Search results for: secondary structure elements

Authors: K. Tejasri, K. Suvarna Vani, S. Prathyusha, S. Ramya

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Proteins are chained sequences of amino acids which are brought together by the peptide bonds. Many varying formations of the chains are possible due to multiple combinations of amino acids and rotation in numerous positions along the chain. Protein structure prediction is one of the crucial goals worked towards by the members of bioinformatics and theoretical chemistry backgrounds. Among the four different structure levels in proteins, we emphasize mainly the secondary level structure. Generally, the secondary protein basically comprises alpha-helix and beta-sheets. Multi-class classification problem of data with disparity is truly a challenge to overcome and has to be addressed for the beta strands. Imbalanced data distribution constitutes a couple of the classes of data having very limited training samples collated with other classes. The secondary structure data is extracted from the protein primary sequence, and the beta-strands are predicted using suitable machine learning algorithms.

Keywords: proteins, secondary structure elements, beta-sheets, beta-strands, alpha-helices, machine learning algorithms

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Authors: Aakansha Gupta, Neha Vadnere, Tapasvi Soni, M. Anbarsi

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Protein secondary structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine and biotechnology. Some aspects of protein functions and genome analysis can be predicted by secondary structure prediction. This is used to help annotate sequences, classify proteins, identify domains, and recognize functional motifs. In this paper, we represent protein secondary structure as a mathematical model. To extract and predict the protein secondary structure from the primary structure, we require a set of parameters. Any constants appearing in the model are specified by these parameters, which also provide a mechanism for efficient and accurate use of data. To estimate these model parameters there are many algorithms out of which the most popular one is the EM algorithm or called the Expectation Maximization Algorithm. These model parameters are estimated with the use of protein datasets like RS126 by using the Bayesian Probabilistic method (data set being categorical). This paper can then be extended into comparing the efficiency of EM algorithm to the other algorithms for estimating the model parameters, which will in turn lead to an efficient component for the Protein Secondary Structure Prediction. Further this paper provides a scope to use these parameters for predicting secondary structure of proteins using machine learning techniques like neural networks and fuzzy logic. The ultimate objective will be to obtain greater accuracy better than the previously achieved.

Keywords: model parameters, expectation maximization algorithm, protein secondary structure prediction, bioinformatics

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Authors: Ghada Badr, Arwa Alturki

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The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: alignment, RNA secondary structure, pairwise, component-based, data mining

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Authors: Jamerson Felipe Pereira Lima, Jeane Cecília Bezerra de Melo

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The difficulty and cost related to obtaining of protein tertiary structure information through experimental methods, such as X-ray crystallography or NMR spectroscopy, helped raising the development of computational methods to do so. An approach used in these last is prediction of tridimensional structure based in the residue chain, however, this has been proved an NP-hard problem, due to the complexity of this process, explained by the Levinthal paradox. An alternative solution is the prediction of intermediary structures, such as the secondary structure of the protein. Artificial Intelligence methods, such as Bayesian statistics, artificial neural networks (ANN), support vector machines (SVM), among others, were used to predict protein secondary structure. Due to its good results, artificial neural networks have been used as a standard method to predict protein secondary structure. Recent published methods that use this technique, in general, achieved a Q3 accuracy between 75% and 83%, whereas the theoretical accuracy limit for protein prediction is 88%. Alternatively, to achieve better results, support vector machines prediction methods have been developed. The statistical evaluation of methods that use different AI techniques, such as ANNs and SVMs, for example, is not a trivial problem, since different training sets, validation techniques, as well as other variables can influence the behavior of a prediction method. In this study, we propose a prediction method based on artificial neural networks, which is then compared with a selected SVM method. The chosen SVM protein secondary structure prediction method is the one proposed by Huang in his work Extracting Physico chemical Features to Predict Protein Secondary Structure (2013). The developed ANN method has the same training and testing process that was used by Huang to validate his method, which comprises the use of the CB513 protein data set and three-fold cross-validation, so that the comparative analysis of the results can be made comparing directly the statistical results of each method.

