Search results for: DNA copy number

Authors: Faisal Nouroz, Mukaramin Mukaramin

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Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Serebryanaya Fatima, Essaih Hind

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The Rosa damascena (Rosa damascena Mill.) is an interesting medicinal plant; it is famous in different countries and has medicinal use in many cultures. The main groups of pharmacological actions of rose oil are connected with anti-inflammatory, antifungal activity, also antioxidant and antibacterial, and antiparasitic properties. We have prepared the quality indicators analysis of the Damascus rose oil. An iodine number, acid number, and oil peroxide number were determined. The following indicators of the quality of rose oil have been studied. The determination was carried out according to the pharmacopoeic methods of analysis of essential oils, the definition of peroxide number (1,971%), iodine number (3,365%), and acid number (0,0526%).

Keywords: Rosa damascene, Rosa damascena Mill., iodine number, acid number, oil peroxide number

Procedia PDF Downloads 48

Authors: Ganesh K. Maurya, Reema Chaudhary, Neha Pandey, Hari S. Misra

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PprA, a pleiotropic protein participating in radioresistance, has been reported for its roles in DNA replication initiation, genome segregation, cell division and DNA repair in polyextremophile Deinococcus radiodurans. Interestingly, expression of deinococcal PprA in E. coli suppresses its growth by reducing the number of colony forming units and provides better resistance against γ-radiation than control. We employed different biochemical and cell biology studies using PprA and its DNA binding/polymerization mutants (K133E & W183R) in E. coli. Cells expressing wild type PprA or its K133E mutant showed reduction in the amount of genomic DNA as well as chromosome copy number in comparison to W183R mutant of PprA and control cells, which suggests the role of PprA protein in regulation of DNA replication initiation in E. coli. Further, E. coli cells expressing PprA or its mutants exhibited different impact on cell morphology than control. Expression of PprA or K133E mutant displayed a significant increase in cell length upto 5 folds while W183R mutant showed cell length similar to uninduced control cells. We checked the interaction of deinococcal PprA and its mutants with E. coli DnaA using Bacterial two-hybrid system and co-immunoprecipitation. We observed a functional interaction of EcDnaA with PprA and K133E mutant but not with W183R mutant of PprA. Further, PprA or K133E mutant has suppressed the ATPase activity of EcDnaA but W183R mutant of PprA failed to do so. These observations suggested that PprA protein regulates DNA replication initiation and cell morphology of surrogate E. coli.

Keywords: DNA replication, radioresistance, protein-protein interaction, cell morphology, ATPase activity

Procedia PDF Downloads 34

Authors: Ganesh K. Maurya, Reema Chaudhary, Neha Pandey, Hari S. Misra

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PprA, a pleiotropic protein participating in radioresistance, has been reported for its roles in DNA replication initiation, genome segregation, cell division and DNA repair in polyextremophile Deinococcus radiodurans. Interestingly, expression of deinococcal PprA in E. coli suppresses its growth by reducing the number of colony forming units and provide better resistance against γ-radiation than control. We employed different biochemical and cell biology studies using PprA and its DNA binding/polymerization mutants (K133E & W183R) in E. coli. Cells expressing wild type PprA or its K133E mutant showed reduction in the amount of genomic DNA as well as chromosome copy number in comparison to W183R mutant of PprA and control cells, which suggests the role of PprA protein in regulation of DNA replication initiation in E. coli. Further, E. coli cells expressing PprA or its mutants exhibited different impact on cell morphology than control. Expression of PprA or K133E mutant displayed a significant increase in cell length upto 5 folds while W183R mutant showed cell length similar to uninduced control cells. We checked the interaction of deinococcal PprA and its mutants with E. coli DnaA using Bacterial two-hybrid system and co-immunoprecipitation. We observed a functional interaction of EcDnaA with PprA and K133E mutant but not with W183R mutant of PprA. Further, PprA or K133E mutant has suppressed the ATPase activity of EcDnaA but W183R mutant of PprA failed to do so. These observations suggested that PprA protein regulates DNA replication initiation and cell morphology of surrogate E. coli.

