect from the background of the mammogram. This paper presents a new method for the identification and removal of the pectoral muscle in medio-Iateral oblique (MLO) view of mammogram using iterative thresholding. Our algorithm also identifies the presence of abnormal axillary lymph nodes, which is a major sign of breast carcinoma, and detects the breast border.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"123 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114842436","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 design of LMS with order adaptation for feedback echo cancellation in hearing aids","authors":"M. Kongpoon, C. Chinrungrueng","doi":"10.1109/CIBEC.2012.6473303","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473303","url":null,"abstract":"This paper describes a design of a hybrid adaptive filter for feedback echo cancellation in hearing aids. The proposed design utilizes a multiplexing direct form (MDF) FIR filter, and the LMS algorithm with order adaptation in order to reduce a requirement of a chip area and to minimize power consumption wasted in activities of non active taps. The proposed design can operate up to 6.25MS/s, and could save 26% of power consumption compared to a conventional fixed order FIR filter with LMS adaptation.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"104 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116741156","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":"Accelerating Iris Recognition algorithms on GPUs","authors":"F. Z. Sakr, M. Taher, A. M. Ei-Bialy, A. Wahba","doi":"10.1109/CIBEC.2012.6473321","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473321","url":null,"abstract":"Current multicore graphic processing units (GPUs) architecture designed for parallel data processing, have become applicable for general purpose computation. An example for image content processing is the automated Iris Recognition System stages, which is a highly computation algorithms. Such tasks are based on the extraction of texture features, which are required to analyze iris content. The localization and extraction processes are highly computation intensive and can benefit from the parallel computation power of GPUs. A scalable parallelization is presented for GPU-based localization and feature extraction, with a demonstrated speedup of 9.6 and 14.8 times, respectively, and 12.4 when taking into account this two system stages with our previous work iris matching on GPU stage speed, compared to that of CPU-based version whole system. We specifically implemented an Iris Recognition System based on Daugman's System for training and classification in C#. We executed the CUDA-C code on a NVIDIA GTX 460 Fermi 336 cores card.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"75 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123982980","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":"Automated identification of exudates for detection of macular edema","authors":"Umer Aftab, M. Akram","doi":"10.1109/CIBEC.2012.6473307","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473307","url":null,"abstract":"Macular edema is an advance stage of diabetic retinopathy which affects central vision of diabetes patients. The main cause of edema is the appearance of exudates near or on macular region in human retina. An automated system for early detection of macular edema should identify all possible exudates present on the surface of retina. In this paper, we present a method for the identification of exudates in colored retinal images which will help in building a computer aided diagnostic system for macular edema. The proposed system consists of three stages i.e. candidate exudate detection, feature extraction and classification. We use filter bank for candidate exudate detection, basic properties of exudates for feature extraction and Gaussian mixture model for classification. This paper presents the performance of our system on three retinal image databases and comparative results with existing methods.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"137 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127154800","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":"The effect of useful life and vendor performance on replacement decision of medical equipment","authors":"B. K. Ouda, N. Saleh, A. Mohamed","doi":"10.1109/CIBEC.2012.6473324","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473324","url":null,"abstract":"Medical equipment management life cycle considers various stages ranging from planning to disposal or replacement. Replacement decision is critical and essential stage of medical equipment. A variety of criteria contributes to make an intelligent replacement decision. We enhance the Fault Tree Analysis (FTA) model for replacement of medical equipment, considering a combination of technical, financial, and safety criteria. The considered criteria are; hazard and alerts, cost, useful life, and vendor support. Throughout this model, we classify medical equipment life status into four groups; replacement, test, surveillance and keep. According to the final event score, the replacement decision is approved or not. Neonatal Intensive Care Unit (NICU) equipment of 12 different types for 3 hospitals, along three years, is utilized to investigate the proposed model. Our model proposes a priority list of equipment that should be replaced. According to the analysis to the proposed factors, the useful life factor is found to be the dominant factor. In addition, a high correlation between vendor performance and expended costs is realized.