Search results for: genetic profiles

Authors: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Wen-Chi Chang

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As the most important non-vascular plants, algae have many research applications, including high species diversity, biofuel sources, adsorption of heavy metals and, following processing, health supplements. With the increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes, an integrated resource for retrieving gene expression data and metabolic pathway is essential for functional analysis and systems biology in algae. However, gene expression profiles and biological pathways are displayed separately in current resources, and making it impossible to search current databases directly to identify the cellular response mechanisms. Therefore, this work develops a novel AlgaePath database to retrieve gene expression profiles efficiently under various conditions in numerous metabolic pathways. AlgaePath, a web-based database, integrates gene information, biological pathways, and next-generation sequencing (NGS) datasets in Chlamydomonasreinhardtii and Neodesmus sp. UTEX 2219-4. Users can identify gene expression profiles and pathway information by using five query pages (i.e. Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-Expression Analysis). The gene expression data of 45 and 4 samples can be obtained directly on pathway maps in C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively. Genes that are differentially expressed between two conditions can be identified in Folds Search. Furthermore, the Gene Group Analysis of AlgaePath includes pathway enrichment analysis, and can easily compare the gene expression profiles of functionally related genes in a map. Finally, Co-Expression Analysis provides co-expressed transcripts of a target gene. The analysis results provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data. More than an effective interface to clarify the transcript response mechanisms in different metabolic pathways under various conditions, AlgaePath is also a data mining system to identify critical mechanisms based on high-throughput sequencing.

Keywords: next-generation sequencing (NGS), algae, transcriptome, metabolic pathway, co-expression

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: G. Bhushan, S. Dhingra, K. K. Dubey

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This paper presents the evaluation of performance (BSFC and BTE), combustion (P_max) and emission (CO, NO_x, HC and smoke opacity) parameters of karanja biodiesel in a single cylinder, four stroke, direct injection diesel engine by considering significant engine input parameters (blending ratio, compression ratio and load torque). Multi-objective optimization of performance, combustion and emission parameters is also carried out in a karanja biodiesel engine using hybrid RSM-NSGA-II technique. The pareto optimum solutions are predicted by running the hybrid RSM-NSGA-II technique. Each pareto optimal solution is having its own importance. Confirmation tests are also conducted at randomly selected few pareto solutions to check the authenticity of the results.

Keywords: genetic algorithm, rsm, biodiesel, karanja

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Authors: Maximilian Cedzich, Ingo Dietz Von Bayer, Roland Jochem

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In order for industrial companies to continue to succeed in dynamic, globalized markets, they must be able to train their employees in an agile manner and at short notice in line with the exogenous conditions that arise. For this purpose, it is indispensable to operate a proactive competence management system for employees that recognizes qualification needs timely in order to be able to address them promptly through qualification measures. However, there are hardly any approaches to be found in the literature that includes systematic, proactive competence management. In order to help close this gap, this publication presents a process model that systematically develops bottom-up, future-oriented target competence profiles based on the tasks of the employees. Concretely, in the first step, the tasks of the individual employees are examined for assumed future conditions. In other words, qualitative scenarios are considered for the individual tasks to determine how they are likely to change. In a second step, these scenario-based future tasks are translated into individual future-related target competencies of the employee using a matrix of generic task properties. The final step pursues the goal of validating the target competence profiles formed in this way within the framework of a management workshop. This process model provides industrial companies with a tool that they can use to determine the competencies required by their own employees in the future and compare them with the actual prevailing competencies. If gaps are identified between the target and the actual, these qualification requirements can be closed in the short term by means of qualification measures.

Keywords: dynamic globalized markets, employee competence management, industrial companies, knowledge management

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Authors: Sheryl Avendaño, Miguel Ospina, Hebert Montegranario

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Full Wave Inversion (FWI) is a variant of seismic tomography for obtaining velocity profiles by an optimization process that combine forward modelling (or solution of wave equation) with the misfit between synthetic and observed data. In this research we are modelling wave propagation in a visco-acoustic medium in the frequency domain. We apply finite differences for the numerical solution of the wave equation with a mix between usual and rotated grids, where density depends on velocity and there exists a damping function associated to a linear dissipative medium. The velocity profiles are obtained from an initial one and the data have been modeled for a frequency range 0-120 Hz. By an iterative procedure we obtain an estimated velocity profile in which are detailed the remarkable features of the velocity profile from which synthetic data were generated showing promising results for our method.

