Search results for: differentially expressed genes

Authors: Yanju Zhang, Joost M. Woltering, Fons J. Verbeek

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It has been established that microRNAs (miRNAs) play an important role in gene expression by post-transcriptional regulation of messengerRNAs (mRNAs). However, the precise relationships between microRNAs and their target genes in sense of numbers, types and biological relevance remain largely unclear. Dissecting the miRNA-target relationships will render more insights for miRNA targets identification and validation therefore promote the understanding of miRNA function. In miRBase, miRanda is the key algorithm used for target prediction for Zebrafish. This algorithm is high-throughput but brings lots of false positives (noise). Since validation of a large scale of targets through laboratory experiments is very time consuming, several computational methods for miRNA targets validation should be developed. In this paper, we present an integrative method to investigate several aspects of the relationships between miRNAs and their targets with the final purpose of extracting high confident targets from miRanda predicted targets pool. This is achieved by using the techniques ranging from statistical tests to clustering and association rules. Our research focuses on Zebrafish. It was found that validated targets do not necessarily associate with the highest sequence matching. Besides, for some miRNA families, the frequency of their predicted targets is significantly higher in the genomic region nearby their own physical location. Finally, in a case study of dre-miR-10 and dre-miR-196, it was found that the predicted target genes hoxd13a, hoxd11a, hoxd10a and hoxc4a of dre-miR- 10 while hoxa9a, hoxc8a and hoxa13a of dre-miR-196 have similar characteristics as validated target genes and therefore represent high confidence target candidates.

Keywords: MicroRNA targets validation, microRNA-target relationships, dre-miR-10, dre-miR-196.

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Authors: Frank Emmert-Streib, Matthias Dehmer

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Inferring the network structure from time series data is a hard problem, especially if the time series is short and noisy. DNA microarray is a technology allowing to monitor the mRNA concentration of thousands of genes simultaneously that produces data of these characteristics. In this study we try to investigate the influence of the experimental design on the quality of the result. More precisely, we investigate the influence of two different types of random single gene perturbations on the inference of genetic networks from time series data. To obtain an objective quality measure for this influence we simulate gene expression values with a biologically plausible model of a known network structure. Within this framework we study the influence of single gene knock-outs in opposite to linearly controlled expression for single genes on the quality of the infered network structure.

Keywords: Dynamic Bayesian networks, microarray data, structure learning, Markov chain Monte Carlo.

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Authors: Jafar Ahmadi, Nafiseh Noormohammadi, Sedigheh Fabriki Ourang

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GRF, Growth regulating factor, genes encode a novel class of plant-specific transcription factors. The GRF proteins play a role in the regulation of cell numbers in young and growing tissues and may act as transcription activations in growth and development of plants. Identification of GRF genes and their expression are important in plants to performance of the growth and development of various organs. In this study, to better understanding the structural and functional differences of GRFs family, 45 GRF proteins sequences in A. thaliana, Z. mays, O. sativa, B. napus, B. rapa, H. vulgare and S. bicolor, have been collected and analyzed through bioinformatics data mining. As a result, in secondary structure of GRFs, the number of alpha helices was more than beta sheets and in all of them QLQ domains were completely in the biggest alpha helix. In all GRFs, QLQ and WRC domains were completely protected except in AtGRF9. These proteins have no trans-membrane domain and due to have nuclear localization signals act in nuclear and they are component of unstable proteins in the test tube.

Keywords: Domain, Gene Family, GRF, Motif.

