Search results for: Gene Family

Authors: Nguyen Viet Tan

Abstract:

The Bahnar is one of 11 indigenous groups living in the Central Highlands of Vietnam. It is one among the four most popular groups in this area, including the Mnong who speak the same language of Mon Khmer family, while both groups of the Jrai and the Rhade belong to the Malayo-Polynesian language family. These groups once captured fertile plateaus, left their cultural and artistic heritage which affected the remaining small groups. Despite the difference in ethnic origins, these groups seem to share similar beliefs, customs and related folk arts after a very long time living beside each other. However, through an in-depth study, this paper points out the fact that the decorative patterns used by the Bahnar are different from the other ethnic groups, especially in color. Based on historical materials from the local museums and some studies in 1980s when all of the ethnic groups in this area had still lived in self-sufficient condition, this paper characterizes the traditional color scheme used by the Bahnar and identifies the difference in decorative motifs of this group compared to the others by pointing out they do not use green in their usual decorative patterns. Moreover, combined with some field surveys recently, through comparative analysis, it also discovers stylistic variations of these patterns in the process of cultural exchange with the other ethnic groups, both in and out of the region, in modern living conditions. This study helps to preserve and promote the traditional values and cultural identity of the Bahnar people in the Central Highlands of Vietnam, avoiding the fusion of styles among groups during the cultural exchange.

Keywords: Bahnar ethic group, decorative patterns, the central highland of Vietnam, traditional color scheme.

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Authors: Jehad Al Dallal, Paul Sorenson

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An application framework provides a reusable design and implementation for a family of software systems. Frameworks are introduced to reduce the cost of a product line (i.e., family of products that share the common features). Software testing is a time consuming and costly ongoing activity during the application software development process. Generating reusable test cases for the framework applications at the framework development stage, and providing and using the test cases to test part of the framework application whenever the framework is used reduces the application development time and cost considerably. Framework Interface Classes (FICs) are classes introduced by the framework hooks to be implemented at the application development stage. They can have reusable test cases generated at the framework development stage and provided with the framework to test the implementations of the FICs at the application development stage. In this paper, we conduct a case study using thirteen applications developed using three frameworks; one domain oriented and two application oriented. The results show that, in general, the percentage of the number of FICs in the applications developed using domain frameworks is, on average, greater than the percentage of the number of FICs in the applications developed using application frameworks. Consequently, the reduction of the application unit testing time using the reusable test cases generated for domain frameworks is, in general, greater than the reduction of the application unit testing time using the reusable test cases generated for application frameworks.

Keywords: FICs, object-oriented framework, object-orientedframework application, software testing.

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Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

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Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: Human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing.

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Authors: Xiaoji Liu, Yonghui Qin

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In this note, we consider a family of iterative formula for computing the weighted Minskowski inverses AM,N in Minskowski space, and give two kinds of iterations and the necessary and sufficient conditions of the convergence of iterations.

Keywords: iterative method, the Minskowski inverse, A

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Authors: Ambika Roy Bardhan

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Kolkata, the City of Joy, is a greying metropolis not only in respect of its concrete jungle but also because of the largest population of 60-plus residents that it shelters among all other cities in India. Declining birth and death rates and a negative growth of population indicate that the city has reached the last stage of demographic transition. Thus, the obvious consequence has been the ageing of its population. With this background, the present paper attempts to study the demographic and socio-economic status of the elderly population in Kolkata. Analysis and findings have been based on secondary data obtained from Census of India of various years, Sample Registration System Reports and reports by HelpAge India. Findings show that the elderly population is increasing continuously. With respect to gender, the male elderly outnumbers the female elderly population. The percentage of households having one elderly member is more in the city due to the emergence of the nuclear families and erosion of joint family system. With respect to socio-economic status, those elderly who are the heads of the family are lower in percentages than those in the other age groups. Also, male elderly as head of the family are greater in percentage than female elderly. Elderly in the category of currently married records the highest percentage followed by widowed, never married and lastly, separated or divorced. Male elderly outnumber the female elderly as currently married, while female elderly outnumbers the male elderly in the category of widowed. In terms of living status, the percentage of elderly who are living alone is highest in Kolkata and the reason for staying alone as no support from children also happens to be highest in this city. The literacy rate and higher level of education is higher among the male than female elderly. Higher percentages of female elderly have been found to be with disability. Disability in movement and multiple disabilities have been found to be more common among the elderly population in Kolkata. Percentages of male literate pensioners are highest than other categories. Also, in terms of levels of education male elderly who are graduate and above other than technical degree are the highest receivers of pension. Also, in terms of working status, elderly as non-workers are higher in percentages with the population of elderly females outnumbering the males. The old age dependency ratio in the city is increasing continuously and the ratio is higher among females than male. Thus, it can be stated that Kolkata is witnessing continuous and rapid ageing of its population. Increasing dependency ratio is likely to create pressure on the working population, available civic, social and health amenities. This requires intervention in the form of planning, formulation and implementation of laws, policies, programs and measures to safeguard and improve the conditions of the elderly in Kolkata.

