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Lung cancer is one of the most serious cancers in the world with the minimum survival rate after the diagnosis as it appears in Computed Tomography scans. Lung nodules may be isolated from (solitary) or attached to (juxtapleural) other structures such as blood vessels or the pleura. Diagnosis of lung nodules according to their location increases the survival rate as it achieves diagnostic and therapeutic quality assurance. In this paper, a Computer Aided Diagnosis (CADx) system is proposed to classify solitary nodules and juxtapleural nodules inside the lungs. Two main auto-diagnostic schemes of supervised learning for lung nodules classification are achieved. In the first scheme, (bounding box + Maximum intensity projection) and (Thresholding + K-means clustering) segmentation approaches are proposed then first- and second-order features are extracted. Fisher score ranking is also used in the first scheme as a feature selection method. The higher five, ten, and fifteen ranks of the feature set are selected. In the first scheme, Support Vector Machine (SVM) classifier is used. In the second scheme, the same segmentation approaches are used with Deep Convolutional neural networks (DCNN) which is a successful tool for deep learning classification. Because of the limited data sample and imbalanced data, tenfold cross-validation and random oversampling are used for the two schemes. For diagnosis of the solitary nodule, the first scheme with SVM achieved the highest accuracy and sensitivity 91.4% and 89.3%, respectively, with radial basis function and applying the (Thresholding + Kmeans clustering) segmentation approach and the higher 15 ranks of the feature set. In the second scheme, DCNN achieved the highest accuracy and sensitivity 96% and 95%, respectively, to detect the solitary nodule when applying the bounding box and maximum intensity projection segmentation approach. Receiver operating characteristic curve is used to evaluate the classifier’s performance. The max. AUC = 90.3% is achieved with DCNN classifier for detecting solitary nodules. This CAD system acts as a second opinion for the radiologist to help in the early diagnosis of lung cancer. The accuracy, sensitivity, and specificity of scheme I (SVM) and scheme II (DCNN) showed promising results in comparison to other published studies.

Recently, the numerical optimization field has attracted the research community to propose and develop various metaheuristic optimization algorithms. This paper presents a new metaheuristic optimization algorithm called Honey Badger Algorithm (HBA). The proposed algorithm is inspired from the intelligent foraging behavior of honey badger, to mathematically develop an efficient search strategy for solving optimization problems. The dynamic search behavior of honey badger with digging and honey finding approaches are formulated into exploration and exploitation phases in HBA. Moreover, with controlled randomization techniques, HBA maintains ample population diversity even towards the end of the search process. To assess the efficiency of HBA, 24 standard benchmark functions, CEC’17 test-suite, and four engineering design problems are solved. The solutions obtained using the HBA have been compared with ten well-known metaheuristic algorithms including Simulated annealing (SA), Particle Swarm Optimization (PSO), Covariance Matrix Adaptation Evolution Strategy (CMA-ES), Success-History based Adaptive Differential Evolution variants with linear population size reduction (L-SHADE), Moth-flame Optimization (MFO), Elephant Herding Optimization (EHO), Whale Optimization Algorithm (WOA), Grasshopper Optimization Algorithm (GOA), Thermal Exchange Optimization (TEO) and Harris hawks optimization (HHO). The experimental results, along with statistical analysis, reveal the effectiveness of HBA for solving optimization problems with complex search-space, as well as, its superiority in terms of convergence speed and exploration–exploitation balance, as compared to other methods used in this study. The source code of HBA is currently available for public at https://www.mathworks.com/matlabcentral/fileexchange/98204-honey-badger-algorithm .