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Authors: S. Bag, S. Ramaiah, P. Anitha, K. M. Kumar, P. Lavanya, V. Sivasakhthi, A. Anbarasu

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Gene networks present a graphical view at the level of gene activities and genetic functions and help us to understand complex interactions in a meaningful manner. In the present study, we have analyzed the gene interaction of PPAR-γ (peroxisome proliferator-activated receptor gamma) by search tool for retrieval of interacting genes. We find PPAR-γ is highly networked by genetic interactions with 10 genes: RXRA (retinoid X receptor, alpha), PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), NCOA1 (nuclear receptor coactivator 1), NR0B2 (nuclear receptor subfamily 0, group B, member 2), HDAC3 (histone deacetylase 3), MED1 (mediator complex subunit 1), INS (insulin), NCOR2 (nuclear receptor co-repressor 2), PAX8 (paired box 8), ADIPOQ (adiponectin) and it augurs well for the fact that obesity and several other metabolic disorders are inter related.

Keywords: Gene networks, NCOA1, PPARγ, PPARGC1A, RXRA.

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Authors: Gee-Cheol Kim, Sang-Hoon Lee, Joo-Won Kang

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In the stadium structure, the significant dynamic responses such as resonance or similar behavior can be occurred by spectator rhythmical activities. Thus, accurate analysis and precise investigation of stadium structure that is subjected to dynamic loads are required for practical design and serviceability check of stadium structures. Moreover, it is desirable to measure and analyze the dynamic loads of spectator activities because these dynamic loads can not be easily expressed in numerical formula. In this study, various dynamic loads induced by spectator movements are measured and analyzed. These dynamic loads induced by spectators movement of stadium structure can be classified into the impact load and the periodic load. These dynamic loads can be expressed as Fourier harmonic load. And, these dynamic loads could be applied for the accurate vibration analysis of a stadium structure.

Keywords: stadium structure, spectator rhythmical activities, vibration analysis.

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Authors: Habibis Saleh, Ishak Hashim

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Conjugate natural convection in a differentially heated square enclosure containing a polygon shaped object is studied numerically in this article. The effect of various polygon types on the fluid flow and thermal performance of the enclosure is addressed for different thermal conductivities. The governing equations are modeled and solved numerically using the built-in finite element method of COMSOL software. It is found that the heat transfer rate remains stable by varying the polygon types.

Keywords: Natural convection, Polygon object, COMSOL

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Authors: O. Grinchuk, E. Motakis, V. Kuznetsov

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Sense-antisense gene pair (SAGP) is a pair of two oppositely transcribed genes sharing a common region on a chromosome. In the mammalian genomes, SAGPs can be organized in more complex sense-antisense gene architectures (CSAGA) in which at least one gene could share loci with two or more antisense partners. Many dozens of CSAGAs can be found in the human genome. However, CSAGAs have not been systematically identified and characterized in context of their role in human diseases including cancers. In this work we characterize the structural-functional properties of a cluster of 5 genes –TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199, termed TNFAIP1 / POLDIP2 module. This cluster is organized as CSAGA in cytoband 17q11.2. Affymetrix U133A&B expression data of two large cohorts (410 atients, in total) of breast cancer patients and patient survival data were used. For the both studied cohorts, we demonstrate (i) strong and reproducible transcriptional co-regulatory patterns of genes of TNFAIP1/POLDIP2 module in breast cancer cell subtypes and (ii) significant associations of TNFAIP1/POLDIP2 CSAGA with amplification of the CSAGA region in breast cancer, (ii) cancer aggressiveness (e.g. genetic grades) and (iv) disease free patient-s survival. Moreover, gene pairs of this module demonstrate strong synergetic effect in the prognosis of time of breast cancer relapse. We suggest that TNFAIP1/ POLDIP2 cluster can be considered as a novel type of structural-functional gene modules in the human genome.

Keywords: Sense-antisense gene pair, complex genome architecture, TMEM97, IFT20, TNFAIP1, POLDIP2, TMEM199, 17q11.2, breast cancer, transcription regulation, survival analysis, prognosis.

