Search results for: copy number variant

Authors: Prateek Kishore, T. M. Muruganandam

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Supersonic wind tunnel nozzles are generally capable of producing a constant Mach number flow in the test section of the wind tunnel. As a result, most of the supersonic vehicles are widely designed using steady state flow characteristics which may have errors while facing unsteady situations. This study aims to explore the possibility of varying the Mach number of the flow during wind tunnel operation. The nozzle walls are restricted to be inflexible for cooling near the throat due to high stagnation temperature requirement of the flow to simulate the conditions as experienced by the vehicle. Two simple independent mechanisms, rotation and translation of nozzle walls have been analyzed and the nozzle ranges have been optimized to vary the Mach number from Mach 2 to Mach 5 using minimum number of nozzles in the wind tunnel.

Keywords: method of characteristics, nozzle, supersonic wind tunnel, variable mach number

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Authors: Areej Isam Barham

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Developing students’ number sense is an essential element in the learning of mathematics. Number sense is one of the foundational ideas in mathematics where students need to understand numbers, representing them in different ways, and realize the relationships among numbers. Number sense also reflects students’ understanding of the meaning of operations, how they related to one another, how to compute fluently and make reasonable estimates. Developing students’ number sense in the mathematics classroom requires good preparation for mathematics teachers, those who will direct their students towards the real understanding of numbers and its implementation in the learning of mathematics. This study describes the development of elementary prospective mathematics teachers’ number sense through a mathematics teaching methods course at Qatar University. The study examined the effect of using the Lesh model in enhancing mathematics prospective teachers’ number sense. Thirty-nine elementary prospective mathematics teachers involved in the current study. The study followed an experimental research approach, and quantitative research methods were used to answer the research questions. Pre-post number sense test was constructed and implemented before and after teaching by using the Lesh model. Data were analyzed using Statistical Packages for Social Sciences (SPSS). Descriptive data analysis and t-test were used to examine the impact of using the Lesh model in enhancing prospective teachers’ number sense. Finding of the study indicated poor number sense and limited numeracy skills before implementing the use of the Lesh model, which highly demonstrate the importance of the study. The results of the study also revealed a positive impact on the use of the Lesh model in enhancing prospective teachers’ number sense with statistically significant differences. The discussion of the study addresses different features and issues related to the participants’ number sense. In light of the study, the research presents recommendations and suggestions for the future development of mathematics prospective teachers’ number sense.

Keywords: number sense, Lesh model, prospective mathematics teachers, development of number sense

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Authors: Karunambigai Mevani Govindasamy, Sathishkumar Ayyappan

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In this paper, we formulate the algorithm to find out the dominating function parameters of Intuitionistic Fuzzy Graphs(IFG). The methodology we adopted here is converting any physical problem into an IFG, and that has been transformed into Intuitionistic Fuzzy Matrix. Using Linear Program Solver software (LiPS), we found the defined parameters for the given IFG. We obtained these parameters for a path and cycle IFG. This study can be extended to other varieties of IFG. In particular, we obtain the definition of edge dominating function, minimal edge dominating function, fractional edge domination number (γ_if^') and upper fractional edge domination number (Γ_if^') of an intuitionistic fuzzy graph. Also, we formulated an algorithm which is appropriate to work on LiPS to find fractional edge domination number and upper fractional edge domination number of an IFG.

Keywords: fractional edge domination number, intuitionistic fuzzy cycle, intuitionistic fuzzy graph, intuitionistic fuzzy path

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Authors: Tuğçe Yücel

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A Wireless Sensor Network(WSN) is a collection of sensor nodes which are deployed randomly in an area for surveillance. Efficient utilization of limited battery energy of sensors for increased network lifetime as well as data security are major design objectives for WSN. Moreover secure transmission of data sensed to a base station for further processing. Producing multiple copies of data packets and sending them on different paths is one of the strategies for this purpose, which leads to redundant energy consumption and hence reduced network lifetime. In this work we develop a restricted multi-copy multipath strategy where data move through ‘frequently’ or ‘heavily’ used sensors is copied by the sensor incident to such central nodes and sent on node-disjoint paths. We develop a mixed integer programing(MIP) model and heuristic approach present some preleminary test results.

