Search results for: genetic model

Authors: Alexandru-Ion Marinescu

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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: Palash Dey, Sudip Talukdar

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In this work, a cross-breed approach is presented for obtaining both the amount of the damage intensity and location of damage existing in thin-walled members. This cross-breed approach is developed based on response surface methodology (RSM) and genetic algorithm (GA). Theoretical finite element (FE) model of cracked angle section thin walled curved beam has been linked to the developed approach to carry out trial experiments to generate response surface functions (RSFs) of free, forced and heterogeneous dynamic response data. Subsequently, the error between the computed response surface functions and measured dynamic response data has been minimized using GA to find out the optimum damage parameters (amount of the damage intensity and location). A single crack of varying location and depth has been considered in this study. The presented approach has been found to reveal good accuracy in prediction of crack parameters and possess great potential in crack detection as it requires only the current response of a cracked beam.

Keywords: damage parameters, finite element, genetic algorithm, response surface methodology, thin walled curved beam

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Authors: Karen Fang

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Investigative genetic genealogy has attracted much interest in both the field of ethics and the public eye due to its global application in criminal cases. Arguments have been made regarding privacy and informed consent, especially with law enforcement using consumer genetic testing results to convict individuals. In the case of public interest, DNA databases have the strong potential to significantly reduce crime, which in turn leads to safer communities and better futures. With the advancement of genetic technologies, the integration of a universal forensic DNA database in violent crimes, crimes against children, and missing person cases is expected to deter crime while protecting one’s privacy. Rather than collecting whole genomes from the whole population, STR profiles can be used to identify unrelated individuals without compromising personal information such as physical appearance, disease risk, and geographical origin, and additionally, reduce cost and storage space. STR DNA profiling is already used in the forensic science field and going a step further benefits several areas, including the reduction in recidivism, improved criminal court case turnaround time, and just punishment. Furthermore, adding individuals to the database as early as possible prevents young offenders and first-time offenders from participating in criminal activity. It is important to highlight that DNA databases should be inclusive and tightly governed, and the misconception on the use of DNA based on crime television series and other media sources should be addressed. Nonetheless, deterrent effects have been observed in countries like the US and Denmark with DNA databases that consist of serious violent offenders. Fewer crimes were reported, and fewer people were convicted of those crimes- a favorable outcome, not even the death penalty could provide. Currently, there is no better alternative than a universal forensic DNA database made up of STR profiles. It can open doors for investigative genetic genealogy and fostering better communities. Expanding the appropriate use of DNA databases is ethically acceptable and positively impacts the public.

Keywords: bioethics, deterrent effects, DNA database, investigative genetic genealogy, privacy, public interest

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Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

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We study the biological effects induced by ionizing radiation in view of therapeutic exposure and the idea of space flights beyond Earth's magnetosphere. In particular, we examine the differences between base pair substitution induction by ionizing radiation in model haploid and diploid yeast Saccharomyces cerevisiae cells. Such mutations are difficult to study in higher eukaryotic systems. In our research, we have used a collection of six isogenic trp5-strains and 14 isogenic haploid and diploid cyc1-strains that are specific markers of all possible base-pair substitutions. These strains differ from each other only in single base substitutions within codon-50 of the trp5 gene or codon-22 of the cyc1 gene. Different mutation spectra for two different haploid genetic trp5- and cyc1-assays and different mutation spectra for the same genetic cyc1-system in cells with different ploidy — haploid and diploid — have been obtained. It was linear function for dose-dependence in haploid and exponential in diploid cells. We suggest that the differences between haploid yeast strains reflect the dependence on the sequence context, while the differences between haploid and diploid strains reflect the different molecular mechanisms of mutations.

Keywords: base pair substitutions, γ-rays, haploid and diploid cells, yeast Saccharomyces cerevisiae

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Authors: Amr A. El Hanafy, Yasser M. Saad, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group).

Keywords: milk yield, beta-casein precursor (CSN2), Saudi camel, molecular markers

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Authors: Marina Nechayeva, Malgorzata Marciniak, Vladimir Przhebelskiy, A. Dragutan, S. Lamichhane, S. Oikawa

