Search results for: grammar-based genetic programming

Authors: Wafa Al Jabri

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Background: In Middle Eastern Islamic Countries (MEICs), there is a high prevalence of genetic blood disorders (GBDs), particularly sickle cell disease and thalassemia. The GBDs are considered a major public health concern, especially with the increase in affected populations along with the associated psychological, social, and financial cost of management. Despite the availability of premarital screening services (PSS) that aim to identify the asymptomatic carriers of GBDs and provide genetic counseling to couples in order toreduce the prevalence of these diseases; yet, the success rate of PSS is very low due to religious and socio-cultural concerns. Purpose: This paper aims to highlight the factors that affect the success of PSS in MEICs. Methods: A literature review of articles located in CINAHL, PubMed, SCOPUS, and MedLinewas carried out using the following terms: “premarital screening,” “success,” “effectiveness,” and “ genetic blood disorders.” Second, a hand search of the reference lists and Google searches were conducted to find studies that did not exist in the primary database searches. Only studies which are conducted in MEICs countries and published in the last five years were included. Studies that were not published in English were excluded. Results: Fourteen articles were included in the review. The results showed that PSS in most of the MEICs was successful in achieving its objective of identifying high-risk marriages; however, the service failed to meetitsultimate goal of reducing the prevalence of GBDs. Various factors seem to hinder the success of PSS, including poor public awareness, late timing of the screening, culture and social stigma, religious beliefs, availability of prenatal diagnosis and therapeutic abortion, emotional factors, and availability of genetic counseling services. However, poor public awareness, late timing of the screening, and unavailability of adequate counseling services were the most common barriers identified. Conclusion: Overcoming the identified barriers by providing effective health education programs, offering the screening test to young adults at an earlier stage, and tailoring the genetic counseling would be crucial steps to provide a framework for an effective PSS in MEICs.

Keywords: premarital screening, success, effectiveness, and genetic blood disorders

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Authors: Viet-Hung Truong, Seung-Eock Kim

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This paper presents a robust software package for practical advanced analysis of space steel framed structures. The pre- and post-processors of the presented software package are coded in the C++ programming language while the solver is written by using the FORTRAN programming language. A user-friendly graphical interface of the presented software is developed to facilitate the modeling process and result interpretation of the problem. The solver employs the stability functions for capturing the second-order effects to minimize modeling and computational time. Both the plastic-hinge and fiber-hinge beam-column elements are available in the presented software. The generalized displacement control method is adopted to solve the nonlinear equilibrium equations.

Keywords: advanced analysis, beam-column, fiber-hinge, plastic hinge, steel frame

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Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Pragyan Paramita Das, Vishwas N. Khatri

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By using the lower- and upper- bound finite elements to limit analysis in conjunction with second-order conic programming (SOCP), the effect of seismic forces on the bearing capacity of surface strip footing resting on dense sand underlain by loose sand deposit is explored. The soil is assumed to obey the Mohr-Coulomb’s yield criterion and an associated flow rule. The angle of internal friction (ϕ) of the top and the bottom layer is varied from 42° to 44° and 32° to 34° respectively. The coefficient of seismic acceleration is varied from 0 to 0.3. The variation of bearing capacity with different thickness of top layer for various seismic acceleration coefficients is generated. A comparison will be made with the available solutions from literature wherever applicable.

Keywords: bearing capacity, conic programming, finite elements, seismic forces

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: adaptation, animals, evolution, genomics

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Authors: Gordana Branković, Dejan Dodig, Vesna Pajić, Vesna Kandić, Desimir Knežević, Nenad Đurić

