Search results for: whole genome sequence

Authors: Usman Qamar, Younus Javed

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Frequent pattern mining is the process of finding a pattern (a set of items, subsequences, substructures, etc.) that occurs frequently in a data set. It was proposed in the context of frequent itemsets and association rule mining. Frequent pattern mining is used to find inherent regularities in data. What products were often purchased together? Its applications include basket data analysis, cross-marketing, catalog design, sale campaign analysis, Web log (click stream) analysis, and DNA sequence analysis. However, one of the bottlenecks of frequent itemset mining is that as the data increase the amount of time and resources required to mining the data increases at an exponential rate. In this investigation a new algorithm is proposed which can be uses as a pre-processor for frequent itemset mining. FASTER (FeAture SelecTion using Entropy and Rough sets) is a hybrid pre-processor algorithm which utilizes entropy and rough-sets to carry out record reduction and feature (attribute) selection respectively. FASTER for frequent itemset mining can produce a speed up of 3.1 times when compared to original algorithm while maintaining an accuracy of 71%.

Keywords: rough-sets, classification, feature selection, entropy, outliers, frequent itemset mining

Procedia PDF Downloads 437

Authors: Abdorrasoul Malekpour, Mohammad Ghorbani Mojtaba Mortazavi, Mohammadreza Fattahi, Mohammad Hassan Meshkibaf, Ali Fakhrzad, Saeid Salehi, Saeideh Zahedi, Amir Ahmadimoghaddam, Parviz Farzadnia Dr., Mohammadreza Hajyani Asl Bs

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Hepatitis B as an infectious disease has eight main genotypes (A–H). The aim of this study is to Bioinformatically identify Rare Codon Clusters (RCC) in proteins structure of HBV. For detection of protein family accession numbers (Pfam) of HBV proteins; used of uni-prot database and Pfam search tool were used. Obtained Pfam IDs were analyzed in Sherlocc program and RCCs in HBV proteins were detected. In further, the structures of TrEMBL entries proteins studied in PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software. Pfam search tool have found nine significant hits and 0 insignificant hits in 3 frames. Results of Pfams studied in the Sherlocc program show this program not identified RCCs in the external core antigen (PF08290) and truncated HBeAg protein (PF08290). By contrast the RCCs become identified in Hepatitis core antigen (PF00906) Large envelope protein S (PF00695), X protein (PF00739), DNA polymerase (viral) N-terminal domain (PF00242) and Protein P (Pf00336). In HBV genome, seven RCC identified that found in hepatitis core antigen, large envelope protein S and DNA polymerase proteins and proteins structures of TrEMBL entries sequences that reported in Sherlocc program outputs are not complete. Based on situation of RCC in structure of HBV proteins, it suggested those RCCs are important in HBV life cycle. We hoped that this study provide a new and deep perspective in protein research and drug design for treatment of HBV.

Keywords: rare codon clusters, hepatitis B virus, bioinformatic study, infectious disease

Procedia PDF Downloads 488

Authors: Soni Nopembri

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The objective of this research is to evaluate the implementation of teaching games for Understanding model by conducting action to physical education teacher who have got long teaching experience. The research applied Participatory Action Research. The subjects of this research were 19 physical education teachers who had got training of Teaching Games for Understanding. Data collection was conducted intensively through a questionnaire, in-depth interview, Focus Group Discussion (FGD), observation, and documentation. The collected data was analysis zed qualitatively and quantitatively. The result showed that physical education teachers had got an appropriate interpretation on TGfU model. Some indicators that were the focus of this research indicated this points; they are: (1) physical education teachers had good understanding toward TGfU model, (2) PE teachers’ competence in applying TGfU model on Physical Education at school were adequate, though some improvement were needed, (3) the influence factors in the implementation of TGfU model, in sequence, were teacher, facilities, environment, and students factors, (4) PE teachers’ perspective toward TGfU model were positively good, although some teachers were less optimistic toward the development of TGfU model in the future.

Keywords: TGfU, physical education teacher, teaching games, FGD

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Authors: Giovanni Forte, Melania De Falco, Antonio Santo

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On 24th August 2016, central Italy was affected by a Mw 6.0 earthquake, representing the main shock of a long seismic sequence, which had a second shock Mw 6.6 on 26th October and lasts still nowadays. After the event, several field survey were carried out in the affected areas, which is made of historical masonry buildings. The post event reconnaissance missions were aimed at collecting information on the damage states of the buildings, the triggering of the landslides and the relationships with site effects. In this paper, the data collected after the event are analyzed considering the role of the geological and geomorphological setting and the ground motion scenario. The buildings displayed an uneven damage distribution, which was affected by both topographic and stratigraphic amplification. As pertains the landslides, which were the most recurrent among the ground failures, consisted mainly of rock falls and subordinately of translational slides. Finally, the collected knowledge showed a strong contribution of the local geological and geomorphological site condition on the resulting damage.

