Search results for: genetic profiles

Authors: Sabitha Rani A., Nagamani V.

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Embelia ribes Burm.f (Family-Myrsinaceae) commonly known as Vidanga or Baibirang, is one of the important medicinal plants of India. The seed extract is reported to be antidiabetic, antitumour, analgesic, anti-inflammatory, antispermatogenic, free radical scavenging activities and widely used in more than 75 Ayurvedic commercial formulations. Among the 100 different species of Embelia, E. ribes is considered as a major source of Embelin, a bioactive compound. Because of high demand and low availability, the seeds of E. ribes are substituted with many cheaper alternatives. Therefore, the present study of RAPD-PCR analysis was undertaken to develop molecular markers for identification of E. ribes. A total of 13 different seed samples of Embelia were collected from different agro-climatic regions of India. The seeds of E.ribes were collected from Kalpetta, Kerala and three different seed samples were collected from traders of Odisha, Madhya Pradesh, Maharastra. The other nine seed samples were collected from local traders which they have collected from different regions of India. Genomic DNA was isolated from different seed samples E. ribes and RAPD-PCR was performed on 13 different seed samples using 47 random primers. Out of all the primers, only 22 primers produced clear and highly-reproducible banding patterns. The 22 selected RAPD primers generated a total of 280 alleles with an average of 12 alleles per primer pair. In the present study, we have identified three RAPD-PCR markers i.e. OPF5_480 bp, OPH11_520 bp and OPH4_530 bp which can be used for genetic fingerprinting of E. ribes. This methodology can be employed for identification of original E. ribes and also distinguishing it from other substitutes and adulterants.

Keywords: Embelia ribes, RAPD-PCR, primers, genetic analysis

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Authors: Begna Tulu, Gobena Ameni

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Understanding the types of Mycobacterium bovis (M. bovis) strains circulating in a country and exploring its zoonotic potential has significant contribution in the effort to design control strategies. The main aim of this study was to review and compile the results of studies conducted on M. bovis genotyping and its zoonotic potential of M. bovis in Ethiopia. A systematic search and review of articles published on M. bovis strains in Ethiopia were made. PubMed and Google Scholar databases were considered for the search while the keywords used were 'Mycobacteria,' 'Mycobacterium bovis,' 'Bovine Tuberculosis' and 'Ethiopia.' Fourteen studies were considered in this review and a total of 31 distinct strains of M. bovis (N=211) were obtained; the most dominant strains were SB0133 (N=62, 29.4%), SB1176 (N=61, 28.9%), and followed by SB0134 and SB1476 each (N=18, 8.5%). The clustering rate of M. bovis strains was found to be 42.0%. On the other hand, 6 strains of M. bovis were reported from human namely; SB0665 (N=4), SB0303 (N=2), SB0982 (N=2), SB0133 (N=1), SB1176 (N=1), and 1 new strain. Similarly, a total of 8 strains (N=13) of M. tuberculosis bacteria were also identified from animal subjects; namely SIT149 (N=3), SIT1 (N=2), SIT1688 (n=2), SIT262 (N=2), SIT53 (N=1), SIT59 (N=1), and one new-Ethiopian strain. The result showed that the genetic diversity of M. bovis strains reported from Ethiopia are less diversified and highly clustered. And also the result underlines that there is an ongoing active transmission of M. bovis and M. tuberculosis between human and animals in Ethiopia because a significant number strains of both type of bacteria were reported from human and animals.

Keywords: mycobacterium bovis, Mycobacterium tuberculosis, zoonotic potential, genetic diversity, Ethiopia

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Authors: Syed Sameer Aga, Saniya Nissar

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The Xeroderma pigmentosum group D gene (XPD) plays a key role in nucleotide excision repair (NER) pathway of the damaged DNA. Genetic polymorphisms in the coding region of the XPD gene may alter DNA repair capacity of the protein and hence can modulate the risk of colorectal cancer (CRC) risk. The aim of the study was to determine the genetic association of XPD Lys751Gln polymorphism with the risk of colorectal cancer (CRC) development. 120 CRC patients and 160 normal controls were assessed for genotype frequencies of XPD Lys751Gln polymorphism using PCR-RFLP technique. We observed a significant association (p < 0.05) between the XPD Lys751Gln polymorphism and the risk of developing CRC (p < 0.05). Additionally, Gln/Gln genotype of the XPD gene doubled the risk for the development of CRC [p < 0.05; OR=2.25 95% CI (1.07-4.7)]. Our results suggest that there is a significant association between the XPD Lys751Gln polymorphism and the risk of CRC.