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The wheat grain quality properties are influenced by genotype, environmental conditions and genotype × environment interaction (GEI). The increasing request of more nutritious wheat products will direct future breeding programmes. Therefore, the aim of investigation was to determine: i) variability of the protein content (PC), wet gluten content (WG) and Zeleny sedimentation volume (ZS); ii) components of variance, heritability in a broad sense (hb2), and expected genetic advance as percent of mean (GAM) for PC, WG, and ZS; iii) correlations between PC, WG, ZS, and most important agronomic traits; in order to assess expected breeding success versus environmental impact for these quality traits. The plant material consisted of 30 genotypes of bread wheat (Triticum aestivum L. ssp. aestivum) and durum wheat (Triticum durum Desf.). The trials were sown at the three test locations in Serbia: Rimski Šančevi, Zemun Polje and Padinska Skela during 2010-2011 and 2011-2012. The experiments were set as randomized complete block design with four replications. The plot consisted of five rows of 1 m2 (5 × 0.2 m × 1 m). PC, WG and ZS were determined by the use of Near infrared spectrometry (NIRS) with the Infraneo analyser (Chopin Technologies, France). PC, WG and ZS, in bread wheat, were in the range 13.4-16.4%, 22.8-30.3%, and 39.4-67.1 mL, respectively, and in durum wheat, in the range 15.3-18.1%, 28.9-36.3%, 37.4-48.3 mL, respectively. The dominant component of variance for PC, WG, and ZS, in bread wheat, was genotype with the genetic variance/GEI variance (VG/VG × E) relation of 3.2, 2.9 and 1.0, respectively, and in durum wheat was GEI with the VG/VG × E relation of 0.70, 0.69 and 0.49, respectively. hb2 and GAM values for PC, WG and ZS, in bread wheat, were 94.9% and 12.6%, 93.7% and 18.4%, and 86.2% and 28.1%, respectively, and in durum wheat, 80.7% and 7.6%, 79.7% and 10.2%, and 74% and 11.2%, respectively. The most consistent through six environments, statistically significant correlations, for bread wheat, were between PC and spike length (-0.312 to -0.637); PC, WG, ZS and grain number per spike (-0.320 to -0.620; -0.369 to -0.567; -0.301 to -0.378, respectively); PC and grain thickness (0.338 to 0.566), and for durum wheat, were between PC, WG, ZS and yield (-0.290 to -0.690; -0.433 to -0.753; -0.297 to -0.660, respectively); PC and plant height (-0.314 to -0.521); PC, WG and spike length (-0.298 to -0.597; -0.293 to -0.627, respectively); PC, WG and grain thickness (0.260 to 0.575; 0.269 to 0.498, respectively); PC, WG and grain vitreousness (0.278 to 0.665; 0.357 to 0.690, respectively). Breeding success can be anticipated for ZS in bread wheat due to coupled high values for hb2 and GAM, suggesting existence of additive genetic effects, and also for WG in bread wheat, due to very high hb2 and medium high GAM. The small, and medium, negative correlations between PC, WG, ZS, and yield or yield components, indicate difficulties to select simultaneously for high quality and yield, depending on linkage for particular genetic arrangements to be broken by recombination.

Keywords: bread and durum wheat, genetic advance, protein and wet gluten content, Zeleny sedimentation volume

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Authors: Paromik Bhattacharyya, Vijay Kumar, Johannes Van Staden

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Micropropagation is an important tool for the conservation of threatened and commercially important plant species of which orchids deserve special attention. Ansellia africana is one such medicinally important orchid species having much commercial significance. Thus, development of regeneration protocols for producing clonally stable regenerates using axillary buds is of much importance. However, for large-scale micropropagation to become not only successful but also acceptable by end-users, somaclonal variations occurring in the plantlets need to be eliminated. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that may account for the somaclonal variations of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach is of utmost importance. In the present study, the clonal integrity of the long term micropropagated A. africana plants were assessed using advanced molecular marker system i.e. Start Codon Targeted Polymorphism (SCoT). Our studies recorded a clonally stable regeneration protocol for A. africana with a very high degree of clonal fidelity amongst the regenerates. The results obtained from these molecular analyses could help in modifying the regeneration protocols for obtaining clonally stable true to type plantlets for sustainable commercial use.

Keywords: medicinal orchid micropropagation, start codon targeted polymorphism (SCoT), RAP), traditional African pharmacopoeia, genetic fidelity

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Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Minjung Kim, Hyunkoo Kang, Jinkoo Kim

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In this study, a seismic retrofit scheme for a reinforced concrete shear wall structure using steel slit dampers was presented. The stiffness and the strength of the slit damper used in the retrofit were verified by cyclic loading test. A genetic algorithm was applied to find out the optimum location of the slit dampers. The effects of the slit dampers on the seismic retrofit of the model were compared with those of jacketing shear walls. The seismic performance of the model structure with optimally positioned slit dampers was evaluated by nonlinear static and dynamic analyses. Based on the analysis results, the simple procedure for determining required damping ratio using capacity spectrum method along with the damper distribution pattern proportional to the inter-story drifts was validated. The analysis results showed that the seismic retrofit of the model structure using the slit dampers was more economical than the jacketing of the shear walls and that the capacity spectrum method combined with the simple damper distribution pattern led to satisfactory damper distribution pattern compatible with the solution obtained from the genetic algorithm.