Keywords: artificial neural networks, protein secondary structure, protein structure prediction, support vector machines

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Authors: Temami Oussama, Bessais Lakhdar, Hamadi Djamal, Abderrahmani Sifeddine

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The analysis of complex structures encourages the engineer to make simplifying assumptions, sometimes attempting the analysis of the whole structure as complex as it is, and it can be done using the finite element method (FEM). In the modeling of complex structures by finite elements, various elements can be used: beam element, membrane element, solid element, plates and shells elements. These elements formulated according to the classical formulation and do not generally share the same nodal degrees of freedom, which complicates the development of a compatible model. The compatibility of the elements with each other is often a difficult problem for modeling complicated structure. This compatibility is necessary to ensure the convergence. To overcome this problem, we have proposed finite elements with a rotational degree of freedom. The study used is based on the strain approach formulation with 2D and 3D formulation with different degrees of freedom at each node. For the comparison and confrontation of results; the finite elements available in ABAQUS/Standard are used.

Keywords: compatibility requirement, complex structures, finite elements, modeling, strain approach

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Authors: Karine B. de Oliveira, Carina F. Dorneles

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The structure level matching is the problem of combining elements of a structure, which can be represented as entities, classes, XML elements, web forms, and so on. This is a challenge due to large number of distinct representations of semantically similar structures. This paper describes a structure-based matching method applied to search for different representations in data sources, considering the similarity between elements of two structures and the data source context. Using real data sources, we have conducted an experimental study comparing our approach with our baseline implementation and with another important schema matching approach. We demonstrate that our proposal reaches higher precision than the baseline.

Keywords: context, data source, index, matching, search, similarity, structure

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Authors: Gelacio JuáRez-Luna, Daniel Enrique GonzáLez-RamíRez, Enrique Tenorio-Montero

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Frame elements coupled with springs elements are used for modelling the development of hinges in segmented tunnels, the spring elements modelled the rotational, transversal and axial failure. These spring elements are equipped with constitutive models to include independently the moment, shear force and axial force, respectively. These constitutive models are formulated based on damage mechanics and experimental test reported in the literature review. The mesh of the segmented tunnels was discretized in the software GID, and the nonlinear analyses were carried out in the finite element software ANSYS. These analyses provide the capacity curve of the primary and secondary lining of a segmented tunnel. Two numerical examples of segmented tunnels show the capability of the spring elements to release energy by the development of hinges. The first example is a segmental concrete lining discretized with frame elements loaded until hinges occurred in the lining. The second example is a tunnel with primary and secondary lining, discretized with a double ring frame model. The outer ring simulates the segmental concrete lining and the inner ring simulates the secondary cast-in-place concrete lining. Spring elements also modelled the joints between the segments in the circumferential direction and the ring joints, which connect parallel adjacent rings. The computed load vs displacement curves are congruent with numerical and experimental results reported in the literature review. It is shown that the modelling of a tunnel with primary and secondary lining with frame elements and springs provides reasonable results and save computational cost, comparing with 2D or 3D models equipped with smeared crack models.

Keywords: damage, hinges, lining, tunnel

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Authors: Lele Zhang, Hui Leng Choo, Alexander Konyukhov, Shuguang Li

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Finite Element (FE) model of simplified e-bike structure was generated by main frame with two tiers, which consisted of pipe, mass, beam, and shell elements (pipe 289, beam188, shell 181, shell 281, combin14, link11, mass21). These elements would be introduced and demonstrated using mathematical formulas. Based on coupling theory, constrain equations was proposed. Exporting all the parameters obtained from theory part, the connection stiffness matrix of the whole e-bike structure between each of these elements was detected.

Keywords: coupling theory, stiffness matrix, e-bike, finite element model

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Authors: Seyyed Abdollah Hojjati

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Review in the areas of secondary education; it is a kind of comparative requires very careful scrutiny in educational structure of different countries,In upcoming review of the basic structure of our educational system in Islamic republic of Iran with somedeveloped countries in the world, Analyzing of strengthsand weaknesses in main areas, A simple review of the above methods do not consider this particular community, Modifythe desired result can be expressed in the secondary school curriculum and academic guidance of under graduate students in a skill-driven and creativity growth, It not just improves the health and dynamism of this period and increases the secondary teachers' authority and the relationship between teacher and student in this course will be meaningful and attractive, But with reduced of false prosperity and guaranteed institutes and quizzes, areas will be provided for students to enjoy the feeling ofthe psychological comfort and to have the highest growth of creativity .

