Search results for: lamina stacking sequence

Authors: Don Anushka Sandaruwan Elvitigala, P. D. S. U. Wickramasinghe, Jehee Lee

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Cystatins are a large superfamily of proteins which act as reversible inhibitors of cysteine proteases. Papain proteases and cysteine cathepsins are predominant substrates of cystatins. Cystatin superfamily can be further clustered into three groups as Stefins, Cystatins, and Kininogens. Among them, stefines are also known as family 1 cystatins which harbors cystatin Bs and cystatin As. In this study, a homologue of family one cystatins more close to cystatin Bs was identified from Korean black rockfish (Sebastes schlegeli) using a prior constructed cDNA (complementary deoxyribonucleic acid) database and designated as RfCyt1. The full-length cDNA of RfCyt1 consisted of 573 bp, with a coding region of 294 bp. It comprised a 5´-untranslated region (UTR) of 55 bp, and 3´-UTR of 263 bp. The coding sequence encodes a polypeptide consisting of 97 amino acids with a predicted molecular weight of 11kDa and theoretical isoelectric point of 6.3. The RfCyt1 shared homology with other teleosts and vertebrate species and consisted conserved features of cystatin family signature including single cystatin-like domain, cysteine protease inhibitory signature of pentapeptide (QXVXG) consensus sequence and N-terminal two conserved neighboring glycine (⁸GG⁹) residues. As expected, phylogenetic reconstruction developed using the neighbor-joining method showed that RfCyt1 is clustered with the cystatin family 1 members, in which more closely with its teleostan orthologues. An SYBR Green qPCR (quantitative polymerase chain reaction) assay was performed to quantify the RfCytB transcripts in different tissues in healthy and immune stimulated fish. RfCyt1 was ubiquitously expressed in all tissue types of healthy animals with gill and spleen being the highest. Temporal expression of RfCyt1 displayed significant up-regulation upon infection with Aeromonas salmonicida. Recombinantly expressed RfCyt1 showed concentration-dependent papain inhibitory activity. Collectively these findings evidence for detectable protease inhibitory and immunity relevant roles of RfCyt1 in Sebastes schlegeli.

Keywords: Sebastes schlegeli, family 1 cystatin, immune stimulation, expressional modulation

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Authors: Norhidayu Muhamad Zain

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Gelatin, a purified protein derived mostly from porcine and bovine sources, is used widely in food manufacturing, pharmaceutical, and cosmetic industries. However, the presence of any porcine-related products are strictly forbidden for Muslim and Jewish consumption. Therefore, analytical methods offering reliable results to differentiate the sources of gelatin are needed. The aim of this study was to differentiate the sources of gelatin (porcine and tilapia fish) using Fourier transform infrared- attenuated total reflection (FTIR-ATR) combined with two dimensional infrared (2DIR) correlation analysis. Porcine gelatin (PG) and tilapia fish gelatin (FG) samples were diluted in distilled water at concentrations ranged from 4-20% (w/v). The samples were then analysed using FTIR-ATR and 2DIR correlation software. The results showed a significant difference in the pattern map of synchronous spectra at the region of 1000 cm⁻¹ to 1100 cm⁻¹ between PG and FG samples. The auto peak at 1080 cm⁻¹ that attributed to C-O functional group was observed at high intensity in PG samples compared to FG samples. Meanwhile, two auto peaks (1080 cm⁻¹ and 1030 cm⁻¹) at lower intensity were identified in FG samples. In addition, using 2D correlation analysis, the original broad water OH bands in 1D IR spectra can be effectively differentiated into six auto peaks located at 3630, 3340, 3230, 3065, 2950 and 2885 cm⁻¹ for PG samples and five auto peaks at 3630, 3330, 3230, 3060 and 2940 cm⁻¹ for FG samples. Based on the rule proposed by Noda, the sequence of the spectral changes in PG samples is as following: NH₃⁺ amino acid > CH₂ and CH₃ aliphatic > OH stretch > carboxylic acid OH stretch > NH in secondary amide > NH in primary amide. In contrast, the sequence was totally in the opposite direction for FG samples and thus both samples provide different 2D correlation spectra ranged from 2800 cm-1 to 3700 cm⁻¹. This method may provide a rapid determination of gelatin source for application in food, pharmaceutical, and cosmetic products.