Keywords: DNA replication, radioresistance, protein-protein interaction, cell morphology, ATPase activity

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Authors: Dandeswar Bisoyi, Preeti Yadav, Utpal Barua

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This study address particular way that verbal information can affect the processing of positive and interesting qualities which help in making the brand attractive to the consumer. Also, it address the development of a communication strategy which is a very important part of the marketing plan we have to take into account many factors. Out of all the product strengths, the strategy has to outline one marked differential which will drive our brand. This is the fundamental base on which the entire creative strategy will be big idea-based.

Keywords: copy writing, advertisement, marketing, branding, recall

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Authors: N. Bachok, N. L. Aleng, N. M. Arifin, A. Ishak, N. Senu

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The problem of laminar fluid flow which results from the shrinking of a permeable surface in a nanofluid has been investigated numerically. The model used for the nanofluid incorporates the effects of Brownian motion and thermophoresis. A similarity solution is presented which depends on the mass suction parameter S, Prandtl number Pr, Lewis number Le, Brownian motion number Nb and thermophoresis number Nt. It was found that the reduced Nusselt number is decreasing function of each dimensionless number.

Keywords: Boundary layer, nanofluid, shrinking sheet, Brownian motion, thermophoresis, similarity solution

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Authors: Md. Shah Alam

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Mushfiq Ahmad has defined a Mixed Number, which is the sum of a scalar and a Cartesian vector. He has also defined the elementary group operations of Mixed numbers i.e. the norm of Mixed numbers, the product of two Mixed numbers, the identity element and the inverse. It has been observed that Mixed Number is consistent with Pauli matrix algebra and a handy tool to work with Dirac electron theory. Its use as a mathematical method in Physics has been studied. (1) We have applied Mixed number in Quantum Mechanics: Mixed Number version of Displacement operator, Vector differential operator, and Angular momentum operator has been developed. Mixed Number method has also been applied to Klein-Gordon equation. (2) We have applied Mixed number in Electrodynamics: Mixed Number version of Maxwell’s equation, the Electric and Magnetic field quantities and Lorentz Force has been found. (3) An associative transformation of Mixed Number numbers fulfilling Lorentz invariance requirement is developed. (4) We have applied Mixed number algebra as an extension of Complex number. Mixed numbers and the Quaternions have isomorphic correspondence, but they are different in algebraic details. The multiplication of unit Mixed number and the multiplication of unit Quaternions are different. Since Mixed Number has properties similar to those of Pauli matrix algebra, Mixed Number algebra is a more convenient tool to deal with Dirac equation.

Keywords: mixed number, special relativity, quantum mechanics, electrodynamics, pauli matrix

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Authors: Ali Reza Tahavvor, Saeed Hosseini, Afshin Karimzadeh Fard

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In this paper the effect of wall waviness of side walls in a two-dimensional wavy enclosure is numerically investigated. Two vertical wavy walls and straight top wall are kept isothermal and the bottom wall temperature is higher and spatially varying with cosinusoidal temperature distribution. A computational code based on Finite-volume approach is used to solve governing equations and SIMPLE method is used for pressure velocity coupling. Test is performed for several different numbers of undulations. The Prandtl number was kept constant and the Ra number denotes that the flow is laminar. Temperature and velocity fields are determined. Therefore, according to the obtained results a correlation is proposed for average Nusselt number as a function of number of side wall waves. The results indicate that the Nusselt number is highly affected by number of waves and increasing it decreases the wavy walls Nusselt number; although the Nusselt number is not highly affected by surface waviness when the number of undulations is below one.

