Search results for: RNA secondary structures

Authors: Shih-Yi Chao

Abstract:

The similarity comparison of RNA secondary structures is important in studying the functions of RNAs. In recent years, most existing tools represent the secondary structures by tree-based presentation and calculate the similarity by tree alignment distance. Different to previous approaches, we propose a new method based on maximum clique detection algorithm to extract the maximum common structural elements in compared RNA secondary structures. A new graph-based similarity measurement and maximum common subgraph detection procedures for comparing purely RNA secondary structures is introduced. Given two RNA secondary structures, the proposed algorithm consists of a process to determine the score of the structural similarity, followed by comparing vertices labelling, the labelled edges and the exact degree of each vertex. The proposed algorithm also consists of a process to extract the common structural elements between compared secondary structures based on a proposed maximum clique detection of the problem. This graph-based model also can work with NC-IUB code to perform the pattern-based searching. Therefore, it can be used to identify functional RNA motifs from database or to extract common substructures between complex RNA secondary structures. We have proved the performance of this proposed algorithm by experimental results. It provides a new idea of comparing RNA secondary structures. This tool is helpful to those who are interested in structural bioinformatics.

Keywords: Clique detection, labeled vertices, RNA secondary structures, subgraph, similarity.

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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: Fetah Eren, Ismail Sahin, Ismail Celik, Ahmet Oguz Akturk

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The aim of this study is to discover secondary school students’ perceptions related to information technologies and the connections between concepts in their cognitive structures. A word association test consisting of six concepts related to information technologies is used to collect data from 244 secondary school students. Concept maps that present students’ cognitive structures are drawn with the help of frequency data. Data are analyzed and interpreted according to the connections obtained as a result of the concept maps. It is determined students associate most with these concepts—computer, Internet, and communication of the given concepts, and associate least with these concepts—computer-assisted education and information technologies. These results show the concepts, Internet, communication, and computer, are an important part of students’ cognitive structures. In addition, students mostly answer computer, phone, game, Internet and Facebook as the key concepts. These answers show students regard information technologies as a means for entertainment and free time activity, not as a means for education.

Keywords: Word association test, cognitive structure, information technology, secondary school.

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Authors: Manpreet Singh, Parvinder Singh Sandhu, Reet Kamal Kaur

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Protein structure determination and prediction has been a focal research subject in the field of bioinformatics due to the importance of protein structure in understanding the biological and chemical activities of organisms. The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time. A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results. However, prediction accuracies of these methods rarely exceed 70%.

Keywords: Protein, Secondary Structure, Prediction, DNA, RNA.

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Authors: Artem Nuriev, Olga Zaitseva

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This paper is devoted to the study of a viscous incompressible flow around a circular cylinder performing harmonic oscillations, especially the steady streaming phenomenon. The research methodology is based on the asymptotic explanation method combined with the computational bifurcation analysis. The research approach develops Schlichting and Wang decomposition method. Present studies allow to identify several regimes of the secondary streaming with different flow structures. The results of the research are in good agreement with experimental and numerical simulation data.

Keywords: Oscillating cylinder, Secondary Streaming, Flow Regimes, Asymptotic and Bifurcation Analysis.

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Authors: Minh Tuan Nguyen, Sang-Wook Lee

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In this study, numerical simulations on laminar flow in sinusoidal wavy shaped tubes were conducted for mean Reynolds number of 250, which is in the range of physiological flow-rate and investigated flow structures, pressure distribution and particle trajectories both in steady and periodic inflow conditions. For extensive comparisons, various wave lengths and amplitudes of sine function for geometry of tube models were employed. The results showed that small amplitude secondary curvature has significant influence on the nature of flow patterns and particle mixing mechanism. This implies that characterizing accurate geometry is essential in accurate predicting of in vivo hemodynamics and may motivate further study on any possibility of reflection of secondary flow on vascular remodeling and pathophysiology.

Keywords: Secondary curvature, Sinusoidal wavy tubes, Mixing Characteristics, Pulsatile flow, Hemodynamics.

