Search results for: pathogen-associated molecular patterns

Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Neha Kulshreshtha

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This paper examines the patterns of 'Mouthing', a non-manual marker, and its distribution in Indian Sign Language (ISL). Linguistic research in Indian Sign Language is an emerging field where much is needed to be done. The little research which has happened focuses on the structure of ISL in terms of physical or manual markers, therefore a study of mouthing patterns would give an insight into the distribution of this particular non-manual marker. Data has been collected with the help of native ISL users through various techniques in which natural signs can be captured, for example, storytelling, informal conversations etc. The aim of the study is to find out the various situations where mouthing is used. Sometimes, the mouthing is not actually the articulation of the word as spoken in the local languages. The paper aims to find out whether the mouthing patterns in ISL are influenced by any local language or they are independent of any influence from the local language or both. Mouthing patterns have been studied in many sign languages and an investigation into ISL will reveal whether it falls in pattern with the other sign languages.

Keywords: Indian sign language, mouthing, non-manual marker, spoken language influence

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Authors: Cao Xi

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This paper reports a study which used eye-tracking to examine the cognitive validity of TEM 8(Test for English Majors, Band 8). The study investigated test takers' reading patterns on four -item types using eye-tracking, and interviews. Thirty participants completed 22 items on a computer, with the Tobii X2 Eye Tracker recording their eye movements on screen. Eleven students further participated in a recall interview while viewing video footage of their gaze patterns on the test. The findings will indicate that first, different reading item types will employ different cognitive processes; then different reading patterns for stronger and weaker test takers’on each item types. The implication of this study is to provide recommendations for the use of eye tracking technology in language research.

Keywords: eye tracking, reading patterns, test for english majors, cognitive validity

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Authors: Sunatda Arayachukiat, Shogo Nobukawa, Masayuki Yamaguchi

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A new self-healing material was developed utilizing molecular entanglements for poly(vinyl butyral) (PVB) containing plasticizers. It was found that PVB shows autonomic self-healing behavior even below the glass transition temperature Tg because of marked molecular motion at surface. Moreover, the plasticizer addition enhances the chain mobility, leading to good healing behavior.

Keywords: Poly(vinyl butyral) (PVB), rheological properties, self-healing behaviour, molecular diffusion

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Authors: W. S. Thulasitha, N. Umasuthan, G. I. Godahewa, Jehee Lee

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In fish, innate immune defense is the first immune response against microbial pathogens which consists of several antimicrobial components. Galectins are one of the carbohydrate binding lectins that have the ability to identify pathogen by recognition of pathogen associated molecular patterns. Galectins play a vital role in the regulation of innate and adaptive immune responses. Rock bream Oplegnathus fasciatus is one of the most important cultured species in Korea and Japan. Considering the losses due to microbial pathogens, present study was carried out to understand the molecular and functional characteristics of a galectin in normal and pathogenic conditions, which could help to establish an understanding about immunological components of rock bream. Complete cDNA of rock bream galectin like protein B (rbGal like B) was identified from the cDNA library, and the in silico analysis was carried out using bioinformatic tools. Genomic structure was derived from the BAC library by sequencing a specific clone and using Spidey. Full length of rbGal like B (contig14775) cDNA containing 517 nucleotides was identified from the cDNA library which comprised of 435 bp in the open reading frame encoding a deduced protein composed of 145 amino acids. The molecular mass of putative protein was predicted as 16.14 kDa with an isoelectric point of 8.55. A characteristic conserved galactose binding domain was located from 12 to 145 amino acids. Genomic structure of rbGal like B consisted of 4 exons and 3 introns. Moreover, pairwise alignment showed that rock bream rbGal like B shares highest similarity (95.9 %) and identity (91 %) with Takifugu rubripes galectin related protein B like and lowest similarity (55.5 %) and identity (32.4 %) with Homo sapiens. Multiple sequence alignment demonstrated that the galectin related protein B was conserved among vertebrates. A phylogenetic analysis revealed that rbGal like B protein clustered together with other fish homologs in fish clade. It showed closer evolutionary link with Takifugu rubripes. Tissue distribution and expression patterns of rbGal like B upon immune challenges were performed using qRT-PCR assays. Among all tested tissues, level of rbGal like B expression was significantly high in gill tissue followed by kidney, intestine, heart and spleen. Upon immune challenges, it showed an up-regulated pattern of expression with Edwardsiella tarda, rock bream irido virus and poly I:C up to 6 h post injection and up to 24 h with LPS. However, In the presence of Streptococcus iniae rbGal like B showed an up and down pattern of expression with the peak at 6 - 12 h. Results from the present study revealed the phylogenetic position and role of rbGal like B in response to microbial infection in rock bream.