Keywords: seismic retrofit, slit dampers, genetic algorithm, jacketing, capacity spectrum method

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Authors: Othman E. Othman, Amira M. Nowier, Medhat El-Denary

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Camels play an important socio-economic role within the pastoral and agricultural system in the dry and semidry zones of Asia and Africa. Camels are economically important animals in Egypt where they are dual purpose animals (meat and milk). The analysis of chemical composition of camel milk showed that the total protein contents ranged from 2.4% to 5.3% and it is divided into casein and whey proteins. The casein fraction constitutes 52% to 89% of total camel milk protein and it divided into 4 fractions namely αs1, αs2, β and κ-caseins which are encoded by four tightly genes. In spite of the important role of casein genes and the effects of their genetic polymorphisms on quantitative traits and technological properties of milk, the studies for the detection of genetic polymorphism of camel milk genes are still limited. Due to this fact, this work focused - using PCR-RFP and sequencing analysis - on the identification of genetic polymorphisms and SNPs of two casein genes in Maghrabi camel breed which is a dual purpose camel breed in Egypt. The amplified fragments at 488-bp of the camel κ-CN gene were digested with AluI endonuclease. The results showed the appearance of three different genotypes in the tested animals; CC with three digested fragments at 203-, 127- and 120-bp, TT with three digested fragments at 203-, 158- and 127-bp and CT with four digested fragments at 203-, 158-, 127- and 120-bp. The frequencies of three detected genotypes were 11.0% for CC, 48.0% for TT and 41.0% for CT genotypes. The sequencing analysis of the two different alleles declared the presence of a single nucleotide polymorphism (C→T) at position 121 in the amplified fragments which is responsible for the destruction of a restriction site (AG/CT) in allele T and resulted in the presence of two different alleles C and T in tested animals. The nucleotide sequences of κ-CN alleles C and T were submitted to GenBank with the accession numbers; KU055605 and KU055606, respectively. The primers used in this study amplified 942-bp fragments spanning from exon 4 to exon 6 of camel αS1-Casein gene. The amplified fragments were digested with two different restriction enzymes; SmlI and AluI. The results of SmlI digestion did not show any restriction site whereas the digestion with AluI endonuclease revealed the presence of two restriction sites AG^CT at positions 68^69 and 631^632 yielding the presence of three digested fragments with sizes 68-, 563- and 293-bp.The nucleotide sequences of this fragment from camel αS1-Casein gene were submitted to GenBank with the accession number KU145820. In conclusion, the genetic characterization of quantitative traits genes which are associated with the production traits like milk yield and composition is considered an important step towards the genetic improvement of livestock species through the selection of superior animals depending on the favorable alleles and genotypes; marker assisted selection (MAS).

Keywords: genetic polymorphism, SNP polymorphism, Maghrabi camels, κ-Casein gene, αS1-Casein gene

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Authors: Alireza Lavaei, Alireza Lohrasbi, Mohammadali M. Shahlaei

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To reduce the overall time of structural optimization for earthquake loads two strategies are adopted. In the first strategy, a neural system consisting self-organizing map and radial basis function neural networks, is utilized to predict the time history responses. In this case, the input space is classified by employing a self-organizing map neural network. Then a distinct RBF neural network is trained in each class. In the second strategy, an improved genetic algorithm is employed to find the optimum design. A 72-bar space truss is designed for optimal weight using exact and approximate analysis for the El Centro (S-E 1940) earthquake loading. The numerical results demonstrate the computational advantages and effectiveness of the proposed method.

