Search results for: essential genes

Authors: Wajeeh Daher, Nimer Baya'a

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High Order Thinking Skills (HOTS) are suggested today as essential for the cognitive development of students and as preparing them for real life skills. Teachers are encouraged to use HOTS activities in the classroom to help their students develop higher order skills and deep thinking. So it is essential to prepare preservice teachers to write and use HOTS activities for their students. This paper describes a model for integrating HOTS activities with GeoGebra in pre-service teachers’ preparation. This model describes four aspects of HOTS activities and working with them: activity components, preparation procedure, strategies and processes used in writing a HOTS activity and types of the HOTS activities. In addition, the paper describes the pre-service teachers' difficulties in preparing and working with HOTS activities, as well as their perceptions regarding the use of these activities and GeoGebra in the mathematics classroom. The paper also describes the contribution of a HOTS activity to pupils' learning of mathematics, where this HOTS activity was prepared and taught by one pre-service teacher.

Keywords: Higher order thinking, HOTS activities, pre-service teachers, teachers' preparation.

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Authors: S. Rezaei, Z. Mirzaei, M. Khalighi, J. Bahrami

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Bridges, as an essential part of road infrastructures, are affected by various deterioration mechanisms over time due to the changes in their performance. As changes in performance can have many negative impacts on society, it is essential to be able to evaluate and measure the performance of bridges throughout their life. This evaluation includes the development or the choice of the appropriate performance indicators, which, in turn, are measured based on the selection of appropriate models for the existing deterioration mechanism. The purpose of this article is a statistical study of indicators and deterioration mechanisms of bridges in order to discover further research capacities in bridges performance assessment. For this purpose, some of the most common indicators of bridge performance, including reliability, risk, vulnerability, robustness, and resilience, were selected. The researches performed on each index based on the desired deterioration mechanisms and hazards were comprehensively reviewed. In addition, the formulation of the indicators and their relationship with each other were studied. The research conducted on the mentioned indicators were classified from the point of view of deterministic or probabilistic method, the level of study (element level, object level, etc.), and the type of hazard and the deterioration mechanism of interest. For each of the indicators, a number of challenges and recommendations were presented according to the review of previous studies.

Keywords: Bridge, deterioration mechanism, lifecycle, performance indicator.

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Authors: I. Nassiri, B. Goliaei, M. Tavassoli

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The ability to distinguish missense nucleotide substitutions that contribute to harmful effect from those that do not is a difficult problem usually accomplished through functional in vivo analyses. In this study, instead current biochemical methods, the effects of missense mutations upon protein structure and function were assayed by means of computational methods and information from the databases. For this order, the effects of new missense mutations in exon 5 of PTEN gene upon protein structure and function were examined. The gene coding for PTEN was identified and localized on chromosome region 10q23.3 as the tumor suppressor gene. The utilization of these methods were shown that c.319G>A and c.341T>G missense mutations that were recognized in patients with breast cancer and Cowden disease, could be pathogenic. This method could be use for analysis of missense mutation in others genes.

Keywords: Bioinformatics, missense mutations, PTEN tumorsuppressor gene.

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Authors: Aníbal Rodríguez Fuentes, Juan V. Lorenzo Ginori, Ricardo Grau Ábalo

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Identifying protein coding regions in DNA sequences is a basic step in the location of genes. Several approaches based on signal processing tools have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new predictor that improves the efficacy of three techniques that use the Fourier Transform to predict coding regions, and that could be computed using an algorithm that reduces the computation load. Some ideas about the combination of the predictor with other methods are discussed. ROC curves are used to demonstrate the efficacy of the proposed predictor, based on the computation of 25 DNA sequences from three different organisms.

Keywords: Bioinformatics, Coding region prediction, Computational load reduction, Digital Signal Processing, Fourier Transform.

