Search results for: gene pair ranking.

Authors: Abeer K. Jameel, Harry Evdorides

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Iraq is a middle income country where the road safety issue is considered one of the leading causes of deaths. To control the road risk issue, the Iraqi Ministry of Planning, General Statistical Organization started to organise a collection system of traffic accidents data with details related to their causes and severity. These data are published as an annual report. In this paper, a review of the available crash data in Iraq will be presented. The available data represent the rate of accidents in aggregated level and classified according to their types, road users’ details, and crash severity, type of vehicles, causes and number of causalities. The review is according to the types of models used in road safety studies and research, and according to the required road safety data in the road constructions tasks. The available data are also compared with the road safety dataset published in the United Kingdom as an example of developed country. It is concluded that the data in Iraq are suitable for descriptive and exploratory models, aggregated level comparison analysis, and evaluation and monitoring the progress of the overall traffic safety performance. However, important traffic safety studies require disaggregated level of data and details related to the factors of the likelihood of traffic crashes. Some studies require spatial geographic details such as the location of the accidents which is essential in ranking the roads according to their level of safety, and name the most dangerous roads in Iraq which requires tactic plan to control this issue. Global Road safety agencies interested in solve this problem in low and middle-income countries have designed road safety assessment methodologies which are basing on the road attributes data only. Therefore, in this research it is recommended to use one of these methodologies.

Keywords: Data availability, Iraq, road safety.

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Authors: Assyl Bari, Olga Berillo, Saltanat Orazova, Anatoliy Ivashchenko

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Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.

Keywords: MicroRNA, mRNA, plant, superoxide dismutase.

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Authors: Yuan-Jye Tseng, Ching-Yen Chen

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In the design cycle, a main design task is to determine the external shape of the product. The external shape of a product is one of the key factors that can affect the customers’ preferences linking to the motivation to buy the product, especially in the case of a consumer electronic product such as a mobile phone. The relationship between the external shape and the customer preferences needs to be studied to enhance the customer’s purchase desire and action. In this research, a design for customer preferences model is developed for investigating the relationships between the external shape and the customer preferences of a product. In the first stage, the names of the geometric features are collected and evaluated from the data of the specified internet web pages using the developed text miner. The key geometric features can be determined if the number of occurrence on the web pages is relatively high. For each key geometric feature, the numerical values are explored using the text miner to collect the internet data from the web pages. In the second stage, a cluster analysis model is developed to evaluate the numerical values of the key geometric features to divide the external shapes into several groups. Several design suggestion cases can be proposed, for example, large model, mid-size model, and mini model, for designing a mobile phone. A customer preference index is developed by evaluating the numerical data of each of the key geometric features of the design suggestion cases. The design suggestion case with the top ranking of the customer preference index can be selected as the final design of the product. In this paper, an example product of a notebook computer is illustrated. It shows that the external shape of a product can be used to drive customer preferences. The presented design for customer preferences model is useful for determining a suitable external shape of the product to increase customer preferences.

Keywords: Cluster analysis, customer preferences, design evaluation, design for customer preferences, product design.

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Authors: O. Onoriode Emoyan, E. Eyitemi Akporhonor, Charles Otobrise

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Polycyclic Aromatic Hydrocarbons (PAHs) are formed mainly because of incomplete combustion of organic materials during industrial, domestic activities or natural occurrence. Their toxicity and contamination of terrestrial and aquatic ecosystem have been established. However, with limited validity index, previous research has focused on PAHs isomer pair ratios of variable physicochemical properties in source identification. The objective of this investigation was to determine the empirical validity of Pearson Correlation Coefficient (PCC) and Cluster Analysis (CA) in PAHs source identification along soil samples of different land uses. Therefore, 16 PAHs grouped, as Endocrine Disruption Substances (EDSs) were determined in 10 sample stations in top and sub soils seasonally. PAHs was determined the use of Varian 300 gas chromatograph interfaced with flame ionization detector. Instruments and reagents used are of standard and chromatographic grades respectively. PCC and CA results showed that the classification of PAHs along pyrolitic and petrogenic organics used in source signature is about the predominance PAHs in environmental matrix. Therefore, the distribution of PAHs in the studied stations revealed the presence of trace quantities of the vast majority of the sixteen PAHs, which may ultimately inhabit the actual source signature authentication. Therefore, factors to be considered when evaluating possible sources of PAHs could be; type and extent of bacterial metabolism, transformation products/substrates, and environmental factors such as salinity, pH, oxygen concentration, nutrients, light intensity, temperature, co-substrates, and environmental medium are hereby recommended as factors to be considered when evaluating possible sources of PAHs.