Keywords: colorectal cancer, polymorphism, RFLP, DNA Repair, NER, XPD

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Authors: Edafe Lucky Okotie, Emmanuel Osawaru Omosigho

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This paper examines the impacts of the introduction of distributed energy generation (DEG) technology into the Nigerian power system as an alternative means of energy generation at distribution ends using Otovwodo 15 MVA, 33/11kV injection substation as a case study. The overall idea is to increase the generated energy in the system, improve the voltage profile and reduce system losses. A photovoltaic-based distributed energy generator (PV-DEG) was considered and was optimally placed in the network using Genetic Algorithm (GA) in Mat. Lab/Simulink environment. The results of simulation obtained shows that the dynamic performance of the network was optimized with DEG-grid integration.

Keywords: distributed energy generation (DEG), genetic algorithm (GA), power quality, total load demand, voltage profile

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Authors: Bin Liu

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As one of the most important tasks in protein sequence analysis, protein remote homology detection has been studied for decades. Currently, the profile-based methods show state-of-the-art performance. Position-Specific Frequency Matrix (PSFM) is widely used profile. However, there exists noise information in the profiles introduced by the amino acids with low frequencies. In this study, we propose a method to remove the noise information in the PSFM by removing the amino acids with low frequencies called Top frequency profile (TFP). Three new matrix transformation methods, including Autocross covariance (ACC) transformation, Tri-gram, and K-separated bigram (KSB), are performed on these profiles to convert them into fixed length feature vectors. Combined with Support Vector Machines (SVMs), the predictors are constructed. Evaluated on two benchmark datasets, and experimental results show that these proposed methods outperform other state-of-the-art predictors.

Keywords: protein remote homology detection, protein fold recognition, top frequency profile, support vector machines

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Authors: Mst. Tuhina-Khatun, Mohamed Hanafi Musa, Mohd Rafii Yosup, Wong Mui Yun, Md. Aktar-Uz-Zaman, Mahbod Sahebi

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Rice is a staple crop of economic importance of most Asian people, and blast is the major constraints for its higher yield. Heritability of plants traits helps plant breeders to make an appropriate selection and to assess the magnitude of genetic improvement through hybridization. Diversity of crop plants is necessary to manage the continuing genetic erosion and address the issues of genetic conservation for successfully meet the future food requirements. Therefore, an experiment was conducted to estimate heritability and to determine the diversity of 27 blast resistant upland rice genotypes based on 18 quantitative traits using randomized complete block design. Heritability value was found to vary from 38 to 93%. The lowest heritability belonged to the character total number of tillers/plant (38%). In contrast, number of filled grains/panicle, and yield/plant (g) was recorded for their highest heritability value viz. 93 and 91% correspondingly. Cluster analysis based on 18 traits grouped 27 rice genotypes into six clusters. Cluster I was the biggest, which comprised 17 genotypes, accounted for about 62.96% of total population. The multivariate analysis suggested that the genotype ‘Chokoto 14’ could be hybridized with ‘IR 5533-55-1-11’ and ‘IR 5533-PP 854-1’ for broadening the gene pool of blast resistant upland rice germplasms for yield and other favorable characters.

Keywords: blast resistant, diversity analysis, heritability, upland rice

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Authors: M. Saiful Islam, M. Mohandes, S. Rehman, S. Badran

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Increasing necessity of wind power is directing us to have precise knowledge on wind resources. Methodical investigation of potential locations is required for wind power deployment. High penetration of wind energy to the grid is leading multi megawatt installations with huge investment cost. This fact appeals to determine appropriate places for wind farm operation. For accurate assessment, detailed examination of wind speed profile, relative humidity, temperature and other geological or atmospheric parameters are required. Among all of these uncertainty factors influencing wind power estimation, vertical extrapolation of wind speed is perhaps the most difficult and critical one. Different approaches have been used for the extrapolation of wind speed to hub height which are mainly based on Log law, Power law and various modifications of the two. This paper proposes a Artificial Neural Network (ANN) and Genetic Algorithm (GA) based hybrid model, namely GA-NN for vertical extrapolation of wind speed. This model is very simple in a sense that it does not require any parametric estimations like wind shear coefficient, roughness length or atmospheric stability and also reliable compared to other methods. This model uses available measured wind speeds at 10m, 20m and 30m heights to estimate wind speeds up to 100m. A good comparison is found between measured and estimated wind speeds at 30m and 40m with approximately 3% mean absolute percentage error. Comparisons with ANN and power law, further prove the feasibility of the proposed method.

Keywords: wind profile, vertical extrapolation of wind, genetic algorithm, artificial neural network, hybrid machine learning

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Authors: S. Yaman, S. Rostami

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In this study, a black box modeling of the coupled-tank system is obtained by using fuzzy sets. The derived model is tested via adaptive neuro fuzzy inference system (ANFIS). In order to achieve a better control performance, the parameters of three different controller types, classical proportional integral controller (PID), fuzzy PID and function tuner method, are tuned by one of the evolutionary computation method, genetic algorithm. All tuned controllers are applied to the fuzzy model of the coupled-tank experimental setup and analyzed under the different reference input values. According to the results, it is seen that function tuner method demonstrates better robust control performance and guarantees the closed loop stability.