Keywords: Amatrice earthquake, damage states, landslides, site effects

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Authors: Muhammad Luqman, Yusuf Kurniawan

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S-Boxes is one of the linear parts of the cryptographic algorithm. The existence of S-Box in the cryptographic algorithm is needed to maintain non-linearity of the algorithm. Nowadays, modern cryptographic algorithms use an S-Box as a part of algorithm process. Despite the fact that several cryptographic algorithms today reuse theoretically secure and carefully constructed S-Boxes, there is an evaluation characteristic that can measure security properties of S-Boxes and hence the corresponding primitives. Analysis of an S-Box usually is done using manual mathematics calculation. Several S-Boxes are presented as a Truth Table without any mathematical background algorithm. Then, it’s rather difficult to determine the strength of Truth Table S-Box without a mathematical algorithm. A comprehensive analysis should be applied to the Truth Table S-Box to determine the characteristic. Several important characteristics should be owned by the S-Boxes, they are Nonlinearity, Balancedness, Algebraic degree, LAT, DAT, differential delta uniformity, correlation immunity and global avalanche criterion. Then, a comprehensive tool will be present to automatically calculate the characteristics of S-Boxes and determine the strength of S-Box. Comprehensive analysis is done on a deterministic process to produce a sequence of S-Boxes characteristic and give advice for a better S-Box construction.

Keywords: cryptographic properties, Truth Table S-Boxes, S-Boxes characteristic, deterministic process

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Authors: Abdullah M. Alzahrani

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The unicellular alga Chlorella vulgaris was isolated from Al-Asfar Lake, which is located in the Al-Ahsa province of Saudi Arabia. Two different isolates were sub-cultured under laboratory conditions. The wild type was grown under a regular concentration of copper, whereas the other isolate was grown under a progressively increasing copper concentration. An Inter Simple Sequence Repeats (ISSR) analysis was performed using DNA isolated from the wild type and tolerant strains. The sum of the scored bands of the wild type was 155, with 100 (64.5%) considered to be polymorphic bands, whereas the resistant strain displayed 147 bands, with 92 (62.6%) considered to be polymorphic bands. The sum of the scored bands of a mixed sample was 117 bands, of which only 4 (3.4%) were considered to be polymorphic. The average Nei's genetic diversity (h) and Shannon-Weiner diversity indices (I) were 0.3891 and 0.5394, respectively. These results clearly indicate that the adaptation to a high level of copper in Chlorella vulgaris is not merely physiological but rather driven by modifications at the genomic level.

Keywords: chlorella vulgaris, copper tolerance, genetic diversity, green algae

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Authors: Murali Aarthy, Sanjeev Kumar Singh

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High risk human papillomaviruses are highly associated with the carcinoma of the cervix and the other genital tumors. Cervical cancer develops through the multistep process in which increasingly severe premalignant dysplastic lesions called cervical intraepithelial neoplastic progress to invasive cancer. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers drives the cells into S-phase creating an environment conducive for viral genome replication and cell proliferation. The replication of the virus occurs in the terminally differentiating epithelium and requires the activation of cellular DNA replication proteins. To date, no suitable drug molecule is available to treat HPV infection whereas identification of potential drug targets and development of novel anti-HPV chemotherapies with unique mode of actions are expected. Hence, our present study aimed to identify the potential inhibitors analogous to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems. A 3D similarity search on the natural small molecule library from natural product database using EGCG identified 11 potential hits based on their similarity score. The structure based docking strategies were implemented in the potential hits and the key interacting residues of protein with compounds were identified through simulation studies and binding free energy calculations. The conformational changes between the apoprotein and the complex were analyzed with the simulation and the results demonstrated that the dynamical and structural effects observed in the protein were induced by the compounds and indicated the dominance to the oncoprotein. Overall, our study provides the basis for the structural insights of the identified potential hits and EGCG and hence, the analogous compounds identified can be potent inhibitors against the HPV 16 E7 oncoprotein.

Keywords: EGCG, oncoprotein, molecular dynamics simulation, analogues

Procedia PDF Downloads 127

Authors: Adi A. Maaita, Hamza A. A. Al Sewadi

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One of the crucial parameters of digital cryptographic systems is the selection of the keys used and their distribution. The randomness of the keys has a strong impact on the system’s security strength being difficult to be predicted, guessed, reproduced or discovered by a cryptanalyst. Therefore, adequate key randomness generation is still sought for the benefit of stronger cryptosystems. This paper suggests an algorithm designed to generate and test pseudo random number sequences intended for cryptographic applications. This algorithm is based on mathematically manipulating a publically agreed upon information between sender and receiver over a public channel. This information is used as a seed for performing some mathematical functions in order to generate a sequence of pseudorandom numbers that will be used for encryption/decryption purposes. This manipulation involves permutations and substitutions that fulfills Shannon’s principle of “confusion and diffusion”. ASCII code characters wereutilized in the generation process instead of using bit strings initially, which adds more flexibility in testing different seed values. Finally, the obtained results would indicate sound difficulty of guessing keys by attackers.