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Authors: Anna Camille V. Flores

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Comics in the Philippines has taken on many uses for the Filipino people. They have been sources of entertainment, education, and political and social commentaries. History has been witnessed to the rise and fall of Philippine comics but the 21^st century is seeing a revival of the medium and the industry. It is within this context that an inquiry about Filipino identity is situated. Employing the analytical framework of postcolonialism, particularly Homi K. Bhabha’s concepts of Hybridity and the Third Space, this study analyzes three contemporary Philippine comics, Trese, Filipino Heroes League, and Dead Balagtas. The study was able to draw three themes that represent how Filipinos inhabit hybrid worlds and hybridized identities. First, the third space emerged through the use of hybrid worlds in the comics. Second, (re)imagined communities are established through the use of intertextual signifiers. Third, (re)negotiated identities are expressed through visual and narrative devices such as the use of Philippine mythology, historical and contemporary contexts, and language. In conclusion, comics can be considered as Third Space where these identities have the agency and opportunity to be expressed and represented.

Keywords: Comics, hybridity and third space, Philippine comics, postcolonialism.

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Authors: C. Juntarasaid, T. Pulngern, S. Chucheepsakul

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A formulation of postbuckling analysis of end supported rods under self-weight has been presented by the variational method. The variational formulation involving the strain energy due to bending and the potential energy of the self-weight, are expressed in terms of the intrinsic coordinates. The variational formulation is accomplished by introducing the Lagrange multiplier technique to impose the boundary conditions. The finite element method is used to derive a system of nonlinear equations resulting from the stationary of the total potential energy and then Newton-Raphson iterative procedure is applied to solve this system of equations. The numerical results demonstrate the postbluckled configurations of end supported rods under self-weight. This finite element method based on variational formulation expressed in term of intrinsic coordinate is highly recommended for postbuckling analysis of end-supported rods under self-weight.

Keywords: Variational method, postbuckling, finite element method, intrinsic coordinate.

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Authors: M. Pandi, K. Premalatha

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A DNA microarray technology is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. It is handled by clustering which reveals the natural structures and identifying the interesting patterns in the underlying data. In this paper, gene based clustering in gene expression data is proposed using Cuckoo Search with Differential Evolution (CS-DE). The experiment results are analyzed with gene expression benchmark datasets. The results show that CS-DE outperforms CS in benchmark datasets. To find the validation of the clustering results, this work is tested with one internal and one external cluster validation indexes.

Keywords: DNA, Microarray, genomics, Cuckoo Search, Differential Evolution, Gene expression data, Clustering.

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Authors: Guyue Zhu, Liangping Hong

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Chinese overall urban design faces a large number of problems such as the neglect of urban characteristics, generalization of content, and difficulty in implementation. Focusing on these issues, this paper proposes the main points of shaping urban characteristics in overall urban design: focuses on core problems in city function and scale, landscape pattern, historical culture, social resources and modern city style and digs the urban characteristic genes. Then, we put forward “core problem location and characteristic gene enhancement” as a kind of overall urban design technical method. Firstly, based on the main problems in urban space as a whole, for the operability goal, the method extracts the key genes and integrates into the multi-dimension system in a targeted manner. Secondly, hierarchical management and guidance system is established which may be in line with administrative management. Finally, by converting the results, action plan is drawn up that can be dynamically implemented. Based on the above idea and method, a practical exploration has been performed in the case of Xiangyang central city.

Keywords: City characteristics, overall urban design, planning implementation, Xiangyang central city.

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Authors: B. Fersadou, H. Kahalerras

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This work deals with the problem of MHD mixed convection in a completely porous and differentially heated vertical channel. The model of Darcy-Brinkman-Forchheimer with the Boussinesq approximation is adopted and the governing equations are solved by the finite volume method. The effects of magnetic field and buoyancy force intensities are given by the Hartmann and Richardson numbers respectively, as well as the Joule heating represented by Eckert number on the velocity and temperature fields, are examined. The main results show an augmentation of heat transfer rate with the decrease of Darcy number and the increase of Ri and Ha when Joule heating is neglected.

Keywords: Heat sources, magnetic field, mixed convection, porous channel.