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Authors: Martin Lisý, Marek Baláš, Michal Špiláček, Zdeněk Skála

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This paper shortly describes various types of biomass and a growing number of facilities utilizing the biomass in the Czech Republic. The considerable part of this paper deals with energy parameters of the most frequently used types of biomass and results of their gasification testing. Sixteen most used "Czech" woody plants and grasses were selected; raw, element and biochemical analyses were performed and basic calorimetric values, ash composition, and ash characteristic temperatures were identified. Later, each biofuel was tested in a fluidized bed gasifier. The essential part of this paper provides results of the gasification of selected biomass types. Operating conditions are described in detail with a focus on individual fuels properties. Gas composition and impurities content are also identified. In terms of operating conditions and gas quality, the essential difference occurred mainly between woody plants and grasses. The woody plants were evaluated as more suitable fuels for fluidized bed gasifiers. Testing results significantly help with a decision-making process regarding suitability of energy plants for growing and with a selection of optimal biomass-treatment technology.

Keywords: Biomass Growing, Biomass Types, Gasification.

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Authors: Li Zong-Cheng

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It is by reason of the unified measure of varieties of resources and the unified processing of the disposal of varieties of resources, that these closely related three of new basic models called the resources assembled node and the disposition integrated node as well as the intelligent organizing node are put forth in this paper; the three closely related quantities of integrative analytical mechanics including the disposal intensity and disposal- weighted intensity as well as the charge of resource charge are set; and then the resources assembled space and the disposition integrated space as well as the intelligent organizing space are put forth. The system of fundamental equations and model of complete factor synergetics is preliminarily approached for the general situation in this paper, to form the analytical base of complete factor synergetics. By the essential variables constituting this system of equations we should set twenty variables respectively with relation to the essential dynamical effect, external synergetic action and internal synergetic action of the system.

Keywords: complex system, disposal of resources, completefactor synergetics, fundamental equation.

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Authors: D. Dib, W. Guebabi, M. B. Guesmi

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The objective of this paper is a contribution to a study of power supply by solar energy system called a common Ferkène north of Algerian desert in the semi-arid area. The optimal exploitation of the system, goes through stages of study and essential design, the choice of the model of the photovoltaic panel, the study of behavior with all the parameters involved in simulation before fixing the trajectory tracking the maximum point the power to extract (MPPT), form the essential platform to shape the design of the solar system set up to supply the town Ferkène without considering the grid. The identification of the common Ferkène by the collection of geographical, meteorological, demographic and electrical provides a basis uniform and important data. The results reflect a valid fictive model for any attempt to study and design a solar system to supply an arid or semi-arid zone by electrical energy from photovoltaic panels.

Keywords: Solar power, photovoltaic panel, Boost converter, supply, design, electric power, Ferkène, Algeria.

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Authors: D. Danesh, M. J. Ryan, A. Abbasi

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Project Portfolio Management (PPM) is an essential component of an organisation’s strategic procedures, which requires attention of several factors to envisage a range of long-term outcomes to support strategic project portfolio decisions. To evaluate overall efficiency at the portfolio level, it is essential to identify the functionality of specific projects as well as to aggregate those findings in a mathematically meaningful manner that indicates the strategic significance of the associated projects at a number of levels of abstraction. PPM success is directly associated with the quality of decisions made and poor judgment increases portfolio costs. Hence, various Multi-Criteria Decision Making (MCDM) techniques have been designed and employed to support the decision-making functions. This paper reviews possible options to enhance the decision-making outcomes in organisational portfolio management processes using the Analytic Hierarchy Process (AHP) both from academic and practical perspectives and will examine the usability, certainty and quality of the technique. The results of the study will also provide insight into the technical risk associated with current decision-making model to underpin initiative tracking and strategic portfolio management.

Keywords: Analytic hierarchy process, decision support systems, multi-criteria decision-making, project portfolio management.

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Authors: Alexandra Oliveros, Miguel Sotaquirá

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DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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Authors: Dong Hoon Lim

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A series of microarray experiments produces observations of differential expression for thousands of genes across multiple conditions. Principal component analysis(PCA) has been widely used in multivariate data analysis to reduce the dimensionality of the data in order to simplify subsequent analysis and allow for summarization of the data in a parsimonious manner. PCA, which can be implemented via a singular value decomposition(SVD), is useful for analysis of microarray data. For application of PCA using SVD we use the DNA microarray data for the small round blue cell tumors(SRBCT) of childhood by Khan et al.(2001). To decide the number of components which account for sufficient amount of information we draw scree plot. Biplot, a graphic display associated with PCA, reveals important features that exhibit relationship between variables and also the relationship of variables with observations.