Keywords: function tuner method (FTM), fuzzy modeling, fuzzy PID controller, genetic algorithm (GA)

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Authors: Ashraf Shebl, Bassam Garah, Radah Youssef

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Sexual assault is usually a hidden crime where the only witnesses are the victim and the assailant. For a variety of reasons, even the victim may be unable to provide a detailed account of the assault or the identity of the perpetrator. Often the case history deteriorates into one person’s word against another. With such limited initial information, the physical and biological evidence collected from the victim, from the crime scene, and from the suspect will play a pivotal role in the objective and scientific reconstruction of the events in question. The aim of work is to examine whether DNA profiles could be recovered from repeated washed clothes after contaminated by semen stains. Fresh semen about 1ml. ( <1 h old) taken from donor was deposited on four types of clothes (cotton, silk, polyester, and jeans). Then leave to dry in room temperature and washed by washing machine at temperature (30°C-60°C) and by hand washing. Some items of clothing were washed once, some twice and others three times. DNA could be extracted from some of these samples even after multiple washing. This study demonstrates that complete DNA profiles can be obtained from washed semen stains on different types of clothes, even after many repeated washing. These results indicated that clothes of the victims must be examined even if they were washed many times.

Keywords: sexual assault, DNA, persistence, clothes

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Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

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Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

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Authors: K. Roushanger, A. Soleymanzadeh

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Weirs are structures often used in irrigation techniques, sewer networks and flood protection. However, the hydraulic behavior of this type of weir is complex and difficult to predict accurately. An accurate flow prediction over a weir mainly depends on the proper estimation of discharge coefficient. In this study, the Genetic Expression Programming (GEP) approach was used for predicting trapezoidal and rectangular sharp-crested side weirs discharge coefficient. Three different performance indexes are used as comparing criteria for the evaluation of the model’s performances. The obtained results approved capability of GEP in prediction of trapezoidal and rectangular side weirs discharge coefficient. The results also revealed the influence of downstream Froude number for trapezoidal weir and upstream Froude number for rectangular weir in prediction of the discharge coefficient for both of side weirs.

Keywords: discharge coefficient, genetic expression programming, trapezoidal weir

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Authors: Hyeon-Seung Kim, Young-Hwan Kim, Sang-Mi Park, Min-Seo Kim, Jong-Myeung Shin, Leen-Seok Kang

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The project budget at the planned stage might be changed by the insufficient government budget or the design change. There are many cases more especially in the case of a project performed for a long period of time. If the actual construction budget is insufficient comparing with the planned budget, the construction schedule should also be changed to match the changed budget. In that case, most project managers change the planned construction schedule by a heuristic approach without a reasonable consideration on the work priority. This study suggests an optimized methodology to modify the construction schedule according to the changed budget. The genetic algorithm was used to optimize the modified construction schedule within the changed budget. And a simulation system of construction cost histogram in accordance with the construction schedule was developed in the BIM (Building Information Modeling) environment.

Keywords: 5D, BIM, GA, cost optimization

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Authors: Shahab Mirzaean Mahabadi, Elham Ebrahimi

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The urban development process in the historical urban context has predominately witnessed two main approaches: the first is the Preservation and conservation of the urban fabric and its value, and the second approach is urban renewal and redevelopment. The latter is generally supported by political and economic aspirations. These two approaches conflict evidently. The authors go through the history of urban planning in order to review the historical development of the mentioned approaches. In this article, various values which are inherent in the historical fabric of a city are illustrated by emphasizing on cultural identity and activity. In the following, it is tried to find an optimized plan which maximizes economic development and minimizes change in historical-cultural sites simultaneously. In the proposed model, regarding the decision maker’s intention, and the variety of functions, the selected zone is divided into a number of components. For each component, different alternatives can be assigned, namely, renovation, refurbishment, destruction, and change in function. The decision Variable in this model is to choose an alternative for each component. A set of decisions made upon all components results in a plan. A plan developed in this way can be evaluated based on the decision maker’s point of view. That is, interactions between selected alternatives can make a foundation for the assessment of urban context to design a historical-cultural landscape. A genetic algorithm (GA) approach is used to search for optimal future land use within the historical-culture landscape for a sustainable high-growth city.

Keywords: urban sustainability, green city, regeneration, genetic algorithm

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Authors: Clara Tramuta, Floris Irene, Daniela Manila Bianchi, Monica Pitti, Giulia Federica Cazzaniga, Lucia Decastelli