Keywords: cryptosystems, information security agreement, key distribution, random numbers

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Authors: Nada Slimane, Foued Theljani, Faouzi Bouani

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The paper addresses the problem of fault diagnosis for systems operating in several modes (normal or faulty) based on states assessment. We use, for this purpose, a methodology consisting of three main processes: 1) sequential data clustering, 2) linear model regression and 3) state filtering. Typically, Kalman Filter (KF) is an algorithm that provides estimation of unknown states using a sequence of I/O measurements. Inevitably, although it is an efficient technique for state estimation, it presents two main weaknesses. First, it merely predicts states without being able to isolate/classify them according to their different operating modes, whether normal or faulty modes. To deal with this dilemma, the KF is endowed with an extra clustering step based fully on sequential version of the k-means algorithm. Second, to provide state estimation, KF requires state space models, which can be unknown. A linear regularized regression is used to identify the required models. To prove its effectiveness, the proposed approach is assessed on a simulated benchmark.

Keywords: clustering, diagnosis, Kalman Filtering, k-means, regularized regression

Procedia PDF Downloads 182

Authors: Salim Omar Raoof

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This study was conducted at the Al-Salam cows’ station for milk production located in Al-Latifiya district - Al-Mahmudiyah district (25 km south of Baghdad governorate) on a sample of (180) Holstein cows imported from Germany by Taj Al-Nahrain company in order to study the effect of the sequence, season and calving year on Total Milk Production (TMP). The lactation period (LP), calving interval, Services per conception and the estimate of the heritability of the studied traits. The results showed that the overall mean of TMP and LP were 3172.53 kg and 237.09-day respectively. The parity effect on TMP in Holstein cows was highly significant (P≤0.01). Total Milk production increased with the advance of parity and mostly reached its maximum value in the 4th and 3rd parity being 3305.87 kg and3286.35 kg per day, respectively. Season of calving has a highly significant (P≤0.01), effect on (TMP). Cows calved in spring had a highest milk production than those calved in other seasons. Season of calving had a highly significant (P≤0.01) effect on services per conception. The result of the study showed the heritability values for TMP, LP, SPC and CL were 0.21, 0.08, 0.08 and 0.07, respectively.

Keywords: cows, non genetic, milk production, heritability

Procedia PDF Downloads 79

Authors: R. A. Eman Elsheikh, Bart Schultz, Abraham Mehari Haile, Hussein S. Adam

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A field experiment was conducted at Gezira research station farm during the winter season in the third week of November 2012, in WadMedani, Sudan (Lat 14.23 W, Long 33.39 E and altitude 405 m above sea level, in deep cracking alkaline heavy clay Vertisols). The objective of this study was to determine the effect of three different irrigation for 10 days (W1), 15 days (W2) and 20 days (W3) and for two rows of 30 cm (S1) and 40 cm (S2), respectively. The experimental design was split plot with three replicates. The sunflower test variety was Hysun 33 cultivar. The seasonal water applied during the study was 6898, 6647, 5256, 5435, 5214, 5416 m3/ha for W1S1, W1S2, W2S1, W2S2, W3S1 and W3S2 respectively. The seed yield obtained for the above treatment in that sequence was 4208, 5542, 5167, 4579, 2931, 2936 kg/ha. The corresponding computed water productivity was 0.61, 0.82, 0.87, 0.95, 0.54, 0.56 kg/m3. The study clearly indicated that the highest seed yield was obtained when the crop was sown at 40 cm row spacing and was irrigated every 10 days (W1S2), followed by W2S1.

Keywords: water productivity, water deficit, sunflower, plant spacing

Procedia PDF Downloads 349

Authors: Camilo Cerda Sarabia, Fernanda Bravo Cornejo, Diego Santibanez Oyarce, Hugo Osses Prado, Esteban Gómez Terán, Belén Diaz Diaz, Raúl Caulier-Cisterna, Jorge Vergara-Quezada, Ana Moya-Beltrán