Keywords: cavity, natural convection, Nusselt number, wavy wall

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Authors: Chao Wu

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Thioredoxin reductase 2 is a mitochondrial enzyme that belongs to the cellular defense against oxidative stress. We deleted mitochondrial Txnrd2 in a KrasG12D-driven pancreatic tumor model. Despite an initial increase in precursor lesions, tumor incidence decreased significantly. We isolated cancer cell lines from these genetically engineered mice and observed an impaired proliferation and colony formation. Reactive Oxygen Species, as determined by DCF fluorescence, were increased. We detected a higher mitochondrial copy number in Txnrd2-deficient cells (KTP). However, measurement of mitochondrial bioenergetics showed no impairment of mitochondrial function and comparable O₂-consumption and extracellular acidification rates. In addition, the mitochondrial complex composition was affected in Txnrd2 deleted cell lines. To gain better insight into the role of Txnrd2, we deleted Txnrd2 in clones from parental KrasG12D cell lines using Crispr/Cas9 technology. The deletion was confirmed by western blot and activity assay. Interestingly, and in line with previous RNA expression analysis, we saw changes in EMT markers in Txnrd2 deleted cell lines and control cell lines. This might help us explain the reduced tumor incidence in KrasG12D; Txnrd2∆panc mice.

Keywords: PDAC, TXNRD2, epithelial-to-mesenchymal-transition, ROS

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: Mohammed Al-Yamani, Yaser Miaji

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DHL Customer Solutions and Innovation Department (CSI) have been experiencing difficulties while comparing quotes for different customers in different years. Currently, the employees are processing data by opening several loaded Excel files where the quotes are and manually copying values to another Excel Workbook where the comparison is made. This project consists of developing a new and effective database for DHL CSI department so that information is stored altogether on the same catalog. That being said, we have been assigned to find an efficient algorithm that can deal with the different formats of the Excel Workbooks to copy and store the express customer rates for core products (DOX, WPX, IMP) for comparisons purposes.

Keywords: DHL, solution design, ORACLE, EXCEL

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Authors: Parisa Khoshvaght, Mehdi Hosseinzadeh

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During the past few years, the Residue Number System (RNS) has been receiving considerable interest due to its parallel and fault-tolerant properties. This system is a useful tool for Digital Signal Processing (DSP) since it can support parallel, carry-free, high-speed and low power arithmetic. One of the drawbacks of Residue Number System is the fractional numbers, that is, the corresponding circuit is very hard to realize in conventional CMOS technology. In this paper, we propose a method in which the numbers of transistors are significantly reduced. The related delay is extremely diminished, in the first glance we use this method to solve concerning problem of one decimal functional number some how this proposition can be extended to generalize the idea. Another advantage of this method is the independency on the kind of moduli.

Keywords: computer arithmetic, residue number system, number system, one-Hot, VLSI

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Authors: Iman Farasat, Howard M. Salis

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Engineered genetic circuits reprogram cellular behavior to act as living computers with applications in detecting cancer, creating self-controlling artificial tissues, and dynamically regulating metabolic pathways. Phenemenological models are often used to simulate and design genetic circuit behavior towards a desired behavior. While such models assume that each circuit component’s function is modular and independent, even small changes in a circuit (e.g. a new promoter, a change in transcription factor expression level, or even a new media) can have significant effects on the circuit’s function. Here, we use statistical thermodynamics to account for the several factors that control transcriptional regulation in bacteria, and experimentally demonstrate the model’s accuracy across 825 measurements in several genetic contexts and hosts. We then employ our first principles model to design, experimentally construct, and characterize a family of signal amplifying genetic circuits (genetic OpAmps) that expand the dynamic range of cell sensors. To develop these models, we needed a new approach to measuring the in vivo binding free energies of transcription factors (TFs), a key ingredient of statistical thermodynamic models of gene regulation. We developed a new high-throughput assay to measure RNA polymerase and TF binding free energies, requiring the construction and characterization of only a few constructs and data analysis (Figure 1A). We experimentally verified the assay on 6 TetR-homolog repressors and a CRISPR/dCas9 guide RNA. We found that our binding free energy measurements quantitatively explains why changing TF expression levels alters circuit function. Altogether, by combining these measurements with our biophysical model of translation (the RBS Calculator) as well as other measurements (Figure 1B), our model can account for changes in TF binding sites, TF expression levels, circuit copy number, host genome size, and host growth rate (Figure 1C). Model predictions correctly accounted for how these 8 factors control a promoter’s transcription rate (Figure 1D). Using the model, we developed a design framework for engineering multi-promoter genetic circuits that greatly reduces the number of degrees of freedom (8 factors per promoter) to a single dimensionless unit. We propose the Ptashne (Pt) number to encapsulate the 8 co-dependent factors that control transcriptional regulation into a single number. Therefore, a single number controls a promoter’s output rather than these 8 co-dependent factors, and designing a genetic circuit with N promoters requires specification of only N Pt numbers. We demonstrate how to design genetic circuits in Pt number space by constructing and characterizing 15 2-repressor OpAmp circuits that act as signal amplifiers when within an optimal Pt region. We experimentally show that OpAmp circuits using different TFs and TF expression levels will only amplify the dynamic range of input signals when their corresponding Pt numbers are within the optimal region. Thus, the use of the Pt number greatly simplifies the genetic circuit design, particularly important as circuits employ more TFs to perform increasingly complex functions.