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This work presents the results obtained by the Regional Reference Centre for Salmonella Typing (CeRTiS) in a retrospective study aimed to investigate, through Pulsed-field Gel Electrophoresis (PFGE) analysis, the genetic relatedness of emerging Salmonella serotypes of human origin circulating in North-West of Italy. Furthermore, the goal of this work was to create a Regional database to facilitate foodborne outbreak investigation and to monitor them at an earlier stage. A total of 112 strains, isolated from 2016 to 2018 in hospital laboratories, were included in this study. The isolates were previously identified as Salmonella according to standard microbiological techniques and serotyping was performed according to ISO 6579-3 and the Kaufmann-White scheme using O and H antisera (Statens Serum Institut®). All strains were characterized by PFGE: analysis was conducted according to a standardized PulseNet protocol. The restriction enzyme XbaI was used to generate several distinguishable genomic fragments on the agarose gel. PFGE was performed on a CHEF Mapper system, separating large fragments and generating comparable genetic patterns. The agarose gel was then stained with GelRed® and photographed under ultraviolet transillumination. The PFGE patterns obtained from the 112 strains were compared using Bionumerics version 7.6 software with the Dice coefficient with 2% band tolerance and 2% optimization. For each serotype, the data obtained with the PFGE were compared according to the geographical origin and the year in which they were isolated. Salmonella strains were identified as follow: S. Derby n. 34; S. Infantis n. 38; S. Napoli n. 40. All the isolates had appreciable restricted digestion patterns ranging from approximately 40 to 1100 kb. In general, a fairly heterogeneous distribution of pulsotypes has emerged in the different provinces. Cluster analysis indicated high genetic similarity (≥ 83%) among strains of S. Derby (n. 30; 88%), S. Infantis (n. 36; 95%) and S. Napoli (n. 38; 95%) circulating in north-western Italy. The study underlines the genomic similarities shared by the emerging Salmonella strains in Northwest Italy and allowed to create a database to detect outbreaks in an early stage. Therefore, the results confirmed that PFGE is a powerful and discriminatory tool to investigate the genetic relationships among strains in order to monitoring and control Salmonellosis outbreak spread. Pulsed-field gel electrophoresis (PFGE) still represents one of the most suitable approaches to characterize strains, in particular for the laboratories for which NGS techniques are not available.

Keywords: emerging Salmonella serotypes, genetic characterization, human strains, PFGE

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Authors: Abrar Al-Hasan

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Objectives: There is ongoing discourse regarding the potential risks to health professionals' reputations and credibility arising from their personal social media use. However, the specific impacts on professional credibility and the health professional-client relationship remain largely unexplored. This study aims to investigate the type and frequency of the content posted by health professionals on their Instagram accounts and its influence on their credibility and the professional-client relationship. Methodology: In a controlled field study, participants reviewed randomly assigned mock Instagram profiles of health professionals. Mock profiles were constructed according to gender (female/male), social media usage (high/low), and social media richness (high/ low), with richness increasing from posts to stories to reels and personal content type (high /low). Participants then rated the profile owners’ credibility on a visual analog scale. An analysis of variance compared these ratings, and mediation analyses assessed the influence of credibility ratings on participants' willingness to become clients of the mock health professional. Results: Results from 315 participants showed that health professionals with personal Instagram profiles displaying high social media richness were perceived as more credible than those with lower social media richness. Low social media usage is perceived as more credible than high social media usage. Personal content type is perceived as less credible as compared to those with low personal content type. Contributions: These findings provide initial evidence of the impact of health professionals' personal online disclosures on credibility and the health professional-client relationship. Understanding public perceptions of professionalism and credibility is essential for informing e-professionalism guidelines and promoting best practices in social media use among health professionals.

Keywords: credibility, consumer behavior, social media, media richness, healthcare professionals

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Authors: Mohammad Haghighi, Amineh Akhondi, Leila Jahangard, Mohammad Ahmadpanah, Masoud Ansari

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Background: According to the recent estimation, approximately 4%-12% percent of Iranians have difficulty in learning to read and spell possibly as a result of developmental dyslexia. The study was planned to investigate spelling error patterns among Persian children with developmental dyslexia and compare that with the errors exhibited by control groups Participants: 90 students participated in this study. 30 students from Grade level five, diagnosed as dyslexics by professionals, 30 normal 5th Grade readers and 30 younger normal readers. There were 15 boys and 15 girls in each of the groups. Qualitative and quantitative methods for analysis of errors were used. Results and conclusion: results of this study indicate similar spelling error profiles among dyslexics and the reading level matched groups, and these profiles were different from age-matched group. However, performances of dyslexic group and reading level matched group were different and inconsistent in some cases.

Keywords: spelling, error types, developmental dyslexia, Persian, writing system, learning disabilities, processing

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Authors: Hanaa H. Abd El Baky, Gamal S. El Baroty, Eman A. Ibrahem

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Microalgae Scenedesmus obliquus, the carotenoides (astaxanine and β-caroteine) were identified as the major bioactive constituents. In this work we prepared functional pre-biotic cakes to increase general mental health. Functional cakes were formulated by adding algal caroteinods at 2 and 4 mg/100g to flower and the cakes were storage for 20 days. Oxidative stability of both function cakes products were examined during storage periods by DPPH and TBA assays, and the results revealed that both values in function food products were significantly much low than that in untreated food products. Data of sensory evaluation revealed that treated biscuit and cakes with algae or algae extracts were significantly acceptable as control for main sensory characteristics (colour, odour/aroma, flavour, texture, the global appreciation, and overall acceptability). Thus, it could be concluded that functional biscuits and cakes (very popular and well balanced nutritional food) had good sensory and nutritional profiles and can be developed as new niche food market.

