Search results for: genetic polymorphisms

Authors: Yue-Tzu Yang, Shu-Ching Liao

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This study presents the numerical simulation of three-dimensional incompressible steady and laminar fluid flow and conjugate heat transfer of a trapezoidal microchannel heat sink using water as a cooling fluid in a silicon substrate. Navier-Stokes equations with conjugate energy equation are discretized by finite-volume method. We perform numerical computations for a range of 50 ≦ Re ≦ 600, 0.05W ≦ P ≦ 0.8W, 20W/cm2 ≦ ≦ 40W/cm2. The present study demonstrates the numerical optimization of a trapezoidal microchannel heat sink design using the response surface methodology (RSM) and the genetic algorithm method (GA). The results show that the average Nusselt number increases with an increase in the Reynolds number or pumping power, and the thermal resistance decreases as the pumping power increases. The thermal resistance of a trapezoidal microchannel is minimized for a constant heat flux and constant pumping power.

Keywords: microchannel heat sinks, conjugate heat transfer, optimization, genetic algorithm method

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Authors: Prittesh Patel, Rushabh Shah, Krishnamurthy Ramar, Vakulbhushan Bhaskar

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The present research work aims at finding genetic differences in the genomes of sugarcane red rot isolates Colletotrichum falcatum Went using Random Amplified Polymorphic DNA (RAPD) and interspersed simple sequence repeat (ISSR) molecular markers. Ten isolates of C. falcatum isolated from different red rot infected sugarcane cultivars stalk were used in present study. The amplified bands were scored across the lanes obtained in 15 RAPD primes and 21 ISSR primes successfully. The data were analysed using NTSYSpc 2.2 software. The results showed 80.6% and 68.07% polymorphism in RPAD and ISSR analysis respectively. Based on the RAPD analysis, ten genotypes were grouped into two major clusters at a cut-off value of 0.75. Geographically distant C. falcatum isolate cfGAN from south Gujarat had a level of similarity with Coimbatore isolate cf8436 presented on separate clade of bootstrapped dendrograms. First and second cluster consisted of five and three isolates respectively, indicating the close relation among them. The 21 ISSR primers produced 119 distinct and scorable loci in that 38 were monomorphic. The number of scorable loci for each primer varied from 2 (ISSR822) to 8 (ISSR807, ISSR823 and ISSR15) with an average of 5.66 loci per primer. Primer ISSR835 amplified the highest number of bands (57), while only 16 bands were obtained by primers ISSR822. Four primers namely ISSR830, ISSR845, ISSR4 and ISSR15 showed the highest value of percentage of polymorphism (100%). The results indicated that both of the marker systems RAPD and ISSR, individually can be effectively used in determination of genetic relationship among C falcatum accessions collected from different parts of south Gujarat.

Keywords: Colletotrichum falcatum, ISSR, RAPD, Red Rot

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Authors: Ming Su, Ziqiang Mu

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This paper proposes a synthesis method for nonuniform linear antenna arrays that combine Gaussian process regression (GPR) and genetic algorithm (GA). In this method, the GPR model can be used to calculate the array radiation pattern in the presence of mutual coupling effects, and then the GA is used to optimize the excitations and locations of the elements so as to generate the desired radiation pattern. In this paper, taking a 9-element nonuniform linear array as an example and the desired radiation pattern corresponding to a Chebyshev distribution as the optimization objective, optimize the excitations and locations of the elements. Finally, the optimization results are verified by electromagnetic simulation software CST, which shows that the method is effective.

Keywords: nonuniform linear antenna arrays, GPR, GA, mutual coupling effects, active element pattern

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Authors: Biswabandhu Bankura, Srikanta Guria, Madhusudan Das

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Purpose: Thyroid peroxidase (TPO) is the key enzyme in the biosynthesis of thyroid hormones. We aimed to identify the spectrum of mutations in the TPO gene leading to hypothyroidism in the population of West Bengal to establish the genetic etiology of the disease. Methods: 200 hypothyroid patients (case) and their corresponding sex and age matched 200 normal individuals (control) were screened depending on their clinical manifestations. Genomic DNA was isolated from peripheral blood samples and TPO gene (Exon 7 to Exon 14) was amplified by PCR. The PCR products were subjected to sequencing to identify mutations. Results: Single nucleotide changes such as Glu 641 Lys, Asp 668 Asn, Thr 725 Pro, Asp 620 Asn, Ser 398 Thr, and Ala 373 Ser were found. Changes in the TPO were assayed in vitro to compare mutant and wild-type activities. Five mutants were enzymatically inactive in the guaiacol and iodide assays. This is a strong indication that the mutations are present at crucial positions of the TPO gene, resulting in inactivated TPO. Key Findings: The results of this study may help to develop a genetic screening protocol for goiter and hypothyroidism in the population of West Bengal.

