Search results for: structural biology.

Authors: Y. H. Mugahed Amran, Raizal S. M. Rashid, Farzad Hejazi, Nor Azizi Safiee, A. A. Abang Ali

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Experimental and analytical studies were accomplished to examine the structural behavior of precast foamed concrete sandwich panel (PFCSP) under vertical in-plane shear load. PFCSP full-scale specimens with total number of six were developed with varying heights to study an important parameter slenderness ratio (H/t). The production technique of PFCSP and the procedure of test setup were described. The results obtained from the experimental tests were analysed in the context of in-plane shear strength capacity, load-deflection profile, load-strain relationship, slenderness ratio, shear cracking patterns and mode of failure. Analytical study of finite element analysis was implemented and the theoretical calculations of the ultimate in-plane shear strengths using the adopted ACI318 equation for reinforced concrete wall were determined aimed at predicting the in-plane shear strength of PFCSP. The decrease in slenderness ratio from 24 to 14 showed an increase of 26.51% and 21.91% on the ultimate in-plane shear strength capacity as obtained experimentally and in FEA models, respectively. The experimental test results, FEA models data and theoretical calculation values were compared and provided a significant agreement with high degree of accuracy. Therefore, on the basis of the results obtained, PFCSP wall has the potential use as an alternative to the conventional load-bearing wall system.

Keywords: Deflection profiles, foamed concrete, load-strain relationships, precast foamed concrete sandwich panel, slenderness ratio, vertical in-plane shear strength capacity.

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Authors: Usha Chouhan, K. R. Pardasani

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Phylogenies ; The evolutionary histories of groups of species are one of the most widely used tools throughout the life sciences, as well as objects of research with in systematic, evolutionary biology. In every phylogenetic analysis reconstruction produces trees. These trees represent the evolutionary histories of many groups of organisms, bacteria due to horizontal gene transfer and plants due to process of hybridization. The process of gene transfer in bacteria and hybridization in plants lead to reticulate networks, therefore, the methods of constructing trees fail in constructing reticulate networks. In this paper a model has been employed to reconstruct phylogenetic network in honey bee. This network represents reticulate evolution in honey bee. The maximum parsimony approach has been used to obtain this reticulate network.

Keywords: Hybridization, HGT, Reticulate networks, Recombination, Species, Parsimony.

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Authors: Essam Al Daoud

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Genome rearrangement is an important area in computational biology and bioinformatics. The basic problem in genome rearrangements is to compute the edit distance, i.e., the minimum number of operations needed to transform one genome into another. Unfortunately, unsigned genome rearrangement problem is NP-hard. In this study an improved ant colony optimization algorithm to approximate the edit distance is proposed. The main idea is to convert the unsigned permutation to signed permutation and evaluate the ants by using Kaplan algorithm. Two new operations are added to the standard ant colony algorithm: Replacing the worst ants by re-sampling the ants from a new probability distribution and applying the crossover operations on the best ants. The proposed algorithm is tested and compared with the improved breakpoint reversal sort algorithm by using three datasets. The results indicate that the proposed algorithm achieves better accuracy ratio than the previous methods.

Keywords: Ant colony algorithm, Edit distance, Genome breakpoint, Genome rearrangement, Reversal sort.

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Authors: Mohammad Reza Pirestani, Mehdi Shafaghati, Amir Ahmad Dehghani

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From the beginning of creation, human being has ever fought against the ecosystem by changes has made in environment. The most environmental changes on the nature have been done after starting the concentrated life in the same region. Dams are one of the most important buildings in water resources and transferring. These buildings have been made from old times without access to hydrological, hydraulically, hydro mechanical information. Dams have positive and negative effects on environment. Constructing a dam relatively causes equal ecological consequences. According to different criteria, environmental effects of dams can lead short term and long term damages. These effects may influence on the situation and treatment of meteorology, biology, culture, ancient works, etc and severely causes to change and complicate it. So considering importance of positive effects of dam construction, it is necessary to minimize negative environmental effects of dams to achieve a stable development. In this article the considered effects and their solutions in influencing on assessment of destructive environmental effects of dams construction have been surveyed and presented.