Keywords: MIP, sensor, telecommunications, WSN

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Authors: Hyeon-Kyo Lim, Tong-Il Jang, Yong-Hee Lee

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For an operator in a nuclear power plant, human error is one of the most dreaded factors that may result in unexpected accidents. The possibility of human errors may be low, but the risk of them would be unimaginably enormous. Thus, for accident prevention, it is quite indispensable to analyze the influence of any factors which may raise the possibility of human errors. During the past decades, not a few research results showed that performance of human operators may vary over time due to lots of factors. Among them, stress is known to be an indirect factor that may cause human errors and result in mental illness. Until now, not a few assessment tools have been developed to assess stress level of human workers. However, it still is questionable to utilize them for human performance anticipation which is related with human error possibility, because they were mainly developed from the viewpoint of mental health rather than industrial safety. Stress level of a person may go up or down with work time. In that sense, if they would be applicable in the safety aspect, they should be able to assess the variation resulted from work time at least. Therefore, this study aimed to compare their applicability for safety purpose. More than 10 kinds of work stress tools were analyzed with reference to assessment items, assessment and analysis methods, and follow-up measures which are known to close related factors with work stress. The results showed that most tools mainly focused their weights on some common organizational factors such as demands, supports, and relationships, in sequence. Their weights were broadly similar. However, they failed to recommend practical solutions. Instead, they merely advised to set up overall counterplans in PDCA cycle or risk management activities which would be far from practical human error prevention. Thus, it was concluded that application of stress assessment tools mainly developed for mental health seemed to be impractical for safety purpose with respect to human performance anticipation, and that development of a new assessment tools would be inevitable if anyone wants to assess stress level in the aspect of human performance variation and accident prevention. As a consequence, as practical counterplans, this study proposed a new scheme for assessment of work stress level of a human operator that may vary over work time which is closely related with the possibility of human errors.

Keywords: human error, human performance, work stress, assessment tool, time-variant, accident prevention

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Authors: Bing Li

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The primitive code-level design patterns (PDP) are the rudimentary programming elements to develop any distributed systems in the generic distributed programming environment, GreatFree. The PDP works with the primitive distributed application programming interfaces (PDA), the distributed modeling, and the distributed concurrency for scaling-up. They not only hide developers from underlying technical details but also support sufficient adaptability to a variety of distributed computing environments. Programming with them, the simplest distributed system, the lightweight messaging two-node client/server (TNCS) system, is constructed rapidly with straightforward and repeatable behaviors, copy-paste-replace (CPR). As any distributed systems are made up of the simplest ones, those PDAs, as well as the PDP, are generic for distributed programming.

Keywords: primitive APIs, primitive code-level design patterns, generic distributed programming, distributed systems, highly patterned development environment, messaging

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Authors: Liang Ming Zhong, Yu Zhong, Wen Zhong, Fei Fei Yin

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Trinary affinity is a description of existence: every object exists as it is known and spoken of, in a system of 2 differences (denoted dif1, dif₂) and 1 similarity (Sim), equivalently expressed as dif₁ / Sim / dif₂ and kn / 0 / tkn (kn = the known, tkn = the 'to be known', 0 = the zero point of knowing). They are mathematically verified and illustrated in this paper by the arrangement of all integers onto 3 columns, where each number exists as a difference in relation to another number as another difference, and the 2 difs as arbitrated by a third number as the Sim, resulting in a trinary affinity or trinity of 3 numbers, of which one is the known, the other the 'to be known', and the third the zero (0) from which both the kn and tkn are measured and specified. Consequently, any number is horizontally specified either as 3n, or as '3n – 1' or '3n + 1', and vertically as 'Cn + c', so that any number seems to occur at the intersection of its X and Y axes and represented by its X and Y coordinates, as any point on Earth’s surface by its latitude and longitude. Technically, i) primes are viewed and treated as progenitors, and composites as descending from them, forming families of composites, each capable of being measured and specified from its own zero called in this paper the realistic zero (denoted 0r, as contrasted to the mathematic zero, 0m), which corresponds to the constant c, and the nature of which separates the composite and prime numbers, and ii) any number is considered as having a magnitude as well as a position, so that a number is verified as a prime first by referring to its descriptive formula and then by making sure that no composite number can possibly occur on its position, by dividing it with factors provided by the composite number formulas. The paper consists of 3 parts: 1) a brief explanation of the trinary affinity of things, 2) the 8 formulas that represent ALL the primes, and 3) families of composite numbers, each represented by a formula. A composite number family is described as 3n + f₁‧f₂. Since there are an infinitely large number of composite number families, to verify the primality of a great probable prime, we have to have it divided with several or many a f₁ from a range of composite number formulas, a procedure that is as laborious as it is the surest way to verifying a great number’s primality. (So, it is possible to substitute planned division for trial division.)

Keywords: trinary affinity, difference, similarity, realistic zero

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Authors: Kazuyoshi Mori

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In this paper, we consider the parametrization of Anantharam’s model within the framework of the factorization approach. In the parametrization, we investigate the number of required parameters of Anantharam’s model. We consider single-input single-output systems in this paper. By the investigation, we find three cases that are (1) there exist plants which require only one parameter and (2) two parameters, and (3) the number of parameters is at most three.