Keywords: Comparative correlation, kinetically, polynuclear aromatic hydrocarbons, thermodynamically- favored PAHs, sources evaluation.

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Authors: Ali Anaissi, Paul J. Kennedy, Madhu Goyal

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Analysis and visualization of microarraydata is veryassistantfor biologists and clinicians in the field of diagnosis and treatment of patients. It allows Clinicians to better understand the structure of microarray and facilitates understanding gene expression in cells. However, microarray dataset is a complex data set and has thousands of features and a very small number of observations. This very high dimensional data set often contains some noise, non-useful information and a small number of relevant features for disease or genotype. This paper proposes a non-linear dimensionality reduction algorithm Local Principal Component (LPC) which aims to maps high dimensional data to a lower dimensional space. The reduced data represents the most important variables underlying the original data. Experimental results and comparisons are presented to show the quality of the proposed algorithm. Moreover, experiments also show how this algorithm reduces high dimensional data whilst preserving the neighbourhoods of the points in the low dimensional space as in the high dimensional space.

Keywords: Linear Dimension Reduction, Non-Linear Dimension Reduction, Principal Component Analysis, Biologists.

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Authors: Dulal Acharjee, Punyaban Patel

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For collecting data from all sensor nodes, some changes in Dynamic Source Routing (DSR) protocol is proposed. At each hop level, route-ranking technique is used for distributing packets to different selected routes dynamically. For calculating rank of a route, different parameters like: delay, residual energy and probability of packet loss are used. A hybrid topology of DMPR(Disjoint Multi Path Routing) and MMPR(Meshed Multi Path Routing) is formed, where braided topology is used in different faulty zones of network. For reducing energy consumption, variant transmission ranges is used instead of fixed transmission range. For reducing number of packet drop, a fuzzy logic inference scheme is used to insert different types of delays dynamically. A rule based system infers membership function strength which is used to calculate the final delay amount to be inserted into each of the node at different clusters. In braided path, a proposed 'Dual Line ACK Link'scheme is proposed for sending ACK signal from a damaged node or link to a parent node to ensure that any error in link or any node-failure message may not be lost anyway. This paper tries to design the theoretical aspects of a model which may be applied for collecting data from any large hanging iron structure with the help of wireless sensor network. But analyzing these data is the subject of material science and civil structural construction technology, that part is out of scope of this paper.

Keywords: Metallic corrosion, Multi Path Routing, DisjointMPR, Meshed MPR, braided path, dual line ACK link, route rankingand Fuzzy Logic.

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Authors: A. D. Parekh, P. R. Tailor, H.R Jivanramajiwala