Keywords: Demographic, Elderly, Population, Socio-economic.

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Authors: Hakan Bostancı, Metin Öztürk

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In this paper, a necessary and sufficient coefficient are given for functions in a class of complex valued meromorphic harmonic univalent functions of the form f = h + g using Salagean operator. Furthermore, distortion theorems, extreme points, convolution condition and convex combinations for this family of meromorphic harmonic functions are obtained.

Keywords: Harmonic mappings, Meromorphic functions, Salagean operator.

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Authors: Mayowa Adeyeye

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This study was conducted to investigate the psychological variables motivating sport participation and involvement among student-athletes of tertiary institutions in southwest Nigeria. One thousand three hundred and fifty (N-1350) studentathletes were randomly selected in all sports from nine tertiary institutions in south-west Nigeria. These tertiary institutions include University of Lagos, Lagos State University, Obafemi Awolowo University, Osun State University, University of Ibadan, University of Agriculture Abeokuta, Federal University of Technology Akungba, University of Ilorin, and Kwara State University. The descriptive survey research method was adopted while a self developed validated Likert type questionnaire named Sport Participation Scale (SPS) was used to elicit opinion from respondents. The test-retest reliability value obtained for the instrument, using Pearson Product Moment Correlation Co-efficient was 0.96. Out of the one thousand three hundred and fifty (N-1350) questionnaire administered, only one thousand two hundred and five (N-1286) were correctly filled, coded and analysed using inferential statistics of Chi-Square (X2) while all the tested hypotheses were set at. 05 alpha level. Based on the findings of this study, the result revealed that several psychological factors influence student athletes to continue participation in sport one which includes love for the game, famous athletes as role model and family support. However, the analysis further revealed that the stipends the student-athletes get from their universities have no influence on their participation and involvement in sport.

Keywords: Family support, peer, role model, sport participation, student-athletes.

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Authors: A. Norezzine, N. Y. Rebouh, M. Souadkia, D. Parpura, A. Gadzhikurbanov, E. A. Gladyr, P. M. Klenovitsky, A. A. Nikishov, A. Dranidis

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This article deals with the genetic characteristics of samples Schwyz-zebu cattle from three farms of the Republic of Tajikistan on 10 microsatellite markers (STS). Hence, the present study was carried out to evaluate the heterozygosity in the population and to characterize this breed by identifying DNA markers using microstatellites. Microsatellites often have multiple alleles and may have heterozygosity frequencies of 70% or more. This makes them highly informative for genetic analysis. A total of ten microsatellite primers were used for microsatellite analysis in genomic DNA of Zebu cattle. The amplified products were analysed for polymorphic alleles and their frequencies. The resulting information can be used in dealing with the conservation and sustainable use of genetic resources of the Tajik Schwyz-zebu cattle.

Keywords: DNA, gene pool, Schwyz-zebu cattle, microsatellite loci.