Keywords: linear systems, parametrization, coprime factorization, number of parameters

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Authors: R. C. Law, Shirley Kang, T. Y. Hin, M. Z. Abdullah

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LED technology has been evolving aggressively in recent years from incandescent bulb during older days to as small as chip scale package. It will continue to stay bright in future. As such, there is tremendous pressure to stay competitive in the market by optimizing products to next level of performance and reliability with the shortest time to market. This changes the conventional way of product design and development to virtual prototyping by means of Computer Aided Engineering (CAE). It comprises of the deployment of Finite Element Method (FEM) and Computational Fluid Dynamic (CFD). FEM accelerates the investigation for early detection of failures such as crack, improve the thermal performance of system and enhance solder joint reliability. CFD helps to simulate the flow pattern of molding material as a function of different temperature, molding parameters settings to evaluate failures like voids and displacement. This paper will briefly discuss the procedures and applications of FEM in thermal stress, solder joint reliability and CFD of compression molding in LED CSP. Integration of virtual prototyping in product development had greatly reduced the time to market. Many successful achievements with minimized number of evaluation iterations required in the scope of material, process setting, and package architecture variant have been materialized with this approach.

Keywords: LED, chip scale packaging (CSP), computational fluid dynamic (CFD), virtual prototyping

Procedia PDF Downloads 287

Authors: Rim Frikha, Nouha Bouayed, Afifa Sellami, Nozha Chakroun, Salima Daoud, Leila Keskes, Tarek Rebai

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Introduction: Recurrent pregnancy loss (RPL) defined as two or more pregnancy losses, is a serious clinical problem. Methylene-tetrahydro-folate-reductase (MTHFR) polymorphisms, commonly the variant C677T is recognized as an inherited thrombophilia which might affect embryonic development and pregnancy success and cause pregnancy complications as RPL. Material and Methods DNA was extracted from peripheral blood samples and PCR-RFLP was performed for the molecular diagnosis of the C677T MTHFR polymorphism among 70 patients (35 couples) with more than 2 fetal losses. Aims and Objective: The aim of this study is to determine the frequency of MTHFR C677T among Tunisian couples with RPL and to critically analyze the available literature on the importance of MTHFR polymorphism testing in the management of RPL. Result and comments: No C677T mutation was detected in the carriers of RPL. This result would be related to sample size and to different criteria (number of abortion), - The association between MTHFR polymorphisms and pregnancy complications has been reported but with controversial results. - A lack of evidence for MTHFR polymorphism testing previously recommended by ACMG (American College of Medical medicine). Our study highlights the importance of screening of MTHFR polymorphism since the real impact of such thrombotic molecular defect on the pregnancy outcome is evident. - Folic supplementation of these patients during pregnancy can prevent such complications and lead to a successful pregnancy outcome.

Keywords: methylenetetrahydrofolate reductase, C677T, recurrent pregnancy loss, genetic testing

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Authors: M. Alipanah, A. Ranjbar, E. Farnad, F. Alipanah

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Entropy generation of an Al2O3-water nanofluid due to heat transfer and fluid friction irreversibility has been investigated in a square cavity subject to different side wall temperatures using a nanofluid for natural convection flow. This study has been carried out for the pertinent parameters in the following ranges: Rayleigh number between 104 to 107 and volume fraction between 0 to 0.05. Based on the obtained dimensionless velocity and temperature values, the distributions of local entropy generation, average entropy generation and average Bejan number are determined. The results are compared for a pure fluid and a nanofluid. It is totally found that the heat transfer and entropy generation of the nanofluid is more than the pure fluid and minimum entropy generation and Nusselt number occur in the pure fluid at any Rayleigh number. Results depict that the addition of nanoparticles to the pure fluid has more effect on the entropy generation as the Rayleigh number goes up.

Keywords: entropy generation, natural convection, bejan number, nuselt number, nanofluid

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Authors: Hari Mohan Kushwaha, Santosh Kumar Sahu

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In the present study, analysis of heat transfer is carried out in the slip flow region for the fluid flowing between two parallel plates by employing the asymmetric heat fluxes at surface of the plates. The flow is assumed to be hydrodynamically and thermally fully developed for the analysis. The second order velocity slip and viscous dissipation effects are considered for the analysis. Closed form expressions are obtained for the Nusselt number as a function of Knudsen number and modified Brinkman number. The limiting condition of the present prediction for Kn = 0, Kn2 = 0, and Brq1 = 0 is considered and found to agree well with other analytical results.