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This presentation is a progress report on a faculty-student research collaboration at CUNY LaGuardia Community College (LaGCC) aimed at designing a small horizontal axis wind turbine optimized for the wind patterns on the roof of our campus. Our project combines statistical and engineering research. Our wind modeling protocol is based upon a recent wind study by a faculty-student research group at MIT, and some of our blade design methods are adopted from a senior engineering project at CUNY City College. Our use of genetic algorithms has been inspired by the work on small wind turbines’ design by David Wood. We combine these diverse approaches in our interdisciplinary project in a way that has not been done before and improve upon certain techniques used by our predecessors. We employ several estimation methods to determine the best fitting parametric probability distribution model for the local wind speed data obtained through correlating short-term on-site measurements with a long-term time series at the nearby airport. The model serves as a foundation for engineering research that focuses on adapting and implementing genetic algorithms (GAs) to engineering optimization of the wind turbine design using Blade Element Momentum Theory. GAs are used to create new airfoils with desirable aerodynamic specifications. Small scale models of best performing designs are 3D printed and tested in the wind tunnel to verify the accuracy of relevant calculations. Genetic algorithms are applied to selected airfoils to determine the blade design (radial cord and pitch distribution) that would optimize the coefficient of power profile of the turbine. Our approach improves upon the traditional blade design methods in that it lets us dispense with assumptions necessary to simplify the system of Blade Element Momentum Theory equations, thus resulting in more accurate aerodynamic performance calculations. Furthermore, it enables us to design blades optimized for a whole range of wind speeds rather than a single value. Lastly, we improve upon known GA-based methods in that our algorithms are constructed to work with XFoil generated airfoils data which enables us to optimize blades using our own high glide ratio airfoil designs, without having to rely upon available empirical data from existing airfoils, such as NACA series. Beyond its immediate goal, this ongoing project serves as a training and selection platform for CUNY Research Scholars Program (CRSP) through its annual Aerodynamics and Wind Energy Research Seminar (AWERS), an undergraduate summer research boot camp, designed to introduce prospective researchers to the relevant theoretical background and methodology, get them up to speed with the current state of our research, and test their abilities and commitment to the program. Furthermore, several aspects of the research (e.g., writing code for 3D printing of airfoils) are adapted in the form of classroom research activities to enhance Calculus sequence instruction at LaGCC.

Keywords: engineering design optimization, genetic algorithms, horizontal axis wind turbine, wind modeling

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Authors: Trupti Diwan

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Predicting student failure at school has changed into a difficult challenge due to both the large number of factors that can affect the reduced performance of students and the imbalanced nature of these kinds of data sets. This paper surveys the two elements needed to make prediction on Students’ Academic Performances which are parameters and methods. This paper also proposes a framework for predicting the performance of engineering students. Genetic programming can be used to predict student failure/success. Ranking algorithm is used to rank students according to their credit points. The framework can be used as a basis for the system implementation & prediction of students’ Academic Performance in Higher Learning Institute.

Keywords: classification, educational data mining, student failure, grammar-based genetic programming

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

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Authors: Ismail El Gayar, Ossama Ismail, Yousri El Gamal

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This paper presented a technique to solve one of the transportation problems that faces us in real life which is the Bus Scheduling Problem. Most of the countries using buses in schools, companies and traveling offices as an example to transfer multiple passengers from many places to specific place and vice versa. This transferring process can cost time and money, so we build a decision support system that can solve this problem. In this paper, a genetic algorithm with the shortest path technique is used to generate a competitive solution to other well-known techniques. It also presents a comparison between our solution and other solutions for this problem.

Keywords: bus scheduling problem, decision support system, genetic algorithm, shortest path

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Authors: Anna Solovyeva, Ivan Levakin, Nickolai Galaktionov, Olga Podgornaya

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Animals that reproduce asexually were thought to have the same genotypes within generations for a long time. However, some refuting examples were found, and mobile genetic elements (MGEs) or transposons are considered to be the most probable source of genetic instability. Dispersed nature and the ability to change their genomic localization enables MGEs to be efficient mutators. Hence the study of MGEs genomic impact requires an appropriate object which comprehends both representative amounts of various MGEs and options to evaluate the genomic influence of MGEs. Animals that reproduce asexually seem to be a decent model to study MGEs impact in genomic variability. We found a small marine trematode Himasthla elongata (Himasthlidae) to be a good model for such investigation as it has a small genome size, diverse MGEs and parthenogenetic stages in the lifecycle. In the current work, clonal diversity of cercaria was traced with an AFLP (Amplified fragment length polymorphism) method, diverse zones from electrophoretic patterns were cloned, and the nature of the fragments explored. Polymorphic patterns of individual cercariae AFLP-based fingerprints are enriched with retrotransposons of different families. The bulk of those sequences are represented by open reading frames of non-Long Terminal Repeats containing elements(non-LTR) yet Long-Terminal Repeats containing elements (LTR), to a lesser extent in variable figments of AFLP array. The CR1 elements expose both in polymorphic and conservative patterns are remarkably more frequent than the other non-LTR retrotransposons. This data was confirmed with shotgun sequencing-based on Illumina HiSeq 2500 platform. Individual cercaria of the same clone (i.e., originated from a single miracidium and inhabiting one host) has a various distribution of MGE families detected in sequenced AFLP patterns. The most numerous are CR1 and RTE-Bov retrotransposons, typical for trematode genomes. Also, we identified LTR-retrotransposons of Pao and Gypsy families among DNA transposons of CMC-EnSpm, Tc1/Mariner, MuLE-MuDR and Merlin families. We detected many of them in H. elongata transcriptome. Such uneven MGEs distribution in AFLP sequences’ sets reflects the different patterns of transposons spreading in cercarial genomes as transposons affect the genome in many ways (ectopic recombination, gene structure interruption, epigenetic silencing). It is considered that they play a key role in the origins of trematode clonal polymorphism. The authors greatly appreciate the help received at the Kartesh White Sea Biological Station of the Russian Academy of Sciences Zoological Institute. This work is funded with RSF 19-74-20102 and RFBR 17-04-02161 grants and the research program of the Zoological Institute of the Russian Academy of Sciences (project number AAAA-A19-119020690109-2).