Keywords: galectin like protein B, immune response, Oplegnathus fasciatus, molecular characterization

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Authors: Rajandeep Kaur, Rajeev Gupta

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Background: Chronic myeloid leukemia (CML) is the most common leukaemia in India. The annual incidence of chronic myeloid leukemia in India was originally reported to be 0.8 to 2.2 per 1,00,000 population. CML is a clonal disorder that is usually easily diagnosed because the leukemic cells of more than 95% of patients have a distinctive cytogenetic abnormality, the Philadelphia chromosome (Ph1). The approval of tyrosine kinase inhibitors (TKIs), which target BCR-ABL1 kinase activity, has significantly reduced the mortality rate associated with chronic myeloid leukemia (CML) and revolutionized treatment. Material and Methods: 80 diagnosed cases of CML were taken. Investigations were done. Bone marrow and molecular studies were also done and with EUTOS, patients were stratified into low and high-risk groups and then treatment with Imatinib was given to all patients and the molecular response was evaluated at 6 months and 12 months follow up with BCR-ABL by RT-PCR quantitative assay. Results: In the study population, out of 80 patients in the study population, 40 were females and 40 were males, with M: F is 1:1. Out of total 80 patients’ maximum patients (54) were in 31-60 years age group. Our study showed a most common symptom of presentation is abdominal discomfort followed by fever. Out of the total 80 patients, 25 (31.3%) patients had high EUTOS scores and 55 (68.8%) patients had low EUTOS scores. On 6 months follow up 36.3% of patients had Complete Molecular Response, 16.3% of patients had Major Molecular Response and 47.5% of patients had No Molecular Response but on 12 months follow up 71.3% of patients had Complete Molecular Response, 16.25% of patients had Major Molecular Response and 12.5% patients had No Molecular Response. Conclusion: In this study, we found a significant correlation between EUTOS score and Molecular response at 6 months and 12 months follow up after Imatinib therapy.

Keywords: chronic myeloid leukemia, European treatment and outcome study score, hematological response, molecular response, tyrosine kinase inhibitor

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Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

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Benzimidazoles are a group of compounds with significant antibacterial, antifungal and anticancer activity. The studied compounds consist of the main benzimidazole structure with different combinations of substituens. This study is based on the two-dimensional and three-dimensional molecular modeling and calculation of molecular descriptors (physicochemical and lipophilicity descriptors) of structurally diverse benzimidazoles. Molecular modeling was carried out by using ChemBio3D Ultra version 14.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The obtained set of molecular descriptors was used in principal component analysis (PCA) of possible similarities and dissimilarities among the studied derivatives. After the molecular modeling, the quantitative structure-property relationship (QSPR) analysis was applied in order to get the mathematical models which can be used in prediction of pKb values of structurally similar benzimidazoles. The obtained models are based on statistically valid multiple linear regression (MLR) equations. The calculated cross-validation parameters indicate the high prediction ability of the established QSPR models. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, chemometrics, molecular modeling, molecular descriptors, QSPR

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Authors: Jannes Quer, Amir Niknejad, Marcus Weber

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Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

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Authors: A. Azari, S. S. K. Seyyedi

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One of the unaddressed and open challenges in the nano-networking is the characteristics of noise. The previous analysis, however, has concentrated on end-to-end communication model with no separate modelings for propagation channel and noise. By considering a separate signal propagation and noise model, the design and implementation of an optimum receiver will be much easier. In this paper, we justify consideration of a separate additive Gaussian noise model of a nano-communication system based on the molecular communication channel for which are applicable for MSK and MOSK modulation schemes. The presented noise analysis is based on the Brownian motion process, and advection molecular statistics, where the received random signal has a probability density function whose mean is equal to the mean number of the received molecules. Finally, the justification of received signal magnitude being uncorrelated with additive non-stationary white noise is provided.