Keywords: seismic inversion, full wave inversion, visco acoustic wave equation, finite diffrence methods

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Authors: Zinhle Cindi, Collet Dandara, Mpiko Ntsekhe, Edson Makambwa, Miguel Larceda

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Background: Warfarin is the most commonly used drug in the management of thromboembolic disease. However, there is a huge variability in the time, number of doses or starting doses for patients to achieve the required international normalised ratio (INR) which is compounded by a narrow therapeutic index. Many genetic-association studies have reported on European and Asian populations which have led to the designing of specific algorithms that are now being used to assist in warfarin dosing. However, very few or no studies have looked at the pharmacogenetics of warfarin in African populations, yet, huge differences in dosage requirements to reach the same INR have been observed. Objective: We set out to investigate the distribution of 3 SNPs CYP4F2 c.1347C > T, VKORC1 g.-1639G > A and VKORC1 c.1173C > T among South African Mixed Ancestry (MA) and Black African patients. Methods: DNA was extracted from 383 participants and subsequently genotyped using PCR/RFLP for the CYP4F2 c.1347 (V433M) (rs2108622), VKORC1 g.-1639 (rs9923231) and VKORC1 c.1173 (rs9934438) SNPs. Results: Comparing the Black and MA groups, significant differences were observed in the distribution of the following genotypes; CYP4F2 c.1347C/T (23% vs. 39% p=0.03). All VKORC1 g.-1639G > A genotypes (p < 0.006) and all VKORC1 c.1173C > T genotypes (p < 0.007). Conclusion: CYP4F2 c.1347T (V433M) reduces CYP4F2 protein levels and therefore expected to affect the amount of warfarin needed to block vitamin k recycling. The VKORC1 g-1639A variant alters transcriptional regulation therefore affecting the function of vitamin k epoxide reductase in vitamin k production. The VKORC1 c.1173T variant reduces the enzyme activity of VKORC1 consequently enhancing the effectiveness of warfarin. These are preliminary results; more genetic characterization is required to understand all the genetic determinants affecting how patients respond to warfarin.

Keywords: algorithms, pharmacogenetics, thromboembolic disease, warfarin

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Authors: Jan Busch, Peter Nyhuis

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Considering the challenges of short product life cycles and growing variant diversity, cost minimization and manufacturing flexibility increasingly gain importance to maintain a competitive edge in today’s global and dynamic markets. In this context, an aerodynamic part feeding system for high-speed industrial assembly applications has been developed at the Institute of Production Systems and Logistics (IFA), Leibniz Universitaet Hannover. The aerodynamic part feeding system outperforms conventional systems with respect to its process safety, reliability, and operating speed. In this paper, a multi-objective optimisation of the aerodynamic feeding system regarding the orientation rate, the feeding velocity and the required nozzle pressure is presented.

Keywords: aerodynamic feeding system, genetic algorithm, multi-objective optimization, workpiece orientation

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Authors: Pamela-Zoe Topalli, Niina Junttila, Päivi M. Niemi, Klaus Ranta

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Adolescents’ biased perceptions about their social competence (SC), whether negatively or positively, serve to influence their socioemotional adjustment such as early feelings of social phobia (nowadays referred to as Social Anxiety Disorder-SAD). Despite the importance of biased self-perceptions in adolescents’ psychosocial adjustment, the extent to which discrepancies between self- and others’ evaluations of one’s SC are linked to social phobic symptoms remains unclear in the literature. This study examined the perceptual discrepancy profiles between self- and peers’ as well as between self- and teachers’ evaluations of adolescents’ SC and the interrelations of these profiles with self-reported social phobic symptoms. The participants were 390 3^rd graders (15 years old) of Finnish lower secondary school (50.8% boys, 49.2% girls). In contrast with variable-centered approaches that have mainly been used by previous studies when focusing on this subject, this study used latent profile analysis (LPA), a person-centered approach which can provide information regarding risk profiles by capturing the heterogeneity within a population and classifying individuals into groups. LPA revealed the following five classes of discrepancy profiles: i) extremely negatively biased perceptions of SC, ii) negatively biased perceptions of SC, iii) quite realistic perceptions of SC, iv) positively biased perceptions of SC, and v) extremely positively biased perceptions of SC. Adolescents with extremely negatively biased perceptions and negatively biased perceptions of their own SC reported the highest number of social phobic symptoms. Adolescents with quite realistic, positively biased and extremely positively biased perceptions reported the lowest number of socio-phobic symptoms. The results point out the negatively and the extremely negatively biased perceptions as possible contributors to social phobic symptoms. Moreover, the association of quite realistic perceptions with low number of social phobic symptoms indicates its potential protective power against social phobia. Finally, positively and extremely positively biased perceptions of SC are negatively associated with social phobic symptoms in this study. However, the profile of extremely positively biased perceptions might be linked as well with the existence of externalizing problems such as antisocial behavior (e.g. disruptive impulsivity). The current findings highlight the importance of considering discrepancies between self- and others’ perceptions of one’s SC in clinical and research efforts. Interventions designed to prevent or moderate social phobic symptoms need to take into account individual needs rather than aiming for uniform treatment. Implications and future directions are discussed.