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Antimicrobial resistance (AMR) represents a significant and rapidly escalating global health threat. Projections estimate that by 2050, AMR infections could claim up to 10 million lives annually. Respiratory infections, in particular, pose a severe risk not only to individual patients but also to the broader public health system. Despite the alarming rise in resistant respiratory infections, AMR within the lung microbiome (microbial community) remains underexplored and poorly characterized. The lungs, as a complex and dynamic microbial environment, host diverse communities of microorganisms whose interactions and resistance mechanisms are not fully understood. Unlike studies that focus on individual genomes, analyzing the entire microbiome provides a comprehensive perspective on microbial interactions, resistance gene transfer, and community dynamics, which are crucial for understanding AMR. However, this holistic approach introduces significant computational challenges and exposes the limitations of traditional analytical methods such as the difficulty of identifying the AMR. Machine learning has emerged as a powerful tool to overcome these challenges, offering the ability to analyze complex genomic data and uncover novel insights into AMR that might be overlooked by conventional approaches. This study investigates microbial resistance within the lung microbiome using unsupervised machine learning approaches to uncover resistance patterns and potential clinical associations. it downloaded and selected lung microbiome data from HumanMetagenomeDB based on metadata characteristics such as relevant clinical information, patient demographics, environmental factors, and sample collection methods. The metadata was further complemented by details on antibiotic usage, disease status, and other relevant descriptions. The sequencing data underwent stringent quality control, followed by a functional profiling focus on identifying resistance genes through specialized databases like Antibiotic Resistance Database (CARD) which contains sequences of AMR gene sequence and resistance profiles. Subsequent analyses employed unsupervised machine learning techniques to unravel the structure and diversity of resistomes in the microbial community. Some of the methods employed were clustering methods such as K-Means and Hierarchical Clustering enabled the identification of sample groups based on their resistance gene profiles. The work was implemented in python, leveraging a range of libraries such as biopython for biological sequence manipulation, NumPy for numerical operations, Scikit-learn for machine learning, Matplotlib for data visualization and Pandas for data manipulation. The findings from this study provide insights into the distribution and dynamics of antimicrobial resistance within the lung microbiome. By leveraging unsupervised machine learning, we identified novel resistance patterns and potential drivers within the microbial community.

Keywords: antibiotic resistance, microbial community, unsupervised machine learning., sequences of AMR gene

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Authors: Salim Omar Raoof

Abstract:

This study was conducted at the Al-Salam cows’ station for milk production located in Al-Latifiya district - Al-Mahmudiyah district (25 km south of Baghdad governorate) on a sample of (180) Holstein cows imported from Germany by Taj Al-Nahrain company, in order to study the effect of the sequence, season and calving year on Total Milk Production (TMP). the lactation period (LP), calving interval, Services per conception and the estimate the heritability of the studied traits. The results showed that the overall mean of TMP and LP were 3172.53 kg and237.09-day respectively. The parity effect on TMP in Holstein cows was highly significant (P≤0.01). total Milk production increased with the advanced of parity and mostly reached its maximum value in the 4th and 3rd parity being 3305.87 kg and3286.35 kg per day, respectively. Season of calving has a highly significant (P≤0.01) effect on (TMP). Cows calved in spring had a highest milk production than that calved in other seasons. Season of calving had highly significant (P≤0.01) effect on services per conception. The result of the study showed the heritability value for TMP, LP, SPC and CL were 0.21 ,0.08 ,0.08 and 0.07 respectively.

Keywords: Holstein, cows, milk production, non-genetic, hertability

Procedia PDF Downloads 66

Authors: Mengying Wang, Dongjing Liu, Holger Schwender, Ping Wang, Hongping Zhu, Tao Wu, Terri H Beaty

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Background: Maternal smoking is a recognized risk factor for nonsyndromic cleft lip with or without cleft palate (NSCL/P). It has been reported that the effect of maternal smoking on oral clefts is mediated through genes that influence nicotine dependence. The polymorphisms of cholinergic receptor nicotinic alpha (CHRNA) and beta (CHRNB) subunits genes have previously shown strong associations with nicotine dependence. Here, we attempted to investigate whether the above genes are associated with clefting risk through testing for potential gene-gene (G×G) and gene-environment (G×E) interaction. Methods: We selected 120 markers in 14 genes associated with nicotine dependence to conduct transmission disequilibrium tests among 806 Chinese NSCL/P case-parent trios ascertained in an international consortium which conducted a genome-wide association study (GWAS) of oral clefts. We applied Cordell’s method using “TRIO” package in R to explore G×G as well as G×E interaction involving environmental tobacco smoke (ETS) based on conditional logistic regression model. Results: while no SNP showed significant association with NSCL/P after Bonferroni correction, we found signals for G×G interaction between 10 pairs of SNPs in CHRNA3, CHRNA5, and CHRNB4 (p<10-8), among which the most significant interaction was found between RS3743077 (CHRNA3) and RS11636753 (CHRNB4, p<8.2×10-12). Linkage disequilibrium (LD) analysis revealed only low level of LD between these markers. However, there were no significant results for G×ETS interaction. Conclusion: This study fails to detect association between nicotine dependence genes and NSCL/P, but illustrates the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P. This study also suggests nicotine dependence genes should be considered as important candidate genes for NSCL/P in future studies.