Keywords: molecular, noise, diffusion, channel

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Authors: Vadivel Ayyasamy

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The present approach deals with the identification of Emotions and classification of Emotional patterns at Phrase-level with respect to Positive and Negative Orientation. The proposed approach considers emotion triggered terms, its co-occurrence terms and also associated sentences for recognizing emotions. The proposed approach uses Part of Speech Tagging and Emotion Actifiers for classification. Here sentence patterns are broken into phrases and Neuro-Fuzzy model is used to classify which results in 16 patterns of emotional phrases. Suitable intensities are assigned for capturing the degree of emotion contents that exist in semantics of patterns. These emotional phrases are assigned weights which supports in deciding the Positive and Negative Orientation of emotions. The approach uses web documents for experimental purpose and the proposed classification approach performs well and achieves good F-Scores.

Keywords: emotions, sentences, phrases, classification, patterns, fuzzy, positive orientation, negative orientation

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Authors: Paweł Stączek, Tomasz Plech, Aleksandra Strzelczyk, Katarzyna Dzitko, Monika Wujec, Edyta Kuśmierz, Piotr Paneth, Agata Paneth

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In this contribution, we will describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile, and molecular modeling evaluation. We have found that one of the tested compounds, 4-benzoyl-1-(2-methyl-furan-3-ylcarbonyl) thiosemicarbazide, remarkably inhibits the activity of S. aureus DNA gyrase with the IC50 below 5 μM. Besides, this compound displays antibacterial activity on Staphylococcus spp. and E. faecalis at non-cytotoxic concentrations in mammalian cells, with minimal inhibitory concentrations (MICs) values at 25 μg/mL. Based on the enzymatic and molecular modeling studies we propose two factors, i.e. geometry of molecule and hydrophobic/hydrophilic balance as important molecular properties for developing thiosemicarbazide derivatives as potent Staphylococcus aureus DNA gyrase inhibitors.

Keywords: bioactivity, drug design, topoisomerase, molecular modeling

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Authors: I. D. Mngutyo, T. T. Gyuse, D. S. A. Alaci, J. Atser

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Streets are public spaces that are meaningful to all people because of lack of restriction on streets. Studies show that conditions, activities and people contribute to the success of public spaces. Also, self-organization potential in activity patterns offers a prospect for the revitalization of an urban area. This potential is mostly ignored hence many African streets appear disorganized giving African urban areas an unplanned look. Therefore, this study aims to analyze street utilization patterns and explore the relationship between the pattern of street use and condition of streets in Makurdi.These activity patterns form a data base for the revitalization of public space. Three major and minor arterials streets in nine out of the eleven wards that make up the built up part of Makurdi were purposively selected as units for measurement. A street activity audit was done on streets for activities that can be observed. For activities that cannot be easily observed 4 questionnaires were randomly administered on each of the three streets giving a total of 108 questionnaires. Multivariate statistical tools such as factor analysis and regression will be used to show emerging streets activity patterns and spatial variation among the nine wards.