Keywords: thyroid peroxidase, hypothyroidism, mutation, in vitro assay, transfection

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Authors: Biswabandhu Bankura, Srikanta Guria, Madhusudan Das

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Purpose: Thyroid peroxidase (TPO) is the key enzyme in the biosynthesis of thyroid hormones. We aimed to identify the spectrum of mutations in the TPO gene leading to hypothyroidism in the population of West Bengal to establish the genetic etiology of the disease. Methods: 200 hypothyroid patients (case) and their corresponding sex and age matched 200 normal individuals (control) were screened depending on their clinical manifestations. Genomic DNA was isolated from peripheral blood samples and TPO gene (Exon 7 to Exon 14) was amplified by PCR. The PCR products were subjected to sequencing to identify mutations. Results: Single nucleotide changes such as Glu 641 Lys, Asp 668 Asn, Thr 725 Pro, Asp 620 Asn, Ser 398 Thr, and Ala 373 Ser were found. Changes in the TPO were assayed in vitro to compare mutant and wild-type activities. Five mutants were enzymatically inactive in the guaiacol and iodide assays. This is a strong indication that the mutations are present at crucial positions of the TPO gene, resulting in inactivated TPO. Key Findings: The results of this study may help to develop a genetic screening protocol for goiter and hypothyroidism in the population of West Bengal.

Keywords: thyroid peroxidase, hypothyroidism, mutation, in vitro assay, transfection

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Authors: Yelin Zhao, Xinxiu Li, Martin Smelik, Oleg Sysoev, Firoj Mahmud, Dina Mansour Aly, Mikael Benson

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Background: Early diagnosis of pancreatic cancer is clinically challenging due to vague, or no symptoms, and lack of biomarkers. Polygenic risk score (PRS) scores may provide a valuable tool to assess increased or decreased risk of PC. This study aimed to develop such PRS by filtering genetic variants identified by GWAS using transcriptional programs identified by single-cell RNA sequencing (scRNA-seq). Methods: ScRNA-seq data from 24 pancreatic ductal adenocarcinoma (PDAC) tumor samples and 11 normal pancreases were analyzed to identify differentially expressed genes (DEGs) in in tumor and microenvironment cell types compared to healthy tissues. Pathway analysis showed that the DEGs were enriched for hundreds of significant pathways. These were clustered into 40 “programs” based on gene similarity, using the Jaccard index. Published genetic variants associated with PDAC were mapped to each program to generate program PRSs (pPRSs). These pPRSs, along with five previously published PRSs (PGS000083, PGS000725, PGS000663, PGS000159, and PGS002264), were evaluated in a European-origin population from the UK Biobank, consisting of 1,310 PDAC participants and 407,473 non-pancreatic cancer participants. Stepwise Cox regression analysis was performed to determine associations between pPRSs with the development of PC, with adjustments of sex and principal components of genetic ancestry. Results: The PDAC genetic variants were mapped to 23 programs and were used to generate pPRSs for these programs. Four distinct pPRSs (P1, P6, P11, and P16) and two published PRSs (PGS000663 and PGS002264) were significantly associated with an increased risk of developing PC. Among these, P6 exhibited the greatest hazard ratio (adjusted HR[95% CI] = 1.67[1.14-2.45], p = 0.008). In contrast, P10 and P4 were associated with lower risk of developing PC (adjusted HR[95% CI] = 0.58[0.42-0.81], p = 0.001, and adjusted HR[95% CI] = 0.75[0.59-0.96], p = 0.019). By comparison, two of the five published PRS exhibited an association with PDAC onset with HR (PGS000663: adjusted HR[95% CI] = 1.24[1.14-1.35], p < 0.001 and PGS002264: adjusted HR[95% CI] = 1.14[1.07-1.22], p < 0.001). Conclusion: Compared to published PRSs, scRNA-seq-based pPRSs may be used not only to assess increased but also decreased risk of PDAC.

Keywords: cox regression, pancreatic cancer, polygenic risk score, scRNA-seq, UK biobank

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Authors: Adrian Ionita, Ana-Maria Ghimes

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The lack of features, design and the lack of promoting an integrated booking application are some of the reasons why most online travel platforms only offer automation of old booking processes, being limited to the integration of a smaller number of services without addressing the user experience. This paper represents a practical study on how to improve travel applications creating user-profiles through data-mining based on neural networks and genetic algorithms. Choices made by users and their ‘friends’ in the ‘social’ network context can be considered input data for a recommendation engine. The purpose of using these algorithms and this design is to improve user experience and to deliver more features to the users. The paper aims to highlight a broader range of improvements that could be applied to travel applications in terms of design and service integration, while the main scientific approach remains the technical implementation of the neural network solution. The motivation of the technologies used is also related to the initiative of some online booking providers that have made the fact that they use some ‘neural network’ related designs public. These companies use similar Big-Data technologies to provide recommendations for hotels, restaurants, and cinemas with a neural network based recommendation engine for building a user ‘DNA profile’. This implementation of the ‘profile’ a collection of neural networks trained from previous user choices, can improve the usability and design of any type of application.