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Authors: R. Lekaviciene, D. Antiniene

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Attempts to split the construct of emotional intelligence (EI) into separate components – ability to understand own and others’ emotions and ability to control own and others’ emotions may be meaningful more theoretically than practically. In real life, a personality encounters various emotional situations that require exhibition of complex EI to solve them. Emotional situation solution tests enable measurement of such undivided EI. The object of the present study is to determine sociodemographic and other factors that are important for emotional situation solutions. The study involved 1,430 participants from various regions of Lithuania. The age of participants varied from 17 years to 27 years. Emotional social and interpersonal situation scale EI-DARL-V2 was used. Each situation had two mandatory answering formats: The first format contained assignments associated with hypothetical theoretical knowledge of how the situation should be solved, while the second format included the question of how the participant would personally resolve the given situation in reality. A questionnaire that contained various sociodemographic data of subjects was also presented. Factors, statistically significant for emotional situation solution, have been determined: gender, family structure, the subject’s relation with his or her mother, mother’s occupation, subjectively assessed financial situation of the family, level of education of the subjects and his or her parents, academic achievement, etc. The best solvers of emotional situations are women with high academic achievements. According to their chosen study profile/acquired profession, they are related to the fields in social sciences and humanities. The worst solvers of emotional situations are men raised in foster homes. They are/were bad students and mostly choose blue-collar professions.

Keywords: Emotional intelligence, emotional situations, solution of situation, young people.

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Authors: Venkatesh Kumar, Kasun Hewage, Rehan Sadiq

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Residential buildings consume significant amounts of energy and produce large amount of emissions and waste. However, there is a substantial potential for energy savings in this sector which needs to be evaluated over the life cycle of residential buildings. Life Cycle Assessment (LCA) methodology has been employed to study the primary energy uses and associated environmental impacts of different phases (i.e., product, construction, use, end of life, and beyond building life) for residential buildings. Four different alternatives of residential buildings in Vancouver (BC, Canada) with a 50-year lifespan have been evaluated, including High Rise Apartment (HRA), Low Rise Apartment (LRA), Single family Attached House (SAH), and Single family Detached House (SDH). Life cycle performance of the buildings is evaluated for embodied energy, embodied environmental impacts, operational energy, operational environmental impacts, total life-cycle energy, and total life cycle environmental impacts. Estimation of operational energy and LCA are performed using DesignBuilder software and Athena Impact estimator software respectively. The study results revealed that over the life span of the buildings, the relationship between the energy use and the environmental impacts are identical. LRA is found to be the best alternative in terms of embodied energy use and embodied environmental impacts; while, HRA showed the best life-cycle performance in terms of minimum energy use and environmental impacts. Sensitivity analysis has also been carried out to study the influence of building service lifespan over 50, 75, and 100 years on the relative significance of embodied energy and total life cycle energy. The life-cycle energy requirements for SDH are found to be a significant component among the four types of residential buildings. The overall disclose that the primary operations of these buildings accounts for 90% of the total life cycle energy which far outweighs minor differences in embodied effects between the buildings.

Keywords: Building simulation, environmental impacts, life cycle assessment, life cycle energy analysis, residential buildings.

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Authors: Arsalan Jabbar, Wajiha Javed, Nelofer Mehboob, Zahid Memon

