Displaying publications 81 - 100 of 133 in total

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  1. Al-Qazzaz NK, Alyasseri ZAA, Abdulkareem KH, Ali NS, Al-Mhiqani MN, Guger C
    Comput Biol Med, 2021 10;137:104799.
    PMID: 34478922 DOI: 10.1016/j.compbiomed.2021.104799
    Stroke is the second foremost cause of death worldwide and is one of the most common causes of disability. Several approaches have been proposed to manage stroke patient rehabilitation such as robotic devices and virtual reality systems, and researchers have found that the brain-computer interfaces (BCI) approaches can provide better results. Therefore, the most challenging tasks with BCI applications involve identifying the best technique(s) that can reveal the neuron stimulus information from the patients' brains and extracting the most effective features from these signals as well. Accordingly, the main novelty of this paper is twofold: propose a new feature fusion method for motor imagery (MI)-based BCI and develop an automatic MI framework to detect the changes pre- and post-rehabilitation. This study investigated the electroencephalography (EEG) dataset from post-stroke patients with upper extremity hemiparesis. All patients performed 25 MI-based BCI sessions with follow up assessment visits to examine the functional changes before and after EEG neurorehabilitation. In the first stage, conventional filters and automatic independent component analysis with wavelet transform (AICA-WT) denoising technique were used. Next, attributes from time, entropy and frequency domains were computed, and the effective features were combined into time-entropy-frequency (TEF) attributes. Consequently, the AICA-WT and the TEF fusion set were utilised to develop an AICA-WT-TEF framework. Then, support vector machine (SVM), k-nearest neighbours (kNN) and random forest (RF) classification technique were tested for MI-based BCI rehabilitation. The proposed AICA-WT-TEF framework with RF classifier achieves the best results compared with other classifiers. Finally, the proposed framework and feature fusion set achieve a significant performance in terms of accuracy measures compared to the state-of-the-art. Therefore, the proposed methods could be crucial for improving the process of automatic MI rehabilitation and are recommended for implementation in real-time applications.
  2. Sudarshan VK, Acharya UR, Ng EY, Tan RS, Chou SM, Ghista DN
    Comput Biol Med, 2016 Apr 1;71:231-40.
    PMID: 26898671 DOI: 10.1016/j.compbiomed.2016.01.028
    Cross-sectional view echocardiography is an efficient non-invasive diagnostic tool for characterizing Myocardial Infarction (MI) and stages of expansion leading to heart failure. An automated computer-aided technique of cross-sectional echocardiography feature assessment can aid clinicians in early and more reliable detection of MI patients before subsequent catastrophic post-MI medical conditions. Therefore, this paper proposes a novel Myocardial Infarction Index (MII) to discriminate infarcted and normal myocardium using features extracted from apical cross-sectional views of echocardiograms. The cross-sectional view of normal and MI echocardiography images are represented as textons using Maximum Responses (MR8) filter banks. Fractal Dimension (FD), Higher-Order Statistics (HOS), Hu's moments, Gabor Transform features, Fuzzy Entropy (FEnt), Energy, Local binary Pattern (LBP), Renyi's Entropy (REnt), Shannon's Entropy (ShEnt), and Kapur's Entropy (KEnt) features are extracted from textons. These features are ranked using t-test and fuzzy Max-Relevancy and Min-Redundancy (mRMR) ranking methods. Then, combinations of highly ranked features are used