Keywords: artificial intelligence, big data, cloud computing, DNA profile, genetic algorithms, machine learning, neural networks, optimization, recommendation system, user profiling

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Authors: Surabhi Maiti, Prajakta Tamhankar, Prachi Uttam Mehta

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Since the accomplishment of the Human Genome Project, there has been an unparalled escalation in the sequencing of genomic data. This project has been the first major vault in the field of medical research, especially in genomics. This project won accolades by using a concept called Bigdata which was earlier, extensively used to gain value for business. Bigdata makes use of data sets which are generally in the form of files of size terabytes, petabytes, or exabytes and these data sets were traditionally used and managed using excel sheets and RDBMS. The voluminous data made the process tedious and time consuming and hence a stronger framework called Hadoop was introduced in the field of genetic sciences to make data processing faster and efficient. This paper focuses on using SPARK which is gaining momentum with the advancement of BigData technologies. Cloud Storage is an effective medium for storage of large data sets which is generated from the genetic research and the resultant sets produced from SPARK analysis.

Keywords: human genome project, Bigdata, genomic data, SPARK, cloud storage, Hadoop

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Authors: Hesham Kozou

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Sensorineural hearing loss (SNHL) poses a significant challenge due to limited access to the inner ear for therapies. Emerging treatments such as regenerative, genetic, and pharmacotherapies offer hope for addressing this condition. This study aims to highlight the potential of cochlear implants and emerging therapies in managing sensorineural hearing loss by improving access to the inner ear. The study is conducted through a review of relevant literature and research articles in the field of cochlear implants and emerging therapies for hearing loss. It outlines how advancements in cochlear implant technologies, electrodes, and surgical techniques can facilitate the delivery of therapies to the inner ear, potentially revolutionizing the treatment of sensorineural hearing loss. The study underscores the potential of cochlear implants and emerging therapies in revolutionizing the treatment landscape for sensorineural hearing loss, emphasizing the feasibility of curing this condition by leveraging technological advancements.

Keywords: therapies for hearing loss management, future of CI as a cochlear delivery channel, regenerative, genetic and pharmacotherapeutic management of hearing loss

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Authors: R. Akbari, M. A. Ehyaei, R. Shahi Shavvon

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Nowadays, solar energy is used for energy purposes such as the use of thermal energy for domestic, industrial and power applications, as well as the conversion of the sunlight into electricity by photovoltaic cells. In this study, the thermodynamic simulation of the solar Rankin cycle with phase change material (paraffin) was first studied. Then energy and exergy analyses were performed. For optimization, a single and multi-objective genetic optimization algorithm to maximize thermal and exergy efficiency was used. The parameters discussed in this paper included the effects of input pressure on turbines, input mass flow to turbines, the surface of converters and collector angles on thermal and exergy efficiency. In the organic Rankin cycle, where solar energy is used as input energy, the fluid selection is considered as a necessary factor to achieve reliable and efficient operation. Therefore, silicon oil is selected for a high-temperature cycle and water for a low-temperature cycle as an operating fluid. The results showed that increasing the mass flow to turbines 1 and 2 would increase thermal efficiency, while it reduces and increases the exergy efficiency in turbines 1 and 2, respectively. Increasing the inlet pressure to the turbine 1 decreases the thermal and exergy efficiency, and increasing the inlet pressure to the turbine 2 increases the thermal efficiency and exergy efficiency. Also, increasing the angle of the collector increased thermal efficiency and exergy. The thermal efficiency of the system was 22.3% which improves to 33.2 and 27.2% in single-objective and multi-objective optimization, respectively. Also, the exergy efficiency of the system was 1.33% which has been improved to 1.719 and 1.529% in single-objective and multi-objective optimization, respectively. These results showed that the thermal and exergy efficiency in a single-objective optimization is greater than the multi-objective optimization.

Keywords: exergy analysis, genetic algorithm, rankine cycle, single and multi-objective function

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Authors: Navab Karimi, Tohid Alizadeh

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An intelligent vision-based system was designed to measure the quality and purity of raisins. A machine vision setup was utilized to capture the images of bulk raisins in ranges of 5-50% mixed pure-impure berries. The textural features of bulk raisins were extracted using Grey-level Histograms, Co-occurrence Matrix, and Local Binary Pattern (a total of 108 features). Genetic Algorithm and neural network regression were used for selecting and ranking the best features (21 features). As a result, the GLCM features set was found to have the highest accuracy (92.4%) among the other sets. Followingly, multiple feature combinations of the previous stage were fed into the second regression (linear regression) to increase accuracy, wherein a combination of 16 features was found to be the optimum. Finally, a Support Vector Machine (SVM) classifier was used to differentiate the mixtures, producing the best efficiency and accuracy of 96.2% and 97.35%, respectively.

Keywords: sun-dried organic raisin, genetic algorithm, feature extraction, ann regression, linear regression, support vector machine, south azerbaijan.

