Search results for: discrete sequence disorder

Authors: M. D. Antoine

Abstract:

When a child is diagnosed with an illness, condition, or developmental disorder, the process involved in understanding and accepting this diagnosis can be a very stressful and isolating experience for parents and families. The healthcare providers’ ability to effectively communicate in such situations represents a vital lifeline for parents. In this context, communication becomes a crucial element not only for getting through the period of grief but also for the future. We mobilized the five stages of grief model to summarize existing literature regarding the ways in which the experience ofan autism spectrum disorder diagnosis disclosurealigns with the experience of grief to explore how this can inform best practices for effective communication with parents through the diagnosis disclosure. Fifteen publications met inclusion criteria. Findings from the scoping review of empirical studies show that parents/families experience grief-like emotions during the diagnosis disclosure. However, grief is not an outcome of the encounter itself. In fact, the experience of the encounter can help mitigate the grief experience. The way parents/families receive and react to the ‘news’ depends on their preparedness, knowledge, and the support received through the experience. Individual communication skills, as well as policies and regulations, should be examined to alleviate adverse reactions in this context. These findings highlight the importance of further research into effective parent-provider communication strategies and their place in supporting quality autism care.

Keywords: autism spectrum disorder, autism spectrum disorder diagnosis, diagnosis disclosure, parent-provider communication, parental grief

Procedia PDF Downloads 157

Authors: Sireesha Tamada, Debraj Bhattacharjee, Pranab K. Dan, Prabha Bhola

Abstract:

The most important component in an automotive transmission system is the gearbox which controls the speed of the vehicle. In an automatic transmission, the right positioning of actuators ensures efficient transmission mechanism embodiment, wherein the challenge lies in formulating the number of actuators associated with modelling a gearbox. Data with respect to actuation and gear shifting sequence has been retrieved from the available literature, including patent documents, and has been used in this proposed heuristics based methodology for modelling actuation sequence in a gear box. This paper presents a methodological approach in designing a gearbox for the purpose of obtaining an optimal shifting sequence. The computational model considers factors namely, the number of stages and gear teeth as input parameters since these two are the determinants of the gear ratios in an epicyclic gear train. The proposed transmission schematic or stick diagram aids in developing the gearbox layout design. The number of iterations and development time required to design a gearbox layout is reduced by using this approach.

Keywords: automatic transmission, gear-shifting, multi-stage planetary gearbox, rank ordered clustering

Procedia PDF Downloads 305

Authors: Chong Wang, Kellem M. Soares, Luis E. Kosteski

Abstract:

The problem of toughening in brittle materials reinforced by fibers is complex, involving all the mechanical properties of fibers, matrix, the fiber/matrix interface, as well as the geometry of the fiber. An appropriate method applicable to the simulation and analysis of toughening is essential. In this work, we performed simulations and analysis of toughening in brittle matrix reinforced by randomly distributed fibers by means of the discrete elements method. At first, we put forward a mechanical model of the contribution of random fibers to the toughening of composite. Then with numerical programming, we investigated the stress, damage and bridging force in the composite material when a crack appeared in the brittle matrix. From the results obtained, we conclude that: (i) fibers with high strength and low elasticity modulus benefit toughening; (ii) fibers with relatively high elastic modulus compared to the matrix may result in considerable matrix damage (spalling effect); (iii) employment of high-strength synthetic fiber is a good option. The present work makes it possible to optimize the parameters in order to produce advanced ceramic with desired performance. We believe combination of the discrete element method (DEM) with the finite element method (FEM) can increase the versatility and efficiency of the software developed.

Keywords: bridging stress, discrete element method, fiber reinforced composites, toughening

Procedia PDF Downloads 428

Authors: Taiki Baba, Tomoaki Hashimoto

Abstract:

The random dither quantization method enables us to achieve much better performance than the simple uniform quantization method for the design of quantized control systems. Motivated by this fact, the stochastic model predictive control method in which a performance index is minimized subject to probabilistic constraints imposed on the state variables of systems has been proposed for linear feedback control systems with random dither quantization. In other words, a method for solving optimal control problems subject to probabilistic state constraints for linear discrete-time control systems with random dither quantization has been already established. To our best knowledge, however, the feasibility of such a kind of optimal control problems has not yet been studied. Our objective in this paper is to investigate the feasibility of stochastic model predictive control problems for linear discrete-time control systems with random dither quantization. To this end, we provide the results of numerical simulations that verify the feasibility of stochastic model predictive control problems for linear discrete-time control systems with random dither quantization.