in the formulation and development of an integrated MII. This calculated novel MII is used to accurately and quickly detect infarcted myocardium by using one numerical value. Also, the highly ranked features are subjected to classification using different classifiers for the characterization of normal and MI LV ultrasound images using a minimum number of features. Our current technique is able to characterize MI with an average accuracy of 94.37%, sensitivity of 91.25% and specificity of 97.50% with 8 apical four chambers view features extracted from only single frame per patient making this a more reliable and accurate classification.
  3. Sudarshan VK, Acharya UR, Ng EY, Tan RS, Chou SM, Ghista DN
    Comput Biol Med, 2016 Apr 1;71:241-51.
    PMID: 26897481 DOI: 10.1016/j.compbiomed.2016.01.029
    Early expansion of infarcted zone after Acute Myocardial Infarction (AMI) has serious short and long-term consequences and contributes to increased mortality. Thus, identification of moderate and severe phases of AMI before leading to other catastrophic post-MI medical condition is most important for aggressive treatment and management. Advanced image processing techniques together with robust classifier using two-dimensional (2D) echocardiograms may aid for automated classification of the extent of infarcted myocardium. Therefore, this paper proposes novel algorithms namely Curvelet Transform (CT) and Local Configuration Pattern (LCP) for an automated detection of normal, moderately infarcted and severely infarcted myocardium using 2D echocardiograms. The methodology extracts the LCP features from CT coefficients of echocardiograms. The obtained features are subjected to Marginal Fisher Analysis (MFA) dimensionality reduction technique followed by fuzzy entropy based ranking method. Different classifiers are used to differentiate ranked features into three classes normal, moderate and severely infarcted based on the extent of damage to myocardium. The developed algorithm has achieved an accuracy of 98.99%, sensitivity of 98.48% and specificity of 100% for Support Vector Machine (SVM) classifier using only six features. Furthermore, we have developed an integrated index called Myocardial Infarction Risk Index (MIRI) to detect the normal, moderately and severely infarcted myocardium using a single number. The proposed system may aid the clinicians in faster identification and quantification of the extent of infarcted myocardium using 2D echocardiogram. This system may also aid in identifying the person at risk of developing heart failure based on the extent of infarcted myocardium.
  4. Vidya KS, Ng EY, Acharya UR, Chou SM, Tan RS, Ghista DN
    Comput Biol Med, 2015 Jul;62:86-93.
    PMID: 25912990 DOI: 10.1016/j.compbiomed.2015.03.033
    Myocardial Infarction (MI) or acute MI (AMI) is one of the leading causes of death worldwide. Precise and timely identification of MI and extent of muscle damage helps in early treatment and reduction in the time taken for further tests. MI diagnosis using 2D echocardiography is prone to inter-/intra-observer variability in the assessment. Therefore, a computerised scheme based on image processing and artificial intelligent techniques can reduce the workload of clinicians and improve the diagnosis accuracy. A Computer-Aided Diagnosis (CAD) of infarcted and normal ultrasound images will be useful for clinicians. In this study, the performance of CAD approach using Discrete Wavelet Transform (DWT), second order statistics calculated from Gray-Level Co-Occurrence Matrix (GLCM) and Higher-Order Spectra (HOS) texture descriptors are compared. The proposed system is validated using 400 MI and 400 normal ultrasound