Keywords: Dam, Environment, Water Resources, Assessment

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Authors: Tarek M. Alguhane, Ayman H. Khalil, M. N. Fayed, Ayman M. Ismail

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This paper deals with different modeling aspects of masonry infill: no infill model, Layered shell infill model, and strut infill model. These models consider the complicated behavior of the in-filled plane frames under lateral load similar to an earthquake load. Three strut infill models are used: NBCC (2005) strut infill model, ASCE/SEI 41-06 strut infill model and proposed strut infill model based on modification to Canadian, NBCC (2005) strut infill model. Pushover and modal analyses of a masonry infill concrete frame with a single storey and an existing 5-storey RC building have been carried out by using different models for masonry infill. The corresponding hinge status, the value of base shear at target displacement as well as their dynamic characteristics have been determined and compared. A validation of the structural numerical models for the existing 5-storey RC building has been achieved by comparing the experimentally measured and the analytically estimated natural frequencies and their mode shapes. This study shows that ASCE/SEI 41-06 equation underestimates the values for the equivalent properties of the diagonal strut while Canadian, NBCC (2005) equation gives realistic values for the equivalent properties. The results indicate that both ASCE/SEI 41-06 and Canadian, NBCC (2005) equations for strut infill model give over estimated values for dynamic characteristic of the building. Proposed modification to Canadian, NBCC (2005) equation shows that the fundamental dynamic characteristic values of the building are nearly similar to the corresponding values using layered shell elements as well as measured field results.

Keywords: Masonry infill, framed structures, RC buildings, non-structural elements.

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Authors: Thomas Jin-Chee Liu

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In this paper, the thermo-electro-structural coupledfield in a cracked metal plate is studied using the finite element analysis. From the computational results, the compressive stresses reveal near the crack tip. This conclusion agrees with the past reference. Furthermore, the compressive condition can retard and stop the crack growth during the Joule heating process.

Keywords: Compressive stress, crack tip, Joule heating, finite element.

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Authors: Vaso K. Kapnopoulou, Piero Caridis

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The fatigue of ship structural details is of major concern in the maritime industry as it can generate fracture issues that may compromise structural integrity. In the present study, a fatigue analysis of the lower hopper knuckle connection of a bulk carrier was conducted using the Finite Element Method by means of ABAQUS/CAE software. The fatigue life was calculated using Miner’s Rule and the long-term distribution of stress range by the use of the two-parameter Weibull distribution. The cumulative damage ratio was estimated using the fatigue damage resulting from the stress range occurring at each load condition. For this purpose, a cargo hold model was first generated, which extends over the length of two holds (the mid-hold and half of each of the adjacent holds) and transversely over the full breadth of the hull girder. Following that, a submodel of the area of interest was extracted in order to calculate the hot spot stress of the connection and to estimate the fatigue life of the structural detail. Two hot spot locations were identified; one at the top layer of the inner bottom plate and one at the top layer of the hopper plate. The IACS Common Structural Rules (CSR) require that specific dynamic load cases for each loading condition are assessed. Following this, the dynamic load case that causes the highest stress range at each loading condition should be used in the fatigue analysis for the calculation of the cumulative fatigue damage ratio. Each load case has a different effect on ship hull response. Of main concern, when assessing the fatigue strength of the lower hopper knuckle connection, was the determination of the maximum, i.e. the critical value of the stress range, which acts in a direction normal to the weld toe line. This acts in the transverse direction, that is, perpendicularly to the ship's centerline axis. The load cases were explored both theoretically and numerically in order to establish the one that causes the highest damage to the location examined. The most severe one was identified to be the load case induced by beam sea condition where the encountered wave comes from the starboard. At the level of the cargo hold model, the model was assumed to be simply supported at its ends. A coarse mesh was generated in order to represent the overall stiffness of the structure. The elements employed were quadrilateral shell elements, each having four integration points. A linear elastic analysis was performed because linear elastic material behavior can be presumed, since only localized yielding is allowed by most design codes. At the submodel level, the displacements of the analysis of the cargo hold model to the outer region nodes of the submodel acted as boundary conditions and applied loading for the submodel. In order to calculate the hot spot stress at the hot spot locations, a very fine mesh zone was generated and used. The fatigue life of the detail was found to be 16.4 years which is lower than the design fatigue life of the structure (25 years), making this location vulnerable to fatigue fracture issues. Moreover, the loading conditions that induce the most damage to the location were found to be the various ballasting conditions.