Keywords: 2 dimensional infrared (2DIR) correlation analysis, Fourier transform infrared- attenuated total reflection (FTIR-ATR), porcine gelatin, tilapia fish gelatin

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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Authors: Nurulhikma Md Isa, Intan Elya Suka, Nur Farhana Roslan, Chew Bee Lynn

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The evolutionarily conserved N-end rule pathway marks proteins for degradation by the Ubiquitin Proteosome System (UPS) based on the nature of their N-terminal residue. Proteins with a destabilizing N-terminal residue undergo a series of condition-dependent N-terminal modifications, resulting in their ubiquitination and degradation. Intensive research has been carried out in Arabidopsis previously. The group VII Ethylene Response Factor (ERFs) transcription factors are the first N-end rule pathway substrates found in Arabidopsis and their role in regulating oxygen sensing. ERFs also function as central hubs for the perception of gaseous signals in plants and control different plant developmental including germination, stomatal aperture, hypocotyl elongation and stress responses. However, nothing is known about the role of this pathway during fruit development and ripening aspect. The plant model system Arabidopsis cannot represent fleshy fruit model system therefore tomato is the best model plant to study. PROTEOLYSIS6 (PRT6) is an E3 ubiquitin ligase of the N-end rule pathway. Two homologs of PRT6 sequences have been identified in tomato genome database using the PRT6 protein sequence from model plant Arabidopsis thaliana. Homology search against Ensemble Plant database (tomato) showed Solyc09g010830.2 is the best hit with highest score of 1143, e-value of 0.0 and 61.3% identity compare to the second hit Solyc10g084760.1. Further homology search was done using NCBI Blast database to validate the data. The result showed best gene hit was XP_010325853.1 of uncharacterized protein LOC101255129 (Solanum lycopersicum) with highest score of 1601, e-value 0.0 and 48% identity. Both Solyc09g010830.2 and uncharacterized protein LOC101255129 were genes located at chromosome 9. Further validation was carried out using BLASTP program between these two sequences (Solyc09g010830.2 and uncharacterized protein LOC101255129) to investigate whether they were the same proteins represent PRT6 in tomato. Results showed that both proteins have 100 % identity, indicates that they were the same gene represents PRT6 in tomato. In addition, we used two different RNAi constructs that were driven under 35S and Polygalacturonase (PG) promoters to study the function of PRT6 during tomato developmental stages and ripening processes.

Keywords: ERFs, PRT6, tomato, ubiquitin

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Authors: Pranjali Sharma, Swati Neogi

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Composite pressure vessels are low weight structures mainly used in a variety of applications such as automobiles, aeronautics and chemical engineering. Fiber reinforced polymer (FRP) composite materials offer the simplicity of design and use, high fuel storage capacity, rapid refueling capability, excellent shelf life, minimal infrastructure impact, high safety due to the inherent strength of the pressure vessel, and little to no development risk. Apart from these preliminary merits, the subsidized weight of composite vessels over metallic cylinders act as the biggest asset to the automotive industry, increasing the fuel efficiency. The result is a lightweight, flexible, non-explosive, and non-fragmenting pressure vessel that can be tailor-made to attune with specific applications. The winding pattern of the composite over-wrap is a primary focus while designing a pressure vessel. The critical stresses in the system depend on the thickness, angle and sequence of the composite layers. The composite over-wrap is wound over a plastic liner, whose geometry can be varied for the ease of winding. In the present study, we aim to optimize the FRP vessel geometry that provides an ease in winding and also aids in weight reduction for enhancing the vessel performance. Finite element analysis is used to study the effect of dome geometry, yielding a design with maximum value of burst pressure and least value of vessel weight. The stress and strain analysis of different dome ends along with the cylindrical portion is carried out in ANSYS 19.2. The failure is predicted using different failure theories like Tsai-Wu theory, Tsai-Hill theory and Maximum stress theory. Corresponding to a given winding sequence, the optimum dome geometry is determined for a fixed internal pressure to identify the theoretical value of burst pressure. Finally, this geometry is used to decrease the number of layers to reach the set value of safety in accordance with the available safety standards. This results in decrease in the weight of the composite over-wrap and manufacturing cost of the pressure vessel. An improvement in the overall weight performance of the pressure vessel gives higher fuel efficiency for its use in automobile applications.

