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Article ; Online: Human cornea thermo-viscoelastic behavior modelling using standard linear solid model.

Ahmed, Hassan M / Salem, Nancy M / Al-Atabany, Walid

2023 Volume 23, Issue 1, Page(s) 250

Abstract: Background: Corneal biomechanics is of great interest to researchers recently. Clinical findings relate them to corneal diseases and to outcomes of refractive surgery. To have a solid understanding of corneal diseases' progression, it is important to ... ...

Abstract	Background: Corneal biomechanics is of great interest to researchers recently. Clinical findings relate them to corneal diseases and to outcomes of refractive surgery. To have a solid understanding of corneal diseases' progression, it is important to understand corneal biomechanics. Also, they are essential for better explaining outcomes of refractive surgeries and their undesired consequences. There is a difficulty for studying corneal biomechanics in-vivo and multiple limitations arise for ex-vivo studies. Hence mathematical modelling is considered as a proper solution to overcome such obstacles. Mathematical modelling of cornea in-vivo allows studying corneal viscoelasticity with taking into consideration all boundary conditions existing in real in-vivo situation. Methods: Three mathematical models are used to simulate corneal viscoelasticity and thermal behavior in two different loading situations: constant and transient loading. Two models of the three are used for viscoelasticity simulation which are Kelvin-Voigt and standard linear solid models. Also, temperature rise due to the ultrasound pressure push is calculated using bioheat transfer model for both the axial direction and as a 2D spatial map using the third model (standard linear solid model). Results: Viscoelasticity simulation results show that standard linear solid model is efficient for describing the viscoelastic behavior of human cornea in both loading conditions. Results show also that the deformation amplitude obtained from standard linear solid model is more reasonable for corneal soft-tissue deformation with respect to corresponding clinical findings than that obtained from Kelvin-Voigt model. Thermal behavior results estimated corneal temperature rise to be roughly 0.2 °C, which conforms with FDA regulations for soft tissue safety. Conclusion: Standard Linear Solid (SLS) model is better describing the human corneal behavior in response to constant and transient load more efficiently. Temperature rise (TR) for the corneal tissue of about 0.2 °C is conforming with FDA regulations and even less than the FDA regulations for soft tissue safety.
MeSH term(s)	Humans ; Cornea/physiology ; Models, Theoretical ; Computer Simulation ; Corneal Diseases ; Viscosity ; Biomechanical Phenomena ; Elasticity
Language	English
Publishing date	2023-06-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2050436-6
ISSN	1471-2415 ; 1471-2415
ISSN (online)	1471-2415
ISSN	1471-2415
DOI	10.1186/s12886-023-02985-3
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Article ; Online: A hybrid deep learning approach for COVID-19 detection based on genomic image processing techniques.

Hammad, Muhammed S / Ghoneim, Vidan F / Mabrouk, Mai S / Al-Atabany, Walid I

Scientific reports

2023 Volume 13, Issue 1, Page(s) 4003

Abstract: The coronavirus disease 2019 (COVID-19) pandemic has been spreading quickly, threatening the public health system. Consequently, positive COVID-19 cases must be rapidly detected and treated. Automatic detection systems are essential for controlling the ... ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic has been spreading quickly, threatening the public health system. Consequently, positive COVID-19 cases must be rapidly detected and treated. Automatic detection systems are essential for controlling the COVID-19 pandemic. Molecular techniques and medical imaging scans are among the most effective approaches for detecting COVID-19. Although these approaches are crucial for controlling the COVID-19 pandemic, they have certain limitations. This study proposes an effective hybrid approach based on genomic image processing (GIP) techniques to rapidly detect COVID-19 while avoiding the limitations of traditional detection techniques, using whole and partial genome sequences of human coronavirus (HCoV) diseases. In this work, the GIP techniques convert the genome sequences of HCoVs into genomic grayscale images using a genomic image mapping technique known as the frequency chaos game representation. Then, the pre-trained convolution neural network, AlexNet, is used to extract deep features from these images using the last convolution (conv5) and second fully-connected (fc7) layers. The most significant features were obtained by removing the redundant ones using the ReliefF and least absolute shrinkage and selection operator (LASSO) algorithms. These features are then passed to two classifiers: decision trees and k-nearest neighbors (KNN). Results showed that extracting deep features from the fc7 layer, selecting the most significant features using the LASSO algorithm, and executing the classification process using the KNN classifier is the best hybrid approach. The proposed hybrid deep learning approach detected COVID-19, among other HCoV diseases, with 99.71% accuracy, 99.78% specificity, and 99.62% sensitivity.
MeSH term(s)	Humans ; COVID-19/diagnosis ; Deep Learning ; Pandemics ; Neural Networks, Computer ; Genomics
Language	English
Publishing date	2023-03-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-30941-0
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Article: Review of Different Sequence Motif Finding Algorithms.