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Authors: Nikol Žižková, Šárka Keprdová, Rostislav Drochytka

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The paper focuses on the study of the properties of cement-based composites produced using secondary crystallization (crystalline additive). In this study, cement mortar made with secondary crystallization was exposed to an aggressive environment and the influence of secondary crystallization on the degradation of the cementitious composite was investigated. The results indicate that the crystalline additive contributed to increasing the resistance of the cement-based composite to the attack of the selected environments (sodium sulphate solution and ammonium chloride solution).

Keywords: Secondary crystallization, cement-based composites, durability.

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Authors: Behnam Shirkhanghah, Vahid Shahbaznejhad-Fard, Houshyar Eimani-Kalesar, Babak Pahlevan

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Flat double-layer grid is from category of space structures that are formed from two flat layers connected together with diagonal members. Increased stiffness and better seismic resistance in relation to other space structures are advantages of flat double layer space structures. The objective of this study is assessment and calculation of Behavior factor of flat double layer space structures. With regarding that these structures are used widely but Behavior factor used to design these structures against seismic force is not determined and exact, the necessity of study is obvious. This study is theoretical. In this study we used structures with span length of 16m and 20 m. All connections are pivotal. ANSYS software is used to non-linear analysis of structures.

Keywords: Behavior factor, Double-layer, Intensified resistance, Non-linear analysis

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Authors: N. Kulakova

Abstract:

Thisresearch paper is dedicated to an actual issue in Latvia and in the whole European Union – development of the secondary materials management. The goal of this paper is to research the development of the secondary materials management in Latvia as a result to point out its main positive aspects and problems. In this research paper the author regards following issues: significance of the secondary materials management, current situation of the waste generation and utilization in Latvia comparing with other EU Member States, main problems and positive aspects of the secondary materials management in Latvia. The research author concludes that in last ten years a great work is done to develop the secondary materials market. Nevertheless following improvements are necessary: implementation of the packaging deposit system, development of the separate waste collection, increasing of the recycling capacity.

Keywords: sustainable development, secondary materials, separate waste collection, packaging deposit system.

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Authors: Yi Yu, Gaoxi Xiao

Abstract:

Community structures widely exist in almost all real-life networks. Extensive researches have been carried out on detecting community structures in complex networks. However, many aspects of how community structures may affect the dynamics and properties of complex networks still remain unclear. In this work, we examine the impacts of community structures on the epidemic spreading and detection in complex networks. Extensive simulation results show that community structures may not help decrease the infection size at steady state, yet they could indeed help slow down the infection spreading. Also, networks with strong community structures may expect to have a smaller average infection size when equipped with a number of sparsely deployed monitors.

Keywords: Complex network, epidemic spreading, infection size, infection monitoring.

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Authors: Abdulqader M. Mohsen, Ahamad Tajudin Khader, Dhanesh Ramachandram, Abdullatif Ghallab

Abstract:

The physical methods for RNA secondary structure prediction are time consuming and expensive, thus methods for computational prediction will be a proper alternative. Various algorithms have been used for RNA structure prediction including dynamic programming and metaheuristic algorithms. Musician's behaviorinspired harmony search is a recently developed metaheuristic algorithm which has been successful in a wide variety of complex optimization problems. This paper proposes a harmony search algorithm (HSRNAFold) to find RNA secondary structure with minimum free energy and similar to the native structure. HSRNAFold is compared with dynamic programming benchmark mfold and metaheuristic algorithms (RnaPredict, SetPSO and HelixPSO). The results showed that HSRNAFold is comparable to mfold and better than metaheuristics in finding the minimum free energies and the number of correct base pairs.

Keywords: Metaheuristic algorithms, dynamic programming algorithms, harmony search optimization, RNA folding, Minimum free energy.