Keywords: comparative, curriculum of secondary education, curriculum, Iran, developed countries

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Authors: Mahmood Niroobakhsh

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This article deals with special structuralism approaches to explain a certain kind of social problem. Widespread presence of poverty is a reminder of deep-rooted unresolved problems of social relations. The expected role from an individual for the social system recognizes poverty derived from an interrelated social structure. By the time, enabled to act on his role in the course of social interaction, reintegration of the poor in society may take place. Poverty and housing type are reflections of the underlying social structure, primarily structure’s elements, systemic interrelations, and the overall strength or weakness of that structure. Poverty varies based on social structure in that the stronger structures are less likely to produce poverty.

Keywords: absolute poverty, relative poverty, social structure, urban poverty

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Authors: Verónica Diaz Quezada

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This research examines the teaching models used by secondary math teachers when teaching logarithmic, quadratic and exponential functions. For this, descriptive case studies have been carried out on 5 secondary teachers. These teachers have been chosen from 3 scientific-humanistic and technical schools, in Chile. Data have been obtained through non-participant class observation and the application of a questionnaire and a rubric to teachers. According to the results, the didactic model that prevails is the one that starts with an interactive strategy, moves to a more content-based structure, and ends with a reinforcement stage. Nonetheless, there is always influence from teachers, their methods, and the group of students.

Keywords: teaching models, math teachers, functions, secondary education

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Authors: Ankita Srivastava, Yogesh K. Garg

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Housing provides comforts and well being leading towards the quality of life. Earlier research had established that landscape elements enhance the residents’ quality of life through its significant experiences occur due to their presence in the housing. This paper tries to identify the preference of landscape elements that enhance residents’ quality of life living in the apartment. Hence, landscape elements that can be planned in the open spaces of housing and quality of life components were identified from the secondary data sources. Experts’ were asked to identify the quality of life components with respect to landscape elements. A questionnaire survey of residents’ living in the apartment housing in Bhopal, India was conducted. The statistical analysis of survey data facilitated to explore the preference of landscape elements for the quality of life in the apartment housing. The final ranking compiled from the experts’ opinion, residents’ perception as well as factor analysis results to have an insight of the preference of landscape elements for the quality of life living in the apartment. Preference of landscape elements present in the paper may provide an overview of planning for apartment housing that may be used by architects, planners and developers for enhancing residents’ quality of life.

Keywords: landscape elements, quality of life, residents, housing

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Authors: Mizam Doğan

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In service life; structures can be damaged if they are subjected to dead and live loads which are greater than design values. For preventing this case; possible loads must be correctly calculated, structure must be designed according to determined loads, and structure must not be used out of its function. If loading case of the structure changes when its function changes; it must be reinforced for continuing it is new function. Reinforcement is a process that is made by increasing the existing strengths of structural system elements of the structure as reinforced concrete walls, beams, and slabs. Reinforcement can be done by casting reinforced concrete, placing steel and fiber structural elements. In this paper, reinforcing of columns and slabs of a structure of which function is changed is studied step by step. This reinforcement is made for increasing vertical and lateral load carrying capacity of the building. Not for repairing damaged structural system.

Keywords: strengthening, RC slabs, seismic load, steel beam, structural irregularity

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Authors: Oossama Tabbabi, Mondher Labidi, Fethi Choubani, J. David

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Modern wireless communication systems require compact design, low cost and simple structure antennas to insure reliability, agility, and high efficiency characteristics. This paper presents a microstrip antenna array designed for 8 GHz applications. To reduce the mutual coupling effects, a Z shape metamaterial structure was imprinted in the microstrip antenna array composed of two elements. Simulation results show the improvement of mutual coupling by adding Z shape metamaterial structure to the antenna substrate. The proposed structure reduces mutual coupling by 19 dB. The simulation has been performed by using HFSS simulator.