Keywords: Scenedesmus obliquus, carotenoids, functional cakes antioxidant, nutritional profiles

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Authors: Inam Ridha, Christine L. Kuryla, Madhuranga Thilakasiri Madugoda Ralalage Don, Norman J. Kleiman, Yunro Chung, Jin Park, Vel Murugan, Joshua LaBaer

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To date, more than 275 million people worldwide have been diagnosed with COVID-19 and the rapid spread of the omicron variant suggests many millions more will soon become infected. Many infections are asymptomatic, while others result in mild to moderate illness. Unfortunately, some infected individuals exhibit more serious symptoms including respiratory distress, thrombosis, cardiovascular disease, multi-organ failure, cognitive difficulties, and, in roughly 2% of cases, death. Studies indicate other coronaviruses can alter the host cell's epigenetic profile and lead to alterations in the immune response. To better understand the mechanism(s) by which SARS-CoV-2 infection causes serious illness, DNA methylation profiles in peripheral blood mononuclear cells (PBMCs) from 90 hospitalized severely ill COVID-19 patients were compared to profiles from uninfected control subjects. Exploratory epigenome-wide DNA methylation analyses were performed using multiplexed methylated DNA immunoprecipitation (MeDIP) followed by pathway enrichment analysis. The findings demonstrated significant DNA methylation changes in infected individuals as compared to uninfected controls. Pathway analysis indicated that apoptosis, cell cycle control, Toll-like receptors (TLR), cytokine interactions, and T cell differentiation were among the most affected metabolic processes. In addition, changes in specific gene methylation were compared to SARS-CoV-2 induced changes in RNA expression using published RNA-seq data from 3 patients with severe COVID-19. These findings demonstrate significant correlations between differentially methylated and differentially expressed genes in a number of critical pathways.

Keywords: COVID19, epigenetics, DNA mathylation, viral infection

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Authors: Sheren H. Salah

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The inverted pendulum is a highly nonlinear and open-loop unstable system. An inverted pendulum (IP) is a pendulum which has its mass above its pivot point. It is often implemented with the pivot point mounted on a cart that can move horizontally and may be called a cart and pole. The characteristics of the inverted pendulum make identification and control more challenging. This paper presents the simulation study of several control strategies for an inverted pendulum system. The goal is to determine which control strategy delivers better performance with respect to pendulum’s angle. The inverted pendulum represents a challenging control problem, which continually moves toward an uncontrolled state. For controlling the inverted pendulum. The simulation study that sliding mode control (SMC) control produced better response compared to Genetic Algorithm Control (GAs) and proportional-integral-derivative(PID) control.

Keywords: Inverted Pendulum (IP) Proportional-Integral-Derivative (PID), Genetic Algorithm Control (GAs), Sliding Mode Control (SMC)

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Authors: Younis Elhaddad, Alfonso Ortega

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Oil production by means of gas lift is a standard technique in oil production industry. To optimize the total amount of oil production in terms of the amount of gas injected is a key question in this domain. Different methods have been tested to propose a general methodology. Many of them apply well-known numerical methods. Some of them have taken into account the power of evolutionary approaches. Our goal is to provide the experts of the domain with a powerful automatic searching engine into which they can introduce their knowledge in a format close to the one used in their domain, and get solutions comprehensible in the same terms, as well. These proposals introduced in the genetic engine the most expressive formal models to represent the solutions to the problem. These algorithms have proven to be as effective as other genetic systems but more flexible and comfortable for the researcher although they usually require huge search spaces to justify their use due to the computational resources involved in the formal models. The first step to evaluate the viability of applying our approaches to this realm is to fully understand the domain and to select an instance of the problem (gas lift optimization) in which applying genetic approaches could seem promising. After analyzing the state of the art of this topic, we have decided to choose a previous work from the literature that faces the problem by means of numerical methods. This contribution includes details enough to be reproduced and complete data to be carefully analyzed. We have designed a classical, simple genetic algorithm just to try to get the same results and to understand the problem in depth. We could easily incorporate the well mathematical model, and the well data used by the authors and easily translate their mathematical model, to be numerically optimized, into a proper fitness function. We have analyzed the 100 curves they use in their experiment, similar results were observed, in addition, our system has automatically inferred an optimum total amount of injected gas for the field compatible with the addition of the optimum gas injected in each well by them. We have identified several constraints that could be interesting to incorporate to the optimization process but that could be difficult to numerically express. It could be interesting to automatically propose other mathematical models to fit both, individual well curves and also the behaviour of the complete field. All these facts and conclusions justify continuing exploring the viability of applying the approaches more sophisticated previously proposed by our research group.