Keywords: AFLP, clonal polymorphism, Himasthla elongata, mobile genetic elements, NGS

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Authors: Rabia Korkmaz Tan, Şebnem Bora

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The major problem encountered when modeling complex systems with agent-based modeling and simulation techniques is the existence of large parameter spaces. A complex system model cannot be expected to reflect the whole of the real system, but by specifying the most appropriate parameters, the actual system can be represented by the model under certain conditions. When the studies conducted in recent years were reviewed, it has been observed that there are few studies for parameter tuning problem in agent based simulations, and these studies have focused on tuning parameters of a single model. In this study, an approach of parameter tuning is proposed by using metaheuristic algorithms such as Genetic Algorithm (GA), Particle Swarm Optimization (PSO), Artificial Bee Colonies (ABC), Firefly (FA) algorithms. With this hybrid structured study, the parameter tuning problems of the models in the different fields were solved. The new approach offered was tested in two different models, and its achievements in different problems were compared. The simulations and the results reveal that this proposed study is better than the existing parameter tuning studies.

Keywords: parameter tuning, agent based modeling and simulation, metaheuristic algorithms, complex systems

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Authors: Amar Khoukhi, Mohamed Shahab

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This paper presents the optimal control problem of mobile robot motion as a nonlinear programming problem (NLP) and solved using a direct method of numerical optimal control. The NLP is initialized with a B-Spline for which node locations are optimized using a genetic search. The system acceleration inputs and sampling periods are considered as optimization variables. Different scenarios with different objectives weights are implemented and investigated. Interesting results are found in terms of complying with the expected behavior of a mobile robot system and time-energy minimization.

Keywords: multi-objective control, non-holonomic systems, mobile robots, nonlinear programming, motion planning, B-spline, genetic algorithm

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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: 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: 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: Antonin Ponsich, Eric Alfredo Rincon Garcia, Roman Anselmo Mora Gutierrez, Miguel Angel Gutierrez Andrade, Sergio Gerardo De Los Cobos Silva, Pedro Lara Velzquez

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The electoral zone design problem consists in redrawing the boundaries of legislative districts for electoral purposes in such a way that federal or state requirements are fulfilled. In Mexico, this process has been historically carried out by the National Electoral Institute (INE), by optimizing an integer nonlinear programming model, in which population equality and compactness of the designed districts are considered as two conflicting objective functions, while contiguity is included as a hard constraint. The solution technique used by the INE is a Simulated Annealing (SA) based algorithm, which handles the multi-objective nature of the problem through an aggregation function. The present work represents the first intent to apply a classical Multi-Objective Evolutionary Algorithm (MOEA), the second version of the Non-dominated Sorting Genetic Algorithm (NSGA-II), to this hard combinatorial problem. First results show that, when compared with the SA algorithm, the NSGA-II obtains promising results. The MOEA manages to produce well-distributed solutions over a wide-spread front, even though some convergence troubles for some instances constitute an issue, which should be corrected in future adaptations of MOEAs to the redistricting problem.

Keywords: multi-objective optimization, NSGA-II, redistricting, zone design problem

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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: 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: Saul A. Torres Z., Eduardo Liceaga C., Alfredo Arias M.