Keywords: Principal component analysis, singular value decomposition, microarray data, SRBCT

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Authors: Seo Young Kim, Toshimitsu Hamasaki

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Microarrays have become the effective, broadly used tools in biological and medical research to address a wide range of problems, including classification of disease subtypes and tumors. Many statistical methods are available for analyzing and systematizing these complex data into meaningful information, and one of the main goals in analyzing gene expression data is the detection of samples or genes with similar expression patterns. In this paper, we express and compare the performance of several clustering methods based on data preprocessing including strategies of normalization or noise clearness. We also evaluate each of these clustering methods with validation measures for both simulated data and real gene expression data. Consequently, clustering methods which are common used in microarray data analysis are affected by normalization and degree of noise and clearness for datasets.

Keywords: Gene expression, clustering, data preprocessing.

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Authors: Nurdan Yildirim, Arif Hepbasli

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Heating, cooling and lighting appliances in buildings account for more than one third of the world’s primary energy demand. Therefore, main components of the building heating systems play an essential role in terms of energy consumption. In this context, efficient energy and exergy utilization in HVAC-R systems has been very essential, especially in developing energy policies towards increasing efficiencies. The main objective of the present study is to assess the performance of a family house with a volume of 326.7 m3 and a net floor area of 121 m2, located in the city of Izmir, Turkey in terms of energetic, exergetic and sustainability aspects. The indoor and exterior air temperatures are taken as 20°C and 1°C, respectively. In the analysis and assessment, various metrics (indices or indicators) such as exergetic efficiency, exergy flexibility ratio and sustainability index are utilized. Two heating options (Case 1: condensing boiler and Case 2: air heat pump) are considered for comparison purposes. The total heat loss rate of the family house is determined to be 3770.72 W. The overall energy efficiencies of the studied cases are calculated to be 49.4% for Case 1 and 54.7% for Case 2. The overall exergy efficiencies, the flexibility factor and the sustainability index of Cases 1 and 2 are computed to be around 3.3%, 0.17 and 1.034, respectively.

Keywords: Buildings, exergy, low exergy, sustainability, efficiency, heating, renewable energy.

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Authors: R. Resmi, M. R. Baiju

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The thermal damping of a dynamic vibrating micromirror is an important factor affecting the design of MEMS based actuator systems. In the development process of new micromirror systems, assessing the extent of energy loss due to thermal damping accurately and predicting the performance of the system is very essential. In this paper, the depth of the thermal penetration layer at different eigenfrequencies and the temperature variation distributions surrounding a vibrating micromirror is analyzed. The thermal penetration depth corresponds to the thermal boundary layer in which energy is lost which is a measure of the thermal damping is found out. The energy is mainly dissipated in the thermal boundary layer and thickness of the layer is an important parameter. The detailed thermoacoustics is used to model the air domain surrounding the micromirror. The thickness of the boundary layer, temperature variations and thermal power dissipation are analyzed for a Si based torsional mode micromirror. It is found that thermal penetration depth decreases with eigenfrequency and hence operating the micromirror at higher frequencies is essential for reducing thermal damping. The temperature variations and thermal power dissipations at different eigenfrequencies are also analyzed. Both frequency-response and eigenfrequency analyses are done using COMSOL Multiphysics software.

Keywords: Eigen frequency analysis, micromirrors, thermal damping, thermoacoustic interactions.

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Authors: Hang T. T. Truong, Ronald S. Laura, Kylie Shaw

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Within Vietnam's system of higher education, its schools of business play a vital role in supporting the country’s economic objectives. However, the crucial contribution of soft skills for maximal success within the business sector has to date not been adequately recognized by its business schools. This being so, the development of the business school curriculum in Vietnam has not been able to 'catch up', so to say, with the burgeoning need of students for a comprehensive soft skills program designed to meet the national and global business objectives of their potential employers. The burden of the present paper is first to reveal the results of our survey in Vietnam which make explicit the extent to which major Vietnamese industrial employers’ value the potential role that soft skill competencies can play in maximizing business success. Our final task will be to determine which soft skills employers discern as best serving to maximize the economic interests of Vietnam within the global marketplace. Semi-structured telephone interviews have been conducted with the 15 representative Head Employers of Vietnam's reputedly largest and most successful of the diverse business enterprises across Vietnam. The findings of the study indicate that all respondents highly value the increasing importance of soft skills in business success. Our critical analysis of respondent data reveals that 19 essential soft skills are deemed by employers as integral to business workplace efficacy and should thus be integrated into the formal business curriculum. We are confident that our study represents the first comprehensive and specific survey yet undertaken within the business sector in Vietnam which accesses and analyses the opinions of representative employers from major companies across the country in regard to the growing importance of 19 specific soft skills essential for maximizing overall business success. Our research findings also reveal that the integration into business school curriculums nationwide of the soft skills we have identified is of paramount importance to advance the national and global economic interests of Vietnam.