Keywords: evolutionary automatic programming, gas lift, genetic algorithms, oil production

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Authors: Usha Barahmand, Ruhollah Heydari Sheikh Ahmad, Sara Alaie Khoraem

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Introduction: The association of epilepsy with several psychological disorders and reduced quality of life has long been recognized. The present study aimed at comparing the personality profiles, quality of life and symptomatology of anxiety and depression in patients with epilepsy and healthy controls. Materials and Methods: Forty seven patients (29 men and 18 women) with diagnosed epilepsy participated in this study. Forty seven healthy controls who matched the patients in age and gender were also recruited. The participants’ personality and psychological profiles were assessed using the Depression, Anxiety, and Stress Scale (DASS-21), the Short-Form Health Survey (SF-36) and the HEXACO Personality Inventory (HEXACO-PI). Scoring algorithms were applied to the SF-36 produce the physical and mental component scores (PCS and MCS). Results: There were statistically significant differences in the total SF-36 score, anxiety, depression and stress scores of the DASS-21 between patients and controls. Anxiety, stress and depression scores significantly correlated inversely with the PCS and MCS. Data analysis showed that females had higher depression scores than males in both patients and controls, while males in both groups scored higher on stress. Patients’ personality scores were also different from those reported by controls on emotional, agreeableness and extroversion. Patients scored higher on emotionality, and lower on agreeableness and extraversion. Patients also scored lower on indices of quality of life. Regression analysis revealed that emotionality, anxiety, stress and MCS accounted for a significant proportion of the variance in severity of epileptic seizures. Conclusion: Stressful situations and psychological conditions as well as the personality trait of neuroticism were related to the occurrence of recurrent epileptic seizures.

Keywords: anxiety, depression, epilepsy, neuroticism, personality, quality of life, stress

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Authors: Shatha A. Yousif, Hatem Jasim, Ali R. Abas, Dheya P. Yousef

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To study the effect of the cross direction in bead wheat, three hybrid combinations (Babyle 113 , Iratome), (Sawa , Tamose2) and (Al Hashymya Al Iraq) were tested for plant height, number of tillers/m, number of grains per spike, weight of grains per spike, 1000-grain weight and grain yield. The results revealed that the direction of the cross had significant effect the number of grain/spike, tillers/m and grain yields. Grain yield was positively and significantly correlated with 1000-grain weight, number of grains per spike and tillers. Depend on the result of heritability and genetic advance it was suggested that 1000-grain weight number of grains per spike and tillers should be given emphasis for future wheat yield improvement programs.

Keywords: correlation, genetic advance, heritability, wheat, yield traits

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Authors: Faheema Khan

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In order to investigate the influence of genetic background on salt tolerance in Soybean (Glycine max) ten soybean genotypes released/notified in India were selected. (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712). The 10-day-old seedlings were subjected to 0, 25, 50, 75, 100, 125, and 150 mM NaCl for 15 days. Plant growth, leaf osmotic adjustment, and RAPD analysis were studied. In comparison to control plants, the plant growth in all genotypes was decreased by salt stress, respectively. Salt stress decreased leaf osmotic potential in all genotypes however the maximum reduction was observed in genotype Pusa-24 followed by PK-416 and Pusa-20. The difference in osmotic adjustment between all the genotypes was correlated with the concentrations of ion examined such as Na+ and the leaf proline concentration. These results suggest that the genotypic variation for salt tolerance can be partially accounted for by plant physiological measures. The genetic polymorphisms between soybean genotypes differing in response to salt stress were characterized using 25 RAPD primers. These primers generated a total of 1640 amplification products, among which 1615 were found to be polymorphic. A very high degree of polymorphism (98.30%) was observed. UPGMA cluster analysis of genetic similarity indices grouped all the genotypes into two major clusters. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings. Our results show that RAPD technique is a sensitive, precise and efficient tool for genomic analysis in soybean genotypes.

Keywords: glycine max, NaCl, RAPD, proteomics

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Authors: Afsaneh Mohammadnejad, Marianne Nygaard, Jan Baumbach, Shuxia Li, Weilong Li, Jesper Lund, Jacob v. B. Hjelmborg, Lene Christensen, Qihua Tan

Abstract:

Cognitive impairment in the elderly is a key issue affecting the quality of life. Despite a strong genetic background in cognition, only a limited number of single nucleotide polymorphisms (SNPs) have been found. These explain a small proportion of the genetic component of cognitive function, thus leaving a large proportion unaccounted for. We hypothesize that one reason for this missing heritability is the misspecified modeling in data analysis concerning phenotype distribution as well as the relationship between SNP dosage and the phenotype of interest. In an attempt to overcome these issues, we introduced a model-free method based on the generalized correlation coefficient (GCC) in a genome-wide association study (GWAS) of cognitive function in twin samples and compared its performance with two popular linear regression models. The GCC-based GWAS identified two genome-wide significant (P-value < 5e-8) SNPs; rs2904650 near ZDHHC2 on chromosome 8 and rs111256489 near CD6 on chromosome 11. The kinship model also detected two genome-wide significant SNPs, rs112169253 on chromosome 4 and rs17417920 on chromosome 7, whereas no genome-wide significant SNPs were found by the linear mixed model (LME). Compared to the linear models, more meaningful biological pathways like GABA receptor activation, ion channel transport, neuroactive ligand-receptor interaction, and the renin-angiotensin system were found to be enriched by SNPs from GCC. The GCC model outperformed the linear regression models by identifying more genome-wide significant genetic variants and more meaningful biological pathways related to cognitive function. Moreover, GCC-based GWAS was robust in handling genetically related twin samples, which is an important feature in handling genetic confounding in association studies.