Keywords: Lower hopper knuckle, high cycle fatigue, finite element method, dynamic load cases.

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Authors: Jun Hee Lee, Young Kyu Kim, Seong Jae Hong, Chamroeun Chhorn, Seung Woo Lee

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Roller-compacted concrete pavement (RCCP), an environmental friendly pavement of which load carry capacity benefitted from both hydration and aggregate interlock from roller compacting, demonstrated a superb structural performance for a relatively small amount of water and cement content. Even though an excellent structural performance can be secured, it is required to investigate roller-compacted concrete (RCC) under environmental loading and its long-term durability under critical conditions. In order to secure long-term durability, an appropriate internal air-void structure is required for this concrete. In this study, a method for improving the long-term durability of RCCP is suggested by analyzing the internal air-void structure and corresponding durability of RCC. The method of improving the long-term durability involves measurements of air content, air voids, and air-spacing factors in RCC that experiences changes in terms of type of air-entraining agent and its usage amount. This test is conducted according to the testing criteria in ASTM C 457, 672, and KS F 2456. It was found that the freezing-thawing and scaling resistances of RCC without any chemical admixture was quite low. Interestingly, an improvement of freezing-thawing and scaling resistances was observed for RCC with appropriate the air entraining (AE) agent content; Relative dynamic elastic modulus was found to be more than 80% for those mixtures. In RCC with AE agent mixtures, large amount of air was distributed within a range of 2% to 3%, and an air void spacing factor ranging between 200 and 300 μm (close to 250 μm, recommended by PCA) was secured. The long-term durability of RCC has a direct relationship with air-void spacing factor, and thus it can only be secured by ensuring the air void spacing factor through the inclusion of the AE in the mixture.

Keywords: RCCP, durability, air spacing factor, surface scaling resistance test, freezing and thawing resistance test.

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Authors: Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid

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Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science and mathematics. Thus, in this paper, the possibility of DNA-based computing to solve an absolute 1-center problem by molecular manipulations is presented. This is truly the first attempt to solve such a problem by DNA-based computing approach. Since, part of the procedures involve with shortest path computation, research works on DNA computing for shortest path Traveling Salesman Problem, in short, TSP are reviewed. These approaches are studied and only the appropriate one is adapted in designing the computation procedures. This DNA-based computation is designed in such a way that every path is encoded by oligonucleotides and the path-s length is directly proportional to the length of oligonucleotides. Using these properties, gel electrophoresis is performed in order to separate the respective DNA molecules according to their length. One expectation arise from this paper is that it is possible to verify the instance absolute 1-center problem using DNA computing by laboratory experiments.

Keywords: DNA computing, operation research, 1-center problem.

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Authors: T. Niknam, M. Nayeripour, B.Bahmani Firouzi

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Clustering techniques have received attention in many areas including engineering, medicine, biology and data mining. The purpose of clustering is to group together data points, which are close to one another. The K-means algorithm is one of the most widely used techniques for clustering. However, K-means has two shortcomings: dependency on the initial state and convergence to local optima and global solutions of large problems cannot found with reasonable amount of computation effort. In order to overcome local optima problem lots of studies done in clustering. This paper is presented an efficient hybrid evolutionary optimization algorithm based on combining Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO), called PSO-ACO, for optimally clustering N object into K clusters. The new PSO-ACO algorithm is tested on several data sets, and its performance is compared with those of ACO, PSO and K-means clustering. The simulation results show that the proposed evolutionary optimization algorithm is robust and suitable for handing data clustering.

Keywords: Ant Colony Optimization (ACO), Data clustering, Hybrid evolutionary optimization algorithm, K-means clustering, Particle Swarm Optimization (PSO).

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Authors: D. Estrella, A. Silva, R. Zapata, H. Rubio

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A total of 100 primary caregivers (mothers, fathers, grandparents) with at least one child or grandchild with a diagnosis of congenital bilateral profound deafness were assessed in order to evaluate the functionality of families with a deaf member, who was evaluated by specialists in audiology, molecular biology, genetics and psychology. After confirmation of the clinical diagnosis, DNA from the patients and parents were analyzed in search of the 35delG deletion of the GJB2 gene to determine who possessed the mutation. All primary caregivers were provided psychological support, regardless of whether or not they had the mutation, and prior and subsequent, the family APGAR test was applied. All parents, grandparents were informed of the results of the genetic analysis during the psychological intervention. The family APGAR, after psychological and genetic counseling, showed that 14% perceived their families as functional, 62% moderately functional and 24% dysfunctional. This shows the importance of psychological support in family functionality that has a direct impact on the quality of life of these families.