Keywords: Business curriculum, business graduates, employers’ perception, soft skills.

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Authors: N. Poomsa-ad, K. Deejing, L. Wiset

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This research is to study the performance of heat pump dryer for drying of kaffir lime leaves under different media and to compare the color values and essential oil content of final products after drying. In the experiments, kaffir lime leaves were dried in the closed-loop system at drying temperatures of 40, 50 and 60 oC. The drying media used in this study were hot air, CO2 and N2 gases. The velocity of drying media in the drying chamber was 0.4 m/s with bypass ratio of 30%. The initial moisture content of kaffir lime leaves was approximately 180-190 % d.b. It was dried until down to a final moisture content of 10% d.b. From the experiments, the results showed that drying rate, the coefficient of performance (COP) and specific energy consumption (SEC) depended on drying temperature. While drying media did not affect on drying rate. The time for kaffir lime leaves drying at 40, 50 and 60 oC was 10, 5 and 3 hours, respectively. The performance of the heat pump system decreased with drying temperature in the range of 2.20-3.51. In the aspect of final product color, the greenness and overall color had a great change under drying temperature at 60 oC rather than drying at 40 and 50 oC. When compared among drying media, the greenness and overall color of product dried with hot air at 60 oC had a great change rather than dried with CO2 and N2.

Keywords: airless drying, drying rate, essential oil content

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Authors: Z. M. Biyasheva, M. Zh. Tleubergenova, Y. A. Zaripova, A. L. Shakirov, V. V. Dyachkov

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In recent years, interest in ecogenetic and biomedical problems related to the effects on the population of radon and its daughter decay products has increased significantly. Of particular interest is the assessment of the consequence of irradiation at hazardous radon areas, which includes the Almaty region due to the large number of tectonic faults that enhance radon emanation. In connection with the foregoing, the purpose of this work was to study the genetic effects of exposure to supernormal radon doses on the alpha-radiation model. Irradiation does not affect the growth of the cell, but rather its ability to differentiate. In addition, irradiation can lead to somatic mutations, morphoses and modifications. These damages most likely occur from changes in the composition of the substances of the cell. Such changes are epigenetic since they affect the regulatory processes of ontogenesis. Variability in the expression of regulatory genes refers to conditional mutations that modify the formation of signs of intraspecific similarity. Characteristic features of these conditional mutations are the dominant type of their manifestation, phenotypic asymmetry and their instability in the generations. Currently, the terms “morphosis” and “modification” are used to describe epigenetic variability, which are maintained in Drosophila melanogaster cultures using linkaged X- chromosomes, and the mutant X-chromosome is transmitted along the paternal line. In this paper, we investigated the epigenetic effects of alpha particles, whose source in nature is mainly radon and its daughter decay products. In the experiment, an isotope of plutonium-238 (Pu²³⁸), generating radiation with an energy of about 5500 eV, was used as a source of alpha particles. In an experiment in the first generation (F₁), deformities or morphoses were found, which can be called "radiation syndromes" or mutations, the manifestation of which is similar to the pleiotropic action of genes. The proportion of morphoses in the experiment was 1.8%, and in control 0.4%. In this experiment, the morphoses in the flies of the first and second generation looked like black spots, or melanomas on different parts of the imago body; "generalized" melanomas; curled, curved wings; shortened wing; bubble on one wing; absence of one wing, deformation of thorax, interruption and violation of tergite patterns, disruption of distribution of ocular facets and bristles; absence of pigmentation of the second and third legs. Statistical analysis by the Chi-square method showed the reliability of the difference in experiment and control at P ≤ 0.01. On the basis of this, it can be considered that alpha particles, which in the environment are mainly generated by radon and its isotopes, have a mutagenic effect that manifests itself, mainly in the formation of morphoses or deformities.