BACKGROUND Non-invasive tests (NITs), such as Fibrosis-4 index (FIB-4) and the aspartate aminotransferase-to-platelet ratio index (APRI), developed using classical statistical methods, are increasingly used for determining liver fibrosis stages and recommended in treatment guidelines replacing the liver biopsy. Application of conventional cutoffs of FIB-4 and APRI resulted in high rates of misclassification of fibrosis stages. AIM There is an unmet need for more accurate NITs that can overcome the limitations of FIB-4 and APRI. PATIENTS AND METHODS Machine learning with the random forest algorithm was used to develop a non-invasive index using retrospective data of 7238 patients with biopsy-proven chronic hepatitis C from two centers in Egypt; derivation dataset (n = 1821) and validation set in the second center (n = 5417). Receiver operator curve analysis was used to define cutoffs for different stages of fibrosis. Performance of the new score was externally validated in cohorts from two other sites in Egypt (n = 560) and seven different countries (n = 1317). Fibrosis stages were determined using the METAVIR score. Results were also compared with three established tools (FIB-4, APRI, and the aspartate aminotransferase-to-alanine aminotransferase ratio [AAR]). RESULTS Age in addition to readily available laboratory parameters such as aspartate, and alanine aminotransferases, alkaline phosphatase, albumin (g/dl), and platelet count (/cm3 ) correlated with the biopsy-derived stage of liver fibrosis in the derivation cohort and were used to construct the model for predicting the fibrosis stage by applying the random forest algorithm, resulting in an FIB-6 index, which can be calculated easily at http://fib6.elriah.info. Application of the cutoff values derived from the derivation group on the validation groups yielded very good performance in ruling out cirrhosis (negative predictive value [NPV] = 97.7%), compensated advance liver disease (NPV = 90.2%), and significant fibrosis (NPV = 65.7%). In the external validation groups from different countries, FIB-6 demonstrated higher sensitivity and NPV than FIB-4, APRI, and AAR. CONCLUSION FIB-6 score is a non-invasive, simple, and accurate test for ruling out liver cirrhosis and compensated advance liver disease in patients with chronic hepatitis C and performs better than APRI, FIB-4, and AAR.

Multiple sclerosis is an autoimmune disease that causes psychological impacts and severe physical disabilities, including motor disabilities and partial blindness. This work introduces an early detection method for multiple sclerosis disease by analyzing transcriptomic microRNA data. By transforming this phenotype classification problem into a text mining problem, multiple sclerosis disease biomarkers can be obtained. To our knowledge, text mining methods have not been introduced previously in transcriptomic data analysis of multiple sclerosis disease. Hence, this work presents a complete predictive model by combining consecutive transcriptomic data preprocessing procedures, followed by the proposed KmerFIDF method as a feature extraction method and linear discriminant analysis for dimensionality reduction. Predictive machine learning methods can then be obtained accordingly. This study describes experimental work on a transcriptomic dataset of noncoding microRNA sequences denoted from relapsing-remitting multiple sclerosis patients before fingolimod treatment and after six consecutive months of treatment. The experimental results of the predictive methods with the proposed model report sensitivity, specificity, F1-score, and average accuracy scores of 96.4, 96.47, 95.6, and 97% with random forest, 92.89, 92.78, 93.2, and 94% with support vector machine and 91.95, 92.2, 93.1, and 94% with logistic regression, respectively. These promising results support the introduced model and the proposed KmerFIDF method in transcriptomic data analysis. Moreover, comparative experiments are conducted with two referenced studies. The obtained results show that the average reported accuracy scores of the proposed model outperform the referenced literature work.

Multiple sclerosis disease is a main cause of non-traumatic disabilities and one of the most common neurological disorders in young adults over many countries. In this work, we introduce a survey study of the utilization of machine learning methods in Multiple Sclerosis early genetic disease detection methods incorporating Microarray data analysis and Single Nucleotide Polymorphism data analysis and explains in details the machine learning methods used in literature. In addition, this study demonstrates the future trends of Next Generation Sequencing data analysis in disease detection and sample datasets of each genetic detection method was included .in addition, the challenges facing genetic disease detection were elaborated.

Several metaheuristic optimization algorithms have been developed to solve the real-world problems recently. This paper proposes a novel metaheuristic algorithm named Henry gas solubility optimization (HGSO), which mimics the behavior governed by Henry’s law to solve challenging optimization problems. Henry’s law is an essential gas law relating the amount of a given gas that is dissolved to a given type and volume of liquid at a fixed temperature. The HGSO algorithm imitates the huddling behavior of gas to balance exploitation and exploration in the search space and avoid local optima. The performance of HGSO is tested on 47 benchmark functions, CEC’17 test suite, and three real-world optimization problems. The results are compared with seven well-known algorithms; the particle swarm optimization (PSO), gravitational search algorithm (GSA), cuckoo search algorithm (CS), grey wolf optimizer (GWO), whale optimization algorithm (WOA), elephant herding algorithm (EHO) and simulated annealing (SA). Additionally, to assess the pairwise statistical performance of the competitive algorithms, a Wilcoxon rank sum test is conducted. The experimental results revealed that HGSO provides competitive and superior results compared to other algorithms when solving challenging optimization problems.