Keywords: adolescence, latent profile analysis, perceptual discrepancies, social competence, social phobia

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Authors: S. Ahmad, C. Yuan, Q. Zhang

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The assorted architectural plasticity of a plant is majorly specified by stooling, a phenomenon tackled by a combination of developmental, environmental and hormonal accelerators of lateral buds. Chrysanthemums (Chrysanthemum morifolium) are one of the most economically important ornamental plants worldwide on the account of having plentiful architectural patterns, diverse shapes and attractive colors. Side branching is the major determinant guaranteeing the consistent demand of cut chrysanthemum in flower industry. Presence of immense number of axillary branches devalues the economic importance of this imperative plant and is a major challenge for mum growers to hold a stake in the cut flower market. Restricting branches to a minimum level, or no branches at all, is the dire need of the day in order to introducing novelty in cut chrysanthemums. Temperature is a potent factor which affects largely the escalation, development of chrysanthemum, and also the genetic expression of various vegetative traits like branching. It affects differently the developmental characteristics and phenotypic expressions of inherent qualities, thereby playing a significant role in differentiating the developmental responses in different cultivars of chrysanthemum. A detailed study pertaining to the affect of temperature on branching in chrysanthemum is a clear lacking throughout the literature on mums. Therefore, searching with temperature as an effective means of reducing side branching to a desired level could be an influencing extension of struggles about how to nullify stooling. This requires plenty of research in order to reveal the extended penetration of temperature in manipulating the genetic control of various important traits like branching, which is a burning issue now a days in producing cut flowers in chrysanthemum. The present review will highlight the impact of temperature on branching control mechanism in chrysanthemum at morpho-physiological, hormonal and molecular levels.

Keywords: branching, chrysanthemum, genetic control, hormonal, morpho-physiological, temperature

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Authors: Jolanta Jonak

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All students demonstrate various learning preferences and learning styles that range from visual, auditory to kinesthetic preferences. These learning preferences are further impacted by individual cognitive profiles hat characterizes itself in linguistic strengths, logical- special, inter-or intra- personal, just to name a few. Students from culturally and linguistically diverse backgrounds (CLD) have an increased risk of being misunderstood by many school systems and even medical personnel. Students with disability, specifically Autism, are faced with another layer of learning differences. Research indicates that large numbers of students are not provided the type of education and types of supports they need in order to be successful in an academic environment. Multiple research findings indicate that significant numbers of school staff self-reports that they do not feel adequately prepared to work with students with disability and different learing profiles. It is very important for the school staff to be educated about different learning needs of students with autism spectrum disorders. Having the knowledge, school staff can avoid unnecessary referrals for office referrals and avoid inaccurate decisions about restrictive learning environments. This presentation will illustrate the cognitive differences in students with autism, how to recognize them, and how to support them through Differentiated Instruction. One way to ensure successful education for students with disability is by providing Differentiated Instruction (DI). DI is quickly gaining its popularity in the Unites States as a scientific- research based instructional approach for all students. This form of support ensures that regardless of the students’ learning preferences and cognitive learning profiles, they have an opportunity to learn through approaches that are suitable to their needs. It is extremely important for the school staff, especially school psychologists who often are the first experts to be consulted by educators, to be educated about differences due to learning preference styles and differentiation needs.

Keywords: special education, autism, differentiation, differences, differentiated instruction

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Authors: S. Hallal, Z. Chami, A. Hadji-Lehtihet, S. Sokhal-Boudella, A. Berhoune, L. Yargui

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Gaucher disease is the most common lysosomal storage in our population, it is due to a deficiency of β –glucosidase acid. The enzyme deficiency causes a pathological accumulation of undegraded substrate in lysosomes. This metabolic overload is responsible for a multisystemic disease with hepatosplenomegaly, anemia, thrombocytopenia, and bone involvement. Neurological involvement is rare. The laboratory diagnosis of Gaucher disease consists of phenotypic diagnosis by determining the enzymatic activity of β - glucosidase by fluorimetric method, a study by genotypic diagnosis in the GBA gene, limiting the search recurrent mutations (N370S, L444P, 84 GG); PCR followed by an enzymatic digestion. Abnormal profiles were verified by sequencing. Monitoring of treated patients is provided by the determination of chitotriosidase. Our experience spaning a period of 6 years (2007-2014) has enabled us to diagnose 78 patients out of a total of 328 requests from the various departments of pediatrics, internal medicine, neurology. Genotypic diagnosis focused on the entire family of 9 children treated at pediatric CHU Mustapha, which help define the clinical form; or 5 of them had type III disease, carrying the L444P mutation in the homozygous state. Three others were composite (N370/L444P) (N370S/other unintended mutation in our study), and only in one family no recurrent mutation has been found. This molecular study permits screening of heterozygous essential for genetic counseling.