Keywords: Deafness, psychological support, family, adaptation to disability.

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Authors: C. Ardil

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The COVID-19 pandemic has revealed the complex and multifaceted relationship between societal structures and public health, emphasizing the need for a holistic approach to understanding pandemic responses. This study utilizes a clinical sociological perspective to analyze the social impacts of pandemics, with a particular focus on how social determinants such as income, education, race, and geographical location influence vulnerability and resilience. It explores the critical role of risk perception, communication strategies, and community dynamics in shaping public adherence to precautionary measures like mask-wearing, social distancing, and vaccination. By examining the ways in which social norms, structural inequalities, and trust in institutions affect public behavior, this study provides insights into the challenges of managing health crises in diverse communities. Comparative case studies and policy analysis are employed to highlight the variations in pandemic responses across different countries and regions, illustrating the importance of coordinated strategies and community-based interventions. The findings underscore that effective pandemic response requires addressing underlying social inequities, fostering community cohesion, and ensuring equitable access to healthcare and information. This study contributes to a deeper understanding of the broader societal implications of pandemics and offers recommendations for building more resilient, inclusive public health systems capable of mitigating the impact of future global health emergencies.

Keywords: Behavioral medicine, clinical sociology, community health, COVID-19, COVID-19 pandemic, epidemiology, infectious diseases, pandemics, precautions, psychology, public health, risks, social determinants, social dynamics, social psychiatry, social psychology, socioeconomic status, structural functionalism

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Authors: Erik Vassøy Olsen, Hirpa G. Lemu

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Inspired by the Formula-1 competition, IMechE (Institute of Mechanical Engineers) and Formula SAE (Society of Mechanical Engineers) organize annual competitions for University and College students worldwide to compete with a single-seat racecar they have designed and built. Design of the chassis or the frame is a key component of the competition because the weight and stiffness properties are directly related with the performance of the car and the safety of the driver. In addition, a reduced weight of the chassis has direct influence on the design of other components in the car. Among others, it improves the power to weight ratio and the aerodynamic performance. As the power output of the engine or the battery installed in the car is limited to 80 kW, increasing the power to weight ratio demands reduction of the weight of the chassis, which represents the major part of the weight of the car. In order to reduce the weight of the car, ION Racing team from University of Stavanger, Norway, opted for a monocoque design. To ensure fulfilment of the competition requirements of the chassis, the monocoque design should provide sufficient torsional stiffness and absorb the impact energy in case of possible collision. The study reported in this article is based on the requirements for Formula Student competition. As part of this study, diverse mechanical tests were conducted to determine the mechanical properties and performances of the monocoque design. Upon a comprehensive theoretical study of the mechanical properties of sandwich composite materials and the requirements of monocoque design in the competition rules, diverse tests were conducted including 3-point bending test, perimeter shear test and test for absorbed energy. The test panels were homemade and prepared with equivalent size of the side impact zone of the monocoque, i.e. 275 mm x 500 mm, so that the obtained results from the tests can be representative. Different layups of the test panels with identical core material and the same number of layers of carbon fibre were tested and compared. Influence of the core material thickness was also studied. Furthermore, analytical calculations and numerical analysis were conducted to check compliance to the stated rules for Structural Equivalency with steel grade SAE/AISI 1010. The test results were also compared with calculated results with respect to bending and torsional stiffness, energy absorption, buckling, etc. The obtained results demonstrate that the material composition and strength of the composite material selected for the monocoque design has equivalent structural properties as a welded frame and thus comply with the competition requirements. The developed analytical calculation algorithms and relations will be useful for future monocoque designs with different lay-ups and compositions.

Keywords: Composite material, formula student, ion racing, monocoque design, structural equivalence.