Prediction of least energy conformation of a protein from its primary structure (chain of amino acids) is an optimization problem associated with a large complex energy landscape. In this study, a simple 2D hydrophobic–hydrophilic model was used to model the protein sequence, which allows the fast and efficient design of genetic algorithm-based protein structure prediction approach. The neighborhood search strategy is integrated into the genetic operator. The neighborhood search guides the genetic operator to regions in the computational space with good solutions. To prevent convergence to local optima, the proposed method employs crowding-based parent replacement strategy, which improves the performance of the algorithm and the ability to deal with multiple numbers of solutions. The proposed algorithm was tested with a standard benchmark of HP sequences and comparative results demonstrate that the proposed system beats most of the evolutionary algorithms for seven sequences. It finds the best energy for a sequence of length [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text].

BackgroundDisorders in deoxyribonucleic acid (DNA) mutations are the common cause of colon cancer. Detection of these mutations is the first step in colon cancer diagnosis. Differentiation among normal and cancerous colon gene sequences is a method used for mutation identification. Early detection of this type of disease can avoid complications that can lead to death. In this study, 55 healthy and 55 cancerous genes for colon cells obtained from the national center for biotechnology information GenBank are used. After applying the electron–ion interaction pseudopotential (EIIP) numbering representation method for the sequences, single-level discrete wavelet transform (DWT) is applied using Haar wavelet. Then, some statistical features are obtained from the wavelet domain. These features are mean, variance, standard deviation, autocorrelation, entropy, skewness, and kurtosis. The resulting values are applied to the k-nearest neighbor (KNN) and support vector machine (SVM) algorithms to obtainsatisfactoryclassification results.ResultsFour important parameters are calculated to evaluate the performance of the classifiers. Accuracy (ACC), F1 score, and Matthews correlation coefficient (MCC) are 95%, 94.74%, and 0.9045%, respectively, for SVM and 97.5%, 97.44%, and 0.9512%, respectively, for KNN.ConclusionThis study has created a novel successful system for colorectal cancer classification and detection with the well-satisfied results. The K-nearest network results are the best with low error for the generated classification system, even though the results of the SVM network are acceptable.

Alzheimer’s disease (AD) is a progressive disease that attacks the brain’s neurons and causes problems in memory, thinking, and reasoning skills. Personalized Medicine (PM) needs a better and more accurate understanding of the relationship between human genetic data and complex diseases like AD. The goal of PM is to tailor the treatment of a case person to his individual properties. PM requires the prediction of a person’s disease from genetic data, and its success depends on the accurate detection of genetic biomarkers. Single Nucleotide polymorphisms (SNPs) are considered the most prevalent type of variation in the human genome. Epistasis has a biological relevance to complex diseases and has an important impact on PM. Detection of the most significant epistasis interactions associated with complex diseases is a big challenge. This paper reviews several machine learning techniques and algorithms to detect the most significant epistasis interactions in Alzheimer’s disease. We discuss many machine learning techniques that can be used for detecting SNPs’ combinations like Random Forests, Support Vector Machines, Multifactor Dimensionality Reduction, Neural Network, and Deep Learning. This review paper highlights the pros and cons of these techniques and explains how they can be applied in an efficient framework to apply knowledge discovery and data mining in AD disease.

Background The computational biology approach has advanced exponentially in protein secondary structure prediction (PSSP), which is vital for the pharmaceutical industry. Extracting protein structure from the laboratory has insufficient information for PSSP that is used in bioinformatics studies. In this paper, the support vector machine (SVM) model and decision tree are presented on the RS126 dataset to address the problem of PSSP. A decision tree is applied for the SVM outcome to obtain the relevant guidelines possible for PSSP. Furthermore, the number of produced rules was fairly small, and they show a greater degree of comprehensibility compared to other rules. Several of the proposed principles have compelling and relevant biological clarification. Results The results confirmed that the existence of a particular amino acid in a protein sequence increases the stability for the forecast of protein secondary structure. The suggested algorithm achieved 85% accuracy for the E|~E classifier. Conclusions The proposed rules can be very important in managing wet laboratory experiments intended at determining protein secondary structure. Lastly, future work will focus mainly on large protein datasets without overfitting and expand the amount of extracted regulations for PSSP.