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Authors: S. K. Lujara, M. M. Kissaka, E. P. Bhalalusesa, L. Trojer

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The Information and Communication Technologies (ICTs), and the Wide World Web (WWW) have fundamentally altered the practice of teaching and learning world wide. Many universities, organizations, colleges and schools are trying to apply the benefits of the emerging ICT. In the early nineties the term learning object was introduced into the instructional technology vernacular; the idea being that educational resources could be broken into modular components for later combination by instructors, learners, and eventually computes into larger structures that would support learning [1]. However in many developing countries, the use of ICT is still in its infancy stage and the concept of learning object is quite new. This paper outlines the learning object design considerations for developing countries depending on learning environment.

Keywords: e-Learning resources, granularity, learning objects, secondary schools.

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Authors: M. J. Park, S. H. Lee, C. H. Lee, O. M. Kwon

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This paper studies a secondary voltage control framework of the microgrids based on the consensus for a communication network of multiagent. The proposed control is designed by the communication network with one-way links. The communication network is modeled by a directed graph. At this time, the concept of sampling is considered as the communication constraint among each distributed generator in the microgrids. To analyze the sampling effects on the secondary voltage control of the microgrids, by using Lyapunov theory and some mathematical techniques, the sufficient condition for such problem will be established regarding linear matrix inequality (LMI). Finally, some simulation results are given to illustrate the necessity of the consideration of the sampling effects on the secondary voltage control of the microgrids.

Keywords: Microgrids, secondary control, multiagent, sampling, LMI.

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Authors: Azlin M. Azmi, T. Zhou, A. Rinoshika, L. Cheng

Abstract:

The turbulent structures in the wake (x/d =10 to 60) of a screen cylinder have been educed to understand the roles of the various structures as evolving downstream by comparing with those obtained in a solid circular cylinder wake at Reynolds number, Re of 7000. Using a wavelet multiresolution technique, the flow structures are decomposed into a number of wavelet components based on their central frequencies. It is observed that in the solid cylinder wake, large-scale structures (of frequencyf₀ and 1.2 f₀) make the largest contribution to the Reynolds stresses although they start to lose their roles significantly at x/d> 20. In the screen cylinder wake, the intermediate-scale structures (2f₀ and 4f₀) contribute the most to the Reynolds stresses atx/d =10 before being taken over by the large-scale structures (f₀) further downstream.

Keywords: Turbulent structure, screen cylinder, vortex, wavelet multiresolution analysis.

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Authors: Manish Kumar

Abstract:

Reinforced cement concrete is getting extensively used for construction of different type of structures for the last one century. During this period, we have constructed many structures like buildings, bridges, industrial structures, pavement, water tanks etc. using this construction material. These structures have been created with huge investment of resources. It is essential to maintain those structures in functional condition. Since deterioration in RCC Structures is a common and natural phenomenon it is required to have a detailed plan, methodology for structural repair and rehabilitation shall be in place for dealing such issues. It is important to know exact reason of distress, type of distress and correct method of repair concrete structures. The different methods of repair are described in paper according to distress category which can be refereed for repair. Major finding of the study is that to protect our structure we need to have maintenance frequency and correct material to be chosen for repair. Also workmanship during repair needs to be taken utmost care for quality repair.

Keywords: Deterioration, functional condition, reinforced cement concrete, resources.

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Authors: Christian A. Romero, Tanja Grkovic, John. R. J. French, D. İpek. Kurtböke, Ronald J. Quinn

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A high-throughput and automated 1H NMR metabolic fingerprinting dereplication approach was used to accelerate the discovery of unknown bioactive secondary metabolites. The applied dereplication strategy accelerated the discovery of new natural products, provided rapid and competent identification and quantification of the known secondary metabolites and avoided time-consuming isolation procedures. The effectiveness of the technique was demonstrated by the isolation and elucidation of arglecins B (1), C (2) and actinofuranosin A (3) from a termite-gut associated Streptomyces sp. (USC 597) grown under solid state fermentation. The structures of these compounds were elucidated by extensive interpretation of 1H, 13C and 2D NMR spectroscopic data. These represent the first report of arglecin analogues isolated from a termite gut-associated Streptomyces species.