Keywords: antenna array, compact design, modern wireless communication, mutual coupling effects

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Authors: Mahyar Maali, Merve Sagiroglu

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Steel, which is one of the base materials we prefer in the building construction, is the material with the highest ratio to weight of carrying capacity. Due to the carrying capacity, lighter and better quality steel in smaller sections and sizes has recently been used as a frame system in cold-formed steel structures. While light steel elements used as secondary frame elements during the past, they have nowadays started to be preferred as the main frame in low/middle story buildings and detached houses with advantages such as quick and easy installation, time-saving, and small amount of scrap. It is also economically ideal because the weight of structure is lighter than other steel profiles. Structural performances and failure modes of cold-formed structures are different from conventional ones due to their thin-walled structures. One of the most important elements of light steel structures to ensure stability is the connection. The screwed connections, which have self-drilling properties with special drilling tools, are widely used in the installation of cold-formed profiles. The length of the screw is selected according to the total thickness of the elements after the screw thickness is determined according to the elements of connections. The thickness of the material depends on the length of the drilling portion at the end of the screw. The shear tests of plates connected with self-drilling screws are carried out depending on the screw length, and their failure modes were evaluated in this study.

Keywords: cold-formed steel, screwed connection, connection, screw length

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Authors: P. P. Woyciechowski

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Calculation of the carbon footprint of cement concrete is a complex process including consideration of the phase of primary life (components and concrete production processes, transportation, construction works, maintenance of concrete structures) and secondary life, including demolition and recycling. Taking into consideration the effect of concrete carbonation can lead to a reduction in the calculated carbon footprint of concrete. In this paper, an example of CO₂ balance for small bridge elements made of Portland cement reinforced concrete was done. The results include the effect of carbonation of concrete in a structure and of concrete rubble after demolition. It was shown that important impact of carbonation on the balance is possible only when rubble carbonation is possible. It was related to the fact that only the sequestration potential in the secondary phase of concrete life has significant value.

Keywords: carbon footprint, balance of carbon dioxide in nature, concrete carbonation, the sequestration potential of concrete

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Authors: Ali Aghazadegan, Ali Shokri, Julia Mullarney

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River confluences are areas where there is a lot of mixing, which is often caused by the formation of shear layers and helical motions. The hydrodynamics of secondary circulation at river confluences with low flow discharge ratios and a 90° junction angle are investigated in this study. The analysis is based on Delft 3D modelling, which includes a three-dimensional time-averaged velocity field, turbulence, and water surface levels that have been validated using laboratory data. Confluence structure was characterized by shear layer, secondary circulation, and mixing at the junction and post confluence channel. This study analysis formation of the shear layer by generation of secondary circulations in variation discharge ratios. The values of streamwise, cross-wise, and vertical components are used to estimate the secondary circulation observed within and downstream of the tributary mouth. These variables are estimated for three horizontal planes at Z = [0.14; 0.07; 0.02] and for eight cross-sections at X = [-0.1; 0.00; 0.10; 0.2; 0.30; 0.4; 0.5; 0.6] within a range of 0.05 Y 0.30.

Keywords: river confluence, shear layer, secondary circulation, hydrodynamics

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Authors: H. Gokdemir

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All structures are subject to vertical and lateral loads. Under these loads, structures make deformations and deformation values of structural elements mustn't exceed their capacity for structural stability. Especially, lateral loads cause critical deformations because of their random directions and magnitudes. Wind load is one of the lateral loads which can act in any direction and any magnitude. Although wind has nearly no effect on reinforced concrete structures, it must be considered for steel structures, roof systems and slender structures like minarets. Therefore, every structure must be able to resist wind loads acting parallel and perpendicular to any side. One of the effective methods for resisting lateral loads is assembling cross steel elements between columns which are called as wind bracing. These cross elements increases lateral rigidity of a structure and prevent exceeding of deformation capacity of the structural system. So, this means cross elements are also effective in resisting earthquake loads too. In this paper; Effects of wind bracing to earthquake resistance of structures are studied. Structure models (with and without wind bracing) are generated and these models are solved under both earthquake and wind loads with different seismic zone parameters. It is concluded by the calculations that; in low-seismic risk zones, wind bracing can easily resist earthquake loads and no additional reinforcement for earthquake loads is necessary. Similarly; in high-seismic risk zones, earthquake cross elements resist wind loads too.