Keywords: Gaucher disease, mutations, N370S, L444P

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Authors: Junghwa An, Sungkyoung Choi, Eun Ye, San Hoon Han, Young-Gun Choi, Chul Oun Jung

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The copper-winged bat (Myotis rufoniger) is the widely distributed medium body-sized bat in Asia, including Korea. This bat population has been decreasing because of habitat loss. This study reported the isolation and characterization of ten polymorphic microsatellite loci in endangered M. rufoniger. To do genetic studies, we use saliva DNA of bats during winter sleep period. The number of alleles per locus ranged from 2 to 9, and the observed and expected heterozygosities ranged from 0.063 to 0.750 and from 0.063 to 0.865, respectively. The average polymorphic information content (PIC) value of these markers was 0.37. Two loci of M. rufoniger showed departure from Hardy-Weinberg equilibrium(HWE). This demonstrated that the ten microsatellite loci can be used as genetic markers for further investigation of the copper-winged bat.

Keywords: copper-winged bat, microsatellite, population genetics, South Korea

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Authors: S. Neelima, P. S. Subramanyam

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A distribution system is an interface between the bulk power system and the consumers. Among these systems, radial distributions system is popular because of low cost and simple design. In distribution systems, the voltages at buses reduces when moved away from the substation, also the losses are high. The reason for a decrease in voltage and high losses is the insufficient amount of reactive power, which can be provided by the shunt capacitors. But the placement of the capacitor with an appropriate size is always a challenge. Thus, the optimal capacitor placement problem is to determine the location and size of capacitors to be placed in distribution networks in an efficient way to reduce the power losses and improve the voltage profile of the system. For this purpose, in this paper, two stage methodologies are used. In the first stage, the load flow of pre-compensated distribution system is carried out using ‘dimension reducing distribution load flow algorithm (DRDLFA)’. On the basis of this load flow the potential locations of compensation are computed. In the second stage, Genetic Algorithm (GA) technique is used to determine the optimal location and size of the capacitors such that the cost of the energy loss and capacitor cost to be a minimum. The above method is tested on IEEE 9 and 34 bus system and compared with other methods in the literature.

Keywords: dimension reducing distribution load flow algorithm, DRDLFA, genetic algorithm, electrical distribution network, optimal capacitors placement, voltage profile improvement, loss reduction

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Authors: Michael Josef Schwerer

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Background: The identification of unknown victims from mass disasters, violent crimes, or terrorist attacks is frequently facilitated through information from missing persons lists, portrait photos, old or recent pictures showing unique characteristics of a person such as scars or tattoos, or simply reference samples from blood relatives for DNA analysis. In contrast, the identification or at least the characterization of an unknown perpetrator from criminal or terrorist actions remains challenging, particularly in the absence of material or data for comparison, such as fingerprints, which had been previously stored in criminal records. In scenarios that result in high levels of destruction of the perpetrator’s corpse, for instance, blast or fire events, the chance for a positive identification using standard techniques is further impaired. Objectives: This study shows the forensic genetic procedures in the Legal Medicine Service of the German Air Force for the identification of unknown individuals, including such cases in which reference samples are not available. Scenarios requiring such efforts predominantly involve aircraft crash investigations, which are routinely carried out by the German Air Force Centre of Aerospace Medicine as one of the Institution’s essential missions. Further, casework by military police or military intelligence is supported based on administrative cooperation. In the talk, data from study projects, as well as examples from real casework, will be demonstrated and discussed with the audience. Methods: Forensic genetic identification in our laboratories involves the analysis of Short Tandem Repeats and Single Nucleotide Polymorphisms in nuclear DNA along with mitochondrial DNA haplotyping. Extended DNA analysis involves phenotypic markers for skin, hair, and eye color together with the investigation of a person’s biogeographic ancestry. Assessment of the biological age of an individual employs CpG-island methylation analysis using bisulfite-converted DNA. Forensic Investigative Genealogy assessment allows the detection of an unknown person’s blood relatives in reference databases. Technically, end-point-PCR, real-time PCR, capillary electrophoresis, pyrosequencing as well as next generation sequencing using flow-cell-based and chip-based systems are used. Results and Discussion: Optimization of DNA extraction from various sources, including difficult matrixes like formalin-fixed, paraffin-embedded tissues, degraded specimens from decomposed bodies or from decedents exposed to blast or fire events, provides soil for successful PCR amplification and subsequent genetic profiling. For cases with extremely low yields of extracted DNA, whole genome preamplification protocols are successfully used, particularly regarding genetic phenotyping. Improved primer design for CpG-methylation analysis, together with validated sampling strategies for the analyzed substrates from, e.g., lymphocyte-rich organs, allows successful biological age estimation even in bodies with highly degraded tissue material. Conclusions: Successful identification of unknown individuals or at least their phenotypic characterization using pigmentation markers together with age-informative methylation profiles, possibly supplemented by family tree search employing Forensic Investigative Genealogy, can be provided in specialized laboratories. However, standard laboratory procedures must be adapted to work with difficult and highly degraded sample materials.