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Authors: Rony Reátegui, Cesar Chácara, Benjamin Castañeda, Rafael Aguilar

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Nowadays, Heritage Building Information Modeling (HBIM) is considered an efficient tool to represent and manage information of Cultural Heritage (CH). The basis of this tool relies on a 3D model generally obtained from a Cloud-to-BIM procedure. There are different methods to create an HBIM model that goes from manual modeling based on the point cloud to the automatic detection of shapes and the creation of objects. The selection of these methods depends on the desired Level of Development (LOD), Level of Information (LOI), Grade of Generation (GOG) as well as on the availability of commercial software. This paper presents the 3D modeling of a stone masonry chapel using Recap Pro, Revit and Dynamo interface following a three-step methodology. The first step consists of the manual modeling of simple structural (e.g., regular walls, columns, floors, wall openings, etc.) and architectural (e.g., cornices, moldings and other minor details) elements using the point cloud as reference. Then, Dynamo is used for generative modeling of complex structural elements such as vaults, infills and domes. Finally, semantic information (e.g., materials, typology, state of conservation, etc.) and pathologies are added within the HBIM model as text parameters and generic models’ families respectively. The application of this methodology allows the documentation of CH following a relatively simple to apply process that ensures adequate LOD, LOI and GOG levels. In addition, the easy implementation of the method as well as the fact of using only one BIM software with its respective plugin for the scan-to-BIM modeling process means that this methodology can be adopted by a larger number of users with intermediate knowledge and limited resources, since the BIM software used has a free student license.

Keywords: Cloud-to-BIM, cultural heritage, generative modeling, HBIM, parametric modeling, Revit.

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Authors: Vinod B. Suryawanshi, Ajit D. Kelkar

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Composite materials, due to their unique properties such as high strength to weight ratio, corrosion resistance, and impact resistance have huge potential as structural materials in automotive, construction and transportation applications. However, these properties often come at higher cost owing to complex design methods, difficult manufacturing processes and raw material cost. Traditionally, tapered laminated composite structures are manufactured using autoclave manufacturing process by ply drop off technique. Autoclave manufacturing though very powerful suffers from high capital investment and higher energy consumption. As per the current trends in composite manufacturing, Out of Autoclave (OoA) processes are looked as emerging technologies for manufacturing the structural composite components for aerospace and defense applications. However, there is a need for improvement among these processes to make them reliable and consistent. In this paper, feasibility of using out of autoclave process to manufacture the variable thickness cantilever beam is discussed. The minimum weight design for the composite beam is obtained using constant stress beam concept by tailoring the thickness of the beam. Ply drop off techniques was used to fabricate the variable thickness beam from glass/epoxy prepregs. Experiments were conducted to measure bending stresses along the span of the cantilever beam at different intervals by applying the concentrated load at the free end. Experimental results showed that the stresses in the bean at different intervals were constant. This proves the ability of OoA process to manufacture the constant stress beam. Finite element model for the constant stress beam was developed using commercial finite element simulation software. It was observed that the simulation results agreed very well with the experimental results and thus validated design and manufacturing approach used.

Keywords: Beams, Composites, Constant Stress, Structures.

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Authors: M. Nabeel Rashin, J. Hemalatha

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Novel Coconut oil nanofluids of various concentrations have been prepared through ultrasonically assisted sol-gel method. The structural and morphological properties of the copper oxide nanoparticle have been analyzed with respectively and it revealed the monoclinic end-centered structure of crystallite and shuttle like flake morphology of agglomerates. Ultrasonic studies have been made for the nanofluids at different temperatures. The molecular interactions responsible for the changes in acoustical parameter with respect to concentration and temperature are discussed.

Keywords: Cutting Fluid, Molecular Interaction, Nanofluids, Ultrasonic

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Authors: Abdelwahed Echchatbi, Adil Rizki, Ali Haddi, Nabil Mrani, Noureddine Elalami

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In this note, the robust static output feedback stabilisation of an induction machine is addressed. The machine is described by a non homogenous bilinear model with structural uncertainties, and the feedback gain is computed via an iterative LMI (ILMI) algorithm.

Keywords: Induction machine, Static output feedback, robust stabilisation.