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Authors: Safa A. Mohammed Ali, Ammar S. Ahamed, Mohammed Khair Abdalla

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The objectives of this study were to estimate the means and genetic parameters of birth and weaning weight of calves of pure Holstein-Friesian cows raised in Sudan. The traits studied were:*Weight at birth *Weight at weaning. The study also included some of the important factors that affected these traits. The data were analyzed using Harvey’s Least Squares and Maximum Likelihood programme. The results obtained showed that the overall mean weight at birth of the calves under study was 34.36±0.94kg. Male calves were found to be heavier than females; the difference between the sexes was highly significant (P<0.001). The mean weight at birth of male calves was 34.27±1.17 kg while that of females was 32.51±1.14kg. The effect of sex of calves, sire and parity of dam were highly significant (P<0.001). The overall mean of weight at weaning was 67.10 ± 5.05 kg, weight at weaning was significantly (p<0.001) effected by sex of calves, sire, year and season of birth have highly significant (P<0.001) effect on either trait. Also estimates heritabilities of birth weight was (0.033±0.015) lower than heritabilities of weaning weight (0.224±0.039), and genetic correlation was 0.563, the phenotypic correlation 0.281, and the environmental correlation 0.268.

Keywords: birth, weaning, weight, friesian

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Authors: Amir Abbas Fatemi, Zahra Tabrizian, Kabir Sadeghi

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To find the location and severity of damage that occurs in a structure, characteristics changes in dynamic and static can be used. The non-destructive techniques are more common, economic, and reliable to detect the global or local damages in structures. This paper presents a non-destructive method in structural damage detection and assessment using GA and static data. Thus, a set of static forces is applied to some of degrees of freedom and the static responses (displacements) are measured at another set of DOFs. An analytical model of the truss structure is developed based on the available specification and the properties derived from static data. The damages in structure produce changes to its stiffness so this method used to determine damage based on change in the structural stiffness parameter. Changes in the static response which structural damage caused choose to produce some simultaneous equations. Genetic Algorithms are powerful tools for solving large optimization problems. Optimization is considered to minimize objective function involve difference between the static load vector of damaged and healthy structure. Several scenarios defined for damage detection (single scenario and multiple scenarios). The static damage identification methods have many advantages, but some difficulties still exist. So it is important to achieve the best damage identification and if the best result is obtained it means that the method is Reliable. This strategy is applied to a plane truss. This method is used for a plane truss. Numerical results demonstrate the ability of this method in detecting damage in given structures. Also figures show damage detections in multiple damage scenarios have really efficient answer. Even existence of noise in the measurements doesn’t reduce the accuracy of damage detections method in these structures.

Keywords: damage detection, finite element method, static data, non-destructive, genetic algorithm

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Authors: Dipti Patra, Guguloth Uma, Smita Pradhan

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Registration is a fundamental task in image processing. It is used to transform different sets of data into one coordinate system, where data are acquired from different times, different viewing angles, and/or different sensors. The registration geometrically aligns two images (the reference and target images). Registration techniques are used in satellite images and it is important in order to be able to compare or integrate the data obtained from these different measurements. In this work, mutual information is considered as a similarity metric for registration of satellite images. The transformation is assumed to be a rigid transformation. An attempt has been made here to optimize the transformation function. The proposed image registration technique hybrid PSO-GA incorporates the notion of Particle Swarm Optimization and Genetic Algorithm and is used for finding the best optimum values of transformation parameters. The performance comparision obtained with the experiments on satellite images found that the proposed hybrid PSO-GA algorithm outperforms the other algorithms in terms of mutual information and registration accuracy.

Keywords: image registration, genetic algorithm, particle swarm optimization, hybrid PSO-GA algorithm and mutual information

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Authors: Manik Sharma, Ganapathy Krishnamurthi

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The cost of some drugs and medical treatments has risen in recent years, that many patients are having to go without. A classification project could make researchers more efficient. One of the more surprising reasons behind the cost is how long it takes to bring new treatments to market. Despite improvements in technology and science, research and development continues to lag. In fact, finding new treatment takes, on average, more than 10 years and costs hundreds of millions of dollars. If successful, we could dramatically improve the industry's ability to model cellular images according to their relevant biology. In turn, greatly decreasing the cost of treatments and ensure these treatments get to patients faster. This work aims at solving a part of this problem by creating a cellular image classification model which can decipher the genetic perturbations in cell (occurring naturally or artificially). Another interesting question addressed is what makes the deep-learning model decide in a particular fashion, which can further help in demystifying the mechanism of action of certain perturbations and paves a way towards the explainability of the deep-learning model.

Keywords: cellular images, genetic perturbations, deep-learning, explainability

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Authors: Nima Farshidfar, Navid Daryasafar

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In this paper, the seismic stability of reinforced soil slopes is studied using pseudo-dynamic analysis. Equilibrium equations that are applicable to the every kind of failure surface are written using Horizontal Slices Method. In written equations, the balance of the vertical and horizontal forces and moment equilibrium is fully satisfied. Failure surface is assumed to be log-spiral, and non-linear equilibrium equations obtained for the system are solved using Newton-Raphson Method. Earthquake effects are applied as horizontal and vertical pseudo-static coefficients to the problem. To solve this problem, a code was developed in MATLAB, and the critical failure surface is calculated using genetic algorithm. At the end, comparing the results obtained in this paper, effects of various parameters and the effect of using pseudo - dynamic analysis in seismic forces modeling is presented.