Hashim, Fatma A / Mabrouk, Mai S / Al-Atabany, Walid

Avicenna journal of medical biotechnology

2019 Volume 11, Issue 2, Page(s) 130–148

Abstract: The DNA motif discovery is a primary step in many systems for studying gene function. Motif discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that help in learning the mechanisms for regulation of gene ... ...

Abstract	The DNA motif discovery is a primary step in many systems for studying gene function. Motif discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that help in learning the mechanisms for regulation of gene expression. Over the past decades, different algorithms were used to design fast and accurate motif discovery tools. These algorithms are generally classified into consensus or probabilistic approaches that many of them are time-consuming and easily trapped in a local optimum. Nature-inspired algorithms and many of combinatorial algorithms are recently proposed to overcome these problems. This paper presents a general classification of motif discovery algorithms with new sub-categories that facilitate building a successful motif discovery algorithm. It also presents a summary of comparison between them.
Language	English
Publishing date	2019-04-01
Publishing country	Iran
Document type	Journal Article ; Review
ZDB-ID	2520683-7
ISSN	2008-4625 ; 2008-2835
ISSN (online)	2008-4625
ISSN	2008-2835
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Article ; Online: Automated brain tumor segmentation from multi-slices FLAIR MRI images.

Eltayeb, Engy N / Salem, Nancy M / Al-Atabany, Walid

Bio-medical materials and engineering

2019 Volume 30, Issue 4, Page(s) 449–462

Abstract: Brain tumors are considered to be a leading cause of cancer death among young people. Early diagnosis is thus essential for treatment. The brain segmentation process is still challenging due to complexity and variation of the tumor structure, intensity ... ...

Abstract	Brain tumors are considered to be a leading cause of cancer death among young people. Early diagnosis is thus essential for treatment. The brain segmentation process is still challenging due to complexity and variation of the tumor structure, intensity similarity between tumor tissues and normal brain tissues. In this paper, a fully automated and reliable brain tumor segmentation system is proposed. This system is able to detect range of slices from a volume that is likely to contain tumor in MRI images. An iterated k-means algorithm is used for the segmentation process in conjunction with a cluster validity index to select the optimal number of clusters. The proposed approach is evaluated using simulated and real MRI of human brain from multimodal brain tumor image segmentation benchmark (BRATS) organized by MICCAI 2012 challenge. Our results achieved average for Dice overlap and Jaccard index for complete tumor region of 91.96% and 98.31% respectively when testing a set of 77 volumes. This shows the robustness of the new technique for clinical routine use.
MeSH term(s)	Adolescent ; Adult ; Algorithms ; Brain/diagnostic imaging ; Brain Neoplasms/diagnostic imaging ; Cluster Analysis ; Female ; Humans ; Image Interpretation, Computer-Assisted/methods ; Magnetic Resonance Imaging/methods ; Male ; Young Adult
Language	English
Publishing date	2019-09-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1066216-9
ISSN	1878-3619 ; 0959-2989
ISSN (online)	1878-3619
ISSN	0959-2989
DOI	10.3233/BME-191066
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Article: Extraspectral Imaging for Improving the Perceived Information Presented in Retinal Prosthesis.