Keywords: streets, utilization patterns, revitalization, urban design, urban, areas, developing countries

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Authors: C. I. Boshoff, S. Steenkamp-Jonker

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Cystic echinococcosis (CE), caused by Echinococcus granulosus is an important parasitic infection in livestock worldwide, with severe zoonotic potential. It is important to understand the variability of Echinococcus granulosus, as genotype variations may influence lifecycle patterns, development rate, and transmission. Cystic Echinococcus samples were collected from domestic animals in Eastern Cape Province, South Africa. A molecular study was performed on 14 hydatid cysts obtained from caprine, ovine and bovine livers in order to determine the Echinococcus granulosus strain present in these hosts. The sequencing of the mitochondrial cytochrome C oxidase subunit I (coxI) gene of the hydatid cysts produced sequences of 400 bp for each sample analysed. These sequences were aligned with those present in GenBank and a phylogenetic tree was constructed. Based on coxI genotype the isolates could be grouped into E. granulosus sensu stricto. The findings of the study represent a pilot molecular study on Echinococcus from domestic animals undertaken in South Africa.

Keywords: Echinococcus granulosus, genotypes, livestock, South Africa

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Authors: Niphattha Hannapha

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This paper examines how the classroom environment influences slow learners’ learning achievement; it focuses on how seating patterns affect students’ behaviours and which patterns best contribute to students’ learning performance. The researcher studied how slow learners’ characteristics and seating patterns influenced their behaviours and performance at Ban Hin Lad School. As a nonparticipant observation, the target groups included 15 slow learners from Prathomsueksa (Grades) 4 and 5. Students’ behaviours were recorded during their learning activities in order to minimize their reading and written expression disorder in Thai language tutorials. The result showed four seating patterns and two behaviors which obstructed students’ learning. The average of both behaviours mostly occurred when students were seated with patterns 1 (the seat facing the door, with the corridor alongside) and 3 (the seat alongside the door, facing the aisle) respectively. Seating patterns 1 and 3 demonstrated visibility (the front and side) of a walking path with two-way movement. However, seating patterns 2 (seating with the door alongside and the aisle at the back) and 4 (sitting with the door at the back and the aisle alongside) demonstrated visibility (the side) of a walking path with one-way movement. In Summary, environmental design is important to enhance concentration in slow learners who have reading and writing disabilities. This study suggests that students should be seated where they can have the least visibility of movement to help them increase continuous learning. That means they can have a better chance of developing reading and writing abilities in comparison with other patterns of seating.

Keywords: slow learning, interior design, interior environment, classroom

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Authors: Sobhan Sobhani

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This study examined the behavioral patterns of student and their determinants according to the "symbolic interaction" sociological perspective in the form of 7 hypotheses. Behavioral patterns of students were classified in 8 categories: religious, scientific, political, artistic, sporting, national, parents and teachers. They were evaluated by student opinions by a five-point Likert rating scale. The statistical population included all male and female students of Islamic Azad University, Behabahan branch, among which 600 patients (268 females and 332 males) were selected randomly. The following statistical methods were used: frequency and percentage, mean, t-test, Pearson correlation coefficient and multi-way analysis of variance. The results obtained from statistical analysis showed that: 1-There is a significant difference between male and female students in terms of disposition to religious figures, artists, teachers and parents. 2-There is a significant difference between students of urban and rural areas in terms of assuming behavioral patterns of religious, political, scientific, artistic, national figures and teachers. 3-The most important criterion for selecting behavioral patterns of students is intellectual understanding with the pattern. 4-The most important factor influencing the behavioral patterns of male and female students is parents followed by friends. 5-Boys are affected by teachers, the Internet and satellite programs more than girls. Girls assume behavioral patterns from books more than boys. 6-There is a significant difference between students in human sciences, technical, medical and engineering disciplines in terms of selecting religious and political figures as behavioral patterns. 7-There is a significant difference between students belonging to different subcultures in terms of assuming behavioral patterns of religious, scientific and cultural figures. 8-Between the first and fourth year students in terms of selecting behavioral patterns, there is a significant difference only in selecting religious figures. 9-There is a significant negative correlation between the education level of parents and the selection of religious and political figures and teachers. 10-There is a significant negative correlation between family income and the selection of political and religious figures.