Keywords: model predictive control, stochastic systems, probabilistic constraints, random dither quantization

Procedia PDF Downloads 263

Authors: Hanqing Yang, Xiang Meng, Qi Li, Weirong Chen

Abstract:

The SOC (state of charge) based droop control has limitations on the load power sharing among different energy storage units, due to the line impedance. In this paper, a distributed control strategy for dispersed energy storage units in the DC microgrid based on discrete consensus is proposed. Firstly, a sparse information communication network is built. Thus, local controllers can communicate with its neighbors using voltage, current and SOC information. An average voltage of grid can be evaluated to compensate voltage offset by droop control, and an objective virtual resistance fulfilling above requirement can be dynamically calculated to distribute load power according to the SOC of the energy storage units. Then, the stability of the whole system and influence of communication delay are analyzed. It can be concluded that this control strategy can improve the robustness and flexibility, because of having no center controller. Finally, a model of DC microgrid with dispersed energy storage units and loads is built, the discrete distributed algorithm is established and communication protocol is developed. The co-simulation between Matlab/Simulink and JADE (Java agent development framework) has verified the effectiveness of proposed control strategy.

Keywords: dispersed energy storage units, discrete consensus algorithm, state of charge, communication delay

Procedia PDF Downloads 256

Authors: Samira Cherid, Samir Bentata, Feyza Zahira Meghoufel, Yamina Sefir, Sabria Terkhi, Fatima Bendahma, Bouabdellah Bouadjemi, Ali Zitouni

Abstract:

Using the transfer-matrix technique and the Kronig Penney model, we numerically and analytically investigate the effect of short-range correlated disorder in random dimer model (RDM) on transmission properties of light in one dimension photonic crystals made of three different materials. Such systems consist of two different structures randomly distributed along the growth direction, with the additional constraint that one kind of these layers appears in pairs. It is shown that the one-dimensional random dimer photonic crystals support two types of extended modes. By shifting of the dimer resonance toward the host fundamental stationary resonance state, we demonstrate the existence of the ballistic response in these systems.

Keywords: photonic crystals, disorder, correlation, transmission

Procedia PDF Downloads 457

Authors: Samba Raju, Chiluveru, Manoj Tripathy

Abstract:

Intelligibility is an essential characteristic of a speech signal, which is used to help in the understanding of information in speech signal. Background noise in the environment can deteriorate the intelligibility of a recorded speech. In this paper, we presented a simple variance subtracted - variable level discrete wavelet transform, which improve the intelligibility of speech. The proposed algorithm does not require an explicit estimation of noise, i.e., prior knowledge of the noise; hence, it is easy to implement, and it reduces the computational burden. The proposed algorithm decides a separate decomposition level for each frame based on signal dominant and dominant noise criteria. The performance of the proposed algorithm is evaluated with speech intelligibility measure (STOI), and results obtained are compared with Universal Discrete Wavelet Transform (DWT) thresholding and Minimum Mean Square Error (MMSE) methods. The experimental results revealed that the proposed scheme outperformed competing methods

Keywords: discrete wavelet transform, speech intelligibility, STOI, standard deviation

Procedia PDF Downloads 129

Authors: Muhammad Umair, Tanveer Hussain, Khubab Shaker, Yasir Nawab, Muhammad Maqsood, Madeha Jabbar

Abstract:

The term comfort is defined as 'the absence of unpleasantness or discomfort' or 'a neutral state compared to the more active state'. Comfort mainly is of three types: sensorial (tactile) comfort, psychological comfort and thermo-physiological comfort. Thermophysiological comfort is determined by the air permeability and moisture management properties of the garment. The aim of this study was to investigate the effect of weave structure and picking sequence on the comfort properties of woven fabrics. Six woven fabrics with two different weave structures i.e. 1/1 plain and 3/1 twill and three different picking sequences: (SPI, DPI, 3PI) were taken as input variables whereas air permeability, wetting time, wicking behavior and overall moisture management capability (OMMC) of fabrics were taken as response variables and a comparison is made of the effect of weave structure and picking sequence on the response variables. It was found that fabrics woven in twill weave design and with simultaneous triple pick insertion (3PI) give significantly better air permeability, shorter wetting time and better water spreading rate, as compared to plain woven fabrics and those with double pick insertion (DPI) or single pick insertion (SPI). It could be concluded that the thermophysiological comfort of woven fabrics may be significantly improved simply by selecting a suitable weave design and picking sequence.

Keywords: air permeability, picking sequence, thermophysiological comfort, weave design

Procedia PDF Downloads 402

Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

Abstract:

Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

Procedia PDF Downloads 215

Authors: Goodarzvand Fatemeh, Soori Rahman, Effatpanah Mohammad, Ajbarnejad Ali

Abstract:

Attention deficit hyperactivity disorder (ADHD) is characterized by a pervasive pattern of developmentally inappropriate inattentive, impulsive and hyperactive behaviors that typically begin during the preschool ages and often persist into adulthood. This disorder is related to autism and schizophrenia and other psychological disorders and clinical conditions such as insulin resistance and they may operate through common pathways, and treatments used exclusively for one of these conditions may prove beneficial for the others. While ADHD is not fully understood as developmental disorder with an etiopathogeny, but studies show that core symptom of disorder was associated with and increased by the interleukins IL-13, where relation of IL-13 with inattention was notable. Regular exercise improves functions associated with attention deficit hyperactivity disorder (ADHD). However, the impact of exercise on cytokines associated with the disease activity remains relatively unexplored. The aim of this study was to examine the effects of 6 weeks high intensity by intervals training (HIIT) on IL-13 levels and insulin resistance in boys with ADHD. Twenty eight boys with ADHD disease in a range of 12-18 year of old participated in this study as the subject. Subjects were divided into control group (n=10) and training group (n=18) randomly. The training group performed progressive HIIT program, 3 days a week for 6 weeks. The control group was in absolute rest at the same time. The results showed that after six weeks of HIIT, IL-13 decreased in the exercise group and these changes achieved (p= 0.002) statistical significance (p < 0.005). The results suggest HIIT with specific intensity and duration utilized in this study had not significant effect on insulin resistance levels in female patients with ADHD (p=0.39), while the difference in the average control and case group was decreased.

Keywords: attention deficit hyperactivity disorder, interleukin 13, insulin resistance, high intensity by intervals training

Procedia PDF Downloads 497

Authors: Mohammed Khamis Albalushi

Abstract:

Background: Somatic symptoms disorders are usually comorbid with depressive disorders despite the fact that there is little evidence for effective treatment for it. Repetitive transcranial magnetic stimulation (rTMS) has been approved by the FDA for mildly resistant depression. From this point, we hypothesized that rTMS delivered over the prefrontal cortex (PFC) may be useful in somatic symptoms disorder. Therefore, in our case report, we want to shed light on the potential effectiveness of rTMS in somatic symptoms disorder. Case Report: A 65-year-old Omani female with multiple medical comorbidities on multiple medications. She presented complaining of multiple somatic complaints in the last 2 years after visiting multiple clinics and underwent several specialists’ examinations, investigations and procedures for somatic treatments; all of them were normal. Then patient was seen by a different psychiatric clinic; multiple anti-depressant and adjuvant anti-psychotic medications were tried, patient still did not improve. The patient was admitted to the hospital for observation and management. Initially, she was preoccupied with her somatic complaint and kept on Fluoxetine and Olanzapine along with that, topiramate was added, but still with minimal improvement. Then rTMS was added to her management plan following Intermittent theta burst (iTBS) rTMS protocol. After completing all sessions of rTMS, the patient was recovering from all her symptoms, and no complaints were reported from her. Conclusion: Our case highlights the importance of investigating more thoroughly in rTMS as a treatment option for Persistent Somatic symptoms Disorder.