Keywords: wind bracings, earthquake, steel structures, vertical and lateral loads

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Authors: Djamal Hamadi, Oussama Temami, Abdallah Zatar, Sifeddine Abderrahmani

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The analysis and design of thin shell structures is a topic of interest in a variety of engineering applications. In structural mechanics problems the analyst seeks to determine the distribution of stresses throughout the structure to be designed. It is also necessary to calculate the displacements of certain points of the structure to ensure that specified allowable values are not exceeded. In this paper a comparative study between displacement and strain based finite elements applied to the analysis of some thin shell structures is presented. The results obtained from some examples show the efficiency and the performance of the strain based approach compared to the well known displacement formulation.

Keywords: displacement formulation, finite elements, strain based approach, shell structures

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Authors: Quoc Van Nguyen, Behzad Fatahi, Aslan S. Hokmabadi

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Performance based seismic design is a modern approach to earthquake-resistant design shifting emphasis from “strength” to “performance”. Soil-Structure Interaction (SSI) can influence the performance level of structures significantly. In this paper, a fifteen storey moment resisting frame sitting on a shallow foundation (footing) with different sizes is simulated numerically using ABAQUS software. The developed three dimensional numerical simulation accounts for nonlinear behaviour of the soil medium by considering the variation of soil stiffness and damping as a function of developed shear strain in the soil elements during earthquake. Elastic-perfectly plastic model is adopted to simulate piles and structural elements. Quiet boundary conditions are assigned to the numerical model and appropriate interface elements, capable of modelling sliding and separation between the foundation and soil elements, are considered. Numerical results in terms of base shear, lateral deformations, and inter-storey drifts of the structure are compared for the cases of soil-structure interaction system with different foundation sizes as well as fixed base condition (excluding SSI). It can be concluded that conventional design procedures excluding SSI may result in aggressive design. Moreover, the size of the foundation can influence the dynamic characteristics and seismic response of the building due to SSI and should therefore be given careful consideration in order to ensure a safe and cost effective seismic design.

Keywords: soil-structure-interaction, seismic response, shallow foundation, abaqus, rayleigh damping

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Authors: Cory A. Bennett

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Teaching and learning through the use of discourse support students’ conceptual understanding by attending to key concepts and relationships. One discourse structure used in primary classrooms is number talks wherein students mentally calculate, discuss, and reason about the appropriateness and efficiency of their strategies. In the secondary mathematics classroom, the mathematics understudy does not often lend itself to mental calculations yet learning to reason, and articulate reasoning, is central to learning mathematics. This qualitative case study discusses how one secondary school in the Middle East adapted the number talk protocol for secondary mathematics classrooms. Several challenges in implementing ‘reasoning talks’ became apparent including shifting current discourse protocols and practices to a more student-centric model, accurately recording and probing student thinking, and specifically attending to reasoning rather than computations.

Keywords: discourse, reasoning, secondary mathematics, teacher development

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Authors: Marianna De Almeida

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Greek secondary education is a highly selective system with regard to the access of students to Greek universities. Since access from elementary to lower secondary education and afterward to upper secondary education is rather liberal and almost free of selective mechanisms, the basic selection process comes after graduating from upper secondary school into play when students go through a highly selective process for university entry. This structure is responsible for the experience of extreme stress on the part of the candidates during a period of at least two years before the entrance examination leading to a radical change in students' everyday life routines. Instead of the school being an important agent for academic and psychological support, it seems that other agents, such as the informal private preparatory school and the student's families, take on the supportive role.