Keywords: transcription factor, synthetic biology, genetic circuit, biophysical model, binding energy measurement

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Authors: Ali Abdi Kordani, Hamid Bigdelirad, Sid Mohammad Boroomandrad

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Operating Urban Bus Transit System is a phenomenon that has a major role in transporting passengers in cities. There are many factors involved in planning and operating an Urban Bus Transit System, one of which is selecting optimized number of stops and scheduling of bus fleet departure. In this paper, we tried to introduce desirable methodology to select number of stops and schedule properly. Selecting the right number of stops causes convenience in accessibility and reduction in travel time and finally increase in public preference of this transportation mode. The achieved results revealed that number of stops must reduce from 33 to 25. Also according to scheduling and conducted economic analysis, the number of buses must decrease from 17 to 11 to have the most appropriate status for the Bus Organization.

Keywords: number of optimized stops, organizing bus system, scheduling, urban transit

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Authors: Sibonakaliso Shadrack Nhlabathi

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In South Africa local governments which are charged with the provision of services and amenities, frequently, face challenges of public protests against what the public perceives to be poor services. Public protests are common, even though the Integrated Development Plan, a central public participation document, which informs local government planning and resources management, ought to be a reflection of the voices of the beneficiary communities. The Integrated Development Plan concept –which evolved from the international discourse on governance, planning, and urban management of the 1990s, and, which bears similarities to the UK’s approaches to urban management and planning– is a significant concept in the planning practice in South Africa. Against this backdrop of the spread of public protests and the supposedly public participation in IDP formulation, this study investigated the extent to which residents of the city of uMhlathuze municipality, South Africa, could use Geographical Information Systems (GIS) Story Maps to enhance public participation in the provision of services and amenities. To this effect, this study collected and analysed data obtained through interactive web maps or hard copy maps; this map data was accompanied by research participants’ attributes data. Research participants identified positive or negative service delivery areas. Positive places were the places which the residents represented as good infrastructural, and amenities areas and weak places were marked as poor amenities. Participants then located each of their identified strong or weak places as points on the GIS Story Maps or on hard copy maps of the city. The information which participants provided was subsequently analysed to produce maps of patterns of service provision. In this way, the study succeeded to identify places that needed attention regarding delivery of services and amenities. Thus, this study advanced service provision through GIS Story Maps.

Keywords: GIS, IPD, South Africa, story maps

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Authors: Nur Irmawati, H. A. Mohammed

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In the present study, mixed convection in a horizontal rectangular duct using Al2O3 is numerically investigated. The effects of different Rayleigh number, Reynolds number and radiation on flow and heat transfer characteristics were studied in detail. This study covers Rayleigh number in the range of 2×106≤Ra≤2×107 and Reynolds number in the range of 100≤Re≤1100. Results reveal that the Nusselt number increases as Reynolds and Rayleigh numbers increase. It was also found that the dimensionless temperature distribution increases as Rayleigh number increases.