Keywords: soil slopes, pseudo-dynamic, genetic algorithm, optimization, limit equilibrium method, log-spiral failure surface

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Authors: Fuad M. Alkoot

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Different experimental technologies such as microarray sequencing have been proposed to generate high-resolution genetic data, in order to understand the complex dynamic interactions between complex diseases and the biological system components of genes and gene products. However, the generated samples have a very large dimension reaching thousands. Therefore, hindering all attempts to design a classifier system that can identify diseases based on such data. Additionally, the high overlap in the class distributions makes the task more difficult. The data we experiment with is generated for the identification of autism. It includes 142 samples, which is small compared to the large dimension of the data. The classifier systems trained on this data yield very low classification rates that are almost equivalent to a guess. We aim at reducing the data dimension and improve it for classification. Here, we experiment with applying a multistage PCA on the genetic data to reduce its dimensionality. Results show a significant improvement in the classification rates which increases the possibility of building an automated system for autism detection.

Keywords: PCA, gene expression, dimensionality reduction, classification, autism

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Authors: Jana Kisková, Dana Gabriková

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Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4-repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance specific haplotype groups of SNPs and interaction of MAOA with others genes (e.g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism

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Authors: Akterono Budiyati, Gita Kusumo, Teguh Putra, Fritzie Rexana, Antonius Kurniawan, Aru Sudoyo, Ahmad Utomo, Andi Utama

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The presence of the programmed death ligand-1 (PD-L1) has been used in multiple clinical trials and approved as biomarker for selecting patients more likely to respond to immune checkpoint inhibitors. However, the expression of PD-L1 is regulated in different ways, which leads to a different significance of its presence. Positive PD-L1 within tumors may result from two mechanisms, induced PD-L1 expression by T-cell presence or genetic mechanism that lead to constitutive PD-L1 expression. Amplification of PD-L1 genes was found as one of genetic mechanism which causes an increase in PD-L1 expression. In case of colorectal cancer (CRC), targeting immune checkpoint inhibitor has been recommended for patients with microsatellite instable (MSI). Although the correlation between PD-L1 expression and MSI status has been widely studied, so far the precise mechanism of PD-L1 gene activation in CRC patients, particularly in MSI population have yet to be clarified. In this present study we have profiled 61 archived formalin fixed paraffin embedded CRC specimens of patients from Medistra Hospital, Jakarta admitted in 2010 - 2016. Immunohistochemistry was performed to measure expression of PD-L1 in tumor cells as well as MSI status using antibodies against PD-L1 and MMR (MLH1, MSH2, PMS2 and MSH6), respectively. PD-L1 expression was measured on tumor cells with cut off of 1% whereas loss of nuclear MMR protein expressions in tumor cells but not in normal or stromal cells indicated presence of MSI. Subset of PD-L1 positive patients was then assessed for copy number variations (CNVs) using single Tube TaqMan Copy Number Assays Gene CD247PD-L1. We also observed KRAS mutation to profile possible genetic mechanism leading to the presence or absence of PD-L1 expression. Analysis of 61 CRC patients revealed 15 patients (24%) expressed PD-L1 on their tumor cell membranes. The prevalence of surface membrane PD-L1 was significantly higher in patients with MSI (87%; 7/8) compared to patients with microsatellite stable (MSS) (15%; 8/53) (P=0.001). Although amplification of PD-L1 gene was not found among PD-L1 positive patients, low-level amplification of PD-L1 gene was commonly observed in MSS patients (75%; 6/8) than in MSI patients (43%; 3/7). Additionally, we found 26% of CRC patients harbored KRAS mutations (16/61), so far the distribution of KRAS status did not correlate with PD-L1 expression. Our data suggest genetic mechanism through amplification of PD-L1 seems not to be the mechanism underlying upregulation of PD-L1 expression in CRC patients. However, further studies are warranted to confirm the results.

Keywords: colorectal cancer, gene amplification, microsatellite instable, programmed death ligand-1

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Authors: M. Kouyate, M. Sangare, S. Samake, S. Keita, H. G. Kim, D. H. Geschwind

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Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder.

Keywords: bioinformatics, endonucleases, autism, Sanger sequencing, point mutations

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Authors: Mia Bahar, Özlem Bozkurt