Keywords: stress, entrance examinations, family support, secondary education

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Authors: Daria Grechishnikova, Maria Poptsova

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Transposable elements play an important role in the evolution of various species from bacteria to human. Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs) are two major classes of retrotransposons that occupy a considerable part of any genome and their copy numbers can range form several hundreds to a million. Both LINEs and SINEs multiply through a copy-and-paste mechanism. LINEs encode proteins, which make them capable of self-propagation while SINEs are parasitic and require the machinery of LINEs to multiply. The mechanisms how LINE and SINE RNA is recognized by the LINE-encoded reverse transcriptase (RT) remain unclear. For some SINE-LINE pairs, it was shown that they share a common 3’-end with a stem-loop structure. Majority of the SINE-LINE pairs do not have a common 3’-end. Recently we have shown that in the human genome Alu-L1 pairs have structurally similar stem-loop structure at the 3’-end. Here we extended our analysis to a wide range of species and analyzed LINEs from 161 different species from Repbase and 217 SINE sequences from SINEBase. It appeared that all of the analyzed sequences contained stem-loop structures at the 3’-end. Here we conclude that it is very likely that a common evolutionary mechanism of transposon RNA recognition requires the presence of stem-loop structures at their 3’-end.

Keywords: LINE, SINE, mechanisms of retrotransposition, retrotransposons, stem-loop, stem-loop structures, transposons

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Authors: Lota Largavista

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This study entitled, ‘The Organizational Structure, Development Features, and Metadiscoursal Elements in the Expository Writing of Freshman College Writers’ aimed to examine essays written by college students. It seeks to examine the organizational structure and development features of the essays and describe their defining characteristics, the linguistic elements at both macrostructural and microstructural discourse levels and the types of textual and interpersonal metadiscourse markers that are employed in order to negotiate meanings with their prospective readers. The different frameworks used to analyze the essays include Toulmin’s ( 1984) model for argument structure, Olson’s ( 2003) three-part essay structure; Halliday and Matthiesen (2004) in Herriman (2011) notions of thematic structure, Danes (1974) thematic progression or method of development, Halliday’s (2004) concept of grammatical and lexical cohesion ;Hyland’s (2005) metadiscourse strategies; and Chung and Nation’s( 2003) four-step scale for technical vocabulary. This descriptive study analyzes qualitatively and quantitatively how freshman students generally express their written compositions. Coding of units is done to determine what linguistic features are present in the essays. Findings revealed that students’ expository essays observe a three-part structure having all three moves, the Introduction, the Body and the Conclusion. Stance assertion, stance support, and emerging moves/strategies are found to be employed in the essays. Students have more marked themes on the essays and also prefer constant theme progression as their method of development. The analysis of salient linguistic elements reveals frequently used cohesive devices and metadiscoursal strategies. Based on the findings, an instructional learning plan is being proposed. This plan is characterized by a genre approach that focuses on expository and linguistic conventions.

Keywords: metadiscourse, organization, theme progression, structure

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Authors: Verónica Díaz Quezada

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Despite the wide variety of educational resources on the market and the advances produced in the technological field, the practice of teaching continues to be supported mainly by textbooks. This article reports on descriptive research with qualitative methodology carried out on secondary school mathematics teachers in a region of Chile, in order to describe the use and the indicators of appreciation that teachers have on the textbooks distributed by the official body to public educational establishments. Data were collected through an open response opinion questionnaire. According to the results, among the texts available for the annual performance of their teaching work, the expository and technological books predominate, to the detriment of comprehensive books. The exhibition structure favors master expositions and repetitive exercises, while, with the technological structure, a productive exercise is attempted, proposing numerous applications with the intention of giving meaning to the different mathematical rules and procedures. In relation to the indicators of appreciation that teachers have regarding the use of mathematics textbooks, the suitability and quality of the teaching resources are verified as the most satisfying characteristic.