Keywords: numerical simulation, mixed convection, horizontal rectangular duct, nanofluids

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Authors: Qinghua Xing, Noha M. Mesbah, Haisheng Wang, Jun Li, Baisuo Zhao

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Droplet digital PCR (ddPCR) is being increasingly adopted for gene detection and quantification because of its higher sensitivity and specificity. According to previous observations and our lab data, it is essential to use endogenous reference genes (RGs) when investigating gene expression at the mRNA level under salt stress. This study aimed to select and validate suitable RGs for gene expression under salt stress using ddPCR. Six candidate RGs were selected based on the tandem mass tag (TMT)-labeled quantitative proteomics of Alkalicoccus halolimnae at four salinities. The expression stability of these candidate genes was evaluated using statistical algorithms (geNorm, NormFinder, BestKeeper and RefFinder). There was a small fluctuation in cycle threshold (Ct) value and copy number of the pdp gene. Its expression stability was ranked in the vanguard of all algorithms, and was the most suitable RG for quantification of expression by both qPCR and ddPCR of A. halolimnae under salt stress. Single RG pdp and RG combinations were used to normalize the expression of ectA, ectB, ectC, and ectD under four salinities. The present study constitutes the first systematic analysis of endogenous RG selection for halophiles responding to salt stress. This work provides a valuable theory and an approach reference of internal control identification for ddPCR-based stress response models.

Keywords: endogenous reference gene, salt stress, ddPCR, RT-qPCR, Alkalicoccus halolimnae

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Authors: Songul Cinaroglu

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Background: Random Forest is an efficient, multi-class machine learning method using for classification, regression and other tasks. This method is operating by constructing each tree using different bootstrap sample of the data. Determining the number of trees in random forests is an open question in the literature for studies about improving classification performance of random forests. Aim: The aim of this study is to analyze whether there is an optimal number of trees in Random Forests and how performance of Random Forests differ according to increase in number of trees using sample health data sets in R programme. Method: In this study we analyzed the performance of Random Forests as the number of trees grows and doubling the number of trees at every iteration using “random forest” package in R programme. For determining minimum and optimal number of trees we performed Mc Nemar test and Area Under ROC Curve respectively. Results: At the end of the analysis it was found that as the number of trees grows, it does not always means that the performance of the forest is better than forests which have fever trees. In other words larger number of trees only increases computational costs but not increases performance results. Conclusion: Despite general practice in using random forests is to generate large number of trees for having high performance results, this study shows that increasing number of trees doesn’t always improves performance. Future studies can compare different kinds of data sets and different performance measures to test whether Random Forest performance results change as number of trees increase or not.

Keywords: classification methods, decision trees, number of trees, random forest

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Authors: A. M. Nasr, W. R. Azzam, K. E. Ebeed

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For bored piles, careful cleaning must be used to reduce the amount of material trapped in the drilled hole; otherwise, the debris' presence might cause the soft toe effect, which would affect the axial resistance. There isn't much comprehensive research on bored piles with debris. In order to investigate the behavior of a single pile, a pile composite foundation, a two pile group, a three pile group and a four pile group investigation conducts, forty-eight numerical tests in which the debris is simulated using foam rubber.1m pile diameter and 10m length with spacing 3D and depth of foundation 1m used in this study. It is found that the existence of debris causes a reduction of bearing capacity by 64.58% and 33.23% for single pile and pile composite foundation, respectively, 23.27% and 24.24% for the number of defective piles / total number of pile =1/2 and 1 respectively for two group pile, 10.23%, 19.42% and 28.47% for the number of defective piles / total number of pile =1/3,2/3 and 1 respectively for three group pile and, this reduction increase with the increase in a number of defective piles / a total number of piles and 7.1%, 13.32%,19.02% and 26.36 for the number of defective piles / total number of pile =1/4,2/4,3/4 and 1 respectively for four group pile and decreases with an increase of number of pile duo to interaction effect.