Keywords: Knudsen number, modified Brinkman number, slip flow, velocity slip

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Authors: L. Musak, J. Valachova, T. Vasicko, O. Osina

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Introduction: Stainless steel is resistant to electrochemical corrosion by passivation. Welders are greatly exposed to welding fumes of toxic metals, which added to this steel. The content of chromium (Cr) in steel was above 11.5%, Ni and Mo from 2 to 6.5%. The aim of the study was the evaluation of occupational exposure to Cr, chromosome analysis and valuation of individual susceptibility polymorphism of gene CCND1 c.870 G>A. Materials and Methods: The exposed group was consisted from 117 welders of stainless steels. The average age was 38.43 years and average exposure time 7.14 years. Smokers represented 40.17%. The control group consisted of 123 non-exposed workers with an average age of 39.74 years and time employment 16.67 years. Smokers accounted for 22.76%. Analysis of Cr in blood and urine was performed by atomic absorption spectrophotometry (AAS Varian SpectraAA 30P) with electrothermal decomposition of the sample in the graphite furnace. For the evaluation of chromosomal aberrations (CA) was used cytogenetic analysis of peripheral blood lymphocytes, gene polymorphism was determined by PCR-RFLP reaction using appropriate primers and restriction enzymes. For statistical analysis was used the Mann-Whitney U-test. Results: The mean Cr level in exposed group was 0.095 mmol/l (0.019 min-max 0.504). No value does exceed the average normal value. The average value Cr in urine was 7.9 mmol/mol creatinine (min 0.026 to max 19.26). The total number of CA was 1.86% in compared to 1.70% controls. (CTA-type 0.90% vs 0.80% and CSA-type 0.96% vs 0.90%). In the number of total CA was observed statistical difference between smokers and non-smokers of exposed group (S-1.57% vs. NS-2.04%, P<0.05). In CCND1 gene polymorphisms was observed the increasing of the total CA with wild-type allele (WT) via heterozygous to the VAR genotype (1.44%<1.82%<2.13%). There was observed a statistically higher incidence of CTA-type aberrations in variant genotypes between exposed and control groups (1.22% vs. 0.59%, P<0.05). Discussion and conclusions: The work place is usually higher source of exposure to harmful factors. Workers need consistently and checked frequently health control. In assessing the risk of adverse effects of metals is important to consider their persistence, behavior and bioavailability. Prolonged exposure to carcinogens may not manifest symptoms of poisoning, but delayed effects may occur, which resulted in a higher incidence of malignant tumors.

Keywords: genotoxicity, chromium, stainless steels, welders

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Authors: Indira Kothalanka

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For individuals born with a cleft palate (CP), there is no separation between the nasal cavity and the oral cavity, due to which they cannot build up enough air pressure in the mouth for speech. Therefore, it is common for them to have speech problems. Common cleft type speech errors include abnormal articulation (compensatory or obligatory) and abnormal resonance (hyper, hypo and mixed nasality). These are generally resolved after palate repair. However, in some individuals, articulation problems do persist even after the palate repair. Such individuals develop variant articulations in an attempt to compensate for the inability to produce the target phonemes. A spectrographic analysis is used to investigate the compensatory articulatory behaviours of pressure consonants in the speech of 10 Telugu speaking individuals aged between 7-17 years with a history of cleft palate. Telugu is a Dravidian language which is spoken in Andhra Pradesh and Telangana states in India. It is a language with the third largest number of native speakers in India and the most spoken Dravidian language. The speech of the informants is analysed using single word list, sentences, passage and conversation. Spectrographic analysis is carried out using PRAAT, speech analysis software. The place and manner of articulation of consonant sounds is studied through spectrograms with the help of various acoustic cues. The types of compensatory articulation identified are glottal stops, palatal stops, uvular, velar stops and nasal fricatives which are non-native in Telugu.

Keywords: cleft palate, compensatory articulation, spectrographic analysis, PRAAT

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Authors: Teguh Sugiarto

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Background: The research aims to explore if there is fraud in a financial statement, use the Act stated that Benford's distribution all digits must compare the number will follow the trend of lower number. Research methods: This research uses all the analysis number being in Benford's law. After receiving the results of the analysis of all the digits, the author makes a distinction between implementation using the scale above and below 5%, the rate of occurrence of difference. With the number which have differences in the range of 5%, then can do the follow-up and the detection of the onset of fraud against the financial statements. The findings: From the research that has been done can be drawn the conclusion that the average of all numbers appear in the financial statements, and compare the rates of occurrence of numbers according to the characteristics of Benford's law. About the existence of errors and fraud in the financial statements of PT medco Energy Tbk did not occur. Conclusions: The study concludes that Benford's law can serve as indicator tool in detecting the possibility of in financial statements to case studies of PT Medco Energy Tbk for the fiscal year 2000-2010.