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Introduction: There are multiple social, individual and cultural factors that influence an individual’s decision to adopt family planning methods especially among non-users in patriarchal societies like Pakistan. Non-users, if targeted efficiently, can contribute significantly to country’s CPR. A research study showed that nonusers if convinced to adopt lactational amenorrhea method can shift to long term methods in future. Research shows that if non users are targeted efficiently a 59% reduction in unintended pregnancies in Saharan Africa and South-Central and South-East Asia is anticipated. Methods: We did secondary data analysis on Pakistan Demographic Heath Survey (2012-13) dataset. Use of contraception (never-use/ever-use) was the outcome variable. At univariate level Chi-square/Fisher Exact test was used to assess relationship of baseline covariates with contraception use. Then variables to be incorporated in the model were checked for multicollinearity, confounding and interaction. Then binary logistic regression (with an urban-rural stratification) was done to find relationship between contraception use and baseline demographic and social variables. Results: The multivariate analyses of the study showed that younger women (≤ 29 years)were more prone to be never users as compared to those who were >30 years and this trend was seen in urban areas (AOR 1.92, CI 1.453-2.536) as well as rural areas (AOR 1.809, CI 1.421-2.303). While looking at regional variation, women from urban Sindh (AOR 1.548, CI 1.142-2.099) and urban Balochistan (AOR 2.403, CI 1.504-3.839) had more never users as compared to other urban regions. Women in the rich wealth quintile were more never users and this was seen both in urban and rural localities (urban (AOR 1.106 CI .753-1.624); rural areas (AOR 1.162, CI .887-1.524)) even though these were not statistically significant. Women idealizing more children (>4) are more never users as compared to those idealizing less children in both urban (AOR 1.854, CI 1.275-2.697) and rural areas (AOR 2.101, CI 1.514-2.916). Women who never lost a pregnancy were more inclined to be nonusers in rural areas (AOR 1.394, CI 1.127-1.723) .Women familiar with only traditional or no method had more never users in rural areas (AOR 1.717, CI 1.127-1.723) but in urban areas it wasn’t significant. Women unaware of Lady Health Worker’s presence in their area were more never users especially in rural areas (AOR 1.276, CI 1.014-1.607). Women who did not visit any care provider were more never users (urban (AOR 11.738, CI 9.112-15.121) rural areas (AOR 7.832, CI 6.243-9.826)). Discussion/Conclusion: This study concluded that government, policy makers and private sector family planning programs should focus on the untapped pool of never users (younger women from underserved provinces, in higher wealth quintiles, who desire more children.). We need to make sure to cover catchment areas where there are less LHWs and less providers as ignorance to modern methods and never been visited by an LHW are important determinants of never use. This all is in sync with previous literate from similar developing countries.

Keywords: Contraception, Demographic and Health Survey, Family Planning, Never users.

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Authors: A. Ghanbari Mardasi, N. Wu, C. Wu

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In this study, a spatial wavelet-based crack localization technique for a thick beam is presented. Wavelet scale in spatial wavelet transformation is optimized to enhance crack detection sensitivity. A windowing function is also employed to erase the edge effect of the wavelet transformation, which enables the method to detect and localize cracks near the beam/measurement boundaries. Theoretical model and vibration analysis considering the crack effect are first proposed and performed in MATLAB based on the Timoshenko beam model. Gabor wavelet family is applied to the beam vibration mode shapes derived from the theoretical beam model to magnify the crack effect so as to locate the crack. Relative wavelet coefficient is obtained for sensitivity analysis by comparing the coefficient values at different positions of the beam with the lowest value in the intact area of the beam. Afterward, the optimal wavelet scale corresponding to the highest relative wavelet coefficient at the crack position is obtained for each vibration mode, through numerical simulations. The same procedure is performed for cracks with different sizes and positions in order to find the optimal scale range for the Gabor wavelet family. Finally, Hanning window is applied to different vibration mode shapes in order to overcome the edge effect problem of wavelet transformation and its effect on the localization of crack close to the measurement boundaries. Comparison of the wavelet coefficients distribution of windowed and initial mode shapes demonstrates that window function eases the identification of the cracks close to the boundaries.

Keywords: Edge effect, scale optimization, small crack locating, spatial wavelet.

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Authors: Mohib ur Rehman, Mohammad Haseeb Anwer, Nadeem Iftikhar

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The need to have standards has always been a priority of all the disciplines in the world. Today, standards such as XML and USB are trying to create a universal interface for their respective areas. The information regarding every family in the discipline addressed, must have a lot in common, known as Metadata. A lot of work has been done in specific domains such as IEEE LOM and MPEG-7 but they do not appeal to the universality of creating Metadata for all entities, where we take an entity (object) as, not restricted to Software Terms. This paper tries to address this problem of universal Metadata Definition which may lead to increase in precision of search.

Keywords: Metadata, Standard, Universal, XML.

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Authors: M. Raissy, M. Shahrani

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The present study was done to evaluate the presence of tetracycline resistance genes in Lactococcus garvieae isolated from cultured rainbow trout, West Iran. The isolates were examined for antimicrobial resistance using disc diffusion method. Of the 49 strains tested, 19 were resistant to tetracycline (38.7%), 32 to enrofloxacin (65.3%), 21 to erythromycin (42.8%), 20 to chloramphenicol and trimetoprim-sulfamethoxazole (40.8%). The strains were then characterized for their genotypic resistance profiles. The results revealed that all 49 isolates contained at least one of the tetracycline resistance genes. Tet (A) was found in 89.4% of tetracycline resistant isolates and the frequency of other gene were as follows: tet (E) 42.1%, tet (B) 47.3%, tet (D) 15.7%, tet (L) 26.3%, tet (K) 52.6%, tet (G) 36.8%, tet (34) 21%, tet (S) 63.1%, tet (C) 57.8%, tet (M) 73.6%, tet (O) 42.1%. The results revealed high levels of antibiotic resistance in L. garvieae strains which is a potential danger for trout culture as well as for public health.