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Authors: Rosarin Rujananon, Poonsuk Prasertsan, Amornrat Phongdara, Tanate Panrat, Jibin Sun, Sugima Rappert, An-Ping Zeng

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In this study, a synthetic pathway was created by assembling genes from Clostridium butyricum and Escherichia coli in different combinations. Among the genes were dhaB1 and dhaB2 from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt) and its activator (GDHtAc), respectively, involved in the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene from E.coli BL21 was also included which codes for an NADPHdependent 1,3-propanediol oxidoreductase isoenzyme (PDORI) reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling analysis indicated that the conformation of fusion protein of YQHD and DHAB1 was favorable for direct molecular channeling of the intermediate 3-HPA. According to the simulation results, the yqhD and dhaB1 gene were assembled in the upstream of dhaB2 to express a fusion protein, yielding the recombinant strain E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing the recombinant enzymes simultaneously but in a non-fusion mode. This is the first report using a gene fusion approach to enhance the biological conversion of glycerol to the value added compound 1,3- PD.

Keywords: Recombinant E.coli, 1, 3-propanediol, glycerol, fusion protein.

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Authors: Minsoo Lee, Yun-mi Kim, Yearn Jeong Kim, Yoon-kyung Lee, Hyejung Yoon

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Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.

Keywords: Ant colony system, biological data, clustering, DNA chip.

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Authors: Bolanle F. Oladejo, Victor T. Odumuyiwa, Amos A. David

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Knowledge is attributed to human whose problemsolving behavior is subjective and complex. In today-s knowledge economy, the need to manage knowledge produced by a community of actors cannot be overemphasized. This is due to the fact that actors possess some level of tacit knowledge which is generally difficult to articulate. Problem-solving requires searching and sharing of knowledge among a group of actors in a particular context. Knowledge expressed within the context of a problem resolution must be capitalized for future reuse. In this paper, an approach that permits dynamic capitalization of relevant and reliable actors- knowledge in solving decision problem following Economic Intelligence process is proposed. Knowledge annotation method and temporal attributes are used for handling the complexity in the communication among actors and in contextualizing expressed knowledge. A prototype is built to demonstrate the functionalities of a collaborative Knowledge Management system based on this approach. It is tested with sample cases and the result showed that dynamic capitalization leads to knowledge validation hence increasing reliability of captured knowledge for reuse. The system can be adapted to various domains.

Keywords: Actors' communication, knowledge annotation, recursive knowledge capitalization, visualization.

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Authors: Zhi-Wei Zheng, Zhong-Qi Liu, Jia-Ling Qiu, Shan-Qing Guo, Zhong-Wei Jia, Chun Hao

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Objectives: The purpose of this study was to understand and examine the association between diurnal mood variation and sexual/health-related status among men who have sex with men (MSM) using data from MSM Chinese Twitter messages. The study consists of 843,745 postings of 377,610 MSM users located in Guangdong that were culled from the MSM Chinese Twitter App. Positive affect, negative affect, sexual related behaviors, and health-related status were measured using the Simplified Chinese Linguistic Inquiry and Word Count. Emotions, including joy, sadness, anger, fear, and disgust were measured using the Weibo Basic Mood Lexicon. A positive sentiment score and a positive emotions score were also calculated. Linear regression models based on a permutation test were used to assess associations between affective states and sexual/health-related status. In the results, 5,871 active MSM users and their 477,374 postings were finally selected. MSM expressed positive affect and joy at 8 a.m. and expressed negative affect and negative emotions between 2 a.m. and 4 a.m. In addition, 25.1% of negative postings were directly related to health and 13.4% reported seeking social support during that sensitive period. MSM who were senior, educated, overweight or obese, self-identified as performing a versatile sex role, and with less followers, more followers, and less chat groups mainly expressed more negative affect and negative emotions. MSM who talked more about sexual-related behaviors had a higher positive sentiment score (β=0.29, p < 0.001) and a higher positive emotions score (β = 0.16, p < 0.001). MSM who reported more on their health status had a lower positive sentiment score (β = -0.83, p < 0.001) and a lower positive emotions score (β = -0.37, p < 0.001). The study concluded that psychological intervention based on an app for MSM should be conducted, as it may improve mental health.