Keywords: rTMS, somatic symptoms disorder, resistive cases, TMS

Procedia PDF Downloads 48

Authors: Smail Tigani, Mohamed Ouzzif

Abstract:

This work presents a discrete quantitative state prediction algorithm with intelligent behavior making it able to self-improve some performance aspects. The specificity of this algorithm is the capacity of self-rectification of the prediction strategy before the final decision. The auto-rectification mechanism is based on two parallel mathematical models. In one hand, the algorithm predicts the next state based on event transition matrix updated after each observation. In the other hand, the algorithm extracts its residues trend with a linear regression representing historical residues data-points in order to rectify the first decision if needs. For a normal distribution, the interactivity between the two models allows the algorithm to self-optimize its performance and then make better prediction. Designed key performance indicator, computed during a Monte Carlo simulation, shows the advantages of the proposed approach compared with traditional one.

Keywords: discrete state, Markov Chains, linear regression, auto-adaptive systems, decision making, Monte Carlo Simulation

Procedia PDF Downloads 485

Authors: Javiera Espinosa, Patricia López, Noelia Santos, Nadia Loro, Esther Moraleda

Abstract:

In recent years, there has been a notable increase in the number of investigations that establish that Down Syndrome and Autism Spectrum Disorder are diagnoses that can coexist together. However, there are also many studies that consider that both diagnoses present neuropsychological, linguistic and adaptive characteristics with a totally different profile. The objective of this research is to question whether there really can be a profile that encompasses both disorders or if they can be incompatible with each other. To this end, a review of the scientific literature of recent years has been carried out. The results indicate that the two lines collect opposite approaches. On the one hand, there is research that supports the increase in comorbidity between Down Syndrome and Autism Spectrum Disorder, and on the other hand, many investigations show a totally different general development profile between the two. The discussion focuses on discussing both lines of work and on proposing future lines of research in this regard.

Keywords: disability, language, speech, down syndrome

Procedia PDF Downloads 57

Authors: A. Bere, H. G. Sithuba, K. Kyei, C. Sigauke

Abstract:

We employ a discrete logit survival model to investigate the risk factors for early alcohol intake among students at two tertiary institutions in Thohoyandou, South Africa. Data were collected from a sample of 744 students using a self-administered questionnaire. Significant covariates were arrived at through a regularization algorithm implemented using the glmmLasso package. The tuning parameter was determined using a five-fold cross-validation algorithm. The baseline hazard was modelled as a smooth function of time through the use of spline functions. The results show that the hazard of initial alcohol intake peaks at the age of about 16 years and that at any given time, being of a male gender, prior use of other drugs, having drinking peers, having experienced negative life events and physical abuse are associated with a higher risk of alcohol intake debut.

Keywords: cross-validation, discrete hazard model, LASSO, smooth baseline hazard

Procedia PDF Downloads 172

Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 149

Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 137

Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

Abstract:

Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

Procedia PDF Downloads 95

Authors: R. Sabre, W. Horrigue, J. C. Simon

Abstract:

This paper is interested in two difficulties encountered in practice when observing a continuous time process. The first is that we cannot observe a process over a time interval; we only take discrete observations. The second is the process frequently observed with a constant additive error. It is important to give an estimator of the spectral density of such a process taking into account the additive observation error and the choice of the discrete observation times. In this work, we propose an estimator based on the spectral smoothing of the periodogram by the polynomial Jackson kernel reducing the additive error. In order to solve the aliasing phenomenon, this estimator is constructed from observations taken at well-chosen times so as to reduce the estimator to the field where the spectral density is not zero. We show that the proposed estimator is asymptotically unbiased and consistent. Thus we obtain an estimate solving the two difficulties concerning the choice of the instants of observations of a continuous time process and the observations affected by a constant error.