Keywords: behavioral patterns, behavioral patterns, male and female students, Islamic Azad University

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Authors: Ling Zhang, Feng Liu

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A matrix is called a ray pattern matrix if its entries are either 0 or a ray in complex plane which originates from 0. A ray pattern A of order n is called spectrally arbitrary if the complex matrices in the ray pattern class of A give rise to all possible nth degree complex polynomial. Otherwise, it is said to be spectrally non-arbitrary ray pattern. We call that a spectrally arbitrary ray pattern A of order n is minimally spectrally arbitrary if any nonzero entry of A is replaced, then A is not spectrally arbitrary. In this paper, we find that is not spectrally arbitrary when n equals to 4 for any θ which is greater than or equal to 0 and less than or equal to n. In this article, we give several ray patterns A(θ) of order n that are not spectrally arbitrary for some θ which is greater than or equal to 0 and less than or equal to n. by using the nilpotent-Jacobi method. One example is given in our paper.

Keywords: spectrally arbitrary, nilpotent matrix , ray patterns, sign patterns

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Authors: Hai Hoang, Thanh Xuan Nguyen Thi, Guillaume Galliero

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Coarse-Grained (CG) molecular simulations have shown to be an efficient way to estimate thermophysical (static and dynamic) properties of fluids. Several strategies have been developed and reported in the literature for defining CG molecular models. Among them, those based on a top-down strategy (i.e. CG molecular models related to macroscopic observables), despite being heuristic, have increasingly gained attention. This is probably due to its simplicity in implementation and its ability to provide reasonable results for not only simple but also complex systems. Regarding simple Force-Fields associated with these CG molecular models, it has been found that the four parameters Mie chain model is one of the best compromises to describe thermophysical static properties (e.g. phase diagram, saturation pressure). However, parameterization procedures of these Mie-chain GC molecular models given in literature are generally insufficient to simultaneously provide static and dynamic (e.g. viscosity) properties. To deal with such situations, we have extended the corresponding states by using a quantity associated with the liquid viscosity. Results obtained from molecular simulations have shown that our approach is able to yield good estimates for both static and dynamic thermophysical properties for various real non-associating fluids. In addition, we will show that on simple (e.g. phase diagram, saturation pressure) and complex (e.g. thermodynamic response functions, thermodynamic energy potentials) static properties, results of our scheme generally provides improved results compared to existing approaches.

Keywords: coarse-grained model, mie potential, molecular simulations, thermophysical properties, phase equilibria

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Authors: Manel Boulakoud, Abdelkader Chouaih, Fodil Hamzaoui

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In the present work we are interested in the determination of the Molecular electrostatic potential (MEP) in Z-3N(2-Ethoxyphenyl), 2-N’(2-Ethoxyphenyl) imino thiazolidin-4-one molecule by ab initio and Density Functional Theory (DFT) in the ground state. The MEP is related to the electronic density and is a very useful descriptor in understanding sites for electrophilic attack and nucleophilic reactions as well as hydrogen bonding interactions. First, geometry optimization was carried out using Hartree–Fock (HF) and DFT methods with 6-311G(d,p) basis set. In order to get more information on the molecule, its stability has been analyzed by natural bond orbital (NBO) analysis. Mulliken population analyses have been calculated. Finally, the molecular electrostatic potential (MEP) and HOMO-LUMO energy levels have been performed. The calculated HOMO and LUMO energies show also the charge transfer within the molecule. The energy gap obtained is about 4 eV which explain the stability of the studied compound. The obtained molecular electrostatic potential from the two methods confirms the nature of the electron charge transfer at the molecular shell and locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: DFT, ab initio, HOMO-LUMO, organic compounds

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Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

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Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: biological molecular networks, essential genes, graph theory, network subgraphs

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Authors: Mario Gianni, Manuel A. Ruiz Garcia, Fiora Pirri

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In this work, we present a Bayesian non-parametric approach to model the motion control of ATVs. The motion control model is based on a Dirichlet Process-Gaussian Process (DP-GP) mixture model. The DP-GP mixture model provides a flexible representation of patterns of control manoeuvres along trajectories of different lengths and discretizations. The model also estimates the number of patterns, sufficient for modeling the dynamics of the ATV.