Keywords: Affect, men who have sex with men, sexual-related behaviors, health-related status, social media.

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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: N. Umasuthan, S. D. N. K. Bathige, W. S. Thulasitha, I. Whang, J. Lee

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The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1^st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure.In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution.A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFkB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.

Keywords: MyD88, Innate immunity, Flagellin, Genomic analysis.

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Authors: Nicolae Bold, Daniel Nijloveanu

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The idea of cropping-system is a method used by farmers. It is an environmentally-friendly method, protecting the natural resources (soil, water, air, nutritive substances) and increase the production at the same time, taking into account some crop particularities. The combination of this powerful method with the concepts of genetic algorithms results into a possibility of generating sequences of crops in order to form a rotation. The usage of this type of algorithms has been efficient in solving problems related to optimization and their polynomial complexity allows them to be used at solving more difficult and various problems. In our case, the optimization consists in finding the most profitable rotation of cultures. One of the expected results is to optimize the usage of the resources, in order to minimize the costs and maximize the profit. In order to achieve these goals, a genetic algorithm was designed. This algorithm ensures the finding of several optimized solutions of cropping-systems possibilities which have the highest profit and, thus, which minimize the costs. The algorithm uses genetic-based methods (mutation, crossover) and structures (genes, chromosomes). A cropping-system possibility will be considered a chromosome and a crop within the rotation is a gene within a chromosome. Results about the efficiency of this method will be presented in a special section. The implementation of this method would bring benefits into the activity of the farmers by giving them hints and helping them to use the resources efficiently.

Keywords: Genetic algorithm, chromosomes, genes, cropping, agriculture.

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Authors: Maysam Mard-Soltani, Mohamad Javad Rasaee, Saeed Khalili, Abdol Karim Sheikhi, Mehdi Hedayati

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Production of specific antibody responses against hTSH is a cumbersome process due to the high identity between the hTSH and the other members of the glycoprotein hormone family (FSH, LH and HCG) and the high identity between the human hTSH and host animals for antibody production. Therefore, two polyclonal antibodies were purified against two recombinant proteins. Four possible ELISA tests were designed based on these antibodies. These ELISA tests were checked against hTSH and other glycoprotein hormones, and their sensitivity and specificity were assessed. Bioinformatics tools were used to analyze the immunological properties. After the immunogen region selection from hTSH protein, c terminal of B hTSH was selected and applied. Two recombinant genes, with these cut pieces (first: two repeats of C terminal of B hTSH, second: tetanous toxin+B hTSH C terminal), were designed and sub-cloned into the pET32a expression vector. Standard methods were used for protein expression, purification, and verification. Thereafter, immunizations of the white New Zealand rabbits were performed and the serums of them were used for antibody titration, purification and characterization. Then, four ELISA tests based on two antibodies were employed to assess the hTSH and other glycoprotein hormones. The results of these assessments were compared with standard amounts. The obtained results indicated that the desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. The raised antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum. Among the four designed tests, the test in which the antibody against first protein was used as capture antibody, and the antibody against second protein was used as detector antibody did not show any hook effect up to 50 miu/l. Both proteins have the ability to induce highly sensitive and specific antibody responses against the hTSH. One of the antibody combinations of these antibodies has the highest sensitivity and specificity in hTSH detection.

Keywords: hTSH, bioinformatics, protein expression, cross reactivity.