Keywords: spectral density, stable processes, aliasing, periodogram

Procedia PDF Downloads 123

Authors: A. Hossein Madadi-Najafabadi, Masoud Nasiri

Abstract:

The discrete element method is a powerful technique for numerical modeling the flow of granular materials such as direct reduced iron. It would enable us to study processes and equipment related to the production and handling of the material. However, the characteristics and properties of the granules have to be adjusted precisely to achieve reliable results in a DEM simulation. The main properties for DEM simulation are size distribution, density, Young's modulus, Poisson's ratio and the contact coefficients of restitution, rolling friction and sliding friction. In the present paper, the mentioned properties are determined for DEM simulation of DRI pellets. A reliable DEM simulation would contribute to optimizing the handling system of DRIs in an iron-making plant. Among the mentioned properties, Young's modulus is the most important parameter, which is usually hard to get for particulate solids. Here, an especial method is utilized to precisely determine this parameter for DRI.

Keywords: discrete element method, direct reduced iron, simulation parameters, granular material

Procedia PDF Downloads 162

Authors: Ngoc Trung Ngo, Buddhima Indraratna, Cholachat Rujikiathmakjornr

Abstract:

For several hundred years, the design of railway tracks has practically remained unchanged. Traditionally, rail tracks are placed on a ballast layer due to several reasons, including economy, rapid drainage, and high load bearing capacity. The primary function of ballast is to distributing dynamic track loads to sub-ballast and subgrade layers, while also providing lateral resistance and allowing for rapid drainage. Upon repeated trainloads, the ballast becomes fouled due to ballast degradation and the intrusion of fines which adversely affects the strength and deformation behaviour of ballast. This paper presents the use of three-dimensional discrete element method (DEM) in studying the shear behaviour of the fouled ballast subjected to direct shear loading. Irregularly shaped particles of ballast were modelled by grouping many spherical balls together in appropriate sizes to simulate representative ballast aggregates. Fouled ballast was modelled by injecting a specified number of miniature spherical particles into the void spaces. The DEM simulation highlights that the peak shear stress of the ballast assembly decreases and the dilation of fouled ballast increases with an increase level of fouling. Additionally, the distributions of contact force chain and particle displacement vectors were captured during shearing progress, explaining the formation of shear band and the evolutions of volumetric change of fouled ballast.

Keywords: railway ballast, coal fouling, discrete element modelling, discrete element method

Procedia PDF Downloads 435

Authors: Xiao Zhou, Jianlin Cheng

Abstract:

A single amino acid mutation can have a significant impact on the stability of protein structure. Thus, the prediction of protein stability change induced by single site mutations is critical and useful for studying protein function and structure. Here, we presented a deep learning network with the dropout technique for predicting protein stability changes upon single amino acid substitution. While using only protein sequence as input, the overall prediction accuracy of the method on a standard benchmark is >85%, which is higher than existing sequence-based methods and is comparable to the methods that use not only protein sequence but also tertiary structure, pH value and temperature. The results demonstrate that deep learning is a promising technique for protein stability prediction. The good performance of this sequence-based method makes it a valuable tool for predicting the impact of mutations on most proteins whose experimental structures are not available. Both the downloadable software package and the user-friendly web server (DNpro) that implement the method for predicting protein stability changes induced by amino acid mutations are freely available for the community to use.

Keywords: bioinformatics, deep learning, protein stability prediction, biological data mining

Procedia PDF Downloads 439

Authors: Ehsan Yadegari

Abstract:

While there are several metaheuristics and exact approaches to solving the Supply Chain Network Design (SCND) problem, there still remains an unfilled gap in using the Teaching-Learning-Based Optimization (TLBO) algorithm. The algorithm has demonstrated desirable results with problems with complicated combinational optimization. The present study introduces a Discrete Self-Study TLBO (DSS-TLBO) with priority-based solution representation that can solve a supply chain network configuration model to lower the total expenses of establishing facilities and the flow of materials. The network features four layers, namely suppliers, plants, distribution centers (DCs), and customer zones. It is designed to meet the customer’s demand through transporting the material between layers of network and providing facilities in the best economic Potential locations. To have a higher quality of the solution and increase the speed of TLBO, a distinct operator was introduced that ensures self-adaptation (self-study) in the algorithm based on the four types of local search. In addition, while TLBO is used in continuous solution representation and priority-based solution representation is discrete, a few modifications were added to the algorithm to remove the solutions that are infeasible. As shown by the results of experiments, the superiority of DSS-TLBO compared to pure TLBO, genetic algorithm (GA) and firefly Algorithm (FA) was established.