Computer-aided diagnosis (CAD) approach is presented as strong frameworks to solve the inaccuracy problems. The major purpose of this paper is to improve a CAD system depended on supervised classification that can be useful in diagnosing and detecting the changes of breast cancers in digitized mammograms earlier, accurately and faster than standard examination programs by applying CAD according to image processing techniques beginning with preprocessing step, segmentation, feature extraction and finally classification stage. The work presented in this study is based on the integration of different features such as shape, texture and invariant moment features. This integration achieved best results for sensitivity and specificity rather than using the one type of features in breast cancer classification. The accuracy of our integration system reached 96% in the automatic mode of ANN while best accuracy accomplished by features result according to invariant moments that reached 97% by ANN in an automatic way. Keywords: Computer-aided diagnosis (CAD), Mammograms, K-nearest neighbor classifier (KNN), Support vector machine (SVM), Artificial neural network (ANN)

Background: Bioinformatics is an interdisciplinary field that combines biology and information technology to study how to deal with the biological data. The DNA motif discovery problem is the main challenge of genome biology and its importance is directly proportional to increasing sequencing technologies which produce large amounts of data. DNA motif is a repeated portion of DNA sequences of major biological interest with important structural and functional features. Motif discovery plays a vital role in the antibody-biomarker identification which is useful for diagnosis of disease and to identify Transcription Factor Binding Sites (TFBSs) that help in learning the mechanisms for regulation of gene expression. Recently, scientists discovered that the TFs have a mutation rate five times higher than the flanking sequences, so motif discovery also has a crucial role in cancer discovery. Methods: Over the past decades, many attempts use different algorithms to design fast and accurate motif discovery tools. These algorithms are generally classified into consensus or probabilistic approach. Results: Many of DNA motif discovery algorithms are time-consuming and easily trapped in a local optimum. Conclusion: Nature-inspired algorithms and many of combinatorial algorithms are recently proposed to overcome the problems of consensus and probabilistic approaches. This paper presents a general classification of motif discovery algorithms with new sub-categories. It also presents a summary comparison between them.

Background Behcet’s disease (BD) is a systemic inflammatory disease of the blood vessels and affects various body parts. This study aimed to determine the association of four single-nucleotide polymorphisms (SNPs) and BD in the Egyptian population using multiple statistical models and show the resulting associations along with previous studies of different populations. Four SNPs were examined for their association with BD: two SNPs from vitamin D receptor gene (FokI and BsmI) were selected and the other two were selected from miR-146a and miR-155. These four SNPs were selected for their association and role with BD in different populations and in the immune system. A marker check was conducted using the Hardy-Weinberg equilibrium and minor allele frequency. The associations were tested using four different statistical models: multiplicative, dominant, recessive, and codominant models. All statistical models used the odd’s ratio (OR) with confidence interval (CI) of 95% to evaluate the association of each SNP. Results BsmI showed association using the four models, while FokI did not show any association through any model. miR-155 showed association using the multiplicative and recessive models. miR-146a showed association using the multiplicative model only. Conclusions As a result, BsmI, miR-155, and miR-146a SNPs could have a role in the development of BD in the Egyptian population, while FokI could have a weak role, if any, in the development of BD in the Egyptian population.

DNA computing is an area of natural computing inspired by molecular biology. It can be used to perform arithmetic and logic operations on information encoded as DNA strands. Due to the rapid development of network technology, E-health care services are helpful for all patients from anywhere at any time. Patients can use these services through a public channel. The security of patients’ privacy is therefore an essential issue in E-health care. In this paper, an encryption scheme is proposed for hiding patient information in a medical image using the Least Significant Bit algorithm, which involves hiding data in the least bit of image pixels. The image is then compressed with a key which is generated from a combination of six stages of chaotic maps and DNA encoding rules that result in encoding data into a DNA format. The proposed security system was applied to six different medical images, including X-ray images, CT images, and MRI images. The results have been evaluated using several evaluation metrics. The proposed scheme appears to be robust.