Keywords: optimization, genetic algorithm, neural networks, self-organizing map

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Authors: Alexander Wachtel, Michael T. Franzen, Walter F. Tichy

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Programming requires years of training. With natural language and end user development methods, programming could become available to everyone. It enables end users to program their own devices and extend the functionality of the existing system without any knowledge of programming languages. In this paper, we describe an Interactive Spreadsheet Processing Module (ISPM), a natural language interface to spreadsheets that allows users to address ranges within the spreadsheet based on inferred table schema. Using the ISPM, end users are able to search for values in the schema of the table and to address the data in spreadsheets implicitly. Furthermore, it enables them to select and sort the spreadsheet data by using natural language. ISPM uses a machine learning technique to automatically infer areas within a spreadsheet, including different kinds of headers and data ranges. Since ranges can be identified from natural language queries, the end users can query the data using natural language. During the evaluation 12 undergraduate students were asked to perform operations (sum, sort, group and select) using the system and also Excel without ISPM interface, and the time taken for task completion was compared across the two systems. Only for the selection task did users take less time in Excel (since they directly selected the cells using the mouse) than in ISPM, by using natural language for end user software engineering, to overcome the present bottleneck of professional developers.

Keywords: natural language processing, natural language interfaces, human computer interaction, end user development, dialog systems, data recognition, spreadsheet

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Authors: Mai A. Ibrahim, Mohammed El-Beltagy, Motaz Khorshid

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Emerging Markets return distributions have shown significance departure from normality were they are characterized by fatter tails relative to the normal distribution and exhibit levels of skewness and kurtosis that constitute a significant departure from normality. Therefore, the classical Markowitz Mean-Variance is not applicable for emerging markets since it assumes normally-distributed returns (with zero skewness and kurtosis) and a quadratic utility function. Moreover, the Markowitz mean-variance analysis can be used in cases of moderate non-normality and it still provides a good approximation of the expected utility, but it may be ineffective under large departure from normality. Higher moments models and median models have been suggested in the literature for asset allocation in this case. Higher moments models have been introduced to account for the insufficiency of the description of a portfolio by only its first two moments while the median model has been introduced as a robust statistic which is less affected by outliers than the mean. Tail risk measures such as Value-at Risk (VaR) and Conditional Value-at-Risk (CVaR) have been introduced instead of Variance to capture the effect of risk. In this research, higher moment models including the Mean-Variance-Skewness (MVS) and Mean-Variance-Skewness-Kurtosis (MVSK) are formulated as single-objective non-linear programming problems (NLP) and median models including the Median-Value at Risk (MedVaR) and Median-Mean Absolute Deviation (MedMAD) are formulated as a single-objective mixed-integer linear programming (MILP) problems. The higher moment models and median models are compared to some benchmark portfolios and tested on real financial data in the Egyptian main Index EGX30. The results show that all the median models outperform the higher moment models were they provide higher final wealth for the investor over the entire period of study. In addition, the results have confirmed the inapplicability of the classical Markowitz Mean-Variance to the Egyptian stock market as it resulted in very low realized profits.

Keywords: Egyptian stock exchange, emerging markets, higher moment models, median models, mixed-integer linear programming, non-linear programming

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Authors: Farzad Jafarpour Taher, Maghsud Solimanpur

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Production planning is one of the complex tasks in multi-product firms that produce a wide range of products. Since resources in mass production companies are limited and different products use common resources, there must be a careful plan so that firms can respond to customer needs efficiently. Azar-battery Company is a firm that provides twenty types of products for its customers. Therefore, careful planning must be performed in this company. In this research, the current conditions of Azar-battery Company were investigated to provide a mathematical programming model to determine the optimum production rate of the products in this company. The production system of this company is multi-stage, multi-product and multi-period. This system is studied in terms of a one-year planning horizon regarding the capacity of machines and warehouse space limitation. The problem has been modeled as a linear programming model with deterministic demand in which shortage is not allowed. The objective function of this model is to minimize costs (including raw materials, assembly stage, energy costs, packaging, and holding). Finally, this model has been solved by Lingo software using the branch and bound approach. Since the computation time was very long, the solver interrupted, and the obtained feasible solution was used for comparison. The proposed model's solution costs have been compared to the company’s real data. This non-optimal solution reduces the total production costs of the company by about %35.