Keywords: Benford law, first digits, all digits number Benford law, financial statement

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Authors: Ahmed Salam, Haithem Benkahla

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Recently, an efficient backward-stable algorithm for computing eigenvalues and vectors of a symmetric and Hamiltonian matrix has been proposed. The method preserves the symmetric and Hamiltonian structures of the original matrix, during the whole process. In this paper, we revisit the method. We derive a way for implementing the reduction of the matrix to the appropriate condensed form. Then, we construct a novel version of the implicit QR-algorithm for computing the eigenvalues and vectors.

Keywords: block implicit QR algorithm, preservation of a double structure, QR algorithm, symmetric and Hamiltonian structures

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Authors: Serkan Aras, Emrah Gulay

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Combining various forecasting models is an important tool for researchers to attain more accurate forecasts. A great number of papers have shown that selecting single models as dissimilar models, or methods based on different information as possible leads to better forecasting performances. However, there is not a certain rule regarding the number of single models to be used in any combining methods. This study focuses on determining the optimal or near optimal number for single models with the help of statistical tests. An extensive experiment is carried out by utilizing some well-known time series data sets from diverse fields. Furthermore, many rival forecasting methods and some of the commonly used combining methods are employed. The obtained results indicate that some statistically significant performance differences can be found regarding the number of the single models in the combining methods under investigation.

Keywords: combined forecast, forecasting, M-competition, time series

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Authors: K. Sanjayani, C. Saraswathy, S. Sreenivasan, S. Sudhahar, D. Suganya, K. S. Neelukumari, N. Vijayarangan

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Double Base Number System (DBNS) is an imminent system of representing a number using two bases namely 2 and 3, which has its application in Elliptic Curve Cryptography (ECC) and Digital Signature Algorithm (DSA).The previous binary method representation included only base 2. DBNS uses an approximation algorithm namely, Greedy Algorithm. By using this algorithm, the number of digits required to represent a larger number is less when compared to the standard binary method that uses base 2 algorithms. Hence, the computational speed is increased and time being reduced. The standard binary method uses binary digits 0 and 1 to represent a number whereas the DBNS method uses binary digit 1 alone to represent any number (canonical form). The greedy algorithm uses two ways to represent the number, one is by using only the positive summands and the other is by using both positive and negative summands. In this paper, arithmetic operations are used for elliptic curve cryptography. Elliptic curve discrete logarithm problem is the foundation for most of the day to day elliptic curve cryptography. This appears to be a momentous hard slog compared to digital logarithm problem. In elliptic curve digital signature algorithm, the key generation requires 160 bit of data by usage of standard binary representation. Whereas, the number of bits required generating the key can be reduced with the help of double base number representation. In this paper, a new technique is proposed to generate key during encryption and extraction of key in decryption.

Keywords: cryptography, double base number system, elliptic curve cryptography, elliptic curve digital signature algorithm

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Authors: Javier Enciso-Benavides, Fredy Fabian, Carlos Castaneda, Luis Alfaro, Alex Choque, Aparicio Aguilar, Javier Enciso

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Background: The use of biomarkers in breast cancer diagnosis, therapy, and prognosis has gained increasing interest. Cancer stem cells (CSCs) are a subpopulation of tumor cells that can drive tumor initiation and may cause relapse. Therefore, due to the importance of diagnosis, therapy, and prognosis, several biomarkers that characterize CSCs have been identified; however, in treatment-naïve triple-negative breast tumors, there is an urgent need to identify new biomarkers and therapeutic targets. According to this, the aim of this study was to identify serum proteins associated with cancer stem cells and pluripotency in women with triple-negative breast tumors in order to subsequently identify a biomarker for this type of breast tumor. Material and Methods: Whole blood samples from 12 women with histopathologically diagnosed triple-negative breast tumors were used after obtaining informed consent from the patient. Blood serum was obtained by conventional procedure and frozen at -80ºC. Identification of cancer stem cell-associated proteins was performed by matrix-assisted laser desorption/ionisation-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS), protein analysis was obtained using the AB Sciex TOF/TOF™ 5800 system (AB Sciex, USA). Sequences not aligned by ProteinPilot™ software were analyzed by Protein BLAST. Results: The following proteins related to pluripotency and cancer stem cells were identified by MALDI TOF/TOF mass spectrometry: A-chain, Serpin A12 [Homo sapiens], AIEBP [Homo sapiens], Alpha-one antitrypsin, AT {internal fragment} [human, partial peptide, 20 aa] [Homo sapiens], collagen alpha 1 chain precursor variant [Homo sapiens], retinoblastoma-associated protein variant [Homo sapiens], insulin receptor, CRA_c isoform [Homo sapiens], Hydroxyisourate hydrolase [Streptomyces scopuliridis], MUCIN-6 [Macaca mulatta], Alpha-actinin-3 [Chrysochloris asiatica], Polyprotein M, CRA_d isoform, partial [Homo sapiens], Transcription factor SOX-12 [Homo sapiens]. Recommendations: The serum proteins identified in this study should be investigated in the exosome of triple-negative breast cancer stem cells and in the blood serum of women without breast cancer. Subsequently, proteins found only in the blood serum of women with triple-negative breast cancer should be identified in situ in triple-negative breast cancer tissue in order to identify a biomarker to study the evolution of this type of cancer, or that could be a therapeutic target. Conclusions: Eleven cancer stem cell-related serum proteins were identified in 12 women with triple-negative breast cancer, of which MUCIN-6, retinoblastoma-associated protein variant, transcription factor SOX-12, and collagen alpha 1 chain are the most representative and have not been studied so far in this type of breast tumor. Acknowledgement: This work was supported by Proyecto CONCYTEC–Banco Mundial “Mejoramiento y Ampliacion de los Servicios del Sistema Nacional de Ciencia Tecnología e Innovacion Tecnologica” 8682-PE (104-2018-FONDECYT-BM-IADT-AV).