Keywords: Gene-Gene Interaction, Maternal Smoking, Nicotine Dependence, Non-Syndromic Cleft Lip with or without Cleft Palate

Procedia PDF Downloads 337

Authors: Jyh-Cherng Chen, Yu-Zen Lin, Wei-Zhi Chen

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Torrefaction is one of waste to energy (WTE) technologies developing in Taiwan recently, which can reduce the moisture and impurities and increase the energy density of biowaste effectively. To understand the torrefaction characteristics of different biowaste and the influences of different torrefaction conditions, four typical biowaste were selected to carry out the torrefaction experiments. The physical and chemical properties of different biowaste prior to and after torrefaction were analyzed and compared. Experimental results show that the contents of elemental carbon and caloric value of the four biowaste were significantly increased after torrefaction. The increase of combustible and caloric value in bamboo was the greatest among the four biowaste. The caloric value of bamboo can be increased from 1526 kcal/kg to 6104 kcal/kg after 300oC and 1 hour torrefaction. The caloric value of torrefied bamboo was almost four times as the original. The increase of elemental carbon content in wood was the greatest (from 41.03% to 75.24%), and the next was bamboo (from 47.07% to 74.63%). The major parameters which affected the caloric value of torrefied biowaste followed the sequence of biowaste kinds, torrefaction time, and torrefaction temperature. The optimal torrefaction conditions of the experiments were bamboo torrefied at 300oC for 3 hours, and the corresponding caloric value of torrefied bamboo was 5953 kcal/kg. This caloric value is similar to that of brown coal or bituminous coal.

Keywords: torrefaction, waste to energy, calorie, biofuel

Procedia PDF Downloads 372

Authors: K. Cartelier, D. Aime, V. Vernoud, J. Buitink, J. M. Prosperi, K. Gallardo, C. Le Signor

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Legumes can produce protein-rich seeds without nitrogen fertilizer through root symbiosis with nitrogen-fixing rhizobia. Rich in lysine, these proteins are used for human nutrition and animal feed. However, the instability of seed protein yield and quality due to environmental fluctuations limits the wider use of legumes such as pea. Breeding efforts are needed to optimize and stabilize seed nutritional value, which requires to identify the genetic determinism of seed protein plasticity in response to the environment. Towards this goal, we have studied the plasticity of protein content and composition of seeds from a collection of 200 Medicago truncatula ecotypes grown under four controlled conditions (optimal, drought, and winter/spring sowing). A quantitative analysis of one-dimensional protein profiles of these mature seeds was performed and plasticity indices were calculated from each abundant protein band. Genome-Wide Association Studies (GWAS) from these data identified major GWAS hotspots, from which a list of candidate genes was obtained. A Gene Ontology Enrichment Analysis revealed an over-representation of genes involved in several amino acid metabolic pathways. This led us to propose that environmental variations are likely to modulate amino acid balance, thus impacting seed protein composition. The selection of candidate genes for controlling the plasticity of seed protein composition was refined using transcriptomics data from developing Medicago truncatula seeds. The pea orthologs of key genes were identified for functional studies by mean of TILLING (Targeting Induced Local Lesions in Genomes) lines in this crop. We will present how this study highlighted mechanisms that could govern seed protein plasticity, providing new cues towards the stabilization of legume seed quality.

Keywords: GWAS, Medicago truncatula, plasticity, seed, storage proteins

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Authors: Elham Saraee, Saurabh Singh, Margrit Betke

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Evaluation of a person’s posture while exercising is important in physical therapy. During a therapy session, a physical therapist or a monitoring system must assure that the person is performing an exercise correctly to achieve the desired therapeutic effect. In this work, we introduce a system called POSTURECHECK for exercise assessment in physical therapy. POSTURECHECK assesses the posture of a person who is exercising with the Proficio robotic arm while being recorded by the Microsoft Kinect interface. POSTURECHECK extracts unique features from the person’s upper body during the exercise, and classifies the sequence of postures as correct or incorrect using Bayesian estimation and majority voting. If POSTURECHECK recognizes an incorrect posture, it specifies what the user can do to correct it. The result of our experiment shows that POSTURECHECK is capable of recognizing the incorrect postures in real time while the user is performing an exercise.

Keywords: Bayesian estimation, majority voting, Microsoft Kinect, PostureCheck, Proficio robotic arm, upper body physical therapy

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Authors: Mohammad Farid

Abstract:

In this paper, we introduce and study an explicit iterative method based on hybrid extragradient method to approximate a common solution of generalized mixed equilibrium problem and fixed point problem for a nonexpansive semigroup in Hilbert space. Further, we prove that the sequence generated by the proposed iterative scheme converge strongly to the common solution of generalized mixed equilibrium problem and fixed point problem for a nonexpansive semigroup. This common solution is the unique solution of a variational inequality problem and is the optimality condition for a minimization problem. The results presented in this paper are the supplement, extension and generalization of the previously known results in this area.

Keywords: generalized mixed equilibrium problem, fixed-point problem, nonexpansive semigroup, variational inequality problem, iterative algorithms, hybrid extragradient method

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Authors: Alexis John de Britto

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Studies were performed to select the superior genotypes based on intra-specific variations, caused by phytogeographical, climatic and edaphic parameters of three anti cancer drug yielding mangrove plants such as Acanthus ilicifolius L., Calophyllum inophyllum L. and Excoecaria agallocha L. using ISSR (Inter Simple Sequence Repeats) markers and phytochemical analysis such as preliminary phytochemical tests, TLC, HPTLC, HPLC and antioxidant tests. The plants were collected from five different geographical locations of the East Coast of south India. Genetic heterozygosity, Nei’s gene diversity, Shannon’s information index and Percentage of polymorphism between the populations were calculated using POPGENE software. Cluster analysis was performed using UPGMA algorithm. AMOVA and correlations between genetic diversity and soil factors were analyzed. Combining the molecular and phytochemical variations superior genotypes were selected. Conservation constraints and methods of efficient exploitation of the species are discussed.