Keywords: multi-period, multi-product production, multi-stage, production planning

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Authors: Prabha Rohatgi

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To obtain an efficient control over a huge amount of inventory of drugs in pharmacy department of any hospital, generally, the medicines are categorized on the basis of their cost ‘ABC’ (Always Better Control), first and then categorize on the basis of their criticality ‘VED’ (Vital, Essential, desirable) for prioritization. About one-third of the annual expenditure of a hospital is spent on medicines. To minimize the inventory investment, the hospital management may like to keep the medicines inventory low, as medicines are perishable items. The main aim of each and every hospital is to provide better services to the patients under certain limited resources. To achieve the satisfactory level of health care services to outdoor patients, a hospital has to keep eye on the wastage of medicines because expiry date of medicines causes a great loss of money though it was limited and allocated for a particular period of time. The objectives of this study are to identify the categories of medicines requiring incentive managerial control. In this paper, to minimize the total inventory cost and the cost associated with the wastage of money due to expiry of medicines, an inventory control model is used as an estimation tool and then nonlinear programming technique is used under limited budget and fixed number of orders to be placed in a limited time period. Numerical computations have been given and shown that by using scientific methods in hospital services, we can give more effective way of inventory management under limited resources and can provide better health care services. The secondary data has been collected from a hospital to give empirical evidence.

Keywords: ABC-VED inventory classification, multi item inventory problem, nonlinear programming technique, optimization of EOQ

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Authors: Elham Jelodari Mamaghani, Christian Prins, Haoxun Chen

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In this paper, there is concentration on collaborative transportation planning (CTP) among multiple carriers with pickup and delivery requests and time windows. This problem is a vehicle routing problem with constraints from standard vehicle routing problems and new constraints from a real-world application. In the problem, each carrier has a finite number of vehicles, and each request is a pickup and delivery request with time window. Moreover, each carrier has reserved requests, which must be served by itself, whereas its exchangeable requests can be outsourced to and served by other carriers. This collaboration among carriers can help them to reduce total transportation costs. A mixed integer programming model is proposed to the problem. To solve the model, a hybrid algorithm that combines Genetic Algorithm and Simulated Annealing (GASA) is proposed. This algorithm takes advantages of GASA at the same time. After tuning the parameters of the algorithm with the Taguchi method, the experiments are conducted and experimental results are provided for the hybrid algorithm. The results are compared with those obtained by a commercial solver. The comparison indicates that the GASA significantly outperforms the commercial solver.

Keywords: centralized collaborative transportation, collaborative transportation with pickup and delivery, collaborative transportation with time windows, hybrid algorithm of GA and SA

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Authors: Mohamed Amine Ben Abdallah, Imed Khemili, Nizar Aifaoui

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This work denotes an insight into dynamic synthesis of multibody systems. A set of mechanism parameters design variable are synthetized based on a desired mechanism response, such as, velocity, acceleration and bodies deformations. Moreover, knowing the work space, for a robot, and mechanism response allow defining optimal parameters mechanism handling with the desired target response. To this end, evolutionary genetic algorithm has been deployed. A demonstrative example for imperfect mechanism has been treated, mainly, a slider crank mechanism with a flexible connecting rod. The transversal deflection of the connecting rod has been chosen as response to identify the mechanism design parameters.

Keywords: dynamic response, evolutionary genetic algorithm, flexible bodies, optimization

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Authors: Yasir Ali, Farhatullah

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The present study was conducted to estimate the genetic variability, heritability and genetic advance in six parental lines and their 56 genotypes derived from five introgressed brassica populations on the basis of morphological and biochemical traits. The experiment was laid out in a randomized complete block design with two replications at The University of Agriculture Peshawar-Pakistan during growing season of 2015-2016. The ANOVA of all traits of F5:6 populations showed highly significant differences (P ≤ 0.01) for all morphological and biochemical traits. Among F5:6 populations, the genotype 2(526) was earlier in flowering (108.65 days), and genotype 14(485) was earlier in maturity (170 days). Tallest plants (182.5 cm), largest main raceme (91.5 cm) and maximum number of pods (80.5) on main raceme were recorded for genotype 17(34). Maximum primary branches plant-1(6.2) and longest pods (10.26 cm) were recorded for genotype 15, while genotype 16(171) had more seeds pod⁻¹ (22) and gave maximum yield plant-1 (30.22 g). The maximum 100-seed weight (0.60 g) was observed for genotype 10(506) while high protein content (22.61%) was recorded for genotype 4(99). Maximum oil content (54.08 %) and low linoleic acid (7.07 %) were produced by genotype (12(138) and low glucosinolate (59.01 µMg⁻¹) was recorded for genotype 21(113). The genotype 27(303) having high oleic acid content (51.73 %) and genotype 1(209) gave low erucic acid (35.97 %). Among the F5:6 populations moderate to high heritability observed for all morphological and biochemical traits coupled with high genetic advance. Cluster analysis grouped the 56 F5:6 populations along their parental lines into seven different groups. Each group was different from the other group on the basis of morphological and biochemical traits. Moreover all the F5:6 populations showed sufficient variability. Genotypes 10(506) and 16(171) were superior for high seed yield⁻¹, 100-seeds weight, and seed pod⁻¹ and are recommended for future breeding program.