Keywords: supply chain network design, teaching–learning-based optimization, improved metaheuristics, discrete solution representation

Procedia PDF Downloads 30

Authors: Dong Tran, Thanh Dac Van, Ly Le

Abstract:

Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

Procedia PDF Downloads 140

Authors: Ryan Tehini

Abstract:

The purpose of this paper is to explore the value of practical experience with Autism Spectrum Disorder (ASD) as a microcosm of mental disorders, in psychology students’ attempt to fully understand it in all of its intricacies. The study follows a one-year program where students of psychology volunteer at a school for Autistic children of ages 3-18. The individual levels of experience with, and theoretical understanding of, ASD varies measurably amongst the volunteers; these volunteers are then intermittently interviewed, observed and surveyed throughout the program in order to determine any decline or growth in their understanding of Autism Spectrum Disorder. A panel of professionals all of whom are active in the world of ASD (headmasters of Autistic schools, psychologists, child development specialists, special needs teachers, parents of autistic children and Occupational Therapists) were used specifically for this study, in order to develop the guideline for understanding ASD that will be used comparatively against the information gained from the volunteers in order to establish the individual results. The paper concludes by illustrating how psychology has a responsibility to the community to understand disorders past what is academic and theoretical, and how increasing student experience with a disorder can aid in a more holistic psychological approach to mental disorders in the future.

Keywords: autism, mental disorders, practical experience, psychology

Procedia PDF Downloads 239

Authors: Shervin Khazaeli, Shahab Haj-zamani

Abstract:

Recently, advanced geotechnical engineering problems related to soil movement, particle loss, and modeling of local failure (i.e. discontinua) as well as modeling the in-contact structures (i.e. continua) are of the great interest among researchers. The aim of this research is to meet the requirements with respect to the modeling of the above-mentioned two different domains simultaneously. To this end, a coupled numerical method is introduced based on Discrete Element Method (DEM) and eXtended-Finite Element Method (X-FEM). In the coupled procedure, DEM is employed to capture the interactions and relative movements of soil particles as discontinua, while X-FEM is utilized to model in-contact structures as continua, which may consist of different types of discontinuities. For verification purposes, the new coupled approach is utilized to examine benchmark problems including different contacts between/within continua and discontinua. Results are validated by comparison with those of existing analytical and numerical solutions. This study proves that extended-finite-discrete element method can be used to robustly analyze not only contact problems, but also other types of discontinuities in continua such as (i) crack formations and propagations, (ii) voids and bimaterial interfaces, and (iii) combination of previous cases. In essence, the proposed method can be used vastly in advanced soil-structure interaction problems to investigate the micro and macro behaviour of the surrounding soil and the response of the embedded structure that contains discontinuities.

Keywords: contact problems, discrete element method, extended-finite element method, soil-structure interaction

Procedia PDF Downloads 481

Authors: Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Fayez Gebali

Abstract:

This paper presents a novel semi-systolic array architecture for an optimized parallel sequence alignment algorithm. This architecture has the advantage that it can be modified to be reused for multiple pass processing in order to increase the number of processing elements that can be packed into a single FPGA and to increase the number of sequences that can be aligned in parallel in a single FPGA. This resolves the potential problem of many FPGA resources left unused for designs that have large values of short read length. When using the previously published conventional hardware design. FPGA implementation results show that, for large values of short read lengths (M>128), the proposed design has a slightly higher speed up and FPGA utilization over the the conventional one.

Keywords: bioinformatics, genome sequence alignment, re-sequencing applications, systolic array

Procedia PDF Downloads 510

Authors: K. Yahia, A. Ghoggal, A. Titaouine, S. E. Zouzou, F. Benchabane

Abstract:

This paper deals with the problem of stator faults diagnosis in induction motors. Using the discrete wavelet transform (DWT) for the current Park’s vector modulus (CPVM) analysis, the inter-turn short-circuit faults diagnosis can be achieved. This method is based on the decomposition of the CPVM signal, where wavelet approximation and detail coefficients of this signal have been extracted. The energy evaluation of a known bandwidth detail permits to define a fault severity factor (FSF). This method has been tested through the simulation of an induction motor using a mathematical model based on the winding-function approach. Simulation, as well as experimental, results show the effectiveness of the used method.