Keywords: cognition, generalized correlation coefficient, GWAS, twins

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Authors: Feng Ji Mervin Goh, Edmund Chee Jian Pua, Stuart Alexander Cook

Abstract:

Dilated cardiomyopathy (DCM) is a common cause of heart failure. Genetic mutations account for 50% of DCM cases with TTN mutations being the most common, accounting for up to 25% of DCM cases. However, the genetic architecture underlying Asian DCM patients is unknown. We evaluated 68 patients (female= 17) with DCM who underwent follow-up at the National Heart Centre, Singapore from 2013 through 2014. Clinical data were obtained and analyzed retrospectively. Genomic DNA was subjected to next-generation targeted sequencing. Nextera Rapid Capture Enrichment was used to capture the exons of a panel of 169 cardiac genes. DNA libraries were sequenced as paired-end 150-bp reads on Illumina MiSeq. Raw sequence reads were processed and analysed using standard bioinformatics techniques. The average age of onset of DCM was 46.1±10.21 years old. The average left ventricular ejection fraction (LVEF), left ventricular diastolic internal diameter (LVIDd), left ventricular systolic internal diameter (LVIDs) were 26.1±11.2%, 6.20±0.83cm, and 5.23±0.92cm respectively. The frequencies of mutations in major DCM-associated genes were as follows TTN (5.88% vs published frequency of 20%), LMNA (4.41% vs 6%), MYH7 (5.88% vs 4%), MYH6 (5.88% vs 4%), and SCN5a (4.41% vs 3%). The average callability at 10 times coverage of each major gene were: TTN (99.7%), LMNA (87.1%), MYH7 (94.8%), MYH6 (95.5%), and SCN5a (94.3%). In conclusion, TTN mutations are not common in Singaporean DCM patients. The frequencies of other major DCM-associated genes are comparable to frequencies published in the current literature.

Keywords: heart failure, dilated cardiomyopathy, genetics, next-generation sequencing

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Authors: Mustafa Malki, Ewan R. Pearson

Abstract:

Tools utilized by health care practitioners to flag potential adverse drug reactions secondary to drug-drug interactions ignore individual genetic variation, which has the potential to markedly alter the severity of these interactions. To our best knowledge, there have been limited published studies on the impact of genetic variation on drug-drug interactions. Therefore, our aim in this project is the discovery of previously unrecognized, clinically important drug-drug-gene interactions (DDGIs) within the list of most commonly used drug combinations in the UK. The UKBB database was utilized to identify the top most frequently prescribed drug combinations in the UK with at least one route of interaction (over than 200 combinations were identified). We have recognised 37 common and unique interacting genes considering all of our drug combinations. Out of around 600 potential genetic variants found in these 37 genes, 100 variants have met the selection criteria (common variant with minor allele frequency ≥ 5%, independence, and has passed HWE test). The association between these variants and the use of each of our top drug combinations has been tested with a case-control analysis under the log-additive model. As the data is cross-sectional, drug intolerance has been identified from the genotype distribution as presented by the lower percentage of patients carrying the risky allele and on the drug combination compared to those free of these risk factors and vice versa with drug tolerance. In GoDARTs database, the same list of common drug combinations identified by the UKBB was utilized here with the same list of candidate genetic variants but with the addition of 14 new SNPs so that we have a total of 114 variants which have met the selection criteria in GoDARTs. From the list of the top 200 drug combinations, we have selected 28 combinations where the two drugs in each combination are known to be used chronically. For each of our 28 combinations, three drug response phenotypes have been identified (drug stop/switch, dose decrease, or dose increase of any of the two drugs during their interaction). The association between each of the three phenotypes belonging to each of our 28 drug combinations has been tested against our 114 candidate genetic variants. The results show replication of four findings between both databases : (1) Omeprazole +Amitriptyline +rs2246709 (A > G) variant in CYP3A4 gene (p-values and ORs with the UKBB and GoDARTs respectively = 0.048,0.037,0.92,and 0.52 (dose increase phenotype)) (2) Simvastatin + Ranitidine + rs9332197 (T > C) variant in CYP2C9 gene (0.024,0.032,0.81, and 5.75 (drug stop/switch phenotype)) (3) Atorvastatin + Doxazosin + rs9282564 (T > C) variant in ABCB1 gene (0.0015,0.0095,1.58,and 3.14 (drug stop/switch phenotype)) (4) Simvastatin + Nifedipine + rs2257401 (C > G) variant in CYP3A7 gene (0.025,0.019,0.77,and 0.30 (drug stop/switch phenotype)). In addition, some other non-replicated, but interesting, significant findings were detected. Our work also provides a great source of information for researchers interested in DD, DG, or DDG interactions studies as it has highlighted the top common drug combinations in the UK with recognizing 114 significant genetic variants related to drugs' pharmacokinetic.