Developments in the field of glass research necessitate the mimicking of the optical properties of glass materials before melting the raw materials, as they are very expensive nowadays. An artificial neural network (ANN) was utilized during this work to train and predict the Judd–Ofelt parameters of various glasses, such as Ω2, Ω4 and Ω6, and the radiative lifetimes of many different types of rare-earth-doped glasses. The optimized ANN architecture for forecasting the Judd–Ofelt parameters were found to be very near to the experimentally measured parameters. Then, the conferred ANN model was employed to predict the Judd–Ofelt parameters of some newly prepared borosilicate glasses. Therein, a new glass system of 0.25 PbO–0.2 SiO2–(0.55 − x) B2O3–x Dy2O3, was prepared in order to employ the melt-quenching technique. The parameter results of the Judd–Ofelt theory, as well as the Ω2, Ω4 and Ω6 and radiative lifetimes showed that the supplementation of Dy2O3 switched the BO4 units to BO3 units with oxygens that were non-bridging atoms, thus weakening the glass frameworks. Therefore, it is very important to use an ANN to predict the Judd–Ofelt parameters of several rare-earth-doped glasses as luminescent materials.

The difficulty and complexity of the real-world numerical optimization problems has grown manifold, which demands efficient optimization methods. To date, various metaheuristic approaches have been introduced, but only a few have earned recognition in research community. In this paper, a new metaheuristic algorithm called Archimedes optimization algorithm (AOA) is introduced to solve the optimization problems. AOA is devised with inspirations from an interesting law of physics Archimedes’ Principle. It imitates the principle of buoyant force exerted upward on an object, partially or fully immersed in fluid, is proportional to weight of the displaced fluid. To evaluate performance, the proposed AOA algorithm is tested on CEC’17 test suite and four engineering design problems. The solutions obtained with AOA have outperformed well-known state-of-the-art and recently introduced metaheuristic algorithms such genetic algorithms (GA), particle swarm optimization (PSO), differential evolution variants L-SHADE and LSHADE-EpSin, whale optimization algorithm (WOA), sine-cosine algorithm (SCA), Harris’ hawk optimization (HHO), and equilibrium optimizer (EO). The experimental results suggest that AOA is a high-performance optimization tool with respect to convergence speed and exploration-exploitation balance, as it is effectively applicable for solving complex problems. The source code is currently available for public from: https://www.mathworks.com/matlabcentral/fileexchange/79822-archimedes-optimization-algorithm

A brain–computer interface (BCI) can be used for people with severe physical disabilities such as ALS, or amyotrophic lateral sclerosis. BCI can allow these individuals to communicate again by creating a new communication channel directly from the brain to an output device. BCI technology can allow paralyzed people to share their intent with others, and thereby demonstrate that direct communication from the brain to the external world is possible, and that it might serve useful functions. In this paper, we propose a system to exploit the P300 signal in the brain, a positive deflection in event-related potentials. The P300 signal can be incorporated into a spelling device. BCI systems include machine learning algorithms (MLA). Their performance depends on the feature extraction and classification techniques employed. This work discusses the performance of different machine learning algorithms. First, a preprocessing step is introduced to the subjects to extract the important features before applying the machine learning algorithms. The presented algorithms are linear discriminant analysis (LDA I and LDA II), support vector machine (SVM I, SVM II, SVM III, and SVM IV), linear regression (LREG), and Bayesian linear discriminant analysis (BLDA). It is found that BLDA and SVMIV classifiers yield the highest performance for both subjects considered in our study.

Cancer is considered one of the most dangerous diseases leading to imminent death during recent decades. It spreads quickly at a frightening pace to all parts of the body and early detection of such diseases may help reduce the risks. Many methods have been used to classify and predict the outcome of cancer, such as image processing techniques, artificial intelligence, and nanotechnology. Out of these methods, artificial intelligence techniques have played an essential role and have provided satisfying results from different investigations in various fields. Considering that cancer is a genetic disease, electron–ion interaction pseudo potential can be used to convert DNA sequences from string shape into number values so that genomic signal processing can be applied for the feature extraction step. In this paper, 51 healthy and 51 cancer genes from multiple cells obtained from the National Center for Biotechnology Information Genbank were used for analysis. Then, 7 invariant moments were extracted into 2 types of learning machine methods: supervised and unsupervised learning. Finally, their results were compared using Receiver Operating Characteristic parameters. From these results, the best accuracy was obtained from the trainable cascade-forward backpropagation network. The calculated parameters were 0.3333, 0.3158, 0.6842, 0.6667, and 67.5% for the Kohonen network, 0.1053, 0.1429, 0.8571, 0.8947, and 87.5% for the feed-forward network, and 0.0000, 0.0909, 0.9091, 1.0000, and 95% for the cascade-forward network for FPR, FNR, TPR, TNR, and accuracy respectively.