Al-Atabany, Walid / Al Yaman, Musa / Degenaar, Patrick

Journal of healthcare engineering

2018 Volume 2018, Page(s) 3493826

Abstract: Retinal prosthesis is steadily improving as a clinical treatment for blindness caused by retinitis pigmentosa. However, despite the continued exciting progress, the level of visual return is still very poor. It is also unlikely that those utilising these ...

Abstract	Retinal prosthesis is steadily improving as a clinical treatment for blindness caused by retinitis pigmentosa. However, despite the continued exciting progress, the level of visual return is still very poor. It is also unlikely that those utilising these devices will stop being legally blind in the near future. Therefore, it is important to develop methods to maximise the transfer of useful information extracted from the visual scene. Such an approach can be achieved by digitally suppressing less important visual features and textures within the scene. The result can be interpreted as a cartoon-like image of the scene. Furthermore, utilising extravisual wavelengths such as infrared can be useful in the decision process to determine the optimal information to present. In this paper, we, therefore, present a processing methodology that utilises information extracted from the infrared spectrum to assist in the preprocessing of the visual image prior to conversion to retinal information. We demonstrate how this allows for enhanced recognition and how it could be implemented for optogenetic forms of retinal prosthesis. The new approach has been quantitatively evaluated on volunteers showing 112% enhancement in recognizing objects over normal approaches.
MeSH term(s)	Equipment Design ; Humans ; Image Processing, Computer-Assisted/methods ; Retina/physiology ; Spectrophotometry, Infrared/methods ; Visual Prosthesis
Language	English
Publishing date	2018-04-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2545054-2
ISSN	2040-2309 ; 2040-2295
ISSN (online)	2040-2309
ISSN	2040-2295
DOI	10.1155/2018/3493826
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Article ; Online: Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the Molecular Level with Real-Time PCR.

Elsayed, Aya M A / Oweda, Mariam / Abushady, Asmaa M / Alhelf, Maha / Khalil, Shaimaa R M / Tawfik, Mohamed S / Al-Atabany, Walid / El-Hadidi, Mohamed

Biochemical genetics

2023

Abstract: Colorectal cancer (CRC) is a prevalent cancer with high morbidity and mortality rates worldwide. Late diagnosis is a significant contributor to low survival rates in a minority of cases. The study aimed to perform a robust pipeline using integrated ... ...

Abstract	Colorectal cancer (CRC) is a prevalent cancer with high morbidity and mortality rates worldwide. Late diagnosis is a significant contributor to low survival rates in a minority of cases. The study aimed to perform a robust pipeline using integrated bioinformatics tools that will enable us to identify potential diagnostic and prognostic biomarkers for early detection of CRC by exploring differentially expressed genes (DEGs). In addition to, testing the capability of replacing chemotherapy with plant extract in CRC treatment by validating it using real-time PCR. RNA-seq data from cancerous and adjacent normal tissues were pre-processed and analyzed using various tools such as FastQC, Kallisto, DESeq@ R package, g:Profiler, GNEMANIA-CytoScape and CytoHubba, resulting in the identification of 1641 DEGs enriched in various signaling routes. MMP7, TCF21, and VEGFD were found to be promising diagnostic biomarkers for CRC. An in vitro experiment was conducted to examine the potential anticancer properties of 5-fluorouracile, Withania somnifera extract, and their combination. The extract was found to exhibit a positive trend in gene expression and potential therapeutic value by targeting the three genes; however, further trials are required to regulate the methylation promoter. Molecular docking tests supported the findings by revealing a stable ligand-receptor complex. In conclusion, the study's analysis workflow is precise and robust in identifying DEGs in CRC that may serve as biomarkers for diagnosis and treatment. Additionally, the identified DEGs can be used in future research with larger sample sizes to analyze CRC survival.
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2168-4
ISSN	1573-4927 ; 0006-2928
ISSN (online)	1573-4927
ISSN	0006-2928
DOI	10.1007/s10528-023-10593-5
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Article ; Online: A scalable data transmission scheme for implantable optogenetic visual prostheses.