images, obtained from 80 patients with MI and 80 normal subjects. The extracted features are ranked based on t-value and fed to the Support Vector Machine (SVM) classifier to obtain the best performance using minimum number of features. The features extracted from DWT coefficients obtained an accuracy of 99.5%, sensitivity of 99.75% and specificity of 99.25%; GLCM have achieved an accuracy of 85.75%, sensitivity of 90.25% and specificity of 81.25%; and HOS obtained an accuracy of 93.0%, sensitivity of 94.75% and specificity of 91.25%. Among the three techniques presented DWT yielded the highest classification accuracy. Thus, the proposed CAD approach may be used as a complementary tool to assist cardiologists in making a more accurate diagnosis for the presence of MI.
  5. Yu L, Mei Q, Mohamad NI, Gu Y, Fernandez J
    Comput Biol Med, 2021 05;132:104302.
    PMID: 33677166 DOI: 10.1016/j.compbiomed.2021.104302
    Anterior knee pain is a commonly documented musculoskeletal disorder among badminton players. However, current biomechanical studies of badminton lunges mainly report kinetic profiles in the lower extremity with few investigations of in-vivo loadings. The objective of this study was to evaluate tissue loadings in the patellofemoral joint via musculoskeletal modelling and Finite Element simulation. The collected marker trajectories, ground reaction force and muscle activation data were used for musculoskeletal modelling to compute knee joint angles and quadricep muscle forces. These parameters were then set as boundary conditions and loads for a quasistatic simulation using the Abaqus Explicit solver. Simulations revealed that the left-forward (LF) and backward lunges showed greater contact pressure (14.98-29.61%) and von Mises stress (14.17-32.02%) than the right-forward and backward lunges; while, loadings in the left-backward lunge were greater than the left-forward lunge by 13-14%. Specifically, the stress in the chondral layer was greater than the contact interface, particularly in the patellar cartilage. These findings suggest that right-side dominant badminton players load higher in the right patellofemoral joint during left-side (backhand) lunges. Knowledge of these tissue loadings may provide implications for the training of badminton footwork, such as musculature development, to reduce cartilage loading accumulation, and prevent anterior knee pain.
  6. Logeswaran R, Eswaran C
    Comput Biol Med, 2007 Aug;37(8):1084-91.
    PMID: 17112496
    Stones in the biliary tract are routinely identified using MRCP (magnetic resonance cholangiopancreatography). The noisy nature of the images, as well as varying intensity, size and location of the stones, defeat most automatic detection algorithms, making computer-aided diagnosis difficult. This paper proposes a multi-stage segment-based scheme for semi-automated detection of choledocholithiasis and cholelithiasis in the MRCP images, producing good performance in tests, differentiating them from "normal" MRCP images. With the high success rate of over 90%, refinement of the scheme could be applicable in the clinical environment as a tool in aiding diagnosis, with possible applications in telemedicine.
  7. Pszczolkowski S, Law ZK, Gallagher RG, Meng D, Swienton DJ, Morgan PS, et al.
    Comput Biol Med, 2019 03;106:126-139.
    PMID: 30711800 DOI: 10.1016/j.compbiomed.2019.01.022
    BACKGROUND: Spontaneous intracerebral haemorrhage (SICH) is a common condition with high morbidity and mortality. Segmentation of haematoma and perihaematoma oedema on medical images provides quantitative outcome measures for clinical trials and may provide important markers of prognosis in people with SICH.