Keywords: debris, Foundation, defective, interaction, board pile

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Authors: Sinuhé Perea Puente

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In several physics systems the whole can be obtained as an exact copy of each of its parts, which facilitates the study of a complex system by looking carefully at its elements, separately. Reducionism offers simplified models which makes the problems easier, but “there’s plenty of room...at the mesoscopic scale”. Here we present a tour for two of its representants: Berry phase and skyrmions, studying some of its basic definitions and properties, and two cases in which both arise together, to finish constraining the scale for our mesoscopic system in the quest of quantum skyrmions, discovering which properties are conserved and which others may be destroyed.

Keywords: condensed mattter, quantum physics, skyrmions, topological defects

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Authors: Laissa Mae Francisco, John Rolex Ingreso, Anna Krizel Menguito, Criselda Robrigado, Rej Maegan Tuazon

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This study aims to determine and describe the existing relationship between number sense proficiency and problem-solving performance of grade seven students from Victorino Mapa High School, Manila. A paper pencil exam containing of 50-item number sense test and 5-item problem-solving test which measures their number sense proficiency and problem-solving performance adapted from McIntosh, Reys, and Bana were used as the research instruments. The data obtained from this study were interpreted and analyzed using the Pearson – Product Moment Coefficient of Correlation to determine the relationship between the two variables. It was found out that students who were low in number sense proficiency tend to be the students with poor problem-solving performance and students with medium number sense proficiency are most likely to have an average problem-solving performance. Likewise, students with high number sense proficiency are those who do excellently in problem-solving performance.

Keywords: number sense, performance, problem solving, proficiency

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Authors: Amel Tayari, Atef Eljerry, Mourad Magherbi

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The paper reports a numerical investigation of the entropy generation analysis due to mixed convection in laminar flow through a channel filled with porous media. The second law of thermodynamics is applied to investigate the entropy generation rate. The Darcy-Brinkman Model is employed. The entropy generation due to heat transfer and friction dissipations has been determined in mixed convection by solving numerically the continuity, momentum and energy equations, using a control volume finite element method. The effects of Darcy number, modified Brinkman number and the Rayleigh number on averaged entropy generation and averaged Nusselt number are investigated. The Rayleigh number varied between 103 ≤ Ra ≤ 105 and the modified Brinkman number ranges between 10-5 ≤ Br≤ 10-1 with fixed values of porosity and Reynolds number at 0.5 and 10 respectively. The Darcy number varied between 10-6 ≤ Da ≤10.

Keywords: entropy generation, porous media, heat transfer, mixed convection, numerical methods, darcy, brinkman

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Authors: Noora Al Muftah, Reda Rawi, Richard Thompson, Halima Bensmail

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Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, mutated cancer genes are potent biomarkers of response to targeted agents. There is an urgent need to identify biomarkers that predict which patients with are most likely to respond to treatment. Systematic efforts to correlate tumor mutational data with biologic dependencies may facilitate the translation of somatic mutation catalogs into meaningful biomarkers for patient stratification. To identify genomic features associated with drug sensitivity and uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we have screened and integrated a panel of several hundred cancer cell lines from different databases, mutation, DNA copy number, and gene expression data for hundreds of cell lines with their responses to targeted and cytotoxic therapies with drugs under clinical and preclinical investigation. We found mutated cancer genes were associated with cellular response to most currently available Glioma cancer drugs and some frequently mutated genes were associated with sensitivity to a broad range of therapeutic agents. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies.

Keywords: cancer, gene network, Lasso, penalized regression, P-values, unbiased estimator

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Authors: Salem Ben Said

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In recent times the decimal number system to which we are accustomed has received serious competition from the binary number system. In this note, an approach is suggested to teaching and learning the binary number system using examples from the real world. More precisely, we will demonstrate the utility of the binary system in describing the optimal strategy to win the Chinese Nim game, and in telegraphy by decoding the hidden message on Perseverance’s Mars parachute written in the language of binary system. Finally, we will answer the question, “why do modern computers prefer the ternary number system instead of the binary system?”. All materials are provided in a format that is conductive to classroom presentation and discussion.