Hou, Zhenyang / Al-Atabany, Walid / Farag, Ramy / Vuong, Quoc C / Mokhov, Andrey / Degenaar, Patrick

Journal of neural engineering

2020 Volume 17, Issue 5, Page(s) 55001

Abstract: Objective: This work described a video information processing scheme for optogenetic forms of visual cortical prosthetics.: Approach: The architecture is designed to perform a processing sequence: Initially simplifying the scene, followed by a ... ...

Abstract	Objective: This work described a video information processing scheme for optogenetic forms of visual cortical prosthetics. Approach: The architecture is designed to perform a processing sequence: Initially simplifying the scene, followed by a pragmatic visual encoding scheme which assumes that initially optical stimulation will be stimulating bulk neural tissue rather than driving individual phosphenes. We demonstrate an optical encoder, combined with what we called a zero-run length encoding (zRLE) video compression and decompression scheme-to wirelessly transfer information to an implantable unit in an efficient manner. In the final step, we have incorporated an even power distribution driver to prevent excessive power fluctuations in the optogenetic driving. Significance: The key novelty in this work centres on the completeness of the scheme, the new zRLE compression algorithm and our even power distributor. Main results: Furthermore, although the paper focusses on the algorithm, we confirm that it can be implemented on real time portable processing hardware which we will use for our visual prosthetics.
MeSH term(s)	Algorithms ; Data Compression ; Optogenetics ; Phosphenes ; Visual Prosthesis
Language	English
Publishing date	2020-10-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2170901-4
ISSN	1741-2552 ; 1741-2560
ISSN (online)	1741-2552
ISSN	1741-2560
DOI	10.1088/1741-2552/abaf2e
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Article: Detection of Simulated Tactile Gratings by Electro-Static Friction Show a Dependency on Bar Width for Blind and Sighted Observers, and Preliminary Neural Correlates in Sighted Observers.

Vuong, Quoc C / Shaaban, Aya M / Black, Carla / Smith, Jess / Nassar, Mahmoud / Abozied, Ahmed / Degenaar, Patrick / Al-Atabany, Walid

Frontiers in neuroscience

2020 Volume 14, Page(s) 548030

Abstract: The three-dimensional micro-structure of physical surfaces produces frictional forces that provide sensory cues about properties of felt surfaces such as roughness. This tactile information activates somatosensory cortices, and frontal and temporal brain ...

Abstract	The three-dimensional micro-structure of physical surfaces produces frictional forces that provide sensory cues about properties of felt surfaces such as roughness. This tactile information activates somatosensory cortices, and frontal and temporal brain regions. Recent advances in haptic-feedback technologies allow the simulation of surface micro-structures via electro-static friction to produce touch sensations on otherwise flat screens. These sensations may benefit those with visual impairment or blindness. The primary aim of the current study was to test blind and sighted participants' perceptual sensitivity to simulated tactile gratings. A secondary aim was to explore which brain regions were involved in simulated touch to further understand the somatosensory brain network for touch. We used a haptic-feedback touchscreen which simulated tactile gratings using digitally manipulated electro-static friction. In Experiment 1, we compared blind and sighted participants' ability to detect the gratings by touch alone as a function of their spatial frequency (bar width) and intensity. Both blind and sighted participants showed high sensitivity to detect simulated tactile gratings, and their tactile sensitivity functions showed both linear and quadratic dependency on spatial frequency. In Experiment 2, using functional magnetic resonance imaging, we conducted a preliminary investigation to explore whether brain activation to physical vibrations correlated with blindfolded (but sighted) participants' performance with simulated tactile gratings outside the scanner. At the neural level, blindfolded (but sighted) participants' detection performance correlated with brain activation in bi-lateral supplementary motor cortex, left frontal cortex and right occipital cortex. Taken together with previous studies, these results suggest that there are similar perceptual and neural mechanisms for real and simulated touch sensations.
Language	English
Publishing date	2020-10-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2411902-7
ISSN	1662-453X ; 1662-4548
ISSN (online)	1662-453X
ISSN	1662-4548
DOI	10.3389/fnins.2020.548030
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Article ; Online: FPGA design for dual-spectrum Visual Scene Preparation in retinal prosthesis.