Keywords: Induction Motors (IMs), Inter-turn Short-Circuits Diagnosis, Discrete Wavelet Transform (DWT), Current Park’s Vector Modulus (CPVM)

Procedia PDF Downloads 546

Authors: Alica Miller

Abstract:

A semiflow is a triple consisting of a Hausdorff topological space $X$, a commutative topological monoid $T$ and a continuous monoid action of $T$ on $X$. The acting monoid $T$ is usually either the discrete monoid $\N_0$ of nonnegative integers (in which case the semiflow can be defined as a pair $(X,f)$ consisting of a phase space $X$ and a continuous function $f:X\to X$), or the monoid $\R_+$ of nonnegative real numbers (the so-called one-parameter monoid). However, it turns out that there are real-life situations where it is useful to consider the acting monoids that are a combination of discrete and continuous monoids. That, for example, happens, when we are observing certain dynamical system at discrete moments, but after some time realize that it would be beneficial to continue our observations in real time. The acting monoid in that case would be $T=\{0, t_0, 2t_0, \dots, (n-1)t_0\} \cup [nt_0,\infty)$ with the operation and topology induced from real numbers. This partly explains the motivation for the level of generality which is pursued in our research. We introduce the PSP monoids, which include all but ``pathological'' monoids, and most of our statements hold for them. The topic of our presentation are some recent results about chaos-related properties in semiflows, indecomposability and sensitivity of semiflows in the described general context.

Keywords: chaos, indecomposability, PSP monoids, semiflow, sensitivity

Procedia PDF Downloads 271

Authors: Elena Jiménez Lidueña, Noelia Santos Muriel, Patricia López Resa, Noelia Pulido García, Esther Moraleda Sepúlveda

Abstract:

In recent years, there has been a notable increase in the number of investigations that establish that Down Syndrome and Autism Spectrum Disorder are diagnoses that can coexist together. However, there are also many studies that consider that both diagnoses present neuropsychological, linguistic and adaptive characteristics with a totally different profiles. The objective of this research is to question whether there really can be a profile that encompasses both disorders or if they can be incompatible with each other. To this end, a review of the scientific literature of recent years has been carried out. The results indicate that the two lines collect opposite approaches. On the one hand, there is research that supports the increase in comorbidity between Down Syndrome and Autism Spectrum Disorder and, on the other hand, shows a totally different general development profile between the two. The discussion focuses on discussing both lines of work and on proposing future lines of research in this regard.

Keywords: Down Syndrome, Autism, comorbidity, linguistic

Procedia PDF Downloads 89

Authors: Anjan Hazra, Nirjhar Dasgupta, Chandan Sengupta, Sauren Das

Abstract:

Tea (Camellia sinensis) has received substantial attention from the scientific world time to time, not only for its commercial importance, but also for its demand to the health-conscious people across the world for its extensive use as potential sources of antioxidant supplement. These health-benefit traits primarily rely on some regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions is being worthwhile for studying the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea the trait-specific Simple Sequence Repeats (SSRs) are yet to be identified, which can be used for marker assisted breeding technique. MicroRNAs are endogenous, noncoding, short RNAs directly involved in regulating gene expressions at the post-transcriptional level. It has been found that diversity in miRNA gene interferes the formation of its characteristic hair pin structure and the subsequent function. In the present study, the precursors of small regulatory RNAs (microRNAs) has been fished out from tea Expressed Sequence Tag (EST) database. Furthermore, the simple sequence repeat motifs within the putative miRNA precursor genes are also identified in order to experimentally validate their existence and function. It is already known that genic-SSR markers are very adept and breeder-friendly source for genetic diversity analysis. So, the potential outcome of this in-silico study would provide some novel clues in understanding the miRNA-triggered polymorphic genic expression controlling specific metabolic pathways, accountable for tea quality.

Keywords: micro RNA, simple sequence repeats, tea quality, trait specific marker

Procedia PDF Downloads 292