Keywords: triple-negative breast cancer, MALDI TOF/TOF MS, serum proteins, cancer stem cells

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Authors: Md Abdullah Al Faruque

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A very large percentage of bridge failures are attributed to scouring around bridge piers and this directly influences public safety. Experiments are carried out in a 12-m long rectangular open channel flume made of transparent tempered glass. A 300 mm thick bed made up of sand particles is leveled horizontally to create the test bed and a 50 mm hollow plastic cylinder is used as a model bridge pier. Tests are carried out with varying flow depths and velocities. Data points of various scour parameters such as scour depth, width, and length are collected based on different flow conditions and visual observations of changes in the stream bed downstream the bridge pier are also made as the scour progresses. Result shows that all three major flow characteristics (flow depth, Froude number and densimetric Froude number) have one way or other affect the scour profile.

Keywords: bridge pier scour, densimetric Froude number, flow depth, Froude number, sand

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Authors: Wen-Yang Hu, Ranli Lu, Mark Maienschein-Cline, Danping Hu, Larisa Nonn, Toshi Shioda, Gail S. Prins

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Background: Genetic mutations are highly associated with increased prostate cancer risk. In addition to whole genome sequencing, somatic mutations can be identified by aligning transcriptome sequences to the human genome. Here we analyzed bulk RNAseq and single cell RNAseq data of human prostate cancer cells and their matched non-cancer cells in benign regions from 4 individual patients. Methods: Sequencing raw reads were aligned to the reference genome hg38 using STAR. Variants were annotated using Annovar with respect to overlap gene annotation information, effect on gene and protein sequence, and SIFT annotation of nonsynonymous variant effect. We determined cancer-specific novel alleles by comparing variant calls in cancer cells to matched benign cells from the same individual by selecting unique alleles that were only detected in the cancer samples. Results: In bulk RNAseq data from 3 patients, the most common variants were the noncoding mutations at UTR3/UTR5, and the major variant types were single-nucleotide polymorphisms (SNP) including frameshift mutations. C>T transversion is the most frequently presented substitution of SNP. A total of 222 genes carrying unique exonic or UTR variants were revealed in cancer cells across 3 patients but not in benign cells. Among them, transcriptome levels of 7 genes (CITED2, YOD1, MCM4, HNRNPA2B1, KIF20B, DPYSL2, NR4A1) were significantly up or down regulated in cancer stem cells. Out of the 222 commonly mutated genes in cancer, 19 have nonsynonymous variants and 11 are damaged genes with variants including SIFT, frameshifts, stop gain/loss, and insertions/deletions (indels). Two damaged genes, activating transcription factor 6 (ATF6) and histone demethylase KDM3A are of particular interest; the former is a survival factor for certain cancer cells while the later positively activates androgen receptor target genes in prostate cancer. Further, single cell RNAseq data of cancer cells and their matched non-cancer benign cells from both primary 2D and 3D tumoroid cultures were analyzed. Similar to the bulk RNAseq data, single cell RNAseq in cancer demonstrated that the exonic mutations are less common than noncoding variants, with SNPs including frameshift mutations the most frequently presented types in cancer. Compared to cancer stem cell enriched-3D tumoroids, 2D cancer cells carried 3-times higher variants, 8-times more coding mutations and 10-times more nonsynonymous SNP. Finally, in both 2D primary and 3D tumoroid cultures, cancer stem cells exhibited fewer coding mutations and noncoding SNP or insertions/deletions than non-stem cancer cells. Summary: Our study demonstrates the usefulness of bulk and single cell RNAseaq data in identifying somatic mutations in prostate cancer, providing an alternative method in screening candidate genes for prostate cancer diagnosis and potential therapeutic targets. Cancer stem cells carry fewer somatic mutations than non-stem cancer cells due to their inherited immortal stand DNA from parental stem cells that explains their long-lived characteristics.