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Authors: Kamolrat Turner, Boontuan Wattanakul

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Critical thinking and creativity are prerequisite skills for working professionals in the 21^st century. A survey conducted in 2014 at the Boromarajonani College of Nursing, Chon Buri, Thailand, revealed that these skills within students across all academic years was at a low to moderate level. An action research study was conducted to develop the EREC IF Model, a framework which includes the concepts of experience, reflection, engagement, culture and language, ICT, and flexibility and fun, to guide pedagogic activities for 75 sophomores of the undergraduate nursing science program at the college. The model was applied to all professional nursing courses. Prior to implementation, workshops were held to prepare lecturers and students. Both lecturers and students initially expressed their discomfort and pointed to the difficulties with the model. However, later they felt more comfortable, and by the end of the project they expressed their understanding and appreciation of the model. A survey conducted four and eight months after implementation found that the critical thinking and creativity skills of the sophomores were significantly higher than those recorded in the pretest. It could be concluded that the EREC IF model is efficient for fostering critical thinking and creativity skills in the undergraduate nursing science program. This model should be used for other levels of students.

Keywords: Critical thinking, creativity, undergraduate nursing students, EREC IF model.

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Authors: Abu Salim Mustafa

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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.

Keywords: Genomic regions of differences, Mycobacterium tuberculosis, peptides, serodiagnosis.

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Authors: Kobra Nalbandi, Bahram Baghban Kohnehrouz, Khalil Alami Saeed

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The low level of foreign genes expression in transgenic plants is a key factor that limits plant genetic engineering. Because of the critical regulatory activity of the promoters on gene transcription, they are studied extensively to improve the efficiency of the plant transgenic system. The strong constitutive promoters, such as CaMV 35S promoter and Ubiqutin 1 maize are usually used in plant biotechnology research. However the expression level of the foreign genes in all tissues is often undesirable. But using a strong seed-specific promoter to limit gene expression in the seed solves such problems. The purpose of this study is to isolate one of the seed specific promoters of Hordeum vulgare. So one of the common varieties of Hordeum vulgare in Iran was selected and their genomes extracted then the D-Hordein promoter amplified using the specific designed primers. Then the amplified fragment of the insert cloned in an appropriate vector and then transformed to E. coli. At last for the final admission of accuracy the cloned fragments sent for sequencing. Sequencing analysis showed that the cloned fragment DHPcontained motifs; like TATA box, CAAT-box, CCGTCC-box, AMYBOX1 and E-box etc., which constituted the seed-specific promoter activity. The results were compared with sequences existing in data banks. D-Hordein promoters of Alger has 99% similarity at 100 % coverage. The results also showed that D-Hordein promoter of barley and HMW promoter of wheat are too similar.

Keywords: Barley, Seed specific promoter, Hordein.

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

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Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: Nevila Alliu, Saimir Heta, Ilma Robo, Vera Ostreni

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Periodontitis as an oral pathology caused by specific bacterial flora functions as a focal infection for the onset and aggravation of arteriosclerosis. These two distant pathologies, since they affect organs at a distance from each other, communicate with each other with correlation at the level of markers of inflammation in the blood. Fluctuations in the level of fibrinogen in the blood, depending on the active or passive phase of the existing periodontitis, affect the promotion of arteriosclerosis. The study is of the brief communication article type with the aim to analyze the effect of non-surgical periodontal treatment on fluctuations in the level of fibrinogen in the blood. The reduction of fibrinogen's level in blood after non-surgical periodontal treatment of periodontitis in the patient's oral cavity, is a common consequence supported by literature sources. Also, the influence of a high amount of fibrinogen in blood on the occurrence of arteriosclerosis at the same patient, is also another important data that again rely on many sources of literature. Thromboembolism and arteriosclerosis, as risk factors expressed in clinical data, have temporary bacteremia in the blood, which can occur significantly and often between phases of non-surgical periodontal treatment of periodontitis, treatments performed with treatment phases and protocols of predetermined treatment. Arterial thromboembolism has a significant factor, such as high levels of fibrinogen in the blood, which are significantly reduced during the period of non-surgical periodontal treatment.