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The present work deals with optimization of cascade refrigeration system using eco friendly refrigerants pair R507A and R23. R507A is azeotropic mixture composed of HFC refrigerants R125/R143a (50%/50% by wt.). R23 is a single component HFC refrigerant used as replacement to CFC refrigerant R13 in low temperature applications. These refrigerants have zero ozone depletion potential and are non-flammable. Optimization of R507AR23 cascade refrigeration system performance parameters such as minimum work required, refrigeration effect, coefficient of performance and exergetic efficiency was carried out in terms of eight operating parameters- combinations using Genetic Algorithm tool. The eight operating parameters include (1) low side evaporator temperature (2) high side condenser temperature (3) temperature difference in the cascade heat exchanger (4) low side condenser temperature (5) low side degree of subcooling (6) high side degree of subcooling (7) low side degree of superheating (8) high side degree of superheating. Results show that for minimum work system should operate at high temperature in low side evaporator, low temperature in high side condenser, low temperature difference in cascade condenser, high temperature in low side condenser and low degree of subcooling and superheating in both side. For maximum refrigeration effect system should operate at high temperature in low side evaporator, high temperature in high side condenser, high temperature difference in cascade condenser, low temperature in low side condenser and higher degree of subcooling in LT and HT side. For maximum coefficient of performance and exergetic efficiency, system should operate at high temperature in low side evaporator, low temperature in high side condenser, low temperature difference in cascade condenser, high temperature in low side condenser and higher degree of subcooling and superheating in low side of the system.

Keywords: Cascade refrigeration system, Genetic Algorithm, R507A, R23,

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Authors: H. Zarei, M. H. Fazel Zarandi, M. Karbasian

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A Decision Support System/Expert System for stock portfolio selection presented where at first step, both technical and fundamental data used to estimate technical and fundamental return and risk (1st phase); Then, the estimated values are aggregated with the investor preferences (2nd phase) to produce convenient stock portfolio. In the 1st phase, there are two expert systems, each of which is responsible for technical or fundamental estimation. In the technical expert system, for each stock, twenty seven candidates are identified and with using rough sets-based clustering method (RC) the effective variables have been selected. Next, for each stock two fuzzy rulebases are developed with fuzzy C-Mean method and Takai-Sugeno- Kang (TSK) approach; one for return estimation and the other for risk. Thereafter, the parameters of the rule-bases are tuned with backpropagation method. In parallel, for fundamental expert systems, fuzzy rule-bases have been identified in the form of “IF-THEN" rules through brainstorming with the stock market experts and the input data have been derived from financial statements; as a result two fuzzy rule-bases have been generated for all the stocks, one for return and the other for risk. In the 2nd phase, user preferences represented by four criteria and are obtained by questionnaire. Using an expert system, four estimated values of return and risk have been aggregated with the respective values of user preference. At last, a fuzzy rule base having four rules, treats these values and produce a ranking score for each stock which will lead to a satisfactory portfolio for the user. The stocks of six manufacturing companies and the period of 2003-2006 selected for data gathering.

Keywords: Stock Portfolio Selection, Fuzzy Rule-Base ExpertSystems, Financial Decision Support Systems, Technical Analysis, Fundamental Analysis.

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Authors: Henrik L. Funke, Lars Ulke-Winter, Sandra Gelbrich, Lothar Kroll

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This work reports about an approach for an automatic adaptation of concrete formulations based on genetic algorithms (GA) to optimize a wide range of different fit-functions. In order to achieve the goal, a method was developed which provides a numerical description of a fibre reinforced concrete (FRC) mixture regarding the production technology and the property spectrum of the concrete. In a first step, the FRC mixture with seven fixed components was characterized by varying amounts of the components. For that purpose, ten concrete mixtures were prepared and tested. The testing procedure comprised flow spread, compressive and bending tensile strength. The analysis and approximation of the determined data was carried out by GAs. The aim was to obtain a closed mathematical expression which best describes the given seven-point cloud of FRC by applying a Gene Expression Programming with Free Coefficients (GEP-FC) strategy. The seven-parametric FRC-mixtures model which is generated according to this method correlated well with the measured data. The developed procedure can be used for concrete mixtures finding closed mathematical expressions, which are based on the measured data.

Keywords: Concrete design, fibre reinforced concrete, genetic algorithms, GEP-FC.