Keywords: Alpha-radiation, genotoxicity, morphoses, radioecology, radon.

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Authors: Mpofu Vongai, Vhurumuku Elaosi

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Many African countries, such as Zimbabwe and South Africa, have curricula reform agendas that include incorporation of Indigenous Knowledge and Nature of Science (NOS) into school Science, Technology, Engineering and Mathematics (STEM) education. It is argued that at high school level, STEM learning, which incorporates understandings of indigenization science and NOS, has the potential to provide a strong foundation for a culturally embedded scientific knowledge essential for their advancement in Science and Technology. Globally, investment in STEM education is recognized as essential for economic development. For this reason, developing countries such as Zimbabwe and South Africa have been investing into training specialized teachers in natural sciences and technology. However, in many cases this training has been detached from the cultural realities and contexts of indigenous learners. For this reason, the STEM curricula reform has provided implementation challenges to teachers. An issue of major concern is the teachers’ pedagogical content knowledge (PCK), which is essential for effective implementation of these STEM curricula. Well-developed Teacher PCK include an understanding of both the nature of indigenous knowledge (NOIK) and of NOS. This paper reports the results of a study that investigated the development of 3 South African and 3 Zimbabwean in-service teachers’ abilities to integrate NOS and NOIK as part of their PCK. A participatory action research design was utilized. The main focus was on capturing, determining and developing teachers STEM knowledge for integrating NOIK and NOS in science classrooms. Their use of indigenous games was used to determine how their subject knowledge for STEM and pedagogical abilities could be developed. Qualitative data were gathered through the use dialogues between the researchers and the in-service teachers, as well as interviewing the participating teachers. Analysis of the data provides a methodological window through which in-service teachers’ PCK can be STEMITIZED and their abilities to integrate NOS and NOIK developed. Implications are raised for developing teachers’ STEM education in universities and teacher training colleges.

Keywords: Indigenous knowledge, nature of science, pedagogical content knowledge, STEM education.

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Authors: Khalid Kaddoura, Tarek Zayed

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Infrastructure assets are essential in urban cities; their purpose is to facilitate the public needs. As a result, their conditions and states shall always be monitored to avoid any sudden malfunction. Sewer systems, one of the assets, are an essential part of the underground infrastructure as they transfer sewer medium to designated areas. However, their conditions are subject to deterioration due to ageing. Therefore, it is of great significance to assess the conditions of pipelines to avoid sudden collapses. Current practices of sewer pipeline assessment rely on industrial protocols that consider distinct defects and grades to conclude the limited average or peak score of the assessed assets. This research aims to enhance the evaluation by integrating the Quality Function Deployment (QFD) and the Decision-Making Trial and Evaluation Laboratory (DEMATEL) methods in assessing the condition of sewer pipelines. The methodology shall study the cause and effect relationship of the systems’ defects to deduce the relative influence weights of each defect. Subsequently, the overall grade is calculated by aggregating the WHAT’s and HOW’s of the House of Quality (HOQ) using the computed relative weights. Thus, this study shall enhance the evaluation of the assets to conclude informative rehabilitation and maintenance plans for decision makers.

Keywords: Condition assessment, DEMATEL, QFD, sewer pipelines.

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Authors: Vita Sterna, Sanita Zute, Inga Jansone, Linda Brunava, Inara Kantane

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Grains, including oats (Avena sativa L.), have been recognized functional foods, because provide beneficial effect on the health of the consumer and decrease the risk of various diseases. Oats are good source of soluble fibre, essential amino acids, unsaturated fatty acids, vitamins and minerals. Oat breeders have developed oat varieties and improved yielding ability potential of oat varieties. Therefore, the aim of investigation was to analyze the composition of perspective oat varieties and breeding lines grains grown in different conditions and evaluate functional properties. In the studied samples content of protein, starch, β-glucans, total dietetic fibre, composition of amino acids and vitamin E were determined. The results of analysis showed that protein content depending of varieties ranged 9.70% to 17.30% total dietary fibre 13.66 g100g-1 to 30.17 g100g-1, content of β-glucans 2.7 g100g-1 to 3.5 g100g-1, amount of vitamin E (α-tocopherol) determined from 4 mgkg-1 to 9.9 mgkg-1. The sums of essential amino acids in oat grain samples were determined from 31.63 gkg-1 to 54.90 gkg-1. It is concluded that amino acids composition of husked and naked oats grown in organic or conventional conditions is close to optimal for human health.