Keywords: identification, forensic genetics, phenotypic markers, CPG methylation, biological age estimation, forensic investigative genealogy

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Authors: Fekadu Gadissa, Kassahun Tesfaye, Kifle Dagne, Mulatu Geleta

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‘Ethiopian dinich’ also called ‘Ethiopian potato’ is one of the economically important ‘orphan’ edible tuber crops indigenous to Ethiopia. We evaluated the morphological and agronomic traits performances of 174 samples from Ethiopia at multiple locations using 12 qualitative and 16 quantitative traits, recorded at the correct growth stages. We observed several morphotypes and phenotypic variations for qualitative traits along with a wide range of mean performance values for all quantitative traits. Analysis of variance for each quantitative trait showed a highly significant (p<0.001) variation among the collections with eventually non-significant variation for environment-traits interaction for all but flower length. A comparatively high phenotypic and genotypic coefficient of variation was observed for plant height, days to flower initiation, days to 50% flowering and tuber number per hill. Moreover, the variability and coefficients of variation due to genotype-environment interaction was nearly zero for all the traits except flower length. High genotypic coefficients of variation coupled with a high estimate of broad sense heritability and high genetic advance as a percent of collection mean were obtained for tuber weight per hill, number of primary branches per plant, tuber number per hill and number of plants per hill. Association of tuber yield per hectare of land showed a large magnitude of positive phenotypic and genotypic correlation with those traits. Principal components analysis revealed 76% of the total variation for the first six principal axes with high factor loadings again from tuber number per hill, number of primary branches per plant and tuber weight. The collections were grouped into four clusters with the weak region (zone) of origin based pattern. In general, there is high genetic-based variability for ‘Ethiopian dinich’ improvement and conservation. DNA based markers are recommended for further genetic diversity estimation for use in breeding and conservation.

Keywords: agro-morphological traits, Ethiopian dinich, genetic diversity, variance components

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Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

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The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance

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Authors: Hesham Abdin, Mohamed Zakaria, Talaat Abd-Elmonaem, Alaa El-Din Sayed Hafez

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Kalman filter algorithm is an estimator known as the workhorse of estimation. It has an important application in missile guidance, especially in lack of accurate data of the target due to noise or uncertainty. In this paper, a Kalman filter is used as a tracking filter in a simulated target-interceptor scenario with noise. It estimates the position, velocity, and acceleration of the target in the presence of noise. These estimations are needed for both proportional navigation and differential geometry guidance laws. A Kalman filter has a good performance at low noise, but a large noise causes considerable errors leads to performance degradation. Therefore, a new technique is required to overcome this defect using tuning factors to tune a Kalman filter to adapt increasing of noise. The values of the tuning factors are between 0.8 and 1.2, they have a specific value for the first half of range and a different value for the second half. they are multiplied by the estimated values. These factors have its optimum values and are altered with the change of the target heading. A genetic algorithm updates these selections to increase the maximum effective range which was previously reduced by noise. The results show that the selected factors have other benefits such as decreasing the minimum effective range that was increased earlier due to noise. In addition to, the selected factors decrease the miss distance for all ranges of this direction of the target, and expand the effective range which leads to increase probability of kill.

Keywords: proportional navigation, differential geometry, Kalman filter, genetic algorithm

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Authors: Hasrat Arjjumend, Sabiha Alam

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The Nagoya Protocol is landmark international legislation governing access to genetic resources and benefit sharing from utilization of genetic resource and traditional knowledge. The field implications of the international law have been assessed by surveying academic/ research institutions, civil society organizations (CSOs) and concerned individuals, who gave their opinions on whether the provider parties (usually developing countries) would ensure effective participation of Indigenous people and local communities (ILCs) in establishing the mechanisms to inform the potential users of traditional knowledge (TK) about their obligations under art. 12.2 of Nagoya Protocol. First of all, involvement and participation of ILCs in suggested clearing-house mechanisms of the Parties are seldom witnessed. Secondly, as respondents expressed, it is doubtful that developing countries would ensure effective participation of ILCs in establishing the mechanisms to inform the potential users of TK about their obligations. Yet, as most of ILCs speak and understand local or indigenous languages, whether the Nagoya Protocol provides or not, it is a felt need that the Parties should disclose information in a language understandable to ILCs. Alternative opinions indicate that if TK held by ILCs is disclosed, the value is gone. Therefore, it should be protected by the domestic law first and should be disclosed then.