Keywords: Compressed Gas Storage, Dome geometry, Theoretical Analysis, Type-4 Composite Pressure Vessel, Improvement in Vessel Weight Performance

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Authors: Milda Nainyte, Viktoras Masevicius

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Biological methylation is a methyl group transfer from S-adenosyl-L-methionine (AdoMet) onto N-, C-, O- or S-nucleophiles in DNA, RNA, proteins or small biomolecules. The reaction is catalyzed by enzymes called AdoMet-dependent methyltransferases (MTases), which represent more than 3 % of the proteins in the cell. As a general mechanism, the methyl group from AdoMet replaces a hydrogen atom of nucleophilic center producing methylated DNA and S-adenosyl-L-homocysteine (AdoHcy). Recently, DNA methyltransferases have been used for the sequence-specific, covalent labeling of biopolymers. Two types of MTase catalyzed labeling of biopolymers are known, referred as two-step and one-step. During two-step labeling, an alkylating fragment is transferred onto DNA in a sequence-specific manner and then the reporter group, such as biotin, is attached for selective visualization using suitable chemistries of coupling. This approach of labeling is quite difficult and the chemical hitching does not always proceed at 100 %, but in the second step the variety of reporter groups can be selected and that gives the flexibility for this labeling method. In the one-step labeling, AdoMet analog is designed with the reporter group already attached to the functional group. Thus, the one-step labeling method would be more comfortable tool for labeling of biopolymers in order to prevent additional chemical reactions and selection of reaction conditions. Also, time costs would be reduced. However, effective AdoMet analog appropriate for one-step labeling of biopolymers and containing cleavable bond, required for reduction of PCR interferation, is still not known. To expand the practical utility of this important enzymatic reaction, cofactors with activated sulfonium-bound side-chains have been produced and can serve as surrogate cofactors for a variety of wild-type and mutant DNA and RNA MTases enabling covalent attachment of these chains to their target sites in DNA, RNA or proteins (the approach named methyltransferase-directed Transfer of Activated Groups, mTAG). Compounds containing hex-2-yn-1-yl moiety has proved to be efficient alkylating agents for labeling of DNA. Herein we describe synthetic procedures for the preparation of N-biotinoyl-N’-(pent-4-ynoyl)cystamine starting from the coupling of cystamine with pentynoic acid and finally attaching the biotin as a reporter group. The synthesis of the first AdoMet based cofactor containing a cleavable reporter group and appropriate for one-step labeling was developed.

Keywords: adoMet analogs, DNA alkylation, cofactor, methyltransferases

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Authors: H. S. Kang

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Coupled electrical and optical model for conversion of electrical energy into coherent optical energy for transmitter-receiver link by solid state device is presented. Probability distribution for travelling laser beam switching time intervals and the number of switchings in the time interval is obtained. Selector function mapping is employed to regulate optical data transmission speed. It is established that regulated laser transmission from PhotoActive Laser transmitter follows principal of invariance. This considerably simplifies design of PhotoActive Laser Transmission networks.

Keywords: computational mathematics, finite difference Markov chain methods, sequence spaces, singularly perturbed differential equations

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure formed by stacked planes of four base paired guanines (G-quartet). Guanine rich DNA sequences appear in many sites of genomic DNA and can potential form G-quadruplexes, such as those occurring at 3'-terminus of the human telomeric DNA. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to down regulate oncogene expression making G-quadruplex an attractive target for anticancer therapy. Many G-quadruplex ligands have been proposed with a planar core to facilitate the pi–pi stacking and electrostatic interactions with the G-quartets. However, many drug candidates are impossibilitated to discriminate a G-quadruplex from a double helix DNA structure. In this context, it is important to investigate the site topology for the interaction of a G-quadruplex with a ligand. In this work, we determine the free energy surface of a G-quadruplex-ligand to study the binding modes of the G-quadruplex (TG4T) with the daunomycin (DM) drug. The complex TG4T-DM is studied using classical molecular dynamics in combination with metadynamics simulations. The metadynamics simulations permit an enhanced sampling of the conformational space with a modest computational cost and obtain free energy surfaces in terms of the collective variables (CV). The free energy surfaces of TG4T-DM exhibit other local minima, indicating the presence of additional binding modes of daunomycin that are not observed in short MD simulations without the metadynamics approach. The results are compared with similar calculations on a different structure (the mutated mu-G4T-DM where the 5' thymines on TG4T-DM have been deleted). The results should be of help to design new G-quadruplex drugs, and understand the differences in the recognition topology sites of the duplex and quadruplex DNA structures in their interaction with ligands.

Keywords: g-quadruplex, cancer, molecular dynamics, metadynamics

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Authors: Misbah Irshad, Faiza Sarfraz

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The problem of approximating surface to surface intersection is considered to be very important in computer aided geometric design and computer aided manufacturing. Although it is a complex problem to handle, its continuous need in the industry makes it an active topic in research. A technique for approximating intersection curves of two parametric surfaces is proposed, which extracts boundary points and turning points from a sequence of intersection points and interpolate them with the help of rational cubic spline functions. The proposed approach is demonstrated with the help of examples and analyzed by calculating error.