Keywords: binary number system, Nim game, telegraphy, computers prefer the ternary system

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Authors: Ladislav Kristoufek, Helen Susannah Moat, Tobias Preis

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Data on the number of people who have committed suicide tends to be reported with a substantial time lag of around two years. We examine whether online activity measured by Google searches can help us improve estimates of the number of suicide occurrences in England before official figures are released. Specifically, we analyse how data on the number of Google searches for the terms “depression” and “suicide” relate to the number of suicides between 2004 and 2013. We find that estimates drawing on Google data are significantly better than estimates using previous suicide data alone. We show that a greater number of searches for the term “depression” is related to fewer suicides, whereas a greater number of searches for the term “suicide” is related to more suicides. Data on suicide related search behaviour can be used to improve current estimates of the number of suicide occurrences.

Keywords: nowcasting, search data, Google Trends, official statistics

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Authors: Belmiloud Mohamed Amine, Sad Chemloul Nord-Eddine

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In this study we investigated numerically heat transfer by mixed convection coupled to radiation in a square cavity; the upper horizontal wall is movable. The purpose of this study is to see the influence of the emissivity and the varying of the Richardson number on the variation of the average Nusselt number. The vertical walls of the cavity are differentially heated, the left wall is maintained at a uniform temperature higher than the right wall, and the two horizontal walls are adiabatic. The finite volume method is used for solving the dimensionless governing equations. Emissivity values used in this study are ranged between 0 and 1, the Richardson number in the range 0.1 to10. The Rayleigh number is fixed to Ra = 10000 and the Prandtl number is maintained constant Pr = 0.71. Streamlines, isothermal lines and the average Nusselt number are presented according to the surface emissivity. The results of this study show that the Richardson number and emissivity affect the average Nusselt number.

Keywords: mixed convection, square cavity, wall emissivity, lid-driven, numerical study

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Authors: Katalin Gombos, Bence Gálik, Krisztina Ildikó Kalács, Krisztina Gödöny, Ákos Várnagy, József Bódis, Attila Gyenesei, Gábor L. Kovács

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Although non-invasive pre-implantation genetic testing for aneuploidy (NIPGT-A) is potentially appropriate to assess chromosomal ploidy of the embryo, practical application of it in a routine IVF center has not been started in the absence of a recommendation. We developed a comprehensive workflow for a clinically applicable strategy for NIPGT-A based on next-generation sequencing (NGS) technology. We performed MALBAC whole genome amplification and NGS on spent blastocyst culture media of Day 3 embryos fertilized with intra-cytoplasmic sperm injection (ICSI). Spent embryonic culture media of morphologically good quality score embryos were enrolled in further analysis with the blank culture media as background control. Chromosomal abnormalities were identified by an optimized bioinformatics pipeline applying a copy number variation (CNV) detecting algorithm. We demonstrate a comprehensive workflow covering both wet- and dry-lab procedures supporting a clinically applicable strategy for NIPGT-A. It can be carried out within 48 h which is critical for the same-cycle blastocyst transfer, but also suitable for “freeze all” and “elective frozen embryo” strategies. The described integrated approach of non-invasive evaluation of embryonic DNA content of the culture media can potentially supplement existing pre-implantation genetic screening methods.

Keywords: next generation sequencing, in vitro fertilization, embryo assessment, non-invasive pre-implantation genetic testing

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Authors: Marielle Leijten, Catherine Meulemans, Sven De Maeyer, Luuk Van Waes

Abstract:

For the diagnosis of Alzheimer's disease (AD), a large variety of neuropsychological tests are available. In some of these tests, linguistic processing - both oral and written - is an important factor. Language disturbances might serve as a strong indicator for an underlying neurodegenerative disorder like AD. However, the current diagnostic instruments for language assessment mainly focus on product measures, such as text length or number of errors, ignoring the importance of the process that leads to written or spoken language production. In this study, it is our aim to describe and test differences between cognitive and impaired elderly on the basis of a selection of writing process variables (inter- and intrapersonal characteristics). These process variables are mainly related to pause times, because the number, length, and location of pauses have proven to be an important indicator of the cognitive complexity of a process. Method: Participants that were enrolled in our research were chosen on the basis of a number of basic criteria necessary to collect reliable writing process data. Furthermore, we opted to match the thirteen cognitively impaired patients (8 MCI and 5 AD) with thirteen cognitively healthy elderly. At the start of the experiment, participants were each given a number of tests, such as the Mini-Mental State Examination test (MMSE), the Geriatric Depression Scale (GDS), the forward and backward digit span and the Edinburgh Handedness Inventory (EHI). Also, a questionnaire was used to collect socio-demographic information (age, gender, eduction) of the subjects as well as more details on their level of computer literacy. The tests and questionnaire were followed by two typing tasks and two picture description tasks. For the typing tasks participants had to copy (type) characters, words and sentences from a screen, whereas the picture description tasks each consisted of an image they had to describe in a few sentences. Both the typing and the picture description tasks were logged with Inputlog, a keystroke logging tool that allows us to log and time stamp keystroke activity to reconstruct and describe text production processes. The main rationale behind keystroke logging is that writing fluency and flow reveal traces of the underlying cognitive processes. This explains the analytical focus on pause (length, number, distribution, location, etc.) and revision (number, type, operation, embeddedness, location, etc.) characteristics. As in speech, pause times are seen as indexical of cognitive effort. Results. Preliminary analysis already showed some promising results concerning pause times before, within and after words. For all variables, mixed effects models were used that included participants as a random effect and MMSE scores, GDS scores and word categories (such as determiners and nouns) as a fixed effect. For pause times before and after words cognitively impaired patients paused longer than healthy elderly. These variables did not show an interaction effect between the group participants (cognitively impaired or healthy elderly) belonged to and word categories. However, pause times within words did show an interaction effect, which indicates pause times within certain word categories differ significantly between patients and healthy elderly.

Keywords: Alzheimer's disease, keystroke logging, matching, writing process

Procedia PDF Downloads 330

Authors: Kazuyoshi Mori

Abstract:

In this paper, we consider the number of parameters for the parametrization of stabilizing controllers for RHinf systems with size 2 × 2. Fortunately, any plant of this model can admit doubly coprime factorization. Thus we can use the Youla parameterization to parametrize the stabilizing contollers . However, Youla parameterization does not give itself the minimal number of parameters. This paper shows that the minimal number of parameters is four. As a result, we show that the Youla parametrization naturally gives the parameterization of stabilizing controllers with minimal numbers.

Keywords: RHinfo, parameterization, number of parameters, multi-input, multi-output systems

Procedia PDF Downloads 386

Authors: Michael Zimba

Abstract:

A duplicated image region may be subjected to a number of attacks such as noise addition, compression, reflection, rotation, and scaling with the intention of either merely mating it to its targeted neighborhood or preventing its detection. In this paper, we present an effective and robust method of detecting duplicated regions inclusive of those affected by the various attacks. In order to reduce the dimension of the image, the proposed algorithm firstly performs discrete wavelet transform, DWT, of a suspicious image. However, unlike most existing copy move image forgery (CMIF) detection algorithms operating in the DWT domain which extract only the low frequency sub-band of the DWT of the suspicious image thereby leaving valuable information in the other three sub-bands, the proposed algorithm simultaneously extracts features from all the four sub-bands. The extracted features are not only more accurate representation of image regions but also robust to additive noise, JPEG compression, and affine transformation. Furthermore, principal component analysis-eigenvalue decomposition, PCA-EVD, is applied to reduce the dimension of the features. The extracted features are then sorted using the more computationally efficient Radix Sort algorithm. Finally, same affine transformation selection, SATS, a duplication verification method, is applied to detect duplicated regions. The proposed algorithm is not only fast but also more robust to attacks compared to the related CMIF detection algorithms. The experimental results show high detection rates.

Keywords: affine transformation, discrete wavelet transform, radix sort, SATS

Procedia PDF Downloads 201