    METHODS: We take advantage of improved contrast seen on magnetic resonance (MR) images of patients with acute and early subacute SICH and introduce an automated algorithm for haematoma and oedema segmentation from these images. To our knowledge, there is no previously proposed segmentation technique for SICH that utilises MR images directly. The method is based on shape and intensity analysis for haematoma segmentation and voxel-wise dynamic thresholding of hyper-intensities for oedema segmentation.

    RESULTS: Using Dice scores to measure segmentation overlaps between labellings yielded by the proposed algorithm and five different expert raters on 18 patients, we observe that our technique achieves overlap scores that are very similar to those obtained by pairwise expert rater comparison. A further comparison between the proposed method and a state-of-the-art Deep Learning segmentation on a separate set of 32 manually annotated subjects confirms the proposed method can achieve comparable results with very mild computational burden and in a completely training-free and unsupervised way.

    CONCLUSION: Our technique can be a computationally light and effective way to automatically delineate haematoma and oedema extent directly from MR images. Thus, with increasing use of MR images clinically after intracerebral haemorrhage this technique has the potential to inform clinical practice in the future.

  8. Salman AM, Ahmed I, Mohd MH, Jamiluddin MS, Dheyab MA
    Comput Biol Med, 2021 06;133:104372.
    PMID: 33864970 DOI: 10.1016/j.compbiomed.2021.104372
    COVID-19 is a major health threat across the globe, which causes severe acute respiratory syndrome (SARS), and it is highly contagious with significant mortality. In this study, we conduct a scenario analysis for COVID-19 in Malaysia using a simple universality class of the SIR system and extensions thereof (i.e., the inclusion of temporary immunity through the reinfection problems and limited medical resources scenarios leads to the SIRS-type model). This system has been employed in order to provide further insights on the long-term outcomes of COVID-19 pandemic. As a case study, the COVID-19 transmission dynamics are investigated using daily confirmed cases in Malaysia, where some of the epidemiological parameters of this system are estimated based on the fitting of the model to real COVID-19 data released by the Ministry of Health Malaysia (MOH). We observe that this model is able to mimic the trend of infection trajectories of COVID-19 pandemic in Malaysia and it is possible for transmission dynamics to be influenced by the reinfection force and limited medical resources problems. A rebound effect in transmission could occur after several years and this situation depends on the intensity of reinfection force. Our analysis also depicts the existence of a critical value in reinfection threshold beyond which the infection dynamics persist and the COVID-19 outbreaks are rather hard to eradicate. Therefore, understanding the interplay between distinct epidemiological factors using mathematical modelling approaches could help to support authorities in making informed decisions so as to control the spread of this pandemic effectively.
  9. Chong SK, Mohamad MS, Mohamed Salleh AH, Choon YW, Chong CK, Deris S
    Comput Biol Med, 2014 Jun;49:74-82.
    PMID: 24763079 DOI: 10.1016/j.compbiomed.2014.03.011
    This paper presents a study on gene knockout strategies to identify candidate genes to be knocked out for improving the production of succinic acid in Escherichia coli. Succinic acid is widely used as a precursor for many chemicals, for example production of antibiotics, therapeutic proteins and food. However, the chemical syntheses of succinic acid using the traditional methods usually result in the production that is far below their theoretical maximums. In silico gene knockout strategies are commonly implemented to delete the gene in E. coli to overcome this problem. In this paper, a hybrid of Ant Colony Optimization (ACO) and Minimization of Metabolic Adjustment (MoMA) is proposed to identify gene knockout strategies to improve the production of succinic acid in E. coli. As a result, the hybrid algorithm generated a list of knockout genes, succinic acid production rate and growth rate for E. coli after gene knockout. The results of the hybrid algorithm were compared with the previous methods, OptKnock and MOMAKnock. It was found that the hybrid algorithm performed better than OptKnock and MOMAKnock in terms of the production rate. The information from the results produced from the hybrid algorithm can be used in wet laboratory experiments to increase the production of succinic acid in E. coli.
  10. Ibitoye MO, Hamzaid NA, Abdul Wahab AK, Hasnan N, Olatunji SO, Davis GM
    Comput Biol Med, 2020 02;117:103614.
    PMID: 32072969 DOI: 10.1016/j.compbiomed.2020.103614
    BACKGROUND AND OBJECTIVE: Using traditional regression modelling, we have previously demonstrated a positive and strong relationship between paralyzed knee extensors' mechanomyographic (MMG) signals and neuromuscular electrical stimulation (NMES)-assisted knee torque in persons with spinal cord injuries. In the present study, a method of estimating NMES-evoked knee torque from the knee extensors' MMG signals using support vector regression (SVR) modelling is introduced and performed in eight persons with chronic and motor complete spinal lesions.

    METHODS: The model was developed to estimate knee torque from experimentally derived MMG signals and other parameters related to torque production, including the knee angle and stimulation intensity, during NMES-assisted knee extension.

    RESULTS: When the relationship between the actual and predicted torques was quantified using the coefficient of determination (R2), with a Gaussian support vector kernel, the R2 value indicated an estimation accuracy of 95% for the training subset and 94% for the testing subset while the polynomial support vector kernel indicated an accuracy of 92% for the training subset and 91% for the testing subset. For the Gaussian kernel, the root mean square error of the model was 6.28 for the training set and 8.19 for testing set, while the polynomial kernels for the training and testing sets were 7.99 and 9.82, respectively.

    CONCLUSIONS: These results showed good predictive accuracy for SVR modelling, which can be generalized, and suggested that the MMG signals from paralyzed knee extensors are a suitable proxy for the NMES-assisted torque produced during repeated bouts of isometric knee extension tasks. This finding has potential implications for using MMG signals as torque sensors in NMES closed-loop systems and provides valuable information for implementing this method in research and clinical settings.