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Obsessive-compulsive disorder (OCD) is a typical, persistent, and long-lasting mental health condition in which a person experiences uncontrollable, recurrent thoughts (or "obsessions") and/or activities (or "compulsions") that they feel compelled to engage in repeatedly. Obsessive-compulsive disorder is both underdiagnosed and undertreated. It frequently manifests in a variety of medical settings and is persistent, expensive, and burdensome. Obsessive-compulsive neurosis was long believed to be a condition that offered valuable insight into the inner workings of the unconscious mind. Obsessive-compulsive disorder is now recognized as a prime example of a neuropsychiatric condition susceptible to particular pharmacotherapeutic and psychotherapy therapies and mediated by pathology in particular neural circuits. An obsessive-compulsive disorder which is called OCD, usually has two components, one cognitive and the other behavioral, although either can occur alone. Obsessions are often repetitive and intrusive thoughts that invade consciousness. These obsessions are incredibly hard to control or dismiss. People who have OCD often engage in rituals to reduce anxiety associated with intrusive thoughts. Once the ritual is formed, the person may feel extreme relief and be free from anxiety until the thoughts of contamination intrude once again. These thoughts are strengthened through a manifestation of negative reinforcement because they allow the person to avoid anxiety and obscurity. These thoughts are described as autogenous, meaning they most likely come from nowhere. These unwelcome thoughts are related to actions which we can describe as Thought Action Fusion. The thought becomes equated with an action, such as if they refuse to perform the ritual, something bad might happen, and so people perform the ritual to escape the intrusive thought. In almost all cases of OCD, the person's life gets extremely disturbed by compulsions and obsessions. Studies show OCD is an estimated 1.1% prevalence, making it a challenging issue with high co-morbidities with other issues like depressive episodes, panic disorders, and specific phobias. The first to reveal brain anomalies in OCD were numerous CT investigations, although the results were inconsistent. A few studies have focused on the orbitofrontal cortex (OFC), anterior cingulate gyrus (AC), and thalamus, structures also implicated in the pathophysiology of OCD by functional neuroimaging studies, but few have found consistent results. However, some studies have found abnormalities in the basal ganglion. There have also been some discussions that OCD might be genetic. OCD has been linked to families in studies of family aggregation, and findings from twin studies show that this relationship is somewhat influenced by genetic variables. Some Research has shown that OCD is a heritable, polygenic condition that can result from de novo harmful mutations as well as common and unusual variants. Numerous studies have also presented solid evidence in favor of a significant additive genetic component to OCD risk, with distinct OCD symptom dimensions showing both common and individual genetic risks.

Keywords: compulsions, obsessions, neuropsychiatric, genetic

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Authors: Alireza Nikbakht Shahbazi, Emadeddin Shirali

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Since optimization issues of water resources are complicated due to the variety of decision making criteria and objective functions, it is sometimes impossible to resolve them through regular optimization methods or, it is time or money consuming. Therefore, the use of modern tools and methods is inevitable in resolving such problems. An accurate and essential utilization policy has to be determined in order to use natural resources such as water reservoirs optimally. Water reservoir programming studies aim to determine the final cultivated land area based on predefined agricultural models and water requirements. Dam utilization rule curve is also provided in such studies. The basic information applied in water reservoir programming studies generally include meteorological, hydrological, agricultural and water reservoir related data, and the geometric characteristics of the reservoir. The system of Dez dam water resources was simulated applying the basic information in order to determine the capability of its reservoir to provide the objectives of the performed plan. As a meta-exploratory method, genetic algorithm was applied in order to provide utilization rule curves (intersecting the reservoir volume). MATLAB software was used in order to resolve the foresaid model. Rule curves were firstly obtained through genetic algorithm. Then the significance of using rule curves and the decrease in decision making variables in the system was determined through system simulation and comparing the results with optimization results (Standard Operating Procedure). One of the most essential issues in optimization of a complicated water resource system is the increasing number of variables. Therefore a lot of time is required to find an optimum answer and in some cases, no desirable result is obtained. In this research, intersecting the reservoir volume has been applied as a modern model in order to reduce the number of variables. Water reservoir programming studies has been performed based on basic information, general hypotheses and standards and applying monthly simulation technique for a statistical period of 30 years. Results indicated that application of rule curve prevents the extreme shortages and decrease the monthly shortages.

Keywords: optimization, rule curve, genetic algorithm method, Dez dam reservoir

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Authors: Mariedel Autriz, Angel Lambio, Renato Vega, Severino Capitan, Rita Laude

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The study was conducted to associate genetic polymorphism of the leptin gene T3469C with reproductive performance in purebred sows. DNA were isolated from hair follicles of 29 Landrace and 24 Large White sows. Amplification of the leptin gene was done followed by Hinf1digestion to determine the base at the T3469C site. Electrophoresis of the digestion products revealed that there were 25 Landrace and 15 Large White sows with the TT genotype while there were 3 Landrace and 6 Large White TC. There was 1 CC for Landrace and 3 for Large White. Significant genotype associations were observed for total litter size born and total born alive. Significant breed differences, on the other hand, was observed for gestation length and average birth weight. Significant breed by genotype interaction was observed in litter size total born and litter size born alive.