Keywords: approximation, parametric surface, spline function, surface intersection

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Authors: Kiwon Yeom

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Change points are abrupt variations in a data sequence. Detection of change points is useful in modeling, analyzing, and predicting time series in application areas such as robotics and teleoperation. In this paper, a change point is defined to be a discontinuity in one of its derivatives. This paper presents a reliable method for detecting discontinuities within a three-dimensional trajectory data. The problem of determining one or more discontinuities is considered in regular and irregular trajectory data from teleoperation. We examine the geometric detection algorithm and illustrate the use of the method on real data examples.

Keywords: change point, discontinuity, teleoperation, abrupt variation

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Authors: J. Trarbach, S. Schosser, B. Vogt

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Decision-makers tend to prefer the first alternative over subsequent alternatives which is called the primacy effect. To reliably measure this effect, we conducted an experiment with real consequences for preference statements. Therefore, we elicit preferences of subjects using a rating scale, i.e. hypothetical preferences, and willingness to pay, i.e. real preferences, for two sequences of pain. Within these sequences, both overall intensity and duration of pain are identical. Hence, a rational decision-maker should be indifferent, whereas the primacy effect predicts a stronger preference for the first sequence. What we see is a primacy effect only for hypothetical preferences. This effect vanishes for real preferences.

Keywords: decision making, primacy effect, real incentives, willingness to pay

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Authors: Sirajo Abubakar, Ismail Ahmad Abir, Muhammad Sabiu Bala, Muhammad Mustapha Adejo, Aravind Shanmugaveloo

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Over the years, land subsidence has been a serious threat mostly to urban areas. Land subsidence is the sudden sinking or gradual downward settling of the ground’s surface with little or no horizontal motion. In most areas, land subsidence is a slow process that covers a large area; therefore, it is sometimes left unnoticed. South of Johor is the area of interest for this project because it is going through rapid urbanization. The objective of this research is to evaluate and identify potential deformations in the south of Johor using integrated remote sensing and 2D resistivity methods. Synthetic aperture radar interferometry (InSAR) which is a remote sensing technique has the potential to map coherent displacements at centimeter to millimeter resolutions. Persistent scatterer interferometry (PSI) stacking technique was applied to Sentinel-1 data to detect the earth deformation in the study area. A dipole-dipole configuration resistivity profiling was conducted in three areas to determine the subsurface features in that area. This subsurface features interpreted were then correlated with the remote sensing technique to predict the possible causes of subsidence and uplifts in the south of Johor. Based on the results obtained, West Johor Bahru (0.63mm/year) and Ulu Tiram (1.61mm/year) are going through uplift due to possible geological uplift. On the other end, East Johor Bahru (-0.26mm/year) and Senai (-1.16mm/year) undergo subsidence due to possible fracture and granitic boulders loading. Land subsidence must be taken seriously as it can cause serious damages to infrastructures and human life. Monitoring land subsidence and taking preventive actions must be done to prevent any disasters.

Keywords: interferometric synthetic aperture radar, persistent scatter, minimum spanning tree, resistivity, subsidence

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: deep learning, disease prediction, end-to-end machine learning, metagenomics, multiple instance learning, precision medicine

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Authors: Yifan Hou, Haibo Liu, Le Jiang, Wandong Su, Binqing Wang

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Road defect detection is crucial for modern urban management and infrastructure maintenance. Traditional road defect detection methods mostly rely on manual labor, which is not only inefficient but also difficult to ensure their reliability. However, existing deep learning-based road defect detection models have poor detection performance in complex environments and lack robustness to multi-scale targets. To address this challenge, this paper proposes a distinct detection framework based on the one stage algorithm network structure. This article designs a deep feature extraction network based on RCSDarknet, which applies channel shuffling to enhance information fusion between tensors. Through repeated stacking of RCS modules, the information flow between different channels of adjacent layer features is enhanced to improve the model's ability to capture target spatial features. In addition, a multi-scale feature fusion mechanism with weighted dual flow paths was adopted to fuse spatial features of different scales, thereby further improving the detection performance of the model at different scales. To validate the performance of the proposed algorithm, we tested it using the RDD2022 dataset. The experimental results show that the enhancement algorithm achieved 84.14% mAP, which is 1.06% higher than the currently advanced YOLOv8 algorithm. Through visualization analysis of the results, it can also be seen that our proposed algorithm has good performance in detecting targets of different scales in complex scenes. The above experimental results demonstrate the effectiveness and superiority of the proposed algorithm, providing valuable insights for advancing real-time road defect detection methods.