Multiple Sclerosis (MS) is an autoimmune disease that severely impacts the central nervous system. Thanks to the evolutionary genetic information studied and published, researches have started to study MS from a genetic perspective. This paper provides a study of six single-nucleotide polymorphisms (SNPs)—MIR137HG (rs1625579), GAS5 (rs2067079), MIR3142HG (rs57095329), MIR146A (rs2910164), MIR155HG (rs767649) and IRAK1 (rs3027898)—and demonstrates their association with MS. This study was applied over an Egyptian dataset of 38 MS patients and 35 controls. Hence, different models were applied, Dominant, Recessive and Genotypic models along with Fisher’s Exact method, Basic case–control analysis and Logistic regression analysis. This paper shows that the SNPs rs1625579, rs57095329, rs767649 and rs3027898 are associated with MS (p value

Coronavirus Disease 2019 (COVID-19) is a sudden viral contagion that appeared at the end of last year in Wuhan city, the Chinese province of Hubei, China. The fast spread of COVID-19 has led to a dangerous threat to worldwide health. Also in the last two decades, several viral epidemics have been listed like the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002/2003, the influenza H1N1 in 2009 and recently the Middle East respiratory syndrome coronavirus (MERS-CoV) which appeared in Saudi Arabia in 2012. In this research, an automated system is created to differentiate between the COVID-19, SARS-CoV and MERS-CoV epidemics by using their genomic sequences recorded in the NCBI GenBank in order to facilitate the diagnosis process and increase the accuracy of disease detection in less time. The selected database contains 76 genes for each epidemic. Then, some features are extracted like a discrete Fourier transform (DFT), discrete cosine transform (DCT) and the seven moment invariants to two different classifiers. These classifiers are the k-nearest neighbor (KNN) algorithm and the trainable cascade-forward back propagation neural network where they give satisfying results to compare. To evaluate the performance of classifiers, there are some effective parameters calculated. They are accuracy (ACC), F1 score, error rate and Matthews correlation coefficient (MCC) that are 100%, 100%, 0 and 1, respectively, for the KNN algorithm and 98.89%, 98.34%, 0.0111 and 0.9754, respectively, for the cascade-forward network.

In this paper, recent algorithms are suggested to repair the issue of motif finding. The proposed algorithms are cuckoo search, modified cuckoo search and finally a hybrid of gravitational search and particle swarm optimization algorithm. Motif finding is the technique of handling expressive motifs successfully in huge DNA sequences. DNA motif finding is important because it acts as a significant function in understanding the approach of gene regulation. Recent results of existing motifs finding programs display low accuracy and can not be used to find motifs in different types of datasets. Practical tests are implemented first on synthetic datasets and then on benchmark real datasets that are based on nature-inspired algorithms. The results revealed that the hybridization of gravitational search algorithm and particle swarm algorithms provides higher precision and recall values and provides average enhancement of F-score up to 0.24, compared to other existing algorithms and tools, and also that cuckoo search and modified cuckoo search have been able to successfully locate motifs in DNA sequences.

Fibrolamellar hepatocellular carcinoma is a unique malignant liver tumor type which arises in young adults and children. It is uncommon variation subtype of hepatocellular carcinoma which remains ineffectively recorded. Learning of cytogenetic changes in fibrolamellar hepatocellular carcinoma has lagged behind the information obtained from alternate entities of hepatocellular carcinoma lately. Gene expression profiling may prompt new biomarkers that may help develop diagnostic precision for distinguishing fibrolamellar hepatocellular carcinoma. The subatomic cytogenetic approach permits positional identification of gains, amplification, and deletion of DNA sequences of the whole tumor genome, to search for recurrent and particular cytogenetic changes in human fibrolamellar hepatocellular carcinoma. In this work, 13 cell lines of fibrolamellar carcinomas and 30 hepatocellular carcinoma samples examined by a single-nucleotide polymorphs array using two techniques to give more accuracy of the results. The majority of the abnormalities found in the fibrolamellar hepatocellular carcinoma positive cases seen as gain in 1q, 4q, 6q, 7p, 8q, 17q, 20q and loss in 1p, 4p-q, 8p, 11p, 13q, 17p, 18q, 19p, and 22q. The ultimate successive were central amplification at 1q (in 54% of 13 samples), 4q (in 54% of 13 samples), 7p (in 46% of 13 samples), and deletions at 19p13 (in 28% of 13 samples). The study revealed 3 distinct structural variations highlights-related genes MDM4, PRDM5, and WHSC1, and these genes are a novel target signature that can help to predict survival of patients with detecting fibrolamellar hepatocellular carcinoma.