Keywords: genetic polymorphism, leptin, swine, T3469C

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Authors: Mohamed Fawzy Elzarei, Yousef Mohammed Al-Dakheel, Ali Mohamed Alseaf

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Modern molecular techniques, like single marker analysis for linked traits to these markers, can provide us with rapid and accurate genetic results. In the last two decades of the last century, the applications of molecular techniques were reached a faraway point in cattle, sheep, and pig. In goats, especially in our region, the application of molecular techniques is still far from other species. As reported by many researchers, microsatellites marker is one of the suitable markers for lie studies. The single marker linked to traits of interest is one technique allowed us to early select animals without the necessity for mapping the entire genome. Simplicity, applicability, and low cost of this technique gave this technique a wide range of applications in many areas of genetics and molecular biology. Also, this technique provides a useful approach for evaluating genetic differentiation, particularly in populations that are poorly known genetically. The expected breeding value (EBV) and yield deviation (YD) are considered as the most parameters used for studying the linkage between quantitative characteristics and molecular markers, since these values are raw data corrected for the non-genetic factors. A total of 17 microsatellites markers (from chromosomes 6, 14, 18, 20 and 23) were used in this study to search for areas that could be responsible for genetic variability for some milk traits and search of chromosomal regions that explain part of the phenotypic variance. Results of single-marker analyses were used to identify the linkage between microsatellite markers and variation in EBVs of these traits, Milk yield, Protein percentage, Fat percentage, Litter size and weight at birth, and litter size and weight at weaning. The estimates of the parameters from forward and backward solutions using stepwise regression procedure on milk yield trait, only two markers, OARCP9 and AGLA29, showed a highly significant effect (p≤0.01) in backward and forward solutions. The forward solution for different equations conducted that R2 of these equations were highly depending on only two partials regressions coefficient (βi,) for these markers. For the milk protein trait, four marker showed significant effect BMS2361, CSSM66 (p≤0.01), BMS2626, and OARCP9 (p≤0.05). By the other way, four markers (MCM147, BM1225, INRA006, andINRA133) showed highly significant effect (p≤0.01) in both backward and forward solutions in association with milk fat trait. For both litter size at birth and at weaning traits, only one marker (BM143(p≤0.01) and RJH1 (p≤0.05), respectively) showed a significant effect in backward and forward solutions. The estimates of the parameters from forward and backward solution using stepwise regression procedure on litter weight at birth (LWB) trait only one marker (MCM147) showed highly significant effect (p≤0.01) and two marker (ILSTS011, CSSM66) showed a significant effect (p≤0.05) in backward and forward solutions.

Keywords: microsatellites marker, estimated breeding value, stepwise regression, milk traits

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Authors: Hyunchul Ahn, William X. S. Wong

Abstract:

Corporate credit rating prediction is one of the most important topics, which has been studied by researchers in the last decade. Over the last decade, researchers are pushing the limit to enhance the exactness of the corporate credit rating prediction model by applying several data-driven tools including statistical and artificial intelligence methods. Among them, multiclass support vector machine (MSVM) has been widely applied due to its good predictability. However, heuristics, for example, parameters of a kernel function, appropriate feature and instance subset, has become the main reason for the critics on MSVM, as they have dictate the MSVM architectural variables. This study presents a hybrid MSVM model that is intended to optimize all the parameter such as feature selection, instance selection, and kernel parameter. Our model adopts genetic algorithm (GA) to simultaneously optimize multiple heterogeneous design factors of MSVM.

Keywords: corporate credit rating prediction, Feature selection, genetic algorithms, instance selection, multiclass support vector machines

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Authors: Iva Košek Bartošová, Andrea Jokešová, Eva Kozlová, Helena Matějová

Abstract:

The paper presents results of a research team from Faculty of Education, University of Hradec Králové in the Czech Republic. It introduces with the most reading methods used in the 1^st classes of a primary school and presents results of a pilot research focused on mastering reading techniques and the quality of reading comprehension of pupils in the first half of a school year during training in teaching reading by an analytic-synthetic method and by a genetic method. These methods of practicing reading skills are the most used ones in the Czech Republic. During the school year 2015/16 there has been a measurement made of two groups of pupils of the 1^st year and monitoring of quantitative and qualitative parameters of reading pupils’ outputs by several methods. Both of these methods are based on different theoretical basis and each of them has a specific educational and methodical procedure. This contribution represents results during a piloting project and draws pilot conclusions which will be verified in the subsequent broader research at the end of the school year of the first class of primary school.

Keywords: analytic-synthetic method of reading, genetic method of reading, reading comprehension, reading literacy, reading methods, reading speed

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Authors: Yushinta Fujaya, Andi Ivo Asphama, Andi Parenrengi, Andi Tenriulo

Abstract:

Blue Swimming crab (Portunus pelagicus) is an important commercial species throughout the subtropical waters and as such constitutes part of the fisheries resources. Data are lacking on the morphological variations of selected fast-growing crabs reared in a pond. This study aimed to analyze the morphological and molecular character of a selected fast-growing crab reared in ponds in South of Sulawesi. The crab seeds were obtained from local fish-trap and hatchery. A study on the growth was carried out in the population of crabs. The dimensions analyzed were carapace width (CW) measured after 3 months of grow out. Morphological character states were examined based on the pattern of spots on the carapace. Molecular analysis was performed using RAPD (Random Amplified Polymorphic DNA). Genetic distance was analysed using TFPGA (Tools for Population Genetic Analyses) version 1.3. The results showed that there were variations in the growth of crabs. These crabs clustered morphologically into three quite distinct groups. The crab with white spots irregularly spread over its carapace was the largest size while the crab with large white spots scattered over the carapace was the smaller size (3%). The crab with small white spots scattered over the carapace was the smallest size found in this study. Molecular analysis showed that there are morphologically and genetically different between groups of crabs. Genetic distances among crabs ranged from 0.1527 to 0.5856. Thus, this study provides information the use of white spots pattern over carapace as indicators to identify the type of blue swimming crabs.