Keywords: roads, defect detection, visualization, deep learning

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Authors: Hernández Eva Selene, Reyna Mary Carmen, Rivera Héctor, Barragán Irving

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We propose an approach that jointly addresses the layout of a facility and the scheduling of a sequence of jobs. In real production, these two problems are interrelated. However, they are treated separately in the literature. Our approach is an extension of the job shop problem with transportation delay, where the location of the machines is selected among possible sites. The model minimizes the makespan, using the short processing times rule with two algorithms; the first one considers all the permutations for the location of machines, and the second only a heuristic to select some specific permutations that reduces computational time. Some instances are proved and compared with literature.

Keywords: layout problem, job shop scheduling problem, concurrent scheduling and layout problem, metaheuristic

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Authors: Shagufta Jabeen, Faez J. Firdaus Abdullah, Zunita Zakaria, Nurulfiza M. Isa, Yung C. Tan, Wai Y. Yee, Abdul R. Omar

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Pasteurella multocida (PM) is an important veterinary opportunistic pathogen particularly associated with septicemic pasteurellosis, pneumonic pasteurellosis and hemorrhagic septicemia in cattle and buffaloes. P. multocida serotype A has been reported to cause fatal pneumonia and septicemia. Pasteurella multocida subspecies multocida of serotype A Malaysian isolate PMTB2.1 was first isolated from buffaloes died of septicemia. In this study, the genome of P. multocida strain PMTB2.1 was sequenced using third-generation sequencing technology, PacBio RS2 system and analyzed bioinformatically via de novo analysis followed by in-depth analysis based on comparative genomics. Bioinformatics analysis based on de novo assembly of PacBio raw reads generated 3 contigs followed by gap filling of aligned contigs with PCR sequencing, generated a single contiguous circular chromosome with a genomic size of 2,315,138 bp and a GC content of approximately 40.32% (Accession number CP007205). The PMTB2.1 genome comprised of 2,176 protein-coding sequences, 6 rRNA operons and 56 tRNA and 4 ncRNAs sequences. The comparative genome sequence analysis of PMTB2.1 with nine complete genomes which include Actinobacillus pleuropneumoniae, Haemophilus parasuis, Escherichia coli and five P. multocida complete genome sequences including, PM70, PM36950, PMHN06, PM3480, PMHB01 and PMTB2.1 was carried out based on OrthoMCL analysis and Venn diagram. The analysis showed that 282 CDs (13%) are unique to PMTB2.1and 1,125 CDs with orthologs in all. This reflects overall close relationship of these bacteria and supports the classification in the Gamma subdivision of the Proteobacteria. In addition, genomic distance analysis among all nine genomes indicated that PMTB2.1 is closely related with other five Pasteurella species with genomic distance less than 0.13. Synteny analysis shows subtle differences in genetic structures among different P.multocida indicating the dynamics of frequent gene transfer events among different P. multocida strains. However, PM3480 and PM70 exhibited exceptionally large structural variation since they were swine and chicken isolates. Furthermore, genomic structure of PMTB2.1 is more resembling that of PM36950 with a genomic size difference of approximately 34,380 kb (smaller than PM36950) and strain-specific Integrative and Conjugative Elements (ICE) which was found only in PM36950 is absent in PMTB2.1. Meanwhile, two intact prophages sequences of approximately 62 kb were found to be present only in PMTB2.1. One of phage is similar to transposable phage SfMu. The phylogenomic tree was constructed and rooted with E. coli, A. pleuropneumoniae and H. parasuis based on OrthoMCL analysis. The genomes of P. multocida strain PMTB2.1 were clustered with bovine isolates of P. multocida strain PM36950 and PMHB01 and were separated from avian isolate PM70 and swine isolates PM3480 and PMHN06 and are distant from Actinobacillus and Haemophilus. Previous studies based on Single Nucleotide Polymorphism (SNPs) and Multilocus Sequence Typing (MLST) unable to show a clear phylogenetic relatedness between Pasteurella multocida and the different host. In conclusion, this study has provided insight on the genomic structure of PMTB2.1 in terms of potential genes that can function as virulence factors for future study in elucidating the mechanisms behind the ability of the bacteria in causing diseases in susceptible animals.