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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: Li Ni, Pen ManMan, Li KenLi

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Clustering is an intensive research for some years because of its multifaceted applications, such as biology, information retrieval, medicine, business and so on. The expectation maximization (EM) is a kind of algorithm framework in clustering methods, one of the ten algorithms of machine learning. Traditionally, optimization of objective function has been the standard approach in EM. Hence, research has investigated the utility of evolutionary computing and related techniques in the regard. Chemical Reaction Optimization (CRO) is a recently established method. So the property embedded in CRO is used to solve optimization problems. This paper presents an algorithm framework (EM-CRO) with modified CRO operators based on EM cluster problems. The hybrid algorithm is mainly to solve the problem of initial value sensitivity of the objective function optimization clustering algorithm. Our experiments mainly take the EM classic algorithm:k-means and fuzzy k-means as an example, through the CRO algorithm to optimize its initial value, get K-means-CRO and FKM-CRO algorithm. The experimental results of them show that there is improved efficiency for solving objective function optimization clustering problems.

Keywords: Chemical reaction optimization, expectation maximization, initial, objective function clustering.

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Authors: Y. Liu, M. K. Bera, L. M. Kyaw, G. Q. Lo, E. F. Chor

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The electrical and structural properties of Hf/Al/Ni/Au (20/100/25/50 nm) ohmic contact to n-GaN are reported in this study. Specific contact resistivities of Hf/Al/Ni/Au based contacts have been investigated as a function of annealing temperature and achieve the lowest value of 1.09´10-6 Ω·cm2 after annealing at 650 oC in vacuum. A detailed mechanism of ohmic contact formation is discussed. By using different chemical analyses, it is anticipated that the formation of Hf-Al-N alloy might be responsible to form low temperature ohmic contacts for the Hf-based scheme to n-GaN.

Keywords: Gallium nitride, ohmic contact, Hafnium

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Authors: Mohammadreza Salek Faramarzi, Touraj Taghikhany

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In this paper, seismic fragility assessment of a recently developed hybrid structural system, known as the strongback system (SBS) is investigated. In this system, to mitigate the occurrence of the soft-story mechanism and improve the distribution of story drifts over the height of the structure, an elastic vertical truss is formed. The strengthened members of the braced span are designed to remain substantially elastic during levels of excitation where soft-story mechanisms are likely to occur and impose a nearly uniform story drift distribution. Due to the distinctive characteristics of near-field ground motions, it seems to be necessary to study the effect of these records on seismic performance of the SBS. To this end, a set of 56 near-field ground motion records suggested by FEMA P695 methodology is used. For fragility assessment, nonlinear dynamic analyses are carried out in OpenSEES based on the recommended procedure in HAZUS technical manual. Four damage states including slight, moderate, extensive, and complete damage (collapse) are considered. To evaluate each damage state, inter-story drift ratio and floor acceleration are implemented as engineering demand parameters. Further, to extend the evaluation of the collapse state of the system, a different collapse criterion suggested in FEMA P695 is applied. It is concluded that SBS can significantly increase the collapse capacity and consequently decrease the collapse risk of the structure during its life time. Comparing the observing mean annual frequency (MAF) of exceedance of each damage state against the allowable values presented in performance-based design methods, it is found that using the elastic vertical truss, improves the structural response effectively.

Keywords: Strongback System, Near-fault, Seismic fragility, Uncertainty, IDA, Probabilistic performance assessment.

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Authors: Joel Arrais, João E. Pereira, João Fernandes, José Luís Oliveira

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The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires typically the simultaneous study of the obtained dataset with data that is available in several distinct public databases. Nevertheless, developing a centralized access to these distributed databases rises up a set of challenges such as: what is the best integration strategy, how to solve nomenclature clashes, how to solve database overlapping data and how to deal with huge datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be publicly downloaded or remotely access through SOAP web services.