Keywords: Brassicaceae, biochemical characterization, introgression, morphological characterization

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Authors: Atilla Bayram

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This paper presents the trajectory tracking control of a spatial redundant hybrid manipulator. This manipulator consists of two parallel manipulators which are a variable geometry truss (VGT) module. In fact, each VGT module with 3-degress of freedom (DOF) is a planar parallel manipulator and their operational planes of these VGT modules are arranged to be orthogonal to each other. Also, the manipulator contains a twist motion part attached to the top of the second VGT module to supply the missing orientation of the endeffector. These three modules constitute totally 7-DOF hybrid (parallel-parallel) redundant spatial manipulator. The forward kinematics equations of this manipulator are obtained, then, according to these equations, the inverse kinematics is solved based on an optimization with the joint limit avoidance. The dynamic equations are formed by using virtual work method. In order to test the performance of the redundant manipulator and the controllers presented, two different desired trajectories are followed by using the computed force control method and a switching control method. The switching control method is combined with the computed force control method and genetic algorithm. In the switching control method, the genetic algorithm is only used for fine tuning in the compensation of the trajectory tracking errors.

Keywords: computed force method, genetic algorithm, hybrid manipulator, inverse kinematics of redundant manipulators, variable geometry truss

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Authors: Ramona Moldovan, Doina Cosman, Sebastian Moldovan, Radu Popp, Victor Pop

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MENTALICA is a project aimed at developing and evaluating a platform that can assist individuals diagnosed with severe mental disorders and their families in managing the consequences associated with severe mental disorders, recurrence risks, prevention strategies and treatment options. MENTALICA is a platform based on guidance issued by some of the most prominent scientific organizations in the world. In order to personalize the information provided, the program explores details about the personal and family history of mental disorders. MENTALICA summarizes the answers and gives respondents a personal assessment. This includes personalized information and support about schizophrenia, bipolar disorder and schizoaffective disorder. MENTALICA includes several modules: Family history tools, Risk assessment tools and Risk factor sheets, Practical guides for patients, Practical guides for families, Guidelines for clinicians. Currently, there are no available guidelines for genetic counselling for mental disorders. Respondents can print out their reports and discuss them with family members or their doctors. We will briefly present the current status of MENTALICA and its implications for patients, professionals and the community.

Keywords: genetic counseling, mental disorders, platform

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Authors: Mamouni Mohammed Dhiya Eddine

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This work aims at studying the exploitation of high-speed networks of clusters for distributed storage. Parallel applications running on clusters require both high-performance communications between nodes and efficient access to the storage system. Many studies on network technologies led to the design of dedicated architectures for clusters with very fast communications between computing nodes. Efficient distributed storage in clusters has been essentially developed by adding parallelization mechanisms so that the server(s) may sustain an increased workload. In this work, we propose to improve the performance of distributed storage systems in clusters by efficiently using the underlying high-performance network to access distant storage systems. The main question we are addressing is: do high-speed networks of clusters fit the requirements of a transparent, efficient and high-performance access to remote storage? We show that storage requirements are very different from those of parallel computation. High-speed networks of clusters were designed to optimize communications between different nodes of a parallel application. We study their utilization in a very different context, storage in clusters, where client-server models are generally used to access remote storage (for instance NFS, PVFS or LUSTRE). Our experimental study based on the usage of the GM programming interface of MYRINET high-speed networks for distributed storage raised several interesting problems. Firstly, the specific memory utilization in the storage access system layers does not easily fit the traditional memory model of high-speed networks. Secondly, client-server models that are used for distributed storage have specific requirements on message control and event processing, which are not handled by existing interfaces. We propose different solutions to solve communication control problems at the filesystem level. We show that a modification of the network programming interface is required. Data transfer issues need an adaptation of the operating system. We detail several propositions for network programming interfaces which make their utilization easier in the context of distributed storage. The integration of a flexible processing of data transfer in the new programming interface MYRINET/MX is finally presented. Performance evaluations show that its usage in the context of both storage and other types of applications is easy and efficient.