Keywords: genetic resources, indigenous people, language, Nagoya protocol, participation, traditional knowledge

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Authors: Monika Szymańska-Czerwińsk, Kinga Zaręba-Marchewka, Krzysztof Niemczuk

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Chlamydiaceae are Gram-negative bacteria distributed worldwide in animals and humans. One of them is Chlamydia gallinacea recently discovered. Available data show that C. gallinacea is dominant chlamydial agent found in poultry in European and Asian countries. The aim of the studies was screening of poultry flocks in order to evaluate frequency of C. gallinacea shedding and genetic diversity. Sampling was conducted in different regions of Poland in 2019-2020. Overall, 1466 cloacal/oral swabs were collected in duplicate from 146 apparently healthy poultry flocks including chickens, turkeys, ducks, geese and quails. Dry swabs were used for DNA extraction. DNA extracts were screened using a Chlamydiaceae 23S rRNA real-time PCR assay. To identify Chlamydia species, specific real-time PCR assays were performed. Furthermore, selected samples were used for sequencing based on ompA gene fragments and variable domains (VD1-2, VD3-4). In total, 10.3% of the tested flocks were Chlamydiaceae-positive (15/146 farms). The presence of Chlamydiaceae was confirmed mainly in chickens (13/92 farms) but also in turkey (1/19 farms) and goose (1/26 farms) flocks. Eleven flocks were identified as C. gallinacea-positive while four flocks remained unclassified. Phylogenetic analysis revealed at least 16 genetic variants of C. gallinacea. Research showed that Chlamydiaceae occur in a poultry flock in Poland. The strains of C. gallinacea as dominant species show genetic variability.

Keywords: C. gallinacea, emerging agent, poultry, real-time PCR

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Authors: Vytautas Galvanauskas, Vykantas Grincas, Rimvydas Simutis

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This paper investigates a possible practical solution for reasonable oxygen supply during the pluripotent stem cells expansion processes, where the stem cells propagate as aggregates in stirred-suspension bioreactors. Low glucose and low oxygen concentrations are preferred for efficient proliferation of pluripotent stem cells. However, strong oxygen limitation, especially inside of cell aggregates, can lead to cell starvation and death. In this research, the oxygen concentration profile inside of stem cell aggregates in a stem cell expansion process was predicted using a modified oxygen diffusion model. This profile can be realized during the stem cells cultivation process by manipulating the oxygen concentration in inlet gas or inlet gas flow. The proposed approach is relatively simple and may be attractive for installation in a real pluripotent stem cell expansion processes.

Keywords: aggregated stem cells, dissolved oxygen profiles, modeling, stirred-tank, 3D expansion

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Authors: Juliana Barcelos Cordeiro, Khashayar Mahani, Farbod Farzan, Mohsen A. Jafari

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Energy disaggregation has been focused by many energy companies since energy efficiency can be achieved when the breakdown of energy consumption is known. Companies have been investing in technologies to come up with software and/or hardware solutions that can provide this type of information to the consumer. On the other hand, not all people can afford to have these technologies. Therefore, in this paper, we present a methodology for breaking down the aggregate consumption and identifying the highdemanding end-uses profiles. These energy profiles will be used to build the forecast model for optimal control purpose. A facility with high cooling load is used as an illustrative case study to demonstrate the results of proposed methodology. We apply a high level energy disaggregation through a pattern recognition approach in order to extract the consumption profile of its rooftop packaged units (RTUs) and present a forecast model for the energy consumption.  

Keywords: energy consumption forecasting, energy efficiency, load disaggregation, pattern recognition approach

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Authors: Asma Naseer Cheema, Attya Bhatti, Jabar Ali, John Peter

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Background: High cholesterol levels, endothelial dysfunction, inefficient coagulation cascade and hyper inflammatory response all are the basis of coronary artery disease (CAD). Several studies are carried out to see the genetic influence of these factors on disease outcome. Objective: The objective of our study was to see the association of 10 putative loci with coronary artery disease in our population. Materials & Methods: We screened our population for 10 putative loci of CAD showing significant association (p < 5x10-8) with candidate genes (regulating the cholesterol metabolism, endothelial function, coagulation cascade and inflammatory response of body). Hardy-Weinberg equilibrium and linkage disequilibrium in cases and controls s were estimated separately. Approximately 5-10 ng of dried DNA in 384 well plate format was used to genotype each sample on the Sequenom iPLEX assay at University of Pittsburgh Genomics and Proteomics Core Laboratories. It was built on single-base primer extension with the MALDI-TOF MS detection possessing high sensitivity and specificity. The SNPs were genotyped through Taqman assay. Hardy Weinberg test was applied. The 10 SNPs were selected as genetic markers for this study (rs579459, rs1561198, rs2954029, rs1122608, rs17114036, rs9515203, rs10947789, rs7173743, rs2895811, rs2075650). Results: Mean age of the patient was 52 ± 11 years. Blood pressure and positive family history was found a significant risk factor for CAD. None of the selected SNPs showed significant association with coronary artery disease in our population (p>0.05). Conclusion: rs579459, rs1561198, rs2954029, rs1122608, rs17114036, rs9515203, rs10947789, rs7173743, rs2895811, rs2075650 are not significant genetic markers for CAD in our population.