Keywords: Actinomycetes, actinofuranosin, antibiotics, arglecins, NMR spectroscopy.

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Authors: Khaleel Sami Hamdan, Dong-Eok Kim, Sang-Ki Moon

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An appropriate model to predict the size of the droplets resulting from the break-up with the structures will help in a better understanding and modeling of the two-phase flow calculations in the simulation of a reactor core loss-of-coolant accident (LOCA). A droplet behavior impacting on a hot surface above the Leidenfrost temperature was investigated. Droplets of known size and velocity were impacted to an inclined plate of hot temperature, and the behavior of the droplets was observed by a high-speed camera. It was found that for droplets of Weber number higher than a certain value, the higher the Weber number of the droplet the smaller the secondary droplets. The COBRA-TF model over-predicted the measured secondary droplet sizes obtained by the present experiment. A simple model for the secondary droplet size was proposed using the mass conservation equation. The maximum spreading diameter of the droplets was also compared to previous correlations and a fairly good agreement was found. A better prediction of the heat transfer in the case of LOCA can be obtained with the presented model.

Keywords: Break-up, droplet, impact, inclined hot plate, Leidenfrost temperature, LOCA.

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Authors: J. Kosikova, B. Vacenovska, M. Vyhnankova

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The paper reports on the subject of recycling and further use of secondary raw materials obtained from solar panels, which is becoming a very up to date topic in recent years. Recycling these panels is very difficult and complex, and the use of resulting secondary raw materials is still not fully resolved. Within the research carried out at the Brno University of Technology, new polymer materials used for industrial floors are being developed. Secondary raw materials are incorporated into these polymers as fillers. One of the tested filler materials was glass obtained from solar panels. The following text describes procedures and results of the tests that were performed on these materials, confirming the possibility of the use of solar panel glass in industrial polymer flooring systems.

Keywords: Fillers, industrial floors, recycling, secondary raw material, solar panel.

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Authors: Hezlina Mohd Hashim, Abdul Mutalib Embong, Zullina H. Shaari

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This study analyses the perceptions of secondary school students about the accounting profession in Malaysia. Fifty five form three and form four students who are taking accounting/commerce subjects were met. Individual-s perception data were collected through questionnaires. The results at the secondary school level suggest that the stereotypical negative image of the accountant ends, with students expressing the positive view of the work of an accountant. There were also gender differences in perceiving the accounting profession. Overall, the results of the study suggest that we are now in line in projecting positive and accurate perceptions of the accounting profession to secondary school students.

Keywords: Perceptions, secondary school students, accounting profession, Malaysia.

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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: Douangmala Kounsana, Xiang Wen, Toru Takahashi

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After a strong earthquake occurs, a secondary disaster due to strong aftershocks, flood, landslide or heavy snow can possible to occur and the secondary disaster due to resident-s action also can possible to happen. However, until now seldom researchers have paid attention at it. This paper focused on the Inhabitant-s action after the strong earthquake occurs when a terrible even becomes calm. An inappropriate behavior of people with disadvantaged climate after the worse earthquake can bring a tragedy to their life.

Keywords: Sichuan Earthquake, Secondary Disaster, Inhabitant's Action, inappropriate behavior.

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Authors: Panchalee Sukjit, Herwig Unger

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IT infrastructures are becoming more and more difficult. Therefore, in the first industrial IT systems, the P2P paradigm has replaced the traditional client server and methods of self-organization are gaining more and more importance. From the past it is known that especially regular structures like grids may significantly improve the system behavior and performance. This contribution introduces a new algorithm based on a biologic analogue, which may provide the growth of several regular structures on top of anarchic grown P2P- or social network structures.