Keywords: distributed storage, remote file access, cluster, high-speed network, MYRINET, zero-copy, memory registration, communication control, event notification, application programming interface

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Authors: Saidatul A'isyah Ahmad Shukri, Haslina Arshad

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This study was conducted to develop an application that provides Augmented Reality experience in identifying halal food products and beverages based on Malaysian Islamic Development Department (JAKIM) database for Muslim consumers in Malaysia. The applications is operating on the mobile device using the Android platform. This application aims to provide a new experience to the user how to use the Android application implements Augmentation Reality technology The methodology used is object-oriented analysis and design (OOAD). The programming language used is JAVA programming using the Android Software Development Kit (SDK) and XML. Android operating system is selected, and it is an open source operating system. Results from the study are implemented to further enhance diversity in presentation of information contained in this application and so can bring users using these applications from different angles.

Keywords: android, augmented reality, food, halal, Malaysia, products, XML

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Authors: H. Naseh, M. Mirshams, M. Mirdamadian, H. R. Fazeley

Abstract:

This paper presents an extension of fuzzy-genetic algorithm multi-objective optimization methodology that could effectively be used to find the overall satisfaction of objective functions (selecting the design variables) in the early stages of design process. The coupling of objective functions due to design variables in an engineering design process will result in difficulties in design optimization problems. In many cases, decision making on design variables conflicts with more than one discipline in system design. In space launch system conceptual design, decision making on some design variable (e.g. oxidizer to fuel mass flow rate O/F) in early stages of the design process is related to objective of liquid propellant engine (specific impulse) and Tanks (structure weight). Then, the primary application of this methodology is the design of a liquid propellant engine with the maximum specific impulse and cylindrical stiffened tank with the minimum weight. To this end, the design problem is established the fuzzy rule set based on designer's expert knowledge with a holistic approach. The independent design variables in this model are oxidizer to fuel mass flow rate, thickness of stringers, thickness of rings, shell thickness. To handle the mentioned problems, a fuzzy-genetic algorithm multi-objective optimization methodology is developed based on Pareto optimal set. Consequently, this methodology is modeled with the one stage of space launch system to illustrate accuracy and efficiency of proposed methodology.

Keywords: cylindrical stiffened tanks, multi-objective, genetic algorithm, fuzzy approach

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Authors: Santosh Kumar Suman, Vinod Kumar Giri

Abstract:

The goal of this paper is to outline a speed controller of a DC motor by choice of a PID parameters utilizing genetic algorithms (GAs), the DC motor is extensively utilized as a part of numerous applications such as steel plants, electric trains, cranes and a great deal more. DC motor could be represented by a nonlinear model when nonlinearities such as attractive dissemination are considered. To provide effective control, nonlinearities and uncertainties in the model must be taken into account in the control design. The DC motor is considered as third order system. Objective of this paper three type of tuning techniques for PID parameter. In this paper, an independently energized DC motor utilizing MATLAB displaying, has been outlined whose velocity might be examined utilizing the Proportional, Integral, Derivative (KP, KI , KD) addition of the PID controller. Since, established controllers PID are neglecting to control the drive when weight parameters be likewise changed. The principle point of this paper is to dissect the execution of optimization techniques viz. The Genetic Algorithm (GA) for improve PID controllers parameters for velocity control of DC motor and list their points of interest over the traditional tuning strategies. The outcomes got from GA calculations were contrasted and that got from traditional technique. It was found that the optimization techniques beat customary tuning practices of ordinary PID controllers.

Keywords: DC motor, PID controller, optimization techniques, genetic algorithm (GA), objective function, IAE

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Authors: Agostinho Antunes

Abstract:

The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: comparative genomics, adaptive evolution, bioinformatics, phylogenetics, genome mining

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Authors: Rithvik Reddy Adapa, Xin Wang

Abstract:

Phasor Measurement Units (PMUs) are very sophisticated measuring devices that find amplitude, phase and frequency of various voltages and currents in a power system. Particle filter is a state estimation technique that uses Bayesian inference. Particle filters are widely used in pose estimation and indoor navigation and are very reliable. This paper studies and compares four different particle filters as PMUs namely, generic particle filter (GPF), genetic algorithm particle filter (GAPF), particle swarm optimization particle filter (PSOPF) and adaptive particle filter (APF). Two different test signals are used to test the performance of the filters in terms of responsiveness and correctness of the estimates.