Keywords: mathematics, secondary school, teachers, textbooks

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Authors: Danny Barash

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Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

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Authors: M. Zain, Thaung H. Aung, Naveed Anwar

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During the service life, a structure may experience extreme loading conditions. The current study proposes a new methodology that covers the effect of uncertainty involved in gravity loadings on key structural elements of new and complex structures by emphasizing on a very realistic assumption that allows the 'Performance-Based Assessment' to be executed on the structure against the gravity loadings. The methodology does not require the complete removal of an element, instead, it permits the incremental reduction in the capacity of key structural elements and preserves the same stiffness of the member in each case of capacity loss. To demonstrate the application of the proposed methodology, a 13 story complex structure is selected that comprises of a diverse structural configuration. The results ensure the structural integrity against the applied gravity loadings, as well as the effectiveness of the proposed methodology.

Keywords: force-deformation relationship, gravity loading, incremental capacity reduction, multi-linear plastic link element, SAP2000, stiffness

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Authors: Natalya G. Filimonova, Mariya G. Ozerova, Irina N. Ermakova

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The long-term strategy of the economic development of Russia up to 2030 is based on the concept of sustainable growth. The determining factor of such development is complex changes in the economic system which may be achieved by making progressive changes in its structure. The structural changes determine the character and the direction of economic development, as well as they include all elements of this system without exception, and their regulated character ensures the most rapid aim achievement. This article has discussed the industrial structure of the agriculture in Russia. With the use of the system of indexes, the article has determined the directions, intensity, and speed of structural shifts. The influence of structural changes on agricultural production development has been found out. It is noticed that the changes in the industrial structure are synchronized with the changes in the organisation and economic structure. Efficiency assessment of structural changes allowed to trace the efficiency of structural changes and elaborate the main directions for agricultural policy improvement.

Keywords: Russian agricultural sectors, sectoral structure, organizational and economic structure, structural changes

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Authors: Janaki Rama Raju Patchamatla, Emani Pavan Kumar

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The idea of increasing the existing train speeds and introduction of the high-speed trains in India as a part of Vision-2020 is really challenging from both economic viability and technical feasibility. More than economic viability, technical feasibility has to be thoroughly checked for safe operation and execution. Trains moving at high speeds need a well-established firm and safe track thoroughly tested against vibration effects. With increased speeds of trains, the track structure and layered soil-structure interaction have to be critically assessed for vibration and displacements. Physical establishment of track, testing and experimentation is a costly and time taking process. Software-based modelling and simulation give relatively reliable, cost-effective means of testing effects of critical parameters like sleeper design and density, properties of track and sub-grade, etc. The present paper reports the applicability of infinite elements in reducing the unrealistic stress-wave reflections from so-called soil-structure interface. The influence of the infinite elements is quantified in terms of the displacement time histories of adjoining soil and the deformation pattern in general. In addition, the railhead response histories at various locations show that the numerical model is realistic without any aberrations at the boundaries. The numerical model is quite promising in its ability to simulate the critical parameters of track design.

Keywords: high speed railway track, finite element method, Infinite elements, vibration analysis, soil-structure interface

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Authors: J. Ramos, V. Gil, A. F. Torres

Abstract:

The nodular iron is a material that has shown great advantages respect to other materials (steel and gray iron) in the production of machine elements. The engineering industry, especially automobile, are potential users of this material. As it is known, the alloying elements modify the properties of steels and castings. Copper has been investigated as a structural modifier of nodular iron, but studies of its mechanical and tribological implications still need to be addressed for industrial use. With the aim of improving the mechanical properties of nodular iron, alloying elements (Mn, Si, and Cu) are added in order to increase their pearlite (or ferrite) structure according to the percentage of the alloying element. In this research (using induction furnace process) nodular iron with three different percentages of copper (residual, 0,5% and 1,2%) was obtained. Chemical analysis was performed by optical emission spectrometry and microstructures were characterized by Optical Microscopy (ASTM E3) and Scanning Electron Microscopy (SEM). The study of mechanical behavior was carried out in a mechanical test machine (ASTM E8) and a Pin on disk tribometer (ASTM G99) was used to assess wear resistance. It is observed that copper increases the pearlite structure improving the wear behavior; tension behavior. This improvement is observed in higher proportion with 0,5% due to the fact that too much increase of pearlite leads to ductility loss.

Keywords: copper, mechanical properties, nodular iron, pearlite structure, wear

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