Keywords: comparative genomics, DNA sequencing, phage, phylogenomics

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Authors: Nikolaos Papadimas, Joanna Bennett, Amir Sakhaei, Timothy Dodwell

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Composite modeling of consolidation processes is playing an important role in the process and part design by indicating the formation of possible unwanted prior to expensive experimental iterative trial and development programs. Composite materials in their uncured state display complex constitutive behavior, which has received much academic interest, and this with different models proposed. Errors from modeling and statistical which arise from this fitting will propagate through any simulation in which the material model is used. A general hyperelastic polynomial representation was proposed, which can be readily implemented in various nonlinear finite element packages. In our case, FEniCS was chosen. The coefficients are assumed uncertain, and therefore the distribution of parameters learned using Markov Chain Monte Carlo (MCMC) methods. In engineering, the approach often followed is to select a single set of model parameters, which on average, best fits a set of experiments. There are good statistical reasons why this is not a rigorous approach to take. To overcome these challenges, A hierarchical Bayesian framework was proposed in which population distribution of model parameters is inferred from an ensemble of experiments tests. The resulting sampled distribution of hyperparameters is approximated using Maximum Entropy methods so that the distribution of samples can be readily sampled when embedded within a stochastic finite element simulation. The methodology is validated and demonstrated on a set of consolidation experiments of AS4/8852 with various stacking sequences. The resulting distributions are then applied to stochastic finite element simulations of the consolidation of curved parts, leading to a distribution of possible model outputs. With this, the paper, as far as the authors are aware, represents the first stochastic finite element implementation in composite process modelling.

Keywords: data-driven , material consolidation, stochastic finite elements, surrogate models

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Authors: Geetanjali Panda, Suvrakanti Chakraborty

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In this paper, Newton-like descent methods are proposed for unconstrained optimization problems, which use q-derivatives of the gradient of an objective function. First, a local scheme is developed with alternative sufficient optimality condition, and then the method is extended to a global scheme. Moreover, a variant of practical Newton scheme is also developed introducing a real sequence. Global convergence of these schemes is proved under some mild conditions. Numerical experiments and graphical illustrations are provided. Finally, the performance profiles on a test set show that the proposed schemes are competitive to the existing first-order schemes for optimization problems.

Keywords: Descent algorithm, line search method, q calculus, Quasi Newton method

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Authors: Naoki Ohshima, Ken Kaminishi

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Four types of dependencies, which are 'Finish-to-start', 'Finish-to-finish', 'Start-to-start' and 'Start-to-finish (S-F)' as logical relationship are modeled based on the definition by 'the predecessor activity is defined as an activity to come before a dependent activity in a schedule' in PMBOK. However, it is found a self-contradiction in the precedence diagram for S-F relationship by PMBOK. In this paper, author would like to validate logical relationship of S-F by Graph Theory and propose a new interpretation of the precedence diagram for S-F relationship.

Keywords: project time management, sequence activity, start-to-finish relationship, precedence diagram, PMBOK

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Authors: Fatemeh Abbasi, Arne Hofemeier, Timo Betz

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Muscle growth and regeneration critically depend on satellite cells (SCs) which are muscle stem cells located between the basal lamina and myofibres. Upon damage, SCs become activated, enter the cell cycle, and give rise to myoblasts that form new myofibres, while a sub-population self-renew and re-populate the muscle stem cell niche. In aged muscle as well as in certain muscle diseases such as muscular dystrophy, some of the SCs lose their regenerative ability. Although it is demonstrated that the chemical composition of SCs quiescent niche is different from the activated niche, the mechanism initially activated in the SCs remains unknown. While extensive research efforts focused on potential chemical activation, no such factor has been identified to the author’s best knowledge. However, it is substantiated that niche mechanics affects SCs behaviors, such as stemness and engraftment. We hypothesize that mechanical stress in the healthy niche (homeostasis) is different from the regenerative niche and that this difference could serve as an early signal activating SCs upon fiber damage. To investigate this hypothesis, we develop a biomimetic system to reconstitute both, the mechanical and the chemical environment of the SC niche. Cells will be confined between two elastic polyacrylamide (PAA) hydrogels with controlled elastic moduli and functionalized surface chemistry. By controlling the distance between the PAA hydrogel surfaces, we vary the compression forces exerted by the substrates on the cells, while the lateral displacement of the upper hydrogel will create controlled shear forces. To establish such a system, a simplified system is presented. We engineered a sandwich-like configuration of two elastic PAA layer with stiffnesses between 1 and 10 kPa and confined a precursor myoblast cell line (C2C12) in between these layers. Our initial observations in this sandwich model indicate that C2C12 cells show different behaviors under mechanical compression if compared to a control one-layer gel without compression. Interestingly, this behavior is stiffness-dependent. While the shape of C2C12 cells in the sandwich consisting of two stiff (10 kPa) layers was much more elongated, showing almost a neuronal phenotype, the cell shape in a sandwich situation consisting of one stiff and one soft (1 kPa) layer was more spherical. Surprisingly, even in proliferation medium and at very low cell density, the sandwich situation stimulated cell differentiation with increased striation and myofibre formation. Such behavior is commonly found for confluent cells in differentiation medium. These results suggest that mechanical changes in stiffness and applied pressure might be a relevant stimulation for changes in muscle cell behavior.