Keywords: crab, portunus pelagicus, morphology, RAPD, Carapace

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Authors: Uswah Khairuddin, Rubiyah Yusof, Nenny Ruthfalydia Rosli

Abstract:

This paper presents a comparative study between k-Nearest Neighbour (k-NN) and Multi-Layer Perceptron Neural Network (MLP-NN) classifier using Genetic Algorithm (GA) as feature selector for wood recognition system. The features have been extracted from the images using Grey Level Co-Occurrence Matrix (GLCM). The use of GA based feature selection is mainly to ensure that the database used for training the features for the wood species pattern classifier consists of only optimized features. The feature selection process is aimed at selecting only the most discriminating features of the wood species to reduce the confusion for the pattern classifier. This feature selection approach maintains the ‘good’ features that minimizes the inter-class distance and maximizes the intra-class distance. Wrapper GA is used with k-NN classifier as fitness evaluator (GA-kNN). The results shows that k-NN is the best choice of classifier because it uses a very simple distance calculation algorithm and classification tasks can be done in a short time with good classification accuracy.

Keywords: feature selection, genetic algorithm, optimization, wood recognition system

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Authors: Alexandru-Ion Marinescu

Abstract:

There exist a plethora of methods in the scientific literature which tackle the well-established task of credit score evaluation. In its most abstract form, a credit scoring algorithm takes as input several credit applicant properties, such as age, marital status, employment status, loan duration, etc. and must output a binary response variable (i.e. “GOOD” or “BAD”) stating whether the client is susceptible to payment return delays. Data imbalance is a common occurrence among financial institution databases, with the majority being classified as “GOOD” clients (clients that respect the loan return calendar) alongside a small percentage of “BAD” clients. But it is the “BAD” clients we are interested in since accurately predicting their behavior is crucial in preventing unwanted loss for loan providers. We add to this whole context the constraint that the algorithm must yield an actual, tractable mathematical formula, which is friendlier towards financial analysts. To this end, we have turned to genetic algorithms and genetic programming, aiming to evolve actual mathematical expressions using specially tailored mutation and crossover operators. As far as data representation is concerned, we employ a very flexible mechanism – LINQ expression trees, readily available in the C# programming language, enabling us to construct executable pieces of code at runtime. As the title implies, they model trees, with intermediate nodes being operators (addition, subtraction, multiplication, division) or mathematical functions (sin, cos, abs, round, etc.) and leaf nodes storing either constants or variables. There is a one-to-one correspondence between the client properties and the formula variables. The mutation and crossover operators work on a flattened version of the tree, obtained via a pre-order traversal. A consequence of our chosen technique is that we can identify and discard client properties which do not take part in the final score evaluation, effectively acting as a dimensionality reduction scheme. We compare ourselves with state of the art approaches, such as support vector machines, Bayesian networks, and extreme learning machines, to name a few. The data sets we benchmark against amount to a total of 8, of which we mention the well-known Australian credit and German credit data sets, and the performance indicators are the following: percentage correctly classified, area under curve, partial Gini index, H-measure, Brier score and Kolmogorov-Smirnov statistic, respectively. Finally, we obtain encouraging results, which, although placing us in the lower half of the hierarchy, drive us to further refine the algorithm.

Keywords: expression trees, financial credit scoring, genetic algorithm, genetic programming, symbolic evolution

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Authors: Seyedmirsajad Mokhtarimousavi, Danial Talebi, Hamidreza Asgari

Abstract:

Gate Assignment Problem (GAP) is one of the most substantial issues in airport operation. In principle, GAP intends to maintain the maximum capacity of the airport through the best possible allocation of the resources (gates) in order to reach the optimum outcome. The problem involves a wide range of dependent and independent resources and their limitations, which add to the complexity of GAP from both theoretical and practical perspective. In this study, GAP was mathematically formulated as a three-objective problem. The preliminary goal of multi-objective formulation was to address a higher number of objectives that can be simultaneously optimized and therefore increase the practical efficiency of the final solution. The problem is solved by applying the second version of Non-dominated Sorting Genetic Algorithm (NSGA-II). Results showed that the proposed mathematical model could address most of major criteria in the decision-making process in airport management in terms of minimizing both airport/airline cost and passenger walking distance time. Moreover, the proposed approach could properly find acceptable possible answers.

Keywords: airport management, gate assignment problem, mathematical modeling, genetic algorithm, NSGA-II

Procedia PDF Downloads 297