  11. Arif MA, Mohamad MS, Abd Latif MS, Deris S, Remli MA, Mohd Daud K, et al.
    Comput Biol Med, 2018 11 01;102:112-119.
    PMID: 30267898 DOI: 10.1016/j.compbiomed.2018.09.015
    Metabolic engineering involves the modification and alteration of metabolic pathways to improve the production of desired substance. The modification can be made using in silico gene knockout simulation that is able to predict and analyse the disrupted genes which may enhance the metabolites production. Global optimization algorithms have been widely used for identifying gene knockout strategies. However, their productions were less than theoretical maximum and the algorithms are easily trapped into local optima. These algorithms also require a very large computation time to obtain acceptable results. This is due to the complexity of the metabolic models which are high dimensional and contain thousands of reactions. In this paper, a hybrid algorithm of Cuckoo Search and Minimization of Metabolic Adjustment is proposed to overcome the aforementioned problems. The hybrid algorithm searches for the near-optimal set of gene knockouts that leads to the overproduction of metabolites. Computational experiments on two sets of genome-scale metabolic models demonstrate that the proposed algorithm is better than the previous works in terms of growth rate, Biomass Product Couple Yield, and computation time.
  12. Rahman T, Khandakar A, Qiblawey Y, Tahir A, Kiranyaz S, Abul Kashem SB, et al.
    Comput Biol Med, 2021 May;132:104319.
    PMID: 33799220 DOI: 10.1016/j.compbiomed.2021.104319
    Computer-aided diagnosis for the reliable and fast detection of coronavirus disease (COVID-19) has become a necessity to prevent the spread of the virus during the pandemic to ease the burden on the healthcare system. Chest X-ray (CXR) imaging has several advantages over other imaging and detection techniques. Numerous works have been reported on COVID-19 detection from a smaller set of original X-ray images. However, the effect of image enhancement and lung segmentation of a large dataset in COVID-19 detection was not reported in the literature. We have compiled a large X-ray dataset (COVQU) consisting of 18,479 CXR images with 8851 normal, 6012 non-COVID lung infections, and 3616 COVID-19 CXR images and their corresponding ground truth lung masks. To the best of our knowledge, this is the largest public COVID positive database and the lung masks. Five different image enhancement techniques: histogram equalization (HE), contrast limited adaptive histogram equalization (CLAHE), image complement, gamma correction, and balance contrast enhancement technique (BCET) were used to investigate the effect of image enhancement techniques on COVID-19 detection. A novel U-Net model was proposed and compared with the standard U-Net model for lung segmentation. Six different pre-trained Convolutional Neural Networks (CNNs) (ResNet18, ResNet50, ResNet101, InceptionV3, DenseNet201, and ChexNet) and a shallow CNN model were investigated on the plain and segmented lung CXR images. The novel U-Net model showed an accuracy, Intersection over Union (IoU), and Dice coefficient of 98.63%, 94.3%, and 96.94%, respectively for lung segmentation. The gamma correction-based enhancement technique outperforms other techniques in detecting COVID-19 from the plain and the segmented lung CXR images. Classification performance from plain CXR images is slightly better than the segmented lung CXR images; however, the reliability of network performance is significantly improved for the segmented lung images, which was observed using the visualization technique. The accuracy, precision, sensitivity, F1-score, and specificity were 95.11%, 94.55%, 94.56%, 94.53%, and 95.59% respectively for the segmented lung images. The proposed approach with very reliable and comparable performance will boost the fast and robust COVID-19 detection using chest X-ray images.
  13. Rahman T, Khandakar A, Abir FF, Faisal MAA, Hossain MS, Podder KK, et al.
    Comput Biol Med, 2022 Apr;143:105284.
    PMID: 35180500 DOI: 10.1016/j.compbiomed.2022.105284
    The reverse transcription-polymerase chain reaction (RT-PCR) test is considered the current gold standard for the detection of coronavirus disease (COVID-19), although it suffers from some shortcomings, namely comparatively longer turnaround time, higher false-negative rates around 20-25%, and higher cost equipment. Therefore, finding an efficient, robust, accurate, and widely available, and accessible alternative to RT-PCR for COVID-19 diagnosis is a matter of utmost importance. This study proposes a complete blood count (CBC) biomarkers-based COVID-19 detection system using a stacking machine learning (SML) model, which could be a fast and less expensive alternative. This study used seven different publicly available datasets, where the largest one consisting of fifteen CBC biomarkers collected from 1624 patients (52% COVID-19 positive) admitted at San Raphael Hospital, Italy from February to May 2020 was used to train and validate the proposed model. White blood cell count, monocytes (%), lymphocyte (%), and age parameters