Keywords: C2C12 cells, compression, force, satellite cells, skeletal muscle

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Authors: A. B. Bolkhir, A. Elshafie, T. K. Yousif

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This paper highlights the methods of error estimation in finite element analysis (FEA) results. It indicates that the modeling error could be eliminated by performing finite element analysis with successively finer meshes or by extrapolating response predictions from an orderly sequence of relatively low degree of freedom analysis results. In addition, the paper eliminates the round-off error by running the code at a higher precision. The paper provides application in finite element analysis results. It draws a conclusion based on results of application of methods of error estimation.

Keywords: finite element analysis (FEA), discretization error, round-off error, mesh refinement, richardson extrapolation, monotonic convergence

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Authors: Cristóbal Moënne-Loccoz, Rodrigo C. Vergara, Vladimir López, Domingo Mery, Diego Cosmelli

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Our daily interaction with computational interfaces is plagued of situations in which we go from inexperienced users to experts through self-motivated exploration of the same task. In many of these interactions, we must learn to find our way through a sequence of decisions and actions before obtaining the desired result. For instance, when drawing cash from an ATM machine, choices are presented in a step-by-step fashion so that a specific sequence of actions must be performed in order to produce the expected outcome. But, as they become experts in the use of such interfaces, do users adopt specific search and learning strategies? Moreover, if so, can we use this information to follow the process of expertise development and, eventually, predict future actions? This would be a critical step towards building truly adaptive interfaces that can facilitate interaction at different moments of the learning curve. Furthermore, it could provide a window into potential mechanisms underlying decision-making behavior in real world scenarios. Here we tackle this question using a simple game interface that instantiates a 4-level binary decision tree (BDT) sequential decision-making task. Participants have to explore the interface and discover an underlying concept-icon mapping in order to complete the game. We develop a Hidden Markov Model (HMM)-based approach whereby a set of stereotyped, hierarchically related search behaviors act as hidden states. Using this model, we are able to track the decision-making process as participants explore, learn and develop expertise in the use of the interface. Our results show that partitioning the problem space into such stereotyped strategies is sufficient to capture a host of exploratory and learning behaviors. Moreover, using the modular architecture of stereotyped strategies as a Mixture of Experts, we are able to simultaneously ask the experts about the user's most probable future actions. We show that for those participants that learn the task, it becomes possible to predict their next decision, above chance, approximately halfway through the game. Our long-term goal is, on the basis of a better understanding of real-world decision-making processes, to inform the construction of interfaces that can establish dynamic conversations with their users in order to facilitate the development of expertise.

Keywords: behavioral modeling, expertise acquisition, hidden markov models, sequential decision-making

Procedia PDF Downloads 251

Authors: Zouhair Issa Ahmed, Ahmed Abdulrasool Ahmed, Falah Hassan Abdulsada

Abstract:

This paper presents a layout of a factory using Pro-Model simulation by choosing the best layout that gives the highest productivity and least work in process. The general problem is to find the best sequence in which jobs pass between the machines which are compatible with the technological constraints and optimal with respect to some performance criteria. The best simulation with Pro-Model program increased productivity and reduced work in process by balancing lines of production compared with the current layout of factory when productivity increased from 45 products to 180 products through 720 hours.

Keywords: scheduling, Pro-Model, simulation, balancing lines of production, layout planning, WIP

Procedia PDF Downloads 633

Authors: J. T. Manhire

Abstract:

A tax authority wants to take actions it knows will foster the greatest degree of voluntary taxpayer compliance to reduce the “tax gap.” This paper suggests that even if a tax authority could attain a state of complete knowledge, there are constraints on whether and to what extent such actions would result in reducing the macro-level tax gap. These limits are not merely a consequence of finite agency resources. They are inherent in the system itself. To show that this is one possible interpretation of the tax gap data, the paper formulates known results in a different way by analyzing tax compliance as a population with a single covariate. This leads to a standard use of the logistic map to analyze the dynamics of non-compliance growth or decay over a sequence of periods. This formulation gives the same results as the tax gap studies performed over the past fifty years in the U.S. given the published margins of error. Limitations and recommendations for future work are discussed, along with some implications for tax policy.