Keywords: CAD, genetic markers, loci, risk factors

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Authors: Prikhil Agrawal, N. Priyanka

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With the increase of millions of users on Internet day by day, it is very essential to maintain highly reliable and secured data communication between various corporations. Although there are various traditional security imparting techniques such as antivirus software, password protection, data encryption, biometrics and firewall etc. But still network security has become the main issue in various leading companies. So IDSs have become an essential component in terms of security, as it can detect various network attacks and respond quickly to such occurrences. IDSs are used to detect unauthorized access to a computer system. This paper describes various intrusion detection techniques using GA approach. The intrusion detection problem has become a challenging task due to the conception of miscellaneous computer networks under various vulnerabilities. Thus the damage caused to various organizations by malicious intrusions can be mitigated and even be deterred by using this powerful tool.

Keywords: genetic algorithm (GA), intrusion detection system (IDS), dataset, network security

Procedia PDF Downloads 269

Authors: Aftab Ahmed, Ghulam Mehboob

Abstract:

The object of presentation is to highlight the importance of condition which is a very rare genetic disorder although Paget’s disease is common but its juvenile type is very rare and a late presentation due to very slow onset and lack of earlier standard management. We present a case of 25 years old male with a chronic history of bone pain and a slow onset of mild swelling, later on diagnosed as juvenile Paget disease of bone. Rarity of this condition with inaccessibility for standard health treatment can lead to a significant delay in presentation and its management. There have been 50 reported cases worldwide according to Genetic Home Reference. There is increased osteoclastic activity along with osteoblastic activity related to gene alteration and osteoprotegrin deficiency. Morbidity of disease is very significant which lead children to become immobilize.

Keywords: juvenile, Paget’s disease, bone, Northern Area of Pakistan

Procedia PDF Downloads 302

Authors: Parker Townes, Prabdeep Panesar, Chunlin Liu, Soo Youn Lee, Dan Devoe, Paul D. Arnold, Jennifer Crosbie, Russell Schachar

Abstract:

Attention-deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) are impairing childhood neurodevelopmental disorders with problems in executive functions. Executive functions are higher-level mental processes essential for daily functioning and goal attainment. There is genetic and neural overlap between ADHD and ASD. The aim of this meta-analysis was to evaluate if pediatric ASD and ADHD have distinct executive function profiles. This review was completed following Cochrane guidelines. Fifty-eight articles were identified through database searching, followed by a blinded screening in duplicate. A meta-analysis was performed for all task performance metrics evaluated by at least two articles. Forty-five metrics from 24 individual tasks underwent analysis. No differences were found between youth with ASD and ADHD in any domain under direct comparison. However, individuals with ASD and ADHD exhibited deficient attention, flexibility, visuospatial abilities, working memory, processing speed, and response inhibition compared to controls. No deficits in planning were noted in either disorder. Only 11 studies included a group with comorbid ASD+ADHD, making it difficult to determine whether common executive function deficits are a function of comorbidity. Further research is needed to determine if comorbidity accounts for the apparent commonality in executive function between ASD and ADHD.

Keywords: autism spectrum disorder, ADHD, neurocognition, executive function, youth

Procedia PDF Downloads 60

Authors: Talaat Ahmed, Amna Babssail

Abstract:

Mangroves are evergreen trees and grow along the coastal areas of Qatar. The largest and oldest area of mangroves can be found around Al-Thakhira and Al-Khor. Other mangrove areas originate from fairly recent plantings by the government, although unfortunately the picturesque mangrove lake in Al-Wakra has now been uprooted. Avicinnia marina is the predominant mangrove species found in the region. Mangroves protect and stabilize low lying coastal land, and provide protection and food sources for estuarine and coastal fishery food chains. They also serve as feeding, breeding and nursery grounds for a variety of fish, crustaceans, reptiles, birds and other wildlife. A total of 21 individuals of A. marina, representing seven diverse Natural and artificial populations, were sampled throughout its range in Qatar. Leaves from 2-3 randomly selected trees at each location were collected. The locations are as follows: Al-Rawis, Ras-Madpak, Fuwairt, Summaseima, Al-khour, AL-Mafjar and Zekreet. Total genomic DNA was extracted using commercial DNeasy Plant System (Qiagen, Inc., Valencia, CA) kit to be used for genetic diversity analysis. Total of 12 (Inter-Simple Sequence Repeat) ISSR primers were used to amplify DNA fragments using genomic DNA. The 12 ISSR primers amplified polymorphic bands among mangrove samples in different areas as well as within each area indicating the existing of variation within each area and among the different areas of mangrove in Qatar. The results could characterize Avicinnia marina populations exist in different areas of Qatar and establish DNA fingerprint documentations for mangrove population to be used in further studies. Moreover, existing of genetic variation within and among Avicinnia marina populations is a strong indication for the ability of such populations to adapt different environmental conditions in Qatar. This study could be a warning to save mangrove in Qatar and save the environment as well.