Al Yaman, Musa / Al-Atabany, Walid / Bystrov, Alex / Degenaar, Patrick

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

2015 Volume 2014, Page(s) 4691–4694

Abstract: A method of Visual Scene Preparation for the patients suffering Retinitis Pigmentosa is implemented in hardware for the first time. The scene is captured with two cameras, one visible spectrum and one infra-red, in order to distinguish between the live ... ...

Abstract	A method of Visual Scene Preparation for the patients suffering Retinitis Pigmentosa is implemented in hardware for the first time. The scene is captured with two cameras, one visible spectrum and one infra-red, in order to distinguish between the live and non-live objects. The live objects are subsequently emphasized in the output image, thus helping a patient to see the most significant detail with the healthy part of the retina. The implementation uses Verilog language and FPGA platform. A system prototype is analyzed and compared to MATLAB results.
MeSH term(s)	Adult ; Algorithms ; Female ; Humans ; Image Processing, Computer-Assisted/instrumentation ; Image Processing, Computer-Assisted/methods ; Male ; Retinitis Pigmentosa/therapy ; Visual Prosthesis
Language	English
Publishing date	2015-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2694-0604
ISSN (online)	2694-0604
DOI	10.1109/EMBC.2014.6944671
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Article ; Online: A head mounted device stimulator for optogenetic retinal prosthesis.

Soltan, Ahmed / Barrett, John Martin / Maaskant, Pleun / Armstrong, Niall / Al-Atabany, Walid / Chaudet, Lionel / Neil, Mark / Sernagor, Evelyne / Degenaar, Patrick

Journal of neural engineering

2018 Volume 15, Issue 6, Page(s) 65002

Abstract: Objective: Our main objective is to demonstrate that compact high radiance gallium nitride displays can be used with conventional virtual reality optics to stimulate an optogenetic retina. Hence, we aim to introduce a non-invasive approach to restore ... ...

Abstract	Objective: Our main objective is to demonstrate that compact high radiance gallium nitride displays can be used with conventional virtual reality optics to stimulate an optogenetic retina. Hence, we aim to introduce a non-invasive approach to restore vision for people with conditions such as retinitis pigmentosa where there is a remaining viable communication link between the retina and the visual cortex. Approach: We design and implement the headset using a high-density µLED matrix, Raspberry Pi, microcontroller from NXP and virtual reality lens. Then, a test platform is developed to evaluate the performance of the headset and the optical system. Furthermore, image simplification algorithms are used to simplify the scene to be sent to the retina. Moreover, in vivo evaluation of the genetically modified retina response at different light intensity is discussed to prove the reliability of the proposed system. Main results: We demonstrate that in keeping with regulatory guidance, the headset displays need to limit their luminance to 90 kcd m Significance: We demonstrate a fully functional 8100-pixel headset system including software/hardware which can operate on a standard consumer battery for periods exceeding a 24 h recharge cycle. The headset is capable of delivering enough light to stimulate the genetically modified retina cells and also keeping the amount of light below the regulation threshold for safety.
MeSH term(s)	Algorithms ; Channelrhodopsins ; Humans ; Optogenetics/methods ; Photic Stimulation ; Prosthesis Design ; Retina/physiology ; Retinitis Pigmentosa/rehabilitation ; Software ; Virtual Reality ; Visual Cortex/physiology ; Visual Prosthesis
Chemical Substances	Channelrhodopsins
Language	English
Publishing date	2018-08-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2170901-4
ISSN	1741-2552 ; 1741-2560
ISSN (online)	1741-2552
ISSN	1741-2560
DOI	10.1088/1741-2552/aadd55
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