Keywords: anti-cancer drug yielding plants, DNA fingerprinting, phytochemical analysis, selection of superior genotypes

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Authors: Mohammad Asadpour, Gholamreza Razmi, Gholamreza Mohammadi, Abolghasem Naghibi

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Cryptosporidium Spp., protozoan parasites of the phylum Apicomplexa, have a wide spectrum of hosts including humans, domestic animals and wild mammals, birds, reptiles, amphibians and fish. Dairy cattle have been identified in numerous reports as a major source of environmental contamination with this pathogen. In this study, a Polymerase Chain Reaction (PCR), Restriction Fragment Length Polymorphism (RFLP) analysis of the Small-Subunit (SSU) rRNA gene was used to detect and identify Cryptosporidium Spp. in 300 fecal specimens from 1 to 30 days pre-wean calves in 10 farms in Mashhad, Iran. Eighty five (28.3%) and forty five (15%) of the specimens were positive for Cryptosporidium by microscopic and PCR examination respectively. Restriction digestion of the PCR products by VSPI and Ssp1 restriction enzymes and analysis of sequence data revealed the presence of C. parvum, bovine genotype in all isolates. Our findings suggest that cattle can be a source of Cryptosporidial infections for humans and animals in Mashhad area. This is the first published description of Cryptosporidium sub genotyping in Mashhad.

Keywords: cryptosporidium, genotype, dairy calves, 18S rRNA, Mashhad

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Authors: Javed Y. Uppal

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In this paper, a case study of a 13 storied multi storied main headquarters building of the Lahore Development Authority Lahore Pakistan has been presented, the 9th floor of which caught fire due to short circuiting and the flare spread through air-conditioning ducts to top three floors, and the building remained under fire for 15 hours before it was quenched. Some columns at the upper 3 floors started crumbling down, which were immediately propped. A visual inspection of site was first carried out, followed by onsite material tests and lab tests for residual strengths, which led to the decision of removal of the top 3 floors in a planned sequence of diamond cutting of middle strips, column strips, and shear walls, in panels and their lifting up by overhead cranes. The waffle slabs were stitched and jacketed with low viscosity polymer layer. The damaged bars were supplemented. The cracked columns were jacketed as well. The validity of rehabilitation procedure was established by load deflection behavior tests and long term performance observation over a period of 5 years. The paper concludes that the procedures adopted could be recommended for such events.

Keywords: fire damage, shotcrete, waffle slabs, delamination, drying cracking, jacketing

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Authors: Mohammad H. Ahmadi, Vahid Haghighatdoost

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Given a set of source locations for a group of friends, and a set of trip plans for each group member as a sequence of Categories-of-Interests (COIs) (e.g., restaurant), and finally a specific COI as a common destination that all group members will gather together, in Meeting Point Based on Trip Plans (MPTPs) queries our goal is to find a Point-of-Interest (POI) from different COIs, such that the aggregate travel distance for the group is minimized. In this work, we considered two cases for aggregate function as Sum and Max. For solving this query, we propose an efficient pruning technique for shrinking the search space. Our approach contains three steps. In the first step, it prunes the search space around the source locations. In the second step, it prunes the search space around the centroid of source locations. Finally, we compute the intersection of all pruned areas as the final refined search space. We prove that the POIs beyond the refined area cannot be part of optimal answer set. The paper also covers an extensive performance study of the proposed technique.

Keywords: meeting point, trip plans, road networks, spatial databases

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Authors: Deepak Choudhary

Abstract:

COEP-Microgrid, a project by the students of College of Engineering Pune aims at establishing a micro grid in the college campus serving as a living laboratory for research and development of novel grid technologies. Proposed micro grid has an AC-bus and DC-bus, interconnected together with a tie line DC-AC converter. In grid-connected mode AC bus of microgrid is synchronized with utility grid. Synchronization with utility grid requires grid and AC bus to have synchronism in frequency, phase sequence and voltage. Power flow requires phase difference between grid and AC bus. Control System is required to effectively regulate power flow between the grid and AC bus. The grid synchronizing control system is composed of frequency and phase control for regulated power flow and voltage control system for reduction of reactive power flow. The control system involves automatic active power flow control. It takes the feedback of DC link Capacitor and changes the power angle accordingly. Control system incorporating voltage, phase and power control was developed for grid-tie inverter. This paper discusses the design, simulation and practical implementation of control system described in various micro grid scenarios.