collected from the patients during hospital admission were found to be important biomarkers for COVID-19 disease prediction using five different feature selection techniques. Our stacking model produced the best performance with weighted precision, sensitivity, specificity, overall accuracy, and F1-score of 91.44%, 91.44%, 91.44%, 91.45%, and 91.45%, respectively. The stacking machine learning model improved the performance in comparison to other state-of-the-art machine learning classifiers. Finally, a nomogram-based scoring system (QCovSML) was constructed using this stacking approach to predict the COVID-19 patients. The cut-off value of the QCovSML system for classifying COVID-19 and Non-COVID patients was 4.8. Six datasets from three different countries were used to externally validate the proposed model to evaluate its generalizability and robustness. The nomogram demonstrated good calibration and discrimination with the area under the curve (AUC) of 0.961 for the internal cohort and average AUC of 0.967 for all external validation cohort, respectively. The external validation shows an average weighted precision, sensitivity, F1-score, specificity, and overall accuracy of 92.02%, 95.59%, 93.73%, 90.54%, and 93.34%, respectively.
  14. Sim KS, Chia FK, Nia ME, Tso CP, Chong AK, Abbas SF, et al.
    Comput Biol Med, 2014 Jun;49:46-59.
    PMID: 24736203 DOI: 10.1016/j.compbiomed.2014.03.003
    A computer-aided detection auto-probing (CADAP) system is presented for detecting breast lesions using dynamic contrast enhanced magnetic resonance imaging, through a spatial-based discrete Fourier transform. The stand-alone CADAP system reduces noise, refines region of interest (ROI) automatically, and detects the breast lesion with minimal false positive detection. The lesions are then classified and colourised according to their characteristics, whether benign, suspicious or malignant. To enhance the visualisation, the entire analysed ROI is constructed into a 3-D image, so that the user can diagnose based on multiple views on the ROI. The proposed method has been applied to 101 sets of digital images, and the results compared with the biopsy results done by radiologists. The proposed scheme is able to identify breast cancer regions accurately and efficiently.
  15. Cheong JK, Popov V, Alchera E, Locatelli I, Alfano M, Menichetti L, et al.
    Comput Biol Med, 2021 11;138:104881.
    PMID: 34583149 DOI: 10.1016/j.compbiomed.2021.104881
    Gold nanorods assisted photothermal therapy (GNR-PTT) is a new cancer treatment technique that has shown promising potential for bladder cancer treatment. The position of the bladder cancer at different locations along the bladder wall lining can potentially affect the treatment efficacy since laser is irradiated externally from the skin surface. The present study investigates the efficacy of GNR-PTT in the treatment of bladder cancer in mice for tumours growing at three different locations on the bladder, i.e., Case 1: closest to skin surface, Case 2: at the bottom half of the bladder, and Case 3: at the side of the bladder. Investigations were carried out numerically using an experimentally validated framework for optical-thermal simulations. An in-silico approach was adopted due to the flexibility in placing the tumour at a desired location along the bladder lining. Results indicate that for the treatment parameters considered (laser power 0.3 W, GNR volume fraction 0.01% v/v), only Case 1 can be used for an effective GNR-PTT. No damage to the tumour was observed in Cases 2 and 3. Analysis of the thermo-physiological responses showed that the effectiveness of GNR-PTT in treating bladder cancer depends not only on the depth of the tumour from the skin surface, but also on the type of tissue that the laser must pass through before reaching the tumour. In addition, the results are reliant on GNRs with a diameter of 10 nm and an aspect ratio of 3.8 - tuned to exhibit peak absorption for the chosen laser wavelength. Results from the present study can be used to highlight the potential for using GNR-PTT for treatment of human bladder cancer. It appears that Cases 2 and 3 suggest that GNR-PTT, where the laser passes through the skin to reach the bladder, may be unfeasible in humans. While this study shows the feasibility of using GNRs for photothermal ablation of bladder cancer, it also identifies the current limitations needed to be overcome for an effective clinical application in the bladder cancer patients.
  16. Ang CYS, Chiew YS, Wang X, Mat Nor MB, Cove ME, Chase JG
    Comput Biol Med, 2022 Dec;151(Pt A):106275.
    PMID: 36375413 DOI: 10.1016/j.compbiomed.2022.106275
    BACKGROUND AND OBJECTIVE: Respiratory mechanics of mechanically ventilated patients evolve significantly with time, disease state and mechanical ventilation (MV) treatment. Existing deterministic data prediction methods fail to comprehensively describe the multiple sources of heterogeneity of biological systems. This research presents two respiratory mechanics stochastic models with increased prediction accuracy and range, offering improved clinical utility in MV treatment.