Keywords: Amino acids, β-glucans, dietetic fibre, nutrition value.

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Authors: Kayoko Yamamoto

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This study focuses on an evaluation of Hokkaido which is the northernmost and largest prefecture by surface area in Japan and particularly on two points: the rivalry between all kinds of land use such as urban land and agricultural and forestry land in various cities and their surrounding areas and the possibilities for forestry biomass in areas other than those mentioned above and grasps which areas require examination of the nature of land use control and guidance through conducting land use analysis at the district level using GIS (Geographic Information Systems). The results of analysis in this study demonstrated that it is essential to divide the whole of Hokkaido into two areas: those within delineated city planning areas and those outside of delineated city planning areas and to conduct an evaluation of each land use control. In delineated urban areas, particularly urban areas, it is essential to re-examine land use from the point of view of compact cities or smart cities along with conducting an evaluation of land use control that focuses on issues of rivalry between all kinds of land use such as urban land and agricultural and forestry land. In areas outside of delineated urban areas, it is desirable to aim to build a specific community recycling range based on forest biomass utilization by conducting an evaluation of land use control concerning the possibilities for forest biomass focusing particularly on forests within and outside of city planning areas.

Keywords: Land Use Control, Urbanization, Forestry Biomass, Geographic Information Systems (GIS), Hokkaido

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Authors: Sing-Wu Liou, Yin-Fu Huang

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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: Violina R. Angelova, Radka V. Ivanova, Givko M. Todorov, Krasimir I. Ivanov

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A field study was conducted to evaluate the efficacy of Salvia sclarea L. for phytoremediation of contaminated soils. The experiment was performed on an agricultural fields contaminated by the Non-Ferrous-Metal Works near Plovdiv, Bulgaria. The content of heavy metals in different parts of Salvia sclarea L. (roots, stems, leaves and inflorescences) was determined by ICP. The essential oil of the Salvia sclarea L. was obtained by steam distillation in laboratory conditions and was analyzed for heavy metals and its chemical composition was determined. Salvia sclarea L. is a plant which is tolerant to heavy metals and can be grown on contaminated soils. Based on the obtained results and using the most common criteria, Salvia sclarea L. can be classified as Pb hyperaccumulator and Cd and Zn accumulators, therefore, this plant has suitable potential for the phytoremediation of heavy metal contaminated soils. Favorable is also the fact that heavy metals do not influence the development of the Salvia sclarea L., as well as on the quality and quantity of the essential oil. For clary sage oil obtained from the processing of clary sage grown on highly contaminated soils, its key odour-determining ingredients meet the quality requirements of the European Pharmacopoeia and BS ISO 7609 regarding Bulgarian clary sage oil and/or have values that are close to the limits of these standards. The possibility of further industrial processing will make Salvia sclarea L. an economically interesting crop for farmers of phytoextraction technology.

Keywords: Clary sage, heavy metals, phytoremediation, polluted soils.

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Authors: Jana Kisková, Dana Gabriková

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Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4- repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance of specific haplotype groups of SNPs and interaction of MAOA with others genes (e. g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: Autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism.

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Authors: Achraf El Allali, John R. Rose

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A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: M. C. Proença

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The tools described in this paper enable the location of burned areas where took place the annihilation of natural habitats and establishes a baseline for major changes in forest ecosystems during recovery. Moreover, the result allows the follow up of the surface fuel loading, allowing the evaluation and guidance of restoration measures to remote areas by phased time planning. This case study implements the evaluation of burned areas that suffered successive wildfires in Portugal mainland during the summer of 2017, killing more than 60 people. The goal is to show that this evaluation can be done with remote sense data free of charges in a simple laptop, with open-source software, describing the not-so-simple methodology step by step, to make it accessible for local workers in the areas attained, where the availability of information is essential for the immediate planning of mitigation measures, such as restoring road access, allocate funds for the recovery of human dwellings and assess further needs for restoration of the ecological system. Wildfires also devastate forest ecosystems having a direct impact on vegetation cover and killing or driving away the animal population, besides loss of all crops in rural areas that are essential as local resources. The economic interests are also attained, as the pinewood burned becomes useless for the noblest applications, so its value decreases, and resin extraction ends for several years.