Keywords: Data integration, biological databases

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

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The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Tom Snir, Eitan Rubin

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Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: Aqsa Jamil, Hiroshi Tamura, Hiroshi Katsuchi, Jiaqi Wang

Abstract:

Yield point represents the upper limit of forces which can be applied on a specimen without causing any permanent deformation. After yielding, the behavior of specimen suddenly changes including the possibility of cracking or buckling. So, the accumulation of damage or type of fracture changes depending on this condition. As it is difficult to accurately detect yield points of the several stress concentration points in structural steel specimens, an effort has been made in this research work to develop a convenient technique using thermography (temperature-based detection) during tensile tests for the precise detection of yield point initiation. To verify the applicability of thermography camera, tests were conducted under different loading conditions and measuring the deformation by installing various strain gauges and monitoring the surface temperature with the help of thermography camera. The yield point of specimens was estimated by the help of temperature dip which occurs due to the thermoelastic effect during the plastic deformation. The scattering of the data has been checked by performing repeatability analysis. The effect of temperature imperfection and light source has been checked by carrying out the tests at daytime as well as midnight and by calculating the signal to noise ratio (SNR) of the noised data from the infrared thermography camera, it can be concluded that the camera is independent of testing time and the presence of a visible light source. Furthermore, a fully coupled thermal-stress analysis has been performed by using Abaqus/Standard exact implementation technique to validate the temperature profiles obtained from the thermography camera and to check the feasibility of numerical simulation for the prediction of results extracted with the help of thermographic technique.

Keywords: Signal to noise ratio, thermoelastic effect, thermography, yield point.

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Authors: Tarunjit S. Butalia, William E. Wolfe

Abstract:

This study demonstrates the use of Class F fly ash in combination with lime or lime kiln dust in the full depth reclamation (FDR) of asphalt pavements. FDR, in the context of this paper, is a process of pulverizing a predetermined amount of flexible pavement that is structurally deficient, blending it with chemical additives and water, and compacting it in place to construct a new stabilized base course. Test sections of two structurally deficient asphalt pavements were reclaimed using Class F fly ash in combination with lime and lime kiln dust. In addition, control sections were constructed using cement, cement and emulsion, lime kiln dust and emulsion, and mill and fill. The service performance and structural behavior of the FDR pavement test sections were monitored to determine how the fly ash sections compared to other more traditional pavement rehabilitation techniques. Service performance and structural behavior were determined with the use of sensors embedded in the road and Falling Weight Deflectometer (FWD) tests. Monitoring results of the FWD tests conducted up to 2 years after reclamation show that the cement, fly ash+LKD, and fly ash+lime sections exhibited two year resilient modulus values comparable to open graded cement stabilized aggregates (more than 750 ksi). The cement treatment resulted in a significant increase in resilient modulus within 3 weeks of construction and beyond this curing time, the stiffness increase was slow. On the other hand, the fly ash+LKD and fly ash+lime test sections indicated slower shorter-term increase in stiffness. The fly ash+LKD and fly ash+lime section average resilient modulus values at two years after construction were in excess of 800 ksi. Additional longer-term testing data will be available from ongoing pavement performance and environmental condition data collection at the two pavement sites.

Keywords: Coal fly ash, full depth reclamation, FWD, pavement rehabilitation

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: Kee-Young Kwahk, Xi Ge, Jun-Hyung Park

Abstract:

This study aims to examine the determinants of purchase intention in C2C e-commerce. Specifically the role of instant messaging in the C2C e-commerce contextis investigated. In addition to instant messaging, we brought in two antecedents of purchase intention - trust and customer satisfaction - to establish a theoretical research model. Structural equation modeling using LISREL was used to analyze the data.We discussed the research findings and suggested some implications for researchers and practitioners.

Keywords: E-commerce, Online marketing, C2C, Purchase Intention

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

Abstract:

The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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Authors: F. Allag, S. Bouharati, M. Belmahdi, R. Zegadi

Abstract:

The rapid expansion of deserts in recent decades as a result of human actions combined with climatic changes has highlighted the necessity to understand biological processes in arid environments. Whereas physical processes and the biology of flora and fauna have been relatively well studied in marginally used arid areas, knowledge of desert soil micro-organisms remains fragmentary. The objective of this study is to conduct a diversity analysis of bacterial communities in unvegetated arid soils. Several biological phenomena in hot deserts related to microbial populations and the potential use of micro-organisms for restoring hot desert environments. Dry land ecosystems have a highly heterogeneous distribution of resources, with greater nutrient concentrations and microbial densities occurring in vegetated than in bare soils. In this work, we found it useful to use techniques of artificial intelligence in their treatment especially artificial neural networks (ANN). The use of the ANN model, demonstrate his capability for addressing the complex problems of uncertainty data.

Keywords: Desert soil, Climatic changes, Bacteria, Vegetation, Artificial neural networks.

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