Abstract:

We seek to develop a UAV for agricultural spraying at a maximum altitude of 5000 meters above sea level, with a payload of 100 liters of fumigant. For the developing the aerodynamic design of the aircraft is using computational tools such as the "Vortex Lattice Athena" software, "MATLAB", "ANSYS FLUENT", "XFoil" package among others. Also methods are being used structured programming, exhaustive analysis of optimization methods and search. The results have a very low margin of error, and the multi-objective problems can be helpful for future developments. Also we developed method for Stability Analysis (Lateral-Directional and Longitudinal).

Keywords: aerodynamics design, optimization, algorithm genetic, multi-objective problem, longitudinal stability, lateral-directional stability

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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

Abstract:

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

Abstract:

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

Procedia PDF Downloads 467

Authors: Tohid Rahimi, Yahya Naderi, Babak Yousefi, Seyed Hossein Hoseini

Abstract:

Today’s modern interconnected power system is highly complex in nature. In this, one of the most important requirements during the operation of the electric power system is the reliability and security. Power and frequency oscillation damping mechanism improve the reliability. Because of power system stabilizer (PSS) low speed response against of major fault such as three phase short circuit, FACTs devise that can control the network condition in very fast time, are becoming popular. However, FACTs capability can be seen in a major fault present when nonlinear models of FACTs devise and power system equipment are applied. To realize this aim, the model of multi-machine power system with FACTs controller is developed in MATLAB/SIMULINK using Sim Power System (SPS) blockiest. Among the FACTs device, Static synchronous series compensator (SSSC) due to high speed changes its reactance characteristic inductive to capacitive, is effective power flow controller. Tuning process of controller parameter can be performed using different method. However, Genetic Algorithm (GA) ability tends to use it in controller parameter tuning process. In this paper, firstly POD controller is used to power oscillation damping. But in this station, frequency oscillation dos not has proper damping situation. Therefore, FOD controller that is tuned using GA is using that cause to damp out frequency oscillation properly and power oscillation damping has suitable situation.

Keywords: power oscillation damping (POD), frequency oscillation damping (FOD), Static synchronous series compensator (SSSC), Genetic Algorithm (GA)

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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: C. Manjula, Lilly Florence

Abstract:

Software technology is developing rapidly which leads to the growth of various industries. Now-a-days, software-based applications have been adopted widely for business purposes. For any software industry, development of reliable software is becoming a challenging task because a faulty software module may be harmful for the growth of industry and business. Hence there is a need to develop techniques which can be used for early prediction of software defects. Due to complexities in manual prediction, automated software defect prediction techniques have been introduced. These techniques are based on the pattern learning from the previous software versions and finding the defects in the current version. These techniques have attracted researchers due to their significant impact on industrial growth by identifying the bugs in software. Based on this, several researches have been carried out but achieving desirable defect prediction performance is still a challenging task. To address this issue, here we present a machine learning based hybrid technique for software defect prediction. First of all, Genetic Algorithm (GA) is presented where an improved fitness function is used for better optimization of features in data sets. Later, these features are processed through Decision Tree (DT) classification model. Finally, an experimental study is presented where results from the proposed GA-DT based hybrid approach is compared with those from the DT classification technique. The results show that the proposed hybrid approach achieves better classification accuracy.

Keywords: decision tree, genetic algorithm, machine learning, software defect prediction

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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 387

Authors: Atefeh Esmailnejad, Gholam Reza Nikbakht Brujeni

Abstract:

The major histocompatibility complex (MHC) is the best-characterized genetic region associated with susceptibility and/or resistance to a wide range of infectious diseases, autoimmune diseases and immune responses to vaccines. It has been demonstrated that there is an association between the MHC and resistance to Marek disease, Newcastle disease, Rous sarcoma tumor, Avian leucosis, Fowl cholera, Salmonellosis and Pasteurellosis in chicken. The present study evaluated the MHC polymorphism and its association with antibody response to Newcastle (ND) vaccine in Iranian native chickens. The MHC polymorphism was investigated using LEI0258 microsatellite locus by PCR-based fragment analysis. LEI0258 microsatellite marker is a genetic indicator for MHC, which is located on microchromosome 16 and strongly associated with serologically defined MHC haplotypes. Antibody titer against ND vaccine was measured by Haemaglutination Inhibition (HI) assay. Statistical analysis was performed using SPSS software (version 21). Total of 13 LEI0258 microsatellite alleles were identified in 72 samples which indicated a high genetic diversity in the population. The association study revealed a significant influence of MHC alleles on immune responses to Newcastle vaccine. 311 and 313 bp alleles were significantly associated with elevated immune responses to Newcastle vaccine (p<0.05). These results would be applicable in designing and improving the populations under selective breeding.

Keywords: chicken, LEI0258, MHC, Newcastle vaccine

Procedia PDF Downloads 409