Keywords: income tax, logistic map, tax compliance, tax law

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Authors: O. Abusaeeda, J. P. O. Evans, D. Downes

Abstract:

We demonstrate the synthesis of intermediary views within a sequence of X-ray images that exhibit depth from motion or kinetic depth effect in a visual display. Each synthetic image replaces the requirement for a linear X-ray detector array during the image acquisition process. Scale invariant feature transform, SIFT, in combination with epipolar morphing is employed to produce synthetic imagery. Comparison between synthetic and ground truth images is reported to quantify the performance of the approach. Our work is a key aspect in the development of a 3D imaging modality for the screening of luggage at airport checkpoints. This programme of research is in collaboration with the UK Home Office and the US Dept. of Homeland Security.

Keywords: X-ray, kinetic depth, KDE, view synthesis

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Authors: Kwan-Ho Kim, Jin-Hong Park

Abstract:

The multi-valued logic (MVL) circuits, which can handle more than two logic states, are one of the promising solutions to overcome the bit density limitations of conventional binary logic systems. Recently, tunneling devices such as Esaki diode and resonant tunneling diode (RTD) have been extensively explored to construct the MVL circuits. These tunneling devices present a negative differential resistance (NDR) phenomenon in which a current decreases as a voltage increases in a specific applied voltage region. Due to this non-monotonic current behavior, the tunneling devices have more than two threshold voltages, consequently enabling construction of MVL circuits. Recently, the emergence of two dimensional (2D) van der Waals (vdW) crystals has opened up the possibility to fabricate such tunneling devices easily. Owing to the defect-free surface of the 2D crystals, a very abrupt junction interface could be formed through a simple stacking process, which subsequently allowed the implementation of a high-performance tunneling device. Here, we report a vdW heterostructure based tunneling device with multiple threshold voltages, which was fabricated with black phosphorus (BP) and hafnium diselenide (HfSe₂). First, we exfoliated BP on the SiO₂ substrate and then transferred HfSe₂ on BP using dry transfer method. The BP and HfSe₂ form type-Ⅲ heterojunction so that the highly doped n+/p+ interface can be easily implemented without additional electrical or chemical doping process. Owing to high natural doping at the junction, record high peak to valley ratio (PVCR) of 16 was observed to the best our knowledge in 2D materials based NDR device. Furthermore, based on this, we first demonstrate the feasibility of the ternary latch by connecting two multi-threshold voltage devices in series.

Keywords: two dimensional van der Waals crystal, multi-valued logic, negative differential resistnace, tunneling device

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

Abstract:

Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Awais Asif

Abstract:

This article investigates fixed point theorems of Chatterjea type F-contraction in the setting of F-metric space. We relax the conditions of F-contraction and define modified F-contraction for two mappings. The study provides fixed point results for both single-valued and multivalued mappings. The results are further extended to common fixed point theorems for two mappings. Moreover, to discuss the applicability of our results, an application is provided, which shows the role of our results in finding the solution to functional equations in dynamic programming. Our results generalize and extend the existing results in the literature.

Keywords: Chatterjea type F-contraction, F-cauchy sequence, F-convergent, multi valued mappings

Procedia PDF Downloads 141

Authors: Jing-Fung Lin, Jer-Jia Sheu

Abstract:

In this study, an approach has been developed for the noise reduction of a muffler. The transmission loss (TL) in the muffler is maximized by the use of a double-chamber muffler, and a baffle with a hole is inserted between chambers. Taguchi method is used to optimize the design for the acoustical performance of the muffler. The TL performance is evaluated by COMSOL software. The excellent parameter combination for the maximum TL is attained as high as 35.30 dB in a wide frequency range from 10 Hz to 1400 Hz. The influence sequence of four parameters on TL is determined by the range analysis. The effects of length and expansion ratio of the first chamber on TL performance for the excellent program were discussed. Comparisons of the TL results from different designs are made.

Keywords: acoustics, baffle, chamber, muffler, Taguchi method, transmission loss

Procedia PDF Downloads 112

Authors: Shahbaz Ahmed

Abstract:

This study is conducted to demonstrate the knowledge of intentional learning and incidental learning. Hypothesis of this experiment is intentional learning is better than incidental learning, participants were demonstrated and were asked to learn the 10 nonsense syllables in a specific sequence from the colored cards in the end they were asked to recall the background color of each card instead of nonsense syllables. Independent variables of the experiment are the colored cards containing nonsense syllables which are to be memorized by the participants, dependent variables are the number of correct responses made by the participant. The findings of the experiment concluded that intentional learning is better than incidental learning, hence hypothesis is proved.

Keywords: intentional learning, incidental learning, non-sense syllable cards, score sheets

Procedia PDF Downloads 532