Keywords: microgrid, Grid-tie inverter, voltage control, automatic power control

Procedia PDF Downloads 664

Authors: Quyen Vu Dang Ha, Oanh Truong Thi, Thuoc Tran Linh, Kent Carpenter, Thinh Doan Vu, Binh Dang Thuy

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Enzyme restriction site associated DNA (EzRAD) has recently emerged as a promising genomic approach for exploring fish genetic diversity on a genome-wide scale. This is a simplified method for genomic genotyping in non-model organisms and applied for SNPs discovery in the population genetics of freshwater and marine fish in the South of Vietnam. The observations of regional-scale differentiation of commercial freshwater fish (smallscale croakers Boesemania microlepis) and marine fish (emperor Lethrinus lentjan) are clarified. Samples were collected along Hau River and coastal area in the south and center Vietnam. 52 DNA samples from Tra Vinh, An Giang Province for Boesemania microlepis and 34 DNA samples of Lethrinus lentjan from Phu Quoc, Nha Trang, Da Nang Province were used to prepare EzRAD libraries from genomic DNA digested with MboI and Sau3AI. A pooled sample of regional EzRAD libraries was sequenced using the HiSeq 2500 Illumina platform. For Boesemania microlepis, the small scale population different from upstream to downstream of Hau river were detected, An Giang population exhibited less genetic diversity (SNPs per individual from 14 to 926), in comparison to Tra Vinh population (from 11 to 2172). For Lethrinus lentjan, the result showed the minor difference between populations in the Northern and the Southern Mekong River. The numbers of contigs and SNPs vary from 1315 to 2455 and from 7122 to 8594, respectively (P ≤ 0.01). The current preliminary study reveals regional scale population disconnection probably reflecting environmental changing. Additional sampling and EzRad libraries need to be implemented for resource management in the Mekong Delta.

Keywords: Boesemania microlepis, EzRAD, Lethrinus lentjan, SNPs

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Authors: Z. Nourmohammadi, F. Farahani, M. Shaker

Abstract:

Aloe is an important commercial crop available in a wide range of species and varieties in international markets. The applications of this plant have been recorded in the ancient cultures of India, Egypt, Greece, Rome and China. Aloe has been used for centuries and is currently being actively studied for medicinal purposes. Aloe is propagated through lateral buds, which is slow, very expensive and low income practice. Nowadays, it has been cultured by in vitro propagation for rapid multiplication of plants, genetic improvement of crops, obtaining disease-free clones and for progressive valuable germplasm. The present study focused on the influence of different phytohormones on rapid in vitro propagation of Aloe plants. We also investigated the effect of gamma radiation on biochemical characters as well as genetic changes. Shoot tip of 2-3 cm were collected from offshoot of Aloe barbadensis and Aloe littoralis, and were inoculated with MS medium containing various concentrations of BA (0.5, 1, 2 mg/l), IAA (0.5, 1 mg/l). The best treatment for a highest shoot number and bud proliferation was MS medium containing 2 mg/l BAP and 0.5 mg/l IAA in A. barbadensis and A. littoralis. Maximum percentage of proliferated shoot buds (90% and 95%) from a single explant were obtained in MS medium after 4-5 weeks of the second and the first subcultures, respectively. Different genome sizes were also indicated among treatments and subcultures. The mixoploids identified in flow cytometery histograms in different treatments. The effect of gamma radiation on A. littoralis showed that by increasing the dose of gamma radiation, amounts of chlorophyll A, B, carotenoids, total protein content and superoxide dismutase were significantly increased compared to control plants. Genetic variation analysis also revealed significant genetic differences between control and gamma radiation treated regenerated plants by AMOVA test. Higher genetic heterozygocity was observed in radiation treated plants. Our findings may provide useful method for improving of Aloe plant proliferation with increasing of useful material such as antioxidant enzymes.

Keywords: aloe, antioxidant enzyme, micropropagation, gamma radiation, genetic variation

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Authors: Kimia Khoshdel Vajari, Saber Saffar

Abstract:

Reducing the residual stresses caused by welding is desirable for the industry. The effect of welding sequence, as well as the effect of yield stress on the number of residual stresses generated in Inconel X750 superalloy sheets and beams, have been investigated. The finite element model used in this research is a three-dimensional thermal and mechanical model, and the type of analysis is indirect coupling. This analysis is done in two stages. First, thermal analysis is performed, and then the thermal changes of the first analysis are used as the applied load in the second analysis. ABAQUS has been used for modeling, and the Dflux subroutine has been used in the Fortran programming environment to move the arc and the molten pool. The results of this study show that the amount of tensile residual stress in symmetric, discontinuous, and symmetric-discontinuous welds is reduced to a maximum of 27%, 54%, and 37% compared to direct welding, respectively. The results also show that the amount of residual stresses created by welding increases linearly with increasing yield stress with a slope of 40%.