Keywords: Dirichlet processes, gaussian mixture models, learning motion patterns, tracked robots for urban search and rescue

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Authors: Y. Megrous, A. Chouaih, F. Hamzaoui

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The crystal structure of 4-Methyl-7-(salicylideneamino)coumarin C17H13NO3has been determined using X-ray diffraction to establish the configuration and stereochemistry of the molecule. This crystal is characterized by its nolinear activity. The molecular electron charge density distribution of the title compound is described accurately using the multipolar model of Hansen and Coppens. The net atomic charge and the molecular dipole moment in-crystal have been determined in order to understand the nature of inter-and intramolecular charge transfer. The study present the thermal motion and the structural analysis obtained from the least-square refinement on F2,this study has also allowed us to determine the electrostatic potential and therefore locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: electron charge density, net atomic charge, molecular dipole moment, X-ray diffraction

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Authors: Dih Ling Luh, Zhi Shih You, Szu Chieh Chen

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Social contact patterns among school-age children play an important role in the epidemiology of infectious disease. Since many of the greatest threats to human health are spread by direct person-to-person contact, understanding the spread of respiratory pathogens and patterns of human interactions are public health priorities. This study used social contact diaries to compare the number of contacts per day per participant across different flu/non-flu seasons and weekend/weekday. We also present contact properties such as sex, age, masking, setting, frequency, duration, and contact types among school-age children (grades 7–8). The sample size with pair-wise comparisons for the seasons (flu/non-flu) and stratification by location were 54 and 83, respectively. There was no difference in the number of contacts during the flu and non-flu seasons, with averages of 16.3 (S.D. = 12.9) and 14.6 (S.D. = 9.5) people, respectively. Weekdays were associated with 23% and 28% more contacts than weekend days during the non-flu and flu seasons, respectively (p < 0.001) (Wilcoxon signed-rank test).

Keywords: contact patterns, behavior, influenza, social mixing

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Authors: Nawaporn Srisarankullawong

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The study on the design of decorative flower patterns from Suan Sunandha Palace is the innovative design using flowers grown in Suan Sunandha Palace as the original sources. The research instrument included: 1) the photographs of flowers in watercolors painted by one of the lady in waiting of Her Royal Highness Princess Saisawareepirom as the source for investigating flowers used to grow in Suan Sunandha Palace, 2) pictures of real flowers used to grow in Suan Sunandha Palace, 3) Adobe Illustrator Program and Adobe Photoshop Program in designing the motif and decorative patterns including the prototype. The researcher chose 3 types of Suan Sunandha Palace flowers; moss rose, orchid, and lignum vitae. The details of the flowers were cut down to make simple motifs which were developed for elaborative decoration. There were 4 motifs adapted from moss roses, 3 motifs adapted from orchids, and 3 motifs adapted from lignum vitae. The patterns were used to decorate photo frames, wrapping paper, and gift boxes or souvenir boxes.

Keywords: Suan Sunandha Palace, design of decorative, flower patterns, decorative flower

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Authors: I-Ling Chang, Jer-An Chen

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The elastic properties and fracture of two-dimensional graphene were calculated purely from the atomic bonding (stretching and bending) based on molecular mechanics method. Considering the representative unit cell of graphene under various loading conditions, the deformations of carbon bonds and the variations of the interlayer distance could be realized numerically under the geometry constraints and minimum energy assumption. In elastic region, it was found that graphene was in-plane isotropic. Meanwhile, the in-plane deformation of the representative unit cell is not uniform along armchair direction due to the discrete and non-uniform distributions of the atoms. The fracture of graphene could be predicted using fracture criteria based on the critical bond length, over which the bond would break. It was noticed that the fracture behavior were directional dependent, which was consistent with molecular dynamics simulation results.