Keywords: prostate cancer, stem cell, genomic mutation, RNAseq

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Authors: Shatha A. Yousif, Qasim M. Zamil, Hasan Y. Al Muhi, Jamal A. Al Shammari

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Potato (Solanum tuberosum L.) is one of the major vegetable crops that are grown world wide because of its economic importance. This experiment investigated the effect of local sands (River Base, Al-Ekader and Karbala) on number and total weight of mini tubers. Statistical analysis revealed that there were no significant differences among sand cultures in number of stem/plant, chlorophyll index and tubers dry weight. River Base sand had the highest plant height (74.9 cm), leaf number/plant number (39.3), leaf area (84.4 dcm2⁄plant), dry weight/plant (26.31), tubers number/plant (8.5), tubers weight/plant (635.53 gm) and potato tuber yields/trove (28.60 kg), whereas the Karbala sand had lower performance. All the characters had positive and significant correlation with yields except the traits number of stem and tuber dry weight.

Keywords: correlation, potato, sand culture, yield

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Authors: N. K. Singh

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In this study the augmentation of heat transfer in a rectangular channel with triangular vortex generators is evaluated. The span wise averaged Nusselt number, mean temperature and total heat flux are compared with and without vortex generators in the channel at a blade angle of 30° for Reynolds numbers 800, 1200, 1600, and 2000. The use of vortex generators increases the span wise averaged Nusselt number compared to the case without vortex generators considerably. At a particular blade angle, increasing the Reynolds number results in an enhancement in the overall performance and span wise averaged Nusselt number was found to be greater at particular location for larger Reynolds number. The total heat flux from the bottom wall with vortex generators was found to be greater than that without vortex generators and the difference increases with increase in Reynolds number.

Keywords: heat transfer, channel with vortex generators, numerical simulation, effect of Reynolds number on heat transfer

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Authors: Behnaz Moradijamei, Michael Higgins

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Identifying community structure is a critical task in analyzing social media data sets often modeled by networks. Statistical models such as the stochastic block model have proven to explain the structure of communities in real-world network data. In this work, we develop a goodness-of-fit test to examine community structure's existence by using a distinguishing property in networks: cyclic structures are more prevalent within communities than across them. To better understand how communities are shaped by the cyclic structure of the network rather than just the number of edges, we introduce a novel method for deciding on the existence of communities. We utilize these structures by using renewal non-backtracking random walk (RNBRW) to the existing goodness-of-fit test. RNBRW is an important variant of random walk in which the walk is prohibited from returning back to a node in exactly two steps and terminates and restarts once it completes a cycle. We investigate the use of RNBRW to improve the performance of existing goodness-of-fit tests for community detection algorithms based on the spectral properties of the adjacency matrix. Our proposed test on community structure is based on the probability distribution of eigenvalues of the normalized retracing probability matrix derived by RNBRW. We attempt to make the best use of asymptotic results on such a distribution when there is no community structure, i.e., asymptotic distribution under the null hypothesis. Moreover, we provide a theoretical foundation for our statistic by obtaining the true mean and a tight lower bound for RNBRW edge weights variance.

Keywords: hypothesis testing, RNBRW, network inference, community structure

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Authors: Atlal El-Assaad

Abstract:

Viruses change with time through mutations and result in new variants that may persist or disappear. A Mutation refers to an actual change in the virus genetic sequence, and a variant is a viral genome that may contain one or more mutations. Critical mutations may cause the virus to be more transmissible, with high disease severity, and more vulnerable to diagnostics, therapeutics, and vaccines. Thus, variants carrying such mutations may increase the risk to human health and are considered variants of concern (VOC). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - the contagious in humans, positive-sense single-stranded RNA virus that caused coronavirus disease 2019 (COVID-19) - has been studied thoroughly, and several variants were revealed across the world with their corresponding mutations. SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins, but prior study and vaccines development focused on genetic mutations in the S protein due to its vital role in allowing the virus to attach and fuse with the membrane of a host cell. Specifically, subunit S1 catalyzes attachment, whereas subunit S2 mediates fusion. In this perspective, we studied all charged amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 in a crystal structure and assessed the effect of different mutations. We generated all missense mutants of SARS-CoV-2 protein amino acids (AAs) within the SARS-CoV-2:CC12.1 complex model. To generate the family of mutants in each complex, we mutated every charged amino acid with all other charged amino acids (Lysine (K), Arginine (R), Glutamic Acid (E), and Aspartic Acid (D)) and studied the new binding of the complex after each mutation. We applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations to determine the effect of each mutation on binding. After analyzing our data, we identified charged amino acids keys for binding. Furthermore, we validated those findings against published experimental genetic data. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants found worldwide.

