{"title":"Cloud-based parallel suffix array construction based on MPI","authors":"A. Abdelhadi, A. Kandil, M. Abouelhoda","doi":"10.1109/MECBME.2014.6783271","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783271","url":null,"abstract":"Massive amount of genomics data are being produced nowadays by Next Generation Sequencing machines. The suffix array is currently the best choice for indexing genomics data, because of its efficiency and large number of applications. In this paper, we address the problem of constructing the suffix array on computer cluster in the cloud. We present a solution that automates the establishment of a computer cluster in a cloud and automatically constructs the suffix array in a distributed fashion over the cluster nodes. This has the advantage of encapsulating all set-up details and execution of the algorithm. The distributed nature of the algorithm we use overcomes the problem that arises when the user wishes, due to cost issues, to use low memory machines in the cloud. Our experiments show that our implementation scales well with the increasing number of processors. The cloud cost is affordable and it provides a cost effective solution.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125193750","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. Khan, Aisha F. Mohammed, Shama A. Al-Hajri, Hajer M. Al Shamari, U. Qidwai, I. Mujeeb, N. Rajpoot
{"title":"A novel system for scoring of hormone receptors in breast cancer histopathology slides","authors":"A. Khan, Aisha F. Mohammed, Shama A. Al-Hajri, Hajer M. Al Shamari, U. Qidwai, I. Mujeeb, N. Rajpoot","doi":"10.1109/MECBME.2014.6783229","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783229","url":null,"abstract":"Grading of breast cancer is often done by an expert pathologist based on their analysis of micro-level structural features of the cancerous tissue specimen as well as the level of presence of certain protein molecules in the specimen. The process of assessment of the level of presence of estrogen and progesterone receptors molecules is subjective by its very nature and therefore, causes large inter-expert and sometimes even intra-expert variability, potentially adding noise to the process of selecting the treatment regime for the patient. Quantification of immunohistochemical stains is critical for an objective assessment of breast cancer histopathology specimens. We present a fast, compact and inexpensive system for scoring the Estrogen and Progesterone hormone receptors in breast cancer histopathology slides using image analysis algorithm. We describe hardware and software issues in the construction of the system, and present a comparison of scores produced by our system to those produced by many expert pathologists.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125864050","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":"Neuronal cell navigation within a microfluidic device","authors":"A. Shamloo","doi":"10.1109/MECBME.2014.6783254","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783254","url":null,"abstract":"In this study, the polarization and navigation of neuronal cells was studied in response to quantified gradients of nerve growth factor (NGF). To accomplish this, a microfluidic device was designed and fabricated to generate stable concentration gradients of biomolecules in a cell culture chamber within a 3D microenvironment. Numerical simulation was implemented to optimize the device geometry for generating a uniform concentration gradient of NGF which was found to remain stable for multiple hours. Neural Stem/ Progenitor Cell (NSCs) migration and differentiation was studied within this microfluidic device in response to NGF concentration and within a 3D environment of collagen matrix. Also, axonal navigation of adult neurons was investigated within the same microenvironment and in response to NGF concentration. This device is expected to have wide applicability in the study of shear-sensitive cells such as neuronal cells and non-adherent cell types as well as in the study of migration through three dimensional matrices.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122393514","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":"An iterative finite difference scheme for buckling of graphene beam subject to axial compressive load","authors":"M. Elgindi, Dongming Wei, M. Ghazy","doi":"10.1109/MECBME.2014.6783211","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783211","url":null,"abstract":"In this paper buckling loads and modes of an Euler beam made of graphene are considered. An eigenvalue problem is formulated with an additional parameter representing material's elastoplasticity. Analytical approximate solution using the perturbation method is presented. This approximate solution is used as a basis for an iterative finite difference scheme to develop a more accurate solution. Deflection at points along the beam are calculated using this iterative finite difference scheme. Convergence with good accuracy is achieved.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122953116","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}
R. Grunert, C. Kretzschmar, C. Rotsch, M. Werner, T. Prietzel
{"title":"Development of an optical measurement system for hip implant surgery to evaluate the leg length and the hip rotation center","authors":"R. Grunert, C. Kretzschmar, C. Rotsch, M. Werner, T. Prietzel","doi":"10.1109/MECBME.2014.6783228","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783228","url":null,"abstract":"The correct leg length and the position of the hip rotation center are the most important parameters for hip implant surgery. Until now there exist no suitable methods to measure it objectively. This paper describes an approach for determining leg length and hip rotation center with an optical measurement system for total hip replacement procedures. A software was programmed by the authors for this application implementing also commercial software solutions. The 3D models of the leg before and after the positioning of the hip implant were created with the Microsoft Kinect camera. Two scanned models of the leg were compared with each other. The difference between the point datasets on the screen is colored visualized and shall show the surgeon if the leg has the same length with the implant as before. During a feasibility study 30 leg models in different positions were compared to evaluate the accuracy, performance and usability of the software and the Kinect camera itself. The accuracy study shows that 96.4% of the 3D-model data points are within a range of 0-10mm. It can be recognized that the application of the Microsoft Kinect camera could be a suitable approach for determining leg length and hip rotation center in a cost-efficient and patient-friendly way.