Keywords: Fibrinogen, refractory periodontitis, atherosclerosis, non-surgical, periodontal treatment.

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Authors: G. Rajamohan, N. Ramesh, P. Kumar

Abstract:

Experiments have been performed to investigate the radiation effects on mixed convection heat transfer for thermally developing airflow in vertical ducts with two differentially heated isothermal walls and two adiabatic walls. The investigation covers the Reynolds number Re = 800 to Re = 2900, heat flux varied from 256 W/m2 to 863 W/m2, hot wall temperature ranges from 27°C to 100 °C, aspect ratios 1 & 0.5 and the emissivity of internal walls are 0.05 and 0.85. In the present study, combined flow visualization was conducted to observe the flow patterns. The effect of surface temperature along the walls was studied to investigate the local Nusselt number variation within the duct. The result shows that flow condition and radiation significantly affect the total Nusselt number and tends to reduce the buoyancy condition.

Keywords: Mixed convection, vertical duct, thermally developing and radiation effects.

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Authors: Trisha Malhotra

Abstract:

Sentiment analysis is a recent field of study that computationally assesses the emotional nature of a body of text. To assess its test-validity, sentiment analysis was carried out on the emotional corpus of text from a personal 15-day mood diary. Self-reported mood scores varied more or less accurately with daily mood evaluation score given by the software. On further assessment, it was found that while sentiment analysis was good at assessing ‘global’ mood, it was not able to ‘locally’ identify and differentially score synonyms of various emotional words. It is further critiqued for treating the intensity of an emotion as universal across cultures. Finally, the software is shown not to account for emotional complexity in sentences by treating emotions as strictly positive or negative. Hence, it is posited that a better output could be two (positive and negative) affect scores for the same body of text.

Keywords: Analysis, data, diary, emotions, mood, sentiment.

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Authors: Nima Shakouri Masouleh, Razieh Bahraminezhad Jooneghani

Abstract:

The study investigated the educational implications that can be derived from the work of a variety of celebrated figures such as Piaget, Vygotsky, and Bruner that will be helpful in the field of language learning. However, the writer believed these views were previously expressed not full–fledged by Comenius who has been described by Howatt (1984) as a genius–the one that the history of language teaching can claim. And we owe to him more than anyone.

Keywords: restructuring, assimilation, equiliberation

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Authors: Mohamed Amine Belmiloud, Nord Eddine Sad Chemloul

Abstract:

In this study, we investigated numerically heat transfer by mixed convection coupled to radiation in a square cavity; the upper horizontal wall is movable. The purpose of this study is to see the influence of the emissivity ε and the varying of the Richardson number Ri on the variation of average Nusselt number Nu. The vertical walls of the cavity are differentially heated, the left wall is maintained at a uniform temperature higher than the right wall, and the two horizontal walls are adiabatic. The finite volume method is used for solving the dimensionless Governing Equations. Emissivity values used in this study are ranged between 0 and 1, the Richardson number in the range 0.1 to 10. The Rayleigh number is fixed to Ra=104 and the Prandtl number is maintained constant Pr=0.71. Streamlines, isothermal lines and the average Nusselt number are presented according to the surface emissivity. The results of this study show that the Richardson number Ri and emissivity ε affect the average Nusselt number.

Keywords: Numerical study, mixed convection, square cavity, wall emissivity, lid-driven.

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Authors: Chrysline Margus N. Piñol, Jenifer DP. De Maligaya, Ahl G. Balitaon

Abstract:

Stable nonzero populations without random deaths caused by the Verhulst factor (Verhulst-free) are a rarity. Majority either grow without bounds or die of excessive harmful mutations. To delay the accumulation of bad genes or diseases, a new environmental parameter Γ is introduced in the simulation. Current results demonstrate that stability may be achieved by setting Γ = 0.1. These steady states approach a maximum size that scales inversely with reproduction age.

Keywords: Aging, mutation accumulation, population dynamics.

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