Keywords: phasor measurement unit, particle filter, genetic algorithm, particle swarm optimisation, state estimation

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Authors: Michael Aupetit, Mahmoud Al-ismail, Khaled Mohamed

Abstract:

Cancer is a major public health problem all over the world. Breast cancer has the highest incidence rate over all cancers for women in Qatar making its study a top priority of the country. Human cancer is a dynamic disease that develops over an extended period through the accumulation of a series of genetic alterations. A Darwinian process drives the tumor cells toward higher malignancy growing the branches of a progression tree in the space of genes expression. Although it is not possible to track these genetic alterations dynamically for one patient, it is possible to reconstruct the progression tree from the aggregation of thousands of tumor cells’ genetic profiles from thousands of different patients at different stages of the disease. Analyzing the progression tree is a way to detect pivotal molecular events that drive the malignant evolution and to provide a guide for the development of cancer diagnostics, prognostics and targeted therapeutics. In this work we present the development of a Visual Analytic web platform CanVis enabling users to upload gene-expression data and analyze their progression tree. The server computes the progression tree based on state-of-the-art techniques and allows an interactive visual exploration of this tree and the gene-expression data along its branching structure helping to discover potential driver genes.

Keywords: breast cancer, progression tree, visual analytics, web platform

Procedia PDF Downloads 416

Authors: Quoc Khanh Dang, Thomas Bourdeaud’huy, Khaled Mesghouni, Armand Toguy´eni

Abstract:

This paper studies a train routing and scheduling problem for busy railway stations. Our objective is to allow trains to be routed in dense areas that are reaching saturation. Unlike traditional methods that allocate all resources to setup a route for a train and until the route is freed, our work focuses on the use of resources as trains progress through the railway node. This technique allows a larger number of trains to be routed simultaneously in a railway node and thus reduces their current saturation. To deal with this problem, this study proposes an abstract model and a mixed-integer linear programming formulation to solve it. The applicability of our method is illustrated on a didactic example.

Keywords: busy railway stations, mixed-integer linear programming, offline railway station management, train platforming, train routing, train scheduling

Procedia PDF Downloads 253

Authors: Hiroaki Fukuda

Abstract:

This paper shows a concurrent development process for modern web application, called Rich Internet Application (RIA), and describes its effect using a non-trivial application development. In the last years, RIAs such as Ajax and Flex have become popular based mainly on high-speed network. RIA provides sophisticated interfaces and user experiences, therefore, the development of RIA requires two kinds of engineer: a developer who implements business logic, and a designer who designs interface and experiences. Although collaborative works are becoming important for the development of RIAs, shared resources such as source code make it difficult. For example, if a design of interface is modified after developers have finished business logic implementations, they need to repeat the same implementations, and also tests to verify application’s behavior. MVC architecture and Object-oriented programming (OOP) enables to dividing an application into modules such as interfaces and logic, however, developers and/or designers have to write pieces of code (e.g., event handlers) that make these modules work as an application. On the other hand, Aspect-oriented programming (AOP) is ex- pected to solve complexity of application software development nowadays. AOP provides methods to separate crosscutting concerns that are scattered pieces of code from primary concerns. In this paper, we provide a concurrent development process for RIAs by introducing AOP concept. This process makes it possible to reduce shared resources between developers and designers, therefore they can perform their tasks concurrently. In addition, we describe experiences of development for a practical application using our proposed development process to show its availability.

Keywords: aspect-oriented programming, concurrent, development process, rich internet application

Procedia PDF Downloads 301

Authors: Grace Onubedo

Abstract:

The primary objective of this research study is to contribute to and deepen the understanding of the realities and conditions for which children recruited by violent extremist organisations in Nigeria live, as well as ascertain the state of their mental health following their reunification with either family or protection workers. The research is intended to contribute to a more focused child protection programming agenda for children associated with armed forces and groups in Nigeria and the wider conflict setting. The extent to which violence has affected the psychological well-being and mental health of children abducted and exposed to activities of Violent Extremist groups remains a largely empirical question. This research attempts to answer the following research questions with the aim of providing further evidences for informed programming: I. What are the demographic characteristics of children associated with armed groups? II. What is the state of their mental health? III. What is the relationship between their background and their mental health?

Keywords: counterterrorism, psychosocial support, psychological distress, children, armed groups

Procedia PDF Downloads 130