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Authors: Bryce Benson, Sooin Lee, Ashwin Belle

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Unrecognized or delayed identification of patient deterioration is a key cause of in-hospitals adverse events. Clinicians rely on vital signs monitoring to recognize patient deterioration. However, due to ever increasing nursing workloads and the manual effort required, vital signs tend to be measured and recorded intermittently, and inconsistently causing large gaps during patient monitoring. Additionally, during deterioration, the body’s autonomic nervous system activates compensatory mechanisms causing the vital signs to be lagging indicators of underlying hemodynamic decline. This study analyzes the predictive efficacy of the Analytic for Hemodynamic Instability (AHI) system, an automated tool that was designed to help clinicians in early identification of deteriorating patients. The lead time analysis in this retrospective observational study assesses how far in advance AHI predicted deterioration prior to the start of an episode of hemodynamic instability (HI) becoming evident through vital signs? Results indicate that of the 362 episodes of HI in this study, 308 episodes (85%) were correctly predicted by the AHI system with a median lead time of 57 minutes and an average of 4 hours (240.5 minutes). Of the 54 episodes not predicted, AHI detected 45 of them while the episode of HI was ongoing. Of the 9 undetected, 5 were not detected by AHI due to either missing or noisy input ECG data during the episode of HI. In total, AHI was able to either predict or detect 98.9% of all episodes of HI in this study. These results suggest that AHI could provide an additional ‘pair of eyes’ on patients, continuously filling the monitoring gaps and consequently giving the patient care team the ability to be far more proactive in patient monitoring and adverse event management.

Keywords: Clinical deterioration prediction, decision support system, early warning system, hemodynamic status, physiologic monitoring.

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Authors: Delly C. Lestari, Linosefa, Ardiana Kusumaningrum, Andi Yasmon, Anis Karuniawati

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The objective of this study is to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) harboring mecA genes from screening isolates among intensive care unit (ICU) patients. All MRSA screening isolates from ICU’s patients of Cipto Mangunkusumo Hospital during 2011 and 2014 were included in this study. Identification and susceptibility test was performed using Vitek2 system (Biomereux®). PCR was conducted to characterize the SCCmec of S. aureus harboring the mecA gene on each isolate. Patient’s history of illness was traced through medical record. 24 isolates from 327 screening isolates were MRSA positive (7.3%). From PCR, we found 17 (70.8%) isolates carrying SCCmec type I, 3 (12.5%) isolates carrying SCCmec type III, and 2 (8.3%) isolates carrying SCCmec type IV. In conclusion, SCCmec type I is the most prevalent MRSA colonization among ICU patients in Cipto Mangunkusumo Hospital.

Keywords: MRSA, mecA genes, ICU, colonization.

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Authors: Cheng-Hong Yang, Yu-Huei Cheng, Hsueh-Wei Chang, Li-Yeh Chuang

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Before performing polymerase chain reactions (PCR), a feasible primer set is required. Many primer design methods have been proposed for design a feasible primer set. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this paper, a particle swarm optimization (PSO) algorithm is proposed to solve primer design problems associated with providing a specific product for PCR experiments. A test set of the gene CYP1A1, associated with a heightened lung cancer risk was analyzed and the comparison of accuracy and running time with the genetic algorithm (GA) and memetic algorithm (MA) was performed. A comparison of results indicated that the proposed PSO method for primer design finds optimal or near-optimal primer sets and effective PCR products in a relatively short time.

Keywords: polymerase chain reaction (PCR), primer design, evolutionary computation, particle swarm optimization (PSO).

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Authors: Chien-Hung Huang, Chia-Wei Weng, Chang-Chih Chiang, Shih-Hua Wu, Chih-Hsien Huang, Ka-Lok Ng

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MicroRNAs (miRNAs) are a class of non-coding RNAs that hybridize to mRNAs and induce either translation repression or mRNA cleavage. Recently, it has been reported that miRNAs could possibly play an important role in human diseases. By integrating miRNA target genes, cancer genes, miRNA and mRNA expression profiles information, a database is developed to link miRNAs to cancer target genes. The database provides experimentally verified human miRNA target genes information, including oncogenes and tumor suppressor genes. In addition, fragile sites information for miRNAs, and