Keywords: Lactococcus garvieae, rainbow trout, tetracycline resistance genes.

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Authors: Marialuisa Gennari, Giancarlo Tamanza, Ilaria Montanari

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Identity development in adolescence is characterized by many risks and challenges, and becomes even more complex by the situation of migration and deafness. In particular, the condition of the second generation of migrant adolescents involves the comparison between the family context in which everybody speaks a language and deals with a specific culture (usually parents’ and relatives’ original culture), the social context (school, peer groups, sports groups), where a foreign language is spoken and a new culture is faced, and finally in the context of the “deaf” world. It is a dialectic involving unsolved differences that have to be treated in a discontinuous process, which will give complex outcomes and chances depending on the process of elaboration of the themes of growth and development, culture and deafness. This paper aims to underline the problems and opportunities for each issue which immigrant deaf adolescents must deal with. In particular, it will highlight the importance of a multifactorial approach for the analysis of personal resources (both intra-psychic and relational); the level of integration of the family of origin in the migration context; the elaboration of the migration event, and finally, the tractability of the condition of deafness. Some psycho-educational support objectives will be also highlighted for the identity development of deaf immigrant adolescents, with particular emphasis on the construction of the adolescents’ useful abilities to decode complex emotions, to develop self-esteem and to get critical thoughts about the inevitable attempts to build their identity. Remarkably, and of importance, the construction of flexible settings which support adolescents in a supple, “decentralized” way in order to avoid the regressive defenses that do not allow for the development of an authentic self.

Keywords: Immigrant deaf adolescents, identity development, personal and social challenges, psycho-educational support.

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Authors: Nilubon Kurubanjerdjit, Nattakarn Iam-On, Ka-Lok Ng

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MicroRNAs are small non-coding RNA found in many different species. They play crucial roles in cancer such as biological processes of apoptosis and proliferation. The identification of microRNA-target genes can be an essential first step towards to reveal the role of microRNA in various cancer types. In this paper, we predict miRNA-target genes for lung cancer by integrating prediction scores from miRanda and PITA algorithms used as a feature vector of miRNA-target interaction. Then, machine-learning algorithms were implemented for making a final prediction. The approach developed in this study should be of value for future studies into understanding the role of miRNAs in molecular mechanisms enabling lung cancer formation.

Keywords: MicroRNA, miRNAs, lung cancer, machine learning, Naïve Bayes, SVM.

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Authors: Monika Neda, Elena Nikonova

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We present a numerical study of the sensitivity of the so called time relaxation family of models of fluid motion with respect to the time relaxation parameter χ on the two dimensional cavity problem. The goal of the study is to compute and compare the sensitivity of the model using finite difference method (FFD) and sensitivity equation method (SEM).

Keywords: Sensitivity, time relaxation, deconvolution, Navier- Stokes equations.

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Authors: Khin May Win, Nan Sai Moon Kham

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Identification of cancer genes that might anticipate the clinical behaviors from different types of cancer disease is challenging due to the huge number of genes and small number of patients samples. The new method is being proposed based on supervised learning of classification like support vector machines (SVMs).A new solution is described by the introduction of the Maximized Margin (MM) in the subset criterion, which permits to get near the least generalization error rate. In class prediction problem, gene selection is essential to improve the accuracy and to identify genes for cancer disease. The performance of the new method was evaluated with real-world data experiment. It can give the better accuracy for classification.

Keywords: Microarray data, feature selection, recursive featureelimination, support vector machines.