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"200 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121856375","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":"Sparse Bayesian image restoration with linear operator uncertainties with application to EEG signal recovery","authors":"L. Chaâri, H. Batatia, J. Tourneret","doi":"10.1109/MECBME.2014.6783225","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783225","url":null,"abstract":"Sparse signal/image recovery is a challenging topic that has captured a great interest during the last decades, especially in the biomedical field. Many techniques generally try to regularize the considered ill-posed inverse problem by defining appropriate priors for the target signal/image. The target regularization problem can then be solved either in a variational or Bayesian context. However, a little interest has been devoted to the uncertainties about the linear operator, which can drastically alter the reconstruction quality. In this paper, we propose a novel method for signal/image recovery that accounts and corrects the linear operator imprecisions. The proposed approach relies on a Bayesian formulation which is applied to EEG signal recovery. Our results show the promising potential of the proposed method compared to other regularization techniques which do not account for any error affecting the linear operator.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116813972","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":"ECG noise reduction using empirical mode decomposition based on combination of instantaneous half period and soft-thresholding","authors":"Sh. Samadi, M. Shamsollahi","doi":"10.1109/MECBME.2014.6783250","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783250","url":null,"abstract":"The electrocardiogram (ECG) signal is widely used for diagnosis of various types of cardiac diseases. However, in practical cases, the signal is corrupted by artifacts through the recording process. Thus, denoising of this type of biological signals seems necessary. Several methods have been suggested in recent years for the purpose of ECG denoising; some of which have been based on Empirical Mode Decomposition (EMD). In this paper, an EMD-based approach is proposed which uses the time interval between two adjacent zero crossings within an Intrinsic Mode Function (IMF), defined as Instantaneous Half Period (IHP), to distinguish noise components from the main ECG signal. Noisy signal is decomposed into several IMFs through an iterative algorithm, called the Sifting process. IMFs are later tested by a predefined threshold; and waveforms with a comparatively small IHP are filtered using soft-thresholding technique. The method is fully data-driven, with the optimum threshold derived from a criterion called Consecutive Mean Square Error (CMSE). The accuracy of the developed EMD-based approach is tested on real ECG data from the MIT-BIH database and compared with one of the previously suggested EMD-based methods. Both quantitative and qualitative results of the work are presented.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"74 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114838168","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}
M. Schertzer, S. Blume, A. Badawi, R. Ben-Mrad, P. Sullivan
{"title":"Characterization of bead-based reactions and mechanical supernatant dilution in digital microfluidic devices","authors":"M. Schertzer, S. Blume, A. Badawi, R. Ben-Mrad, P. Sullivan","doi":"10.1109/MECBME.2014.6783269","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783269","url":null,"abstract":"Discrete flow microfluidic devices have been identified as a technology that can be used to efficiently deliver health care services by reducing the cycle times and reagent consumption of biological protocols and medical diagnostic procedures. These devices also have the potential to reduce overhead costs by performing these applications at the point of care. Digital microfluidic devices are one promising discrete flow microfluidic platform that can individually create, manipulate, and mix droplets through the application of asymmetric electric fields. The work presented here suggests that (1) monitoring electrical properties of droplets during specific chemical reactions and (2) supernatant dilution via mechanical filtration can be integrated into digital microfluidic immunoassay devices. Measurement of electrical properties during the bead based chemical reaction between p-nitrophenyl phosphate and particles with bound antibodies conjugated to alkaline phosphatase resulted in measureable difference in capacitance and resistance when compared to the control particles. A single filtration cycle using the mechanical supernatant dilution method demonstrated here reduced the fluorescence intensity in particle laden droplet by approximately 80%.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131364148","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}
H. Mousa, Y. Al-saboni, B. Al-Habash, M. S. El Din, H. Al-Nashash
{"title":"Visual aid for Optic Nerve Hypoplasia patients","authors":"H. Mousa, Y. Al-saboni, B. Al-Habash, M. S. El Din, H. Al-Nashash","doi":"10.1109/MECBME.2014.6783222","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783222","url":null,"abstract":"There is an increase in the number of children patients suffering from Optic Nerve Hypoplasia (ONH) especially in the past few decades. In this paper, we introduce an eye-tracking based smart vision device that aids ONH patients. The device makes use of cameras connected to displays with a processing unit that acts to modify the displayed image optimize patient's vision. The proposed system encompasses the best features of currently available aids together with an added feature of eye-tracking and being user friendly. It can also capture, enhance and display a caption of the surrounding for the low vision users. Obtained results confirm the ability of the device to provide the required magnification together with eye movements tracking and adjust focus accordingly.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134546440","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 low voltage and low power current-mode field programmable analog computational unit","authors":"M. Al-Absi, A. Hussein, M. Abuelma'atti","doi":"10.1109/MECBME.2014.6783204","DOIUrl":"https://doi.org/10.1109/MECBME.2014.6783204","url":null,"abstract":"A new current-mode analog computational unit (ACU) is presented. The ACU can be digitally programmed to produce multiplying, squaring and inverse functions. The design is based on using MOSFETs operating in subthreshold region to achieve ultra-low power dissipation. The circuit is operated from a ± 0.75V DC supply. The proposed circuit has been simulated using Tanner in 0.35μm TSMC CMOS process. Simulation results confirm the functionality of the circuit. The total power consumption is 2.3μW, total harmonic distortion is 1.1%, maximum nonlinearity error is 0.3% and the bandwidth is 2.3MHz.","PeriodicalId":384055,"journal":{"name":"2nd Middle East Conference on Biomedical Engineering","volume":"75 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132696217","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}