Keywords: adverse drug reactions, common drug combinations, drug-drug-gene interactions, pharmacogenomics

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Authors: E. A. Mlybari, M. S. Elbisy, A. H. Alshahri, O. M. Albarakati

Abstract:

Sea level rise threatens to increase the impact of future storms and hurricanes on coastal communities. Accurate sea level change prediction and supplement is an important task in determining constructions and human activities in coastal and oceanic areas. In this study, support vector machines (SVM) is proposed to predict daily tidal levels along the Jeddah Coast, Saudi Arabia. The optimal parameter values of kernel function are determined using a genetic algorithm. The SVM results are compared with the field data and with back propagation (BP). Among the models, the SVM is superior to BPNN and has better generalization performance.

Keywords: tides, prediction, support vector machines, genetic algorithm, back-propagation neural network, risk, hazards

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Authors: Saeid Jalilzadeh

Abstract:

PID controllers are widely used to control the industrial plants because of their robustness and simple structures. Tuning of the controller's parameters to get a desired response is difficult and time consuming. With the development of computer technology and artificial intelligence in automatic control field, all kinds of parameters tuning methods of PID controller have emerged in endlessly, which bring much energy for the study of PID controller, but many advanced tuning methods behave not so perfect as to be expected. Honey Bee algorithm (HBA) and genetic algorithm (GA) are extensively used for real parameter optimization in diverse fields of study. This paper describes an application of HBA and GA to the problem of designing a PID controller whose parameters comprise proportionality constant, integral constant and derivative constant. Presence of three parameters to optimize makes the task of designing a PID controller more challenging than conventional P, PI, and PD controllers design. The suitability of the proposed approach has been demonstrated through computer simulation using MATLAB/SIMULINK.

Keywords: controller, GA, optimization, PID, PSO

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Authors: Parinaz Arashnia, Farzad Hatami, Saeed Ghaffarpour Jahromi

Abstract:

Using steel in bridges’ construction because of their desired tensile and compressive strength and light weight especially in large spans was widely popular. Disadvantages of steel such as corrosion, buckling and weaknesses in high temperature and unsuitable weld could be solve with using Fibres Reinforced Polymer (FRP) profiles. The FRP is a remarkable class of composite polymers that can improve structural elements behaviour like corrosion resistance, fir resistance with good proofing and electricity and magnetic non-conductor. Nowadays except FRP reinforced bars and laminates, FRP I-beams are made and studied. The main reason for using FRP profiles is, prevent of corrosion and increase the load carrying capacity and durability, especially in large spans in bridges’ deck. In this paper, behaviour of I-section glass fibres reinforced polymer (GFRP) beam is discussed under point loads with numerical models and results has been compared and verified with experimental tests.

Keywords: glass fibres reinforced polymer, composite, I-section beam, durability, finite element method, numerical model

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Authors: Dheyaa W. Abbood, Rafa H. AL-Suhaili, May S. Saleh

Abstract:

A model using the artificial neural networks and genetic algorithm technique is developed for obtaining optimum dimensions of the foundation length and protections of small hydraulic structures. The procedure involves optimizing an objective function comprising a weighted summation of the state variables. The decision variables considered in the optimization are the upstream and downstream cutoffs length sand their angles of inclination, the foundation length, and the length of the downstream soil protection. These were obtained for a given maximum difference in head, depth of impervious layer and degree of anisotropy.The optimization carried out subjected to constraints that ensure a safe structure against the uplift pressure force and sufficient protection length at the downstream side of the structure to overcome an excessive exit gradient. The Geo-studios oft ware, was used to analyze 1200 different cases. For each case the length of protection and volume of structure required to satisfy the safety factors mentioned previously were estimated. An ANN model was developed and verified using these cases input-output sets as its data base. A MatLAB code was written to perform a genetic algorithm optimization modeling coupled with this ANN model using a formulated optimization model. A sensitivity analysis was done for selecting the cross-over probability, the mutation probability and level ,the number of population, the position of the crossover and the weights distribution for all the terms of the objective function. Results indicate that the most factor that affects the optimum solution is the number of population required. The minimum value that gives stable global optimum solution of this parameters is (30000) while other variables have little effect on the optimum solution.

Keywords: inclined cutoff, optimization, genetic algorithm, artificial neural networks, geo-studio, uplift pressure, exit gradient, factor of safety

Procedia PDF Downloads 302