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Authors: Minh T. N. Le, Cathleen Teh, Ng Shyh-Chang, Vladimir Korzh, Harvey F. Lodish, Bing Lim

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MicroRNAs are an important class of gene expression regulators that are involved in many biological processes including embryogenesis. miR-125b is a conserved microRNA that is enriched in the nervous system. We have previously reported the function of miR-125b in neuronal differentiation of human cell lines. We also discovered the function of miR-125b in regulating p53 in human and zebrafish. Here we further characterize the brain defects in zebrafish embryos injected with morpholinos against miR-125b. Our data confirm the essential role of miR-125b in brain morphogenesis particularly in maintaining the balance between proliferation, cell death and differentiation. We identified lunatic fringe (lfng) as an additional target of miR-125b in human and zebrafish and suggest that lfng may mediate the function of miR-125b in neurogenesis. Together, this report reveals new insights into the function of miR- 125b during neural development of zebrafish.

Keywords: microRNA, miR-125b, neurogenesis, zebrafish.

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Authors: Seyeon Park, Mi Jang

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Tumor cells have an invasive and metastatic phenotype that is the main cause of death for cancer patients. Tumor establishment and penetration consists of a series of complex processes involving multiple changes in gene expression. In this study, intraperitoneal administration of a high concentration of ascorbic acid inhibited tumor establishment and decreased tumor mass in BALB/C mice implanted with S-180 sarcoma cancer cells. To identify proteins involved in the ascorbic acid-mediated inhibition of tumor progression, changes in the tumor proteome associated with ascorbic acid treatment of BALB/C mice implanted with S-180 were investigated using two-dimensional gel electrophoresis and mass spectrometry. Twenty protein spots were identified whose expression was different between control and ascorbic acid treatment groups.

Keywords: Ascorbic acid, Proteomic analysis, S-180 implantedBALB/C mouse

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Authors: Mustafa Qaseem Hielat, Ahmad Mohammad Al-Shabatat

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Jordan exerts many efforts to nurture their academically gifted students in special schools since 2001. During the past nine years of launching these schools, their learning and excellence environments were believed to be distinguished compared to public schools. This study investigated the environments of gifted students compared with other non-gifted, using a survey instrument that measures the dimensions of family, peers, teachers, school- support, society, and resources –dimensions rooted deeply in supporting gifted education, learning, and achievement. A total number of 109 were selected from excellence schools for academically gifted students, and 119 non-gifted students were selected from public schools. Around 8.3% of the non-gifted students reported that they “Never" received any support from their surrounding environments, 14.9% reported “Seldom" support, 23.7% reported “ Often" support, 26.0% reported “Frequent" support, and 32.8% reported “Very frequent" support. Where the gifted students reported more “Never" support than the non-gifted did with 11.3%, “Seldom" support with 15.4%, “Often" support with 26.6%, “Frequent" support with 29.0%, and reported “Very frequent" support less than the non-gifted students with 23.6%. Unexpectedly, statistical differences were found between the two groups favoring non-gifted students in perception of their surrounding environments in specific dimensions, namely, school- support, teachers, and society. No statistical differences were found in the other dimensions of the survey, namely, family, peers, and resources. As the differences were found in teachers, school- support, and society, the nurturing environments for the excellence schools need to be revised to adopt more creative teaching styles, rich school atmosphere and infrastructures, interactive guiding for the students and their parents, promoting for the excellence environments, and re-build successful identification models. Thus, families, schools, and society should increase their cooperation, communication, and awareness of the gifted supportive environments. However, more studies to investigate other aspects of promoting academic giftedness and excellence are recommended.

Keywords: Academic giftedness, Supportive environment, Excellence schools, Gifted grouping, Gifted nurturing.