Keywords: DNA fingerprint, Avicinnia marina, genetic analysis, Qatar

Procedia PDF Downloads 372

Authors: Fuad M. Alkoot

Abstract:

DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: biometrics, genetic data, identity verification, k nearest neighbor

Procedia PDF Downloads 229

Authors: Şeyma Özçirak Ergün, Ergün Şakalar, Emrah Yalazi̇, Nebahat Şahi̇n

Abstract:

Food irradiation is a usage of exposing food to ionising radiation (IR) such as gamma rays. IR has been used to decrease the number of harmful microorganisms in the food such as spices. Excessive usage of IR can cause damage to both food and people who consuming food. And also it causes to damages on food DNA. Generally, IR detection techniques were utilized in literature for spices are Electron Spin Resonance (ESR), Thermos Luminescence (TL). Storage creates negative effect on IR detection method then analyses of samples have been performed without storage in general. In the experimental part, red pepper (Capsicum annuum) and mint (Mentha piperita) as spices were exposed to 0, 0.272, 0.497, 1.06, 3.64, 8.82, and 17.42 kGy ionize radiation. ESR was applied to samples irradiated. DNA isolation from irradiated samples was performed using GIDAGEN Multi Fast DNA isolation kit. The DNA concentration was measured using a microplate reader spectrophotometer (Infinite® 200 PRO-Life Science–Tecan). The concentration of each DNA was adjusted to 50 ng/µL. Genomic DNA was imaged by UV transilluminator (Gel Doc XR System, Bio-Rad) for the estimation of genomic DNA bp-fragment size after IR. Thus, agarose gel profiles of irradiated spices were obtained to determine the change of band profiles. Besides, samples were examined at three different time periods (0, 3, 6 months storage) to show the feasibility of developed method. Results of gel electrophoresis showed especially degradation of DNA of irradiated samples. In conclusion, this study with gel electrophoresis can be used as a basis for the identification of the dose of irradiation by looking at degradation profiles at specific amounts of irradiation. Agarose gel results of irradiated samples were confirmed with ESR analysis. This method can be applied widely to not only food products but also all biological materials containing DNA to predict radiation-induced damage of DNA.

Keywords: DNA, electrophoresis, gel electrophoresis, ionizeradiation

Procedia PDF Downloads 235

Authors: I. Boroňová, J. Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, S. Mačeková, J. Poráčová, M. M. Blaščáková

Abstract:

Osteoporosis is a common multifactorial disease with a strong genetic component characterized by reduced bone mass and increased risk of fractures. Genetic factors play an important role in the pathogenesis of osteoporosis. The aim of our study was to identify the genotype and allele distribution of T245G polymorphism in OPG gene in Slovak postmenopausal women. A total of 200 unrelated Slovak postmenopausal women with diagnosed osteoporosis and 200 normal controls were genotyped for T245G (rs3134069) polymorphism of OPG gene. Genotyping was performed using the Custom Taqman®SNP Genotyping assays. Genotypes and alleles frequencies showed no significant differences (p=0.5551; p=0.6022). The results of the present study confirm the importance of T245G polymorphism in OPG gene in the pathogenesis of osteoporosis.

Keywords: OPG gene, T245G polymorphism, osteoporosis, T245G polymorphism, real-time PCR

Procedia PDF Downloads 387

Authors: Abdurrahim Guler

Abstract:

Immigrants who came to a new country experience some socio-cultural difficulties which are different from theirs. The study aims to investigate how Syrian Refugees manage their life in Turkey and the relationship between acculturation profiles and demographic background of Syrian refugees who came to Turkey after civil war has intensified in Syria. Data are collected from 280 adult Syrian refugees who were born in Syria. The study adopts bi-dimensional acculturation approach stating that both heritage and dominant host cultures can live together. Results suggest that demographic backgrounds, religion, and religiosity are significantly linked to both heritage and dominant host culture. Syrian refugees who are not affiliated with Islam are found to significantly preserve their ethnic/heritage culture. Generally, Syrian refugees are more willing to integrate Turkish society but not to assimilate. The results also confirmed acculturation process as a bi-dimensional, not a zero-sum game since we found a significant positive correlation between the heritage and the dominant host cultures which assume the independence and orthogonal of involvements in the dominant host and heritage cultures.

Keywords: acculturation, demographic backgrounds, heritage culture, religion, Syrian refugees

Procedia PDF Downloads 205