Keywords: Image processing, remote sensing, wildfires, burned areas, SENTINEL-2.

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Authors: Francis Jegede

Abstract:

This paper examines essential issues relating to the rise and nature of violent extremism involving non-state actors and groups in the early 21^st century. The global trends in terrorism and violent extremism are examined in relation to Western governments’ counter terror operations. The paper analyses the existing legal framework for fighting violent extremism and terrorism and highlights the inherent limitations of the current International Law of War in dealing with the growing challenges posed by terrorists and violent extremist groups. The paper discusses how terrorist groups use civilians, women and children as tools and weapon of war to fuel their campaign of terror and suggests ways in which the international community could deal with the challenge of fighting terrorist groups without putting civilians, women and children in harm way. The paper emphasises the need to uphold human rights values and respect for the law of war in our response to global terrorism. The paper poses the question as to whether the current legal framework for dealing with terrorist groups is sufficient without contravening the essential provisions and ethos of the International Law of War and Human Rights. While the paper explains how terrorist groups flagrantly disregard the rule of law and disrespect human rights in their campaign of terror, it also notes instances in which the current Western strategy in fighting terrorism may be viewed or considered as conflicting with human rights and international law.

Keywords: Terrorism, law of war, international law, violent extremism.

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Authors: M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid

Abstract:

Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Keywords: Simulated annealing, genetic algorithm, sequence alignment, multiple sequence alignment.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: L. Almulla

Abstract:

Native plants are better adapted to the local environment providing a more natural effect on landscape projects; their use will both conserve natural resources and produce sustainable greenery. Continuation of evaluation of additional native plants is essential to increase diversity of plant resources for greenery projects. Therefore, in this project an effort was made to study the mass multiplication of further native plants for greenery applications. Standardization of vegetative propagation methods is essential for conservation and sustainable utilization of native plants in restoration projects. Moreover, these simple propagation methods can be readily adapted by the local nursery sector in Kuwait. In the present study, various treatments were used to mass multiply selected plants using vegetative parts to secure maximum rooting and initial growth. Soft or semi-hardwood cuttings of selected native plants were collected from mother plants and subjected to different treatments. Pennisetum divisum can be vegetatively propagated by cuttings/off-shoots. However, Tamarix aucheriana showed maximum number of rooted cuttings and stronger vigor seedlings with the lowest growth hormone concentration. Standardizing the propagation techniques for the native plant species will add to the rehabilitation and landscape revegetation projects in Kuwait.

Keywords: Kuwait desert, landscape, rooting percentage vegetative propagation.

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Authors: Ayat Bani Rashaid, Zain Khasawneh, Mazin Alqhazo, Shreen Nusair, Mohammad El-Khateeb, Mahmoud Bashtawi

Abstract:

Autism Spectrum disorder (ASD) is a psychiatric disorder with unknown etiology that mainly affects children in the first three years of life. Alterations of amino acid levels are believed to contribute to ASD. The levels of six essential amino acids (methionine, histidine, valine, leucine, threonine, and phenylalanine), five conditional amino acids (proline, tyrosine, glutamine, cysteine, and cystine), and five non-essential amino acids (asparagine, aspartic acid, alanine, serine, and glutamic acid) in hair samples of children with ASD (n = 25) were analyzed and compared to corresponding levels in healthy age-matched controls (n = 25). The results showed that the levels of methionine, alanine, and asparagine were significantly lower in the hair samples of ASD group compared to those of the control group (p ≤ 0.05). However, the levels of glutamic acid were significantly higher in the ASD group than the control group (p ≤ 0.05). The current findings could contribute towards further understanding of ASD etiology and provide specialists with a hair amino acid profile utilized as a biomarker for early diagnosis of ASD. Such biomarkers could participate in future developments of therapies that reduce ASD-related symptoms.

Keywords: Autism spectrum disorder, amino acids, liquid chromatography-tandem mass spectrometry, human hair.

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