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Authors: Syahril Ridzuan Ab Rahim, Ibrahim Ahmad, Mohd Azizi Chik, Ahmad Zafir Md. Rejab, and U. Hashim

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This research presents the development of simulation modeling for WIP management in semiconductor fabrication. Manufacturing simulation modeling is needed for productivity optimization analysis due to the complex process flows involved more than 35 percent re-entrance processing steps more than 15 times at same equipment. Furthermore, semiconductor fabrication required to produce high product mixed with total processing steps varies from 300 to 800 steps and cycle time between 30 to 70 days. Besides the complexity, expansive wafer cost that potentially impact the company profits margin once miss due date is another motivation to explore options to experiment any analysis using simulation modeling. In this paper, the simulation model is developed using existing commercial software platform AutoSched AP, with customized integration with Manufacturing Execution Systems (MES) and Advanced Productivity Family (APF) for data collections used to configure the model parameters and data source. Model parameters such as processing steps cycle time, equipment performance, handling time, efficiency of operator are collected through this customization. Once the parameters are validated, few customizations are made to ensure the prior model is executed. The accuracy for the simulation model is validated with the actual output per day for all equipments. The comparison analysis from result of the simulation model compared to actual for achieved 95 percent accuracy for 30 days. This model later was used to perform various what if analysis to understand impacts on cycle time and overall output. By using this simulation model, complex manufacturing environment like semiconductor fabrication (fab) now have alternative source of validation for any new requirements impact analysis.

Keywords: Advanced Productivity Family (APF), Complementary Metal Oxide Semiconductor (CMOS), Manufacturing Execution Systems (MES), Work In Progress (WIP).

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Authors: Hui Hsin Huang

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The downstream manufactures will order their materials from different upstream suppliers to maintain a certain level of the demand. This paper proposes a bivariate model to portray this phenomenon of material demand. We use empirical data to estimate the parameters of model and evaluate the RMSD of model calibration. The results show that the model has better fitness.

Keywords: Farlie-Gumbel-Morgenstern family of bivariate distributions, multi-source ordering, materials demand quantity, recency, ordering time.

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Authors: Neelima Gupta, Seema Aggarwal

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Most of the biclustering/projected clustering algorithms are based either on the Euclidean distance or correlation coefficient which capture only linear relationships. However, in many applications, like gene expression data and word-document data, non linear relationships may exist between the objects. Mutual Information between two variables provides a more general criterion to investigate dependencies amongst variables. In this paper, we improve upon our previous algorithm that uses mutual information for biclustering in terms of computation time and also the type of clusters identified. The algorithm is able to find biclusters with mixed relationships and is faster than the previous one. To the best of our knowledge, none of the other existing algorithms for biclustering have used mutual information as a similarity measure. We present the experimental results on synthetic data as well as on the yeast expression data. Biclusters on the yeast data were found to be biologically and statistically significant using GO Tool Box and FuncAssociate.

Keywords: Biclustering, mutual information.

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Authors: Laura Lukmanto, Harya Widiputra, Lukas

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Studies in economics domain tried to reveal the correlation between stock markets. Since the globalization era, interdependence between stock markets becomes more obvious. The Dynamic Interaction Network (DIN) algorithm, which was inspired by a Gene Regulatory Network (GRN) extraction method in the bioinformatics field, is applied to reveal important and complex dynamic relationship between stock markets. We use the data of the stock market indices from eight countries around the world in this study. Our results conclude that DIN is able to reveal and model patterns of dynamic interaction from the observed variables (i.e. stock market indices). Furthermore, it is also found that the extracted network models can be utilized to predict movement of the stock market indices with a considerably good accuracy.

Keywords: complex dynamic relationship, dynamic interaction network, interactive stock markets, stock market interdependence.

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Authors: Fuad M. Alkoot

Abstract:

DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: Biometrics, identity verification, genetic data, k-nearest neighbor.

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Authors: Nadia H. Mohammed, Anmar Al-Taie, Fadia H. Al-Sultany

Abstract:

Although breast cancer prevalence continues to increase, mortality has been decreasing as a result of early detection and improvement in adjuvant systemic therapy. Nevertheless, this disease required further efforts to understand and identify the associated potential risk factors that could play a role in the prevalence of this malignancy among Iraqi women. The objective of this study was to assess the perception of certain predictive risk factors on the prevalence of breast cancer types among a sample of Iraqi women diagnosed with breast cancer. This was a retrospective observational study carried out at National Cancer Research Center in College of Medicine, Baghdad University from November 2017 to January 2018. Data of 100 patients with breast cancer whose biopsies examined in the National Cancer Research Center were included in this study. Data were collected to structure a detailed assessment regarding the patients’ demographic, medical and cancer records. The majority of study participants (94%) suffered from ductal breast cancer with mean age 49.57 years. Among those women, 48.9% were obese with body mass index (BMI) 35 kg/m². 68.1% of them had positive family history of breast cancer and 66% had low parity. 40.4% had stage II ductal breast cancer followed by 25.5% with stage III. It was found that 59.6% and 68.1% had positive oestrogen receptor sensitivity and positive human epidermal growth factor (HER2/neu) receptor sensitivity respectively. In regard to the impact of prediction of certain variables on the incidence of ductal breast cancer, positive family history of breast cancer (P < 0.0001), low parity (P< 0.0001), stage I and II breast cancer (P = 0.02) and positive HER2/neu status (P < 0.0001) were significant predictive factors among the study participants. The results from this study provide relevant evidence for a significant positive and potential association between certain risk factors and the prevalence of breast cancer among Iraqi women.

Keywords: Ductal breast cancer, hormone sensitivity, Iraq, risk factors.

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Authors: Sing-Wu Liou, Yin-Fu Huang

Abstract:

For identifying the discriminative sequence features between exons and introns, a new paradigm, rescaled-range frameshift analysis (RRFA), was proposed. By RRFA, two new sequence features, the frameshift sensitivity (FS) and the accumulative penta-mer complexity (APC), were discovered which were further integrated into a new feature of larger scale, the persistency in anti-mutation (PAM). The feature-validation experiments were performed on six model organisms to test the power of discrimination. All the experimental results highly support that FS, APC and PAM were all distinguishing features between exons and introns. These identified new sequence features provide new insights into the sequence composition of genes and they have great potentials of forming a new basis for recognizing the exonintron boundaries in gene sequences.

Keywords: Exon-Intron Discrimination, Rescaled-Range Frameshift Analysis, Frameshift Sensitivity, Accumulative Sequence Complexity

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Authors: Anna V. Zhdanova, Uwe Keller

Abstract:

We summarize information that facilitates choosing an ontology language for knowledge intensive applications. This paper is a short version of the ontology language state-of-the-art and evolution analysis carried out for choosing an ontology language in the IST Esperonto project. At first, we analyze changes and evolution that took place in the filed of Semantic Web languages during the last years, in particular, around the ontology languages of the RDF/S and OWL family. Second, we present current trends in development of Semantic Web languages, in particular, rule support extensions for Semantic Web languages and emerging ontology languages such as WSMO languages.

Keywords: OWL, RDF/S, Semantic Web Languages, WSML

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Authors: Maysam Mard-Soltani, Mohamad Javad Rasaee, Saeed Khalili, Abdol Karim Sheikhi, Mehdi Hedayati

Abstract:

Production of specific antibody responses against hTSH is a cumbersome process due to the high identity between the hTSH and the other members of the glycoprotein hormone family (FSH, LH and HCG) and the high identity between the human hTSH and host animals for antibody production. Therefore, two polyclonal antibodies were purified against two recombinant proteins. Four possible ELISA tests were designed based on these antibodies. These ELISA tests were checked against hTSH and other glycoprotein hormones, and their sensitivity and specificity were assessed. Bioinformatics tools were used to analyze the immunological properties. After the immunogen region selection from hTSH protein, c terminal of B hTSH was selected and applied. Two recombinant genes, with these cut pieces (first: two repeats of C terminal of B hTSH, second: tetanous toxin+B hTSH C terminal), were designed and sub-cloned into the pET32a expression vector. Standard methods were used for protein expression, purification, and verification. Thereafter, immunizations of the white New Zealand rabbits were performed and the serums of them were used for antibody titration, purification and characterization. Then, four ELISA tests based on two antibodies were employed to assess the hTSH and other glycoprotein hormones. The results of these assessments were compared with standard amounts. The obtained results indicated that the desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. The raised antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum. Among the four designed tests, the test in which the antibody against first protein was used as capture antibody, and the antibody against second protein was used as detector antibody did not show any hook effect up to 50 miu/l. Both proteins have the ability to induce highly sensitive and specific antibody responses against the hTSH. One of the antibody combinations of these antibodies has the highest sensitivity and specificity in hTSH detection.

Keywords: hTSH, bioinformatics, protein expression, cross reactivity.

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