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"102 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134214187","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":"The influence of bar position on implant-retained mandibular overdenture a three dimensional finite element analysis","authors":"S. Fawzi","doi":"10.1109/CIBEC.2012.6473304","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473304","url":null,"abstract":"To evaluate the effect of bar position in implant-retained mandibular overdenture on stress distribution induced in bone surrounding the implant, a three dimensional (3D) model is designed by simulating an edentulous mandible, restored with mandibular overdenture and retained by 4 widely separated implants. All parameters were fixed except for the position of the bar segments. Vertical and oblique loads were applied on one working side. The stress distribution around the implants in each case was recorded and compared to correlate the induced stress magnitude to the bar structure. Stress distribution induced in the bone surrounding the implants showed minimal changes under the application of vertical loads, while under oblique load, connecting the two anterior implants, resulted in a better stress distribution. Using a one piece bar connection or two pieces bar connection of the four widely separated implants might lead to posterior buccal bone resorption in the working side as the stresses induced bypassed the bone yield strength.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"120 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115986224","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}
A. Elnokrashy, M. Hassan, T. Hosny, A. Ali, A. Megawer, Y. M. Kadah
{"title":"Multipass GPU surface rendering in 4D ultrasound","authors":"A. Elnokrashy, M. Hassan, T. Hosny, A. Ali, A. Megawer, Y. M. Kadah","doi":"10.1109/CIBEC.2012.6473330","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473330","url":null,"abstract":"4D ultrasound imaging extends the real-time ca-pability of ultrasound to display a real-time volume, which can then be explored by the sonographer. Surface Rendering is one of the common modes used to display the 3D datasets. Surface shading is required to visualize the surface and en-hances the surface contrast. Here, we show a surface rendering implementation based on three passes. In the first pass, ray casting is used with edge detection algorithm and then the edges are stored to viewing plan distance in the z-buffer of the 2D rendered image. In the second pass, filtration of the z-buffer is performed. This stage is so critical because the fuzzy nature of the ultrasound dataset then shade the 2D rendered image using image space shading. Finally, the third pass applies additional image processing mainly image smoothing on the rendered 2D image. The new method is applied to render volumes acquired on a research system and quality and computation time results show potential for clinical utility.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"14 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132152861","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":"Low cost, compact and pulsated constant current microcontroller based nerve locator","authors":"H. A. Alzomor, B. K. Ouda","doi":"10.1109/CIBEC.2012.6473315","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473315","url":null,"abstract":"Regional anesthesia is preferred to global anesthesia when applicable due to its safety, low cost and patient preference. Successful regional anesthesia depends upon precise location of the peripheral nerve or nerve plexus. Locating peripheral nerves is usually done using nerve stimulation which is considered by many to be the current `gold standard'. In order to generate a nerve impulse by electrical means, a threshold stimulus of current must be applied to the nerve “rheobase”. The technique depends on stimulating muscular twitching at a close distance to the nerve without actually touching it. In this paper, a design for μcontroller-based nerve locator is introduced. The current delivered to the nerve is maintained constant in the proposed design for a wide range of load impedances. The device is tested and used to locate the nerves in the limbs of the animal. Moreover, the device tested successfully against IEC safety standards and compared to prior arts. The comparison is based on five characteristics which are waveform, current intensity, impulse duration, maximum load and functionality. Based on that rules the proposed design is able to achieve reasonably high scores that put it on the second place among 22 available nerve stimulators.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121871534","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":"Constructing a functional Fourier volume rendering pipeline on heterogeneous platforms","authors":"M. Abdellah, A. Eldeib, A. Shaarawi","doi":"10.1109/CIBEC.2012.6473295","DOIUrl":"https://doi.org/10.1109/CIBEC.2012.6473295","url":null,"abstract":"Volume rendering became a crucial and significant tool in the medical field. This was due to the rapid evolution of imaging modalities such as Magnetic Resonance Imaging (MRI) machines, Computed Tomography (CT) scanners. Volume rendering techniques vary from category to another depending basically on the employed modality and eventually on the target application. Although spatial-domain volume rendering techniques have gained a wide acceptance during the past decades, however, they suffer from performance bottlenecks due to their O(N3) complexity for a volume of size N3. Fourier Volume Rendering (FVR) is an alternative technique that works on the k-space representation of the volume with reduced complexity of O(N2logN) for generating projection images of the spatial volume that look like X-ray ones. In this work, a functional hybrid implementation of the FVR pipeline on Central Processing Units (CPUs) and Graphics Processing Units (GPUs) is presented.","PeriodicalId":416740,"journal":{"name":"2012 Cairo International Biomedical Engineering Conference (CIBEC)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130290903","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}