Keywords: SARS-CoV-2, variant, ionic amino acid, protein-protein interactions, missense mutation, AESOP

Procedia PDF Downloads 113

Authors: Zoltan Horvath, Dora Nagy

Abstract:

In this research, it was examined whether individual COVID variants cause differences in the lactate curve of cyclists. After all, the virus variants attacked different organs in our body during the infections. During our tests, we used a traditional lactate step test, the results of which were compared with the values before the infection. In the tests, it has been proven that different virus variants show unique lactate curves. In this way, based on the lactate curve, it is possible to identify which variant caused the disease. Thanks to this, it has been shorten the return time, because we can apply the best return protocol after infection to the competitors.

Keywords: COVID-Sars19, lactate, virus mutation, lactate profile

Procedia PDF Downloads 67

Authors: Teguh Sugiarto, Amir Mohamadian Amiri

Abstract:

Background: This study aims to explore if there is fraud in the company's financial report distribution using the number first digit Lucas, Fibonacci and Benford. Research methods: In this study, the author uses a number model contained in the first digit of the model Lucas, Fibonacci and Benford, to make a distinction between implementation by using the scale above and below 5%, the rate of occurrence of a difference against the digit number contained on Lucas, Fibonacci and Benford. If there is a significant difference above and below 5%, then the process of follow-up and detection of occurrence of fraud against the financial statements can be made. Findings: From research that has been done can be concluded that the number of frequency levels contained in the financial statements of PT Bank BRI Tbk in a year in the same conscientious results for model Lucas, Fibonacci and Benford.

Keywords: Lucas, Fibonacci, Benford, first digit

Procedia PDF Downloads 274

Authors: A. Khaleel, S. Gao

Abstract:

Both steady and unsteady turbulent mixed convection heat transfer in a 3D lid-driven enclosure, which has constant heat flux on the middle of bottom wall and with isothermal moving sidewalls, is reported in this paper for working fluid with Prandtl number Pr = 0.71. The other walls are adiabatic and stationary. The dimensionless parameters used in this research are Reynolds number, Re = 5000, 10000 and 15000, and Richardson number, Ri = 1 and 10. The simulations have been done by using different turbulent methods such as RANS, URANS, and LES. The effects of using different k- models such as standard, RNG and Realizable k- model are investigated. Interesting behaviours of the thermal and flow fields with changing the Re or Ri numbers are observed. Isotherm and turbulent kinetic energy distributions and variation of local Nusselt number at the hot bottom wall are studied as well. The local Nusselt number is found increasing with increasing either Re or Ri number. In addition, the turbulent kinetic energy is discernibly affected by increasing Re number. Moreover, the LES results have shown a good ability of this method in predicting more detailed flow structures in the cavity.

Keywords: mixed convection, lid-driven cavity, turbulent flow, RANS model, large Eddy simulation

Procedia PDF Downloads 211

Authors: Saroj Bijarnia, Preety Singh

Abstract:

We propose a simple and effective biometrics system based on face verification across aging using a new variant of texture feature, Pyramid Binary Pattern. This employs Local Binary Pattern along with its hierarchical information. Dimension reduction of generated texture feature vector is done using Principal Component Analysis. Support Vector Machine is used for classification. Our proposed method achieves an accuracy of 92:24% and can be used in an automated age-invariant face verification system.

Keywords: biometrics, age invariant, verification, support vector machine

Procedia PDF Downloads 354

Authors: Kamel Allaw, Jocelyne Adjizian Gerard, Makram Chehayeb, Nada Badaro Saliba

Abstract:

In developing countries, such as Lebanon, the demographic data are hardly available due to the absence of the mechanization of population system. The aim of this study is to evaluate, using only remote sensing data, the correlations between the number of population and the characteristics of roads network (length of primary roads, length of secondary roads, total length of roads, density and percentage of roads and the number of intersections). In order to find the influence of the different factors on the demographic data, we studied the degree of correlation between each factor and the number of population. The results of this study have shown a strong correlation between the number of population and the density of roads and the number of intersections.

Keywords: population, road network, statistical correlations, remote sensing

Procedia PDF Downloads 163