Keywords: P2P, Pattern generation, Grid, Social network, Inheritance, Reproduction

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Authors: Shanthi Thomas

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This research paper presents the current practices of teacher professional development, perceived as beneficial by teachers themselves, in a private secondary school in Brunei Darussalam. This is part of the findings of a larger qualitative study on teacher empowerment, using ethnographic methods for data collection, i.e. participant observation, interviews and document analysis. The field work was carried out over a period of six months in 2013. An analysis of the field data revealed multiple pathways of teacher professional development existing in the school. The results indicate that school leaders, the teacher community in the school, students, and the teachers themselves were the agents in a school that facilitated teacher empowerment. Besides contributing to the knowledge base on teacher professional development, the results of this study provide directions for educational policy makers in their efforts to enhance professional development in secondary schools of similar characteristics. For school leaders and the teacher community, these findings offer guidelines for maximizing the opportunities for these professional development practices, by strengthening collegiality and by using the existing structures optimally for the benefit of all concerned.

Keywords: Colleagues and the wider teacher community, school leaders, self-driven professional development, teacher professional development.

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Authors: Pamela L. Knox, Linda R. Guthrie

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Trauma in early life is widely regarded as a cause for adult mental health problems. This study explores the role of secondary trauma on later functioning in a sample of 359 university students enrolled in undergraduate psychology classes in the United States. Participants were initially divided into four groups based on 1) having directly experienced trauma (assaultive violence), 2) having directly experienced trauma and secondary traumatization through the unanticipated death of a close friend or family member or witnessing of an injury or shocking even), 3) having no experience of direct trauma but having experienced indirect trauma (secondary trauma), or 4) reporting no exposure. Participants completed a battery of measures on concepts associated with psychological functioning which included measures of psychological well-being, problem solving, coping and resiliency. Findings discuss differences in psychological functioning and resilience based on participants who experienced secondary traumatization and assaultive violence versus secondary traumatization alone.

Keywords: Psychological Functioning, Resiliency, Trauma, Abuse

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Authors: Ellen. A. Kalinga

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Moodle is an open source learning management system that enables creation of a powerful and flexible learning environment. Many organizations, especially learning institutions have customized Moodle open source LMS for their own use. In general open source LMSs are of great interest due to many advantages they offer in terms of cost, usage and freedom to customize to fit a particular context. Tanzania Secondary School e- Learning (TanSSe-L) system is the learning management system for Tanzania secondary schools. TanSSe-L system was developed using a number of methods, one of them being customization of Moodle Open Source LMS. This paper presents few areas on the way Moodle OS LMS was customized to produce a functional TanSSe-L system fitted to the requirements and specifications of Tanzania secondary schools’ context.

Keywords: LMS, Moodle, e-Learning, Tanzania, Secondary school.

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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: Cory A. Bennett

Abstract:

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: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

Abstract:

Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: Ehrenstorfer Barbara, Peherstorfer Tanja, Nový Jan

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Urbanization and regionalization are two different approaches when it comes to economical structures and development, infrastructure and mobility, quality of life and living, education, social cohesion and many other topics. At first glance, the structures associated with urbanization and regionalization seems to be contradicting. This paper discusses possibilities of transfer and cooperation between rural and urban structures. An empirical investigation contributed to reveal scenarios of supposable forms of exchange and cooperation of remote rural areas and big cities.

Keywords: Learning Regions, Quality of Life and Living, Regional and Rural Development, Social Innovation.

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Authors: Viktória Sugár, Zoltán Laczó, András Horkai, Gyula Kiss, Attila Talamon

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The majority of the building stock of Budapest inner districts was built around the turn of the 19^th and 20^th century. Although the structural stability of the buildings is not questioned, as the load bearing structures are in sufficient state, the secondary structures are aged, resulting unsatisfactory energetic state. The renovation of these historical buildings requires special methodology and technology: their ornamented facades and custom-made fenestration cannot be insulated or exchanged with conventional solutions without damaging the heritage values. The present paper aims to introduce and systematize the possible technological solutions for heritage respecting energy retrofit in case of a historical residential building stock. Through case study, the possible energy saving potential is also calculated using multiple renovation scenarios.

Keywords: Energy efficiency, heritage, historical building, renovation, technical solutions.

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