The DNA motif discovery (MD) problem is the main challenge of genome biology, and its importance is directly proportional to increasing sequencing technologies. MD plays a vital role in the identification of transcription factor binding sites that help in learning the mechanisms for regulation of gene expression. Metaheuristic algorithms are promising techniques for eliciting motif from DNA genomic sequences, but often fail to demonstrate robust performance by overcoming the inherent challenges in complex gene sequences, making search environment extremely non-convex for optimization methods. This paper proposes a novel modified Henry gas solubility optimization (MHGSO) algorithm for motif discovery which elicits a functional motif in DNA genomic sequences. In our approach, a new stage that captures the main characteristics of the motifs in DNA sequences is proposed, and MHGSO imitates the motifs characteristics for accurate detection of target motif. The performance of the MHGSO algorithm is validated using both synthetic and real datasets. Results confirm the stability and superiority of the proposed algorithm compared to state-of-the-art algorithms including MEME, DREME, XXmotif, PMbPSO, and MACS. Based on several evaluation matrices, MHGSO outperforms the competitor techniques in terms of nucleotide-level correlation coefficient, recall, precision, F-score, Cohen’s Kappa, and statistical validation measures.

Computerized analysis of pigmented skin lesions (PSLs) is a lively space of survey that dates back over 25 years. Recently, different automated computer-based systems stand to be a helpful tool. Physicians’ usage for ABCD worldwide as the main tool of diagnosis and self-examination make it the common reference for different skin cancer diagnosis models. This system is comprised of the main four key warning signs of the ABCD model that can be detected by visual inspection and more accurately identified by the automated system to diagnose melanoma. Based on the image area identified as PSL, through pre-processing and segmentation step, the features will then be detected regarding ABCD rule. According to what ABCD stands for, the proposed study extracts Asymmetry, Border and Color features, in addition to various parameters introduce parameter “D.” Finally, as the worldwide definition of ABCD rule of cancer diagnoses was discussed, this research also makes the final decision according to the Total Dermoscopic Score (TDS) Index, in addition to another three popular machine learning classifiers. ANN, SVM, and K-nearest neighbor were used for classification of the segmented lesions in addition to the traditional TDS. This research shows perfect results for calculating the ABCD score automatically, which reflects its viability. Different experiments developed in regard to features variety and different classification methods to reach 98.1%, 95%, and 98.75% classification accuracy when dermoscopic images were classified by TDS, Automatic ANN, and linear SVM, respectively, where the clinical images reached perfect accuracy 100% when classified by linear SVM, and very promising result 98.75% as per automatic ANN. This system considered to be the first promising digitalized system for traditional TDS regarding the achieved accuracy and using of a simple Graphical User Interface (GUI) to facilitate user easy use.

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.

Lumbar total disc replacement (LTDR) is a surgical procedure for the treatment of degenerative disc disease (DDD) and lumbar spinal distortion to preserve range of motion (ROM). The SB Charite™ is the first device for LTDR but it produces more complications and long-term issues, causing a shortage of SB Charite™ disc. Currently, the evolution of lumbar disc arthroplasty based on some criteria like prosthetics structure, biomechanical model, tissue engineering and biomaterials approach. The optimal biomechanical model is based on kinematic and kinetic parameters together to ensure a long-term implantation with a lower rate of damage from disc implant in the spinal column. The finite element method (FEE) of human lumbar spinal is advanced to support biomechanical modeling techniques which are related to biomaterials guideline for choosing better material for implantation. Therefore, this paper presented a 3D biomechanical FEM model of L1 to L3 lumbar spines by different types of discs and materials. We applied a compressive force, and compressive force plus extension moment to this model to calculate Tresca stress of annulus fibers, strain and von Mises stress on the vertebral endplate at each intervertebral level under COMSOL Multiphysics® software.