    METHODS: Two stochastic models (SM2 and SM3) were developed using retrospective patient respiratory elastance (Ers) from two clinical cohorts which were averaged over time intervals of 10 and 30 min respectively. A stochastic model from a previous study (SM1) was used to benchmark performance. The stochastic models were clinically validated on an independent retrospective clinical cohort of 14 patients. Differences in predictive ability were evaluated using the difference in percentile lines and cumulative distribution density (CDD) curves.

    RESULTS: Clinical validation shows all three models captured more than 98% (median) of future Ers data within the 5th - 95th percentile range. Comparisons of stochastic model percentile lines reported a maximum mean absolute percentage difference of 5.2%. The absolute differences of CDD curves were less than 0.25 in the ranges of 5 

  17. Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW
    Comput Biol Med, 2021 12;139:104947.
    PMID: 34678481 DOI: 10.1016/j.compbiomed.2021.104947
    Alzheimer's Disease (AD) is a neurodegenerative disease that affects cognition and is the most common cause of dementia in the elderly. As the number of elderly individuals increases globally, the incidence and prevalence of AD are expected to increase. At present, AD is diagnosed clinically, according to accepted criteria. The essential elements in the diagnosis of AD include a patients history, a physical examination and neuropsychological testing, in addition to appropriate investigations such as neuroimaging. The omics-based approach is an emerging field of study that may not only aid in the diagnosis of AD but also facilitate the exploration of factors that influence the development of the disease. Omics techniques, including genomics, transcriptomics, proteomics and metabolomics, may reveal the pathways that lead to neuronal death and identify biomolecular markers associated with AD. This will further facilitate an understanding of AD neuropathology. In this review, omics-based approaches that were implemented in studies on AD were assessed from a bioinformatics perspective. Current state-of-the-art statistical and machine learning approaches used in the single omics analysis of AD were compared based on correlations of variants, differential expression, functional analysis and network analysis. This was followed by a review of the approaches used in the integration and analysis of multi-omics of AD. The strengths and limitations of multi-omics analysis methods were explored and the issues and challenges associated with omics studies of AD were highlighted. Lastly, future studies in this area of research were justified.
  18. Supakar R, Satvaya P, Chakrabarti P
    Comput Biol Med, 2022 Dec;151(Pt A):106225.
    PMID: 36306576 DOI: 10.1016/j.compbiomed.2022.106225
    Normal life can be ensured for schizophrenic patients if diagnosed early. Electroencephalogram (EEG) carries information about the brain network connectivity which can be used to detect brain anomalies that are indicative of schizophrenia. Since deep learning is capable of automatically extracting the significant features and make classifications, the authors proposed a deep learning based model using RNN-LSTM to analyze the EEG signal data to diagnose schizophrenia. The proposed model used three dense layers on top of a 100 dimensional LSTM. EEG signal data of 45 schizophrenic patients and 39 healthy subjects were used in the study. Dimensionality reduction algorithm was used to obtain an optimal feature set and the classifier was run with both sets of data. An accuracy of 98% and 93.67% were obtained with the complete feature set and the reduced feature set respectively. The robustness of the model was evaluated using model performance measure and combined performance measure. Outcomes were compared with the outcome obtained with traditional machine learning classifiers such as Random Forest, SVM, FURIA, and AdaBoost, and the proposed model was found to perform better with the complete dataset. When compared with the result of the researchers who worked with the same set of data using either CNN or RNN, the proposed model's accuracy was either better or comparable to theirs.