Keywords: residual stress, X750 superalloy, finite element, welding, thermal analysis

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Authors: D. Leibman, D. Wolf, A. Gal-On

Abstract:

Viral diseases of tomato crops result in heavy yield losses and may even jeopardize the production of these crops. Classical tomato breeding for disease resistance against Tomato yellow leaf curl virus (TYLCV), leads to partial resistance associated with a number of recessive genes. To author’s best knowledge Pepino mosaic virus (PepMV) genetic resistance is not yet available. The generation of viral resistance by means of genetic engineering was reported and implemented for many crops, including tomato. Transgenic resistance against viruses is based, in most cases, on Post Transcriptional Gene Silencing (PTGS), an endogenous mechanism which destroys the virus genome. In this work, we developed immunity against PepMV and TYLCV in a tomato based on a PTGS mechanism. Tomato plants were transformed with a hairpin-construct-expressed transgene-derived double-strand-RNA (tr-dsRNA). In the case of PepMV, the binary construct harbored three consecutive fragments of the replicase gene from three different PepMV strains (Italian, Spanish and American), to provide resistance against a range of virus strains. In the case of TYLCV, the binary vector included three consecutive fragments of the IR, V2 and C2 viral genes constructed in a hairpin configuration. Selected transgenic lines (T0) showed a high accumulation of transgene siRNA of 21-24 bases, and T1 transgenic lines showed complete immunity to PepMV and TYLCV. Graft inoculation displayed immunity of the transgenic scion against PepMV and TYLCV. The study presents the engineering of resistance in tomato against two serious diseases, which will help in the production of high-quality tomato. However, unfortunately, these resistant plants have not been implemented due to public ignorance and opposition against breeding by genetic engineering.

Keywords: PepMV, PTGS, TYLCV, tr-dsRNA

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Authors: Promise Ekpo Osaine, Daniel Melesse

Abstract:

Image captioning is an active area of research in the multi-modal artificial intelligence (AI) community as it connects vision and language understanding, especially in settings where it is required that a model understands the content shown in an image and generates semantically and grammatically correct descriptions. In this project, we followed a standard approach to a deep learning-based image captioning model, injecting architecture for the encoder-decoder setup, where the encoder extracts image features, and the decoder generates a sequence of words that represents the image content. As such, we investigated image encoders, which are ResNet101, InceptionResNetV2, EfficientNetB7, EfficientNetV2M, and CLIP. As a caption generation structure, we explored long short-term memory (LSTM). The CLIP-LSTM model demonstrated superior performance compared to the encoder-decoder models, achieving a BLEU-1 score of 0.904 and a BLEU-4 score of 0.640. Additionally, among the CNN-LSTM models, EfficientNetV2M-LSTM exhibited the highest performance with a BLEU-1 score of 0.896 and a BLEU-4 score of 0.586 while using a single-layer LSTM.

Keywords: multi-modal AI systems, image captioning, encoder, decoder, BLUE score

Procedia PDF Downloads 77

Authors: Eyhab El-Kharashi, Maher El-Dessouki

Abstract:

The paper is dedicated to precise assessment of the induction motor output energy during the unbalanced operation. Since many years ago and until now the voltage complex unbalance factor (CVUF) is used only to assess the output energy of the induction motor while this output energy for asymmetry supply voltage does not depend on the value of unbalanced voltage only but also on the machine parameters. The paper illustrates the variation of the two unbalance factors, complex voltage unbalance factor (CVUF) and impedance unbalance factor (IUF), with positive sequence voltage component, reveals that degree and manner of unbalance in supply voltage. From this point of view the paper delineates the current unbalance factor (CUF) to exactly reflect the output energy during unbalanced operation. The paper proceeds to illustrate the importance of using this factor in the multi-machine system to precise prediction of the output energy during the unbalanced operation. The use of the proposed unbalance factor (CUF) avoids the accumulation of the error due to more than one machine in the system which is expected if only the complex voltage unbalance factor (CVUF) is used.

Keywords: induction motor, electromagnetic torque, voltage unbalance, energy conversion

Procedia PDF Downloads 557

Authors: Apotiola Z. O., Anyakorah C. I., Kuforiji O. O.

Abstract:

Sensory and microbial properties of fresh and canned Calocybe indica (milky mushroom) were evaluated. The mushroom was grown under a controlled environment with hardwood (Cola nitida) and rice bran substrate (4:1) canned in a brine solution of salt and citric acid. Analysis was carried out using standard methods. The overall acceptability ranged between 5.62 and 6.50, with sample S30 adjudged the best. In all, significant differences p<0.01 exist in the panelist judgment. Thus, the incorporation of salt and citric acid at 3.5g and 1.5g, respectively, improved sensory attributes such as texture, aroma, color, and overall acceptability. There was no coliform and fungi growth on the samples throughout the storage period. The bacterial count, on the other hand, was observed only in the fifth and sixth week of the storage period which varied between 0.2 to 0.9 x 103 cfu/g. The highest value was observed in sample S20 of the sixth week of storage, while the lowest value was recorded in sample S30 of the sixth week of storage. Based on 16S rRNA gene sequencing, bacterial species were taxonomically confirmed as Bacillus thuringiensis. The percentile compositions and Sequence ID of the bacterial species in the mushroom was 90%.

Keywords: bacterial count, microbial property, sensory, sawdust, texture

Procedia PDF Downloads 62