Keywords: energy minimization, fracture, graphene, molecular mechanics

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Authors: Jing Zhao, Yongqing Bai, Qiaofang Shi, Huaihao Zhang

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Advances in software technology enable computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: upper-division undergraduate, computer-based learning, laboratory instruction, molecular modeling

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

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Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: Iqbal Ahmed Chowdhury

Abstract:

Diarrhea is considered to be one of the influential factors of child death in Bangladesh. While it is known that diarrhea is a water-driven disease, due to the lack of studies, little is known about the extent to which various feeding patterns contribute to such an incidence. Our paper intends to fill this gap by looking into different feeding patterns and their influence on diarrhea incidence among children in Bangladesh. Using data collected for the Demographic and Health Survey, 2014, this paper reveals that feeding patterns can influence the diarrhea incidence among this group of children to a great extent. This paper finds that the incidence of diarrhea is likely to elevate if diarrhea-affected children are fed plain water from any source and any kind of juice. However, breastfeeding, feeding soup or clear broth, prescribed baby food, and clean water from a tube well tend to help fight diarrhea incidence among children in Bangladesh. The results are found to be consistent even after controlling for sociodemographic variables, including age and sex of children, age and education qualification of the parent, and the number of children in the family. The results of this study could contribute to treating diarrhea among children in Bangladesh as well as similar other countries in the world.

Keywords: feeding patterns, diarrhea, Bangladesh, children

Procedia PDF Downloads 79

Authors: Salem El-Tohami Ashoor

Abstract:

Here we show that the reduction of [Cr(ArN(CH2)3NAr)2Cl2] (1) where (Ar = 2,6-Pri2C6H3) and in presence of NaCp (2) (Cp= C5H5 = cyclopentadien), with a center coordination η5 interaction between Cp as co-ligand and chromium metal center, this was optimization by using density functional theory (DFT) and then was comparing with experimental data, also other possibility of Cp interacted with ion metal were tested like η1 ,η2 ,η3 and η4 under optimization system. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP ( Becke)( Lee–Yang–Parr ) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [Cr(ArN(CH2)3NAr)2(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of chromium cyclopentadienyl. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Chromium(III) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

Procedia PDF Downloads 475

Authors: Tomáš Ludík, Jiří Barta, Josef Navrátil

Abstract:

Natural or human made disasters have a significant negative impact on the environment. At the same time there is an extensive effort to support management and decision making in emergency situations by information technologies. Therefore the purpose of the paper is to propose a design patterns applicable in emergency management, enabling better analysis and design of emergency management processes and therefore easier development and deployment of information systems in the field of emergency management. It will be achieved by detailed analysis of existing emergency management legislation, contingency plans, and information systems. The result is a set of design patterns focused at emergency management processes that enable easier design of emergency plans or development of new information system. These results will have a major impact on the development of new information systems as well as to more effective and faster solving of emergencies.

Keywords: analysis and design, Business Process Modelling Notation, contingency plans, design patterns, emergency management

Procedia PDF Downloads 456

Authors: Armin Shirbazo, Mohammad Vahab, Hamed Lamei Ramandi, Jalal Fahimpour

Abstract:

One of the most effective ways for increasing production in wells that are faced with problems such as pressure depletion and low rate is hydraulic fracturing. Hydraulic fracturing is creating a high permeable path through the reservoir and simulated area around the wellbore. This is very important for low permeability reservoirs, which their production is uneconomical. In this study, the influence of the fracturing pattern in multi-stage fractured horizontal wells is analyzed for a tight, heavy oil reservoir to explore the impact of fracturing patterns on improving oil recovery. The horizontal well has five transverse fractures with the same fracture length, width, height, and conductivity properties. The fracture patterns are divided into four distinct shapes: uniform shape, diamond shape, U shape, and W shape. The results show that different fracturing patterns produce various cumulative production after ten years, and the best pattern can be selected based on the most cumulative production. The result also illustrates that optimum design in fracturing can boost the production up to 3% through the permeability distribution around the wellbore and reservoir.

Keywords: multi-stage fracturing, horizontal well, fracture patterns, fracture length, number of stages

Procedia PDF Downloads 189