  19. Al-Shuhaib MBS, Al-Kafajy FR, Badi MA, AbdulAzeez S, Marimuthu K, Al-Juhaishi HAI, et al.
    Comput Biol Med, 2018 09 01;100:17-26.
    PMID: 29960146 DOI: 10.1016/j.compbiomed.2018.06.019
    Because of variable inconvenient living conditions in some places around the world, it is difficult to collect reliable physiological data for ostriches. Therefore, this study aims to provide a comprehensive in silico insight for the nature of polymorphism of important genetic loci that are related to physiological and reproductive traits. Sixty-nine mature ostriches ranging over half of Iraq were screened. Six exonic genetic loci, including cytochrome c oxidase I (COX1), cytochrome b (CYTB), secretogranin V (SCG5), feather keratin 2-like (FK2), prolactin (PRL) and placenta growth factor (PGF) were genotyped by PCR-single stranded conformation polymorphism (SSCP). Thirty-six novel SNPs, including seventeen nonsynonymous (ns) SNPs, were observed. Several computational software programs were utilized to assess the extent of the nsSNPs on their corresponding proteins structure, function and stability. The results showed several deleterious functional and stability changes in almost all the proteins studied. The total severity of each missense mutation was evaluated and compared with other nsSNPs accumulatively. It is evident from the extensive cumulative in silico computation that both p.E34D and p.E60K in PGF have the highest deleterious effect. The cumulative predictions from the present study are an impressive guide for the genotypes of African ostriches, which bypassed the expensive protocols for wet laboratory screening, to identify the effects of variants. To the best of our knowledge, this is the first investigation of its kind on the analyses and prediction outcome of missense mutations in African ostrich populations. The highly deleterious nsSNPs in the placenta growth factor are possible adaptive mutations which might be associated with adaptation in extreme and new environments. The flow and protocol of the computational predictions can be extended for various wild animals to identify the molecular nature of adaptations.
  20. Leong SS, Vijayananthan A, Yaakup NA, Shah N, Ng KH, Acharya UR, et al.
    Comput Biol Med, 2016 11 01;78:58-64.
    PMID: 27658262 DOI: 10.1016/j.compbiomed.2016.09.006
    OBJECTIVE: To determine the reproducibility of three-dimensional (3D) ultrasound (US) over two-dimensional (2D) US in characterizing atherosclerotic carotid plaques using inter- and intra-observer agreement metrics.

    METHODS: A Total of 51 patients with 105 carotid artery plaques were screened using 3D and 2D US probes attached to the same US scanner. Two independent observers characterized the plaques based on the morphological features namely echotexture, echogenicity and surface characteristics. The scores assigned to each morphological feature were used to determine intra- and inter-observer performance. The level of agreement was measured using Kappa coefficient.

    RESULTS: The first observer with 2D US showed fair (k=0.4-0.59) and very strong (k>0.8) with 3D US intra-observer agreements using three morphological features. The second observer indicated moderate strong (k=0.6-0.79) with 2D US and very strong with 3D US (k>0.8) intra-observer performances. Moderate strong (k=0.6-0.79) and very strong (k>0.8) inter-observer agreements were reported with 2D US and 3D US respectively. The results with 2D and 3D US were correlated 62% using only echotexture and 56% using surface morphology coupled with echogenicity. 3D US gave a lower score than 2D 71% of the time (p=0.005) in disagreement cases.

    CONCLUSION: High reproducibility in carotid plaque characterization was obtained using 3D US rather than 2D US. Hence, it can be a preferred imaging modality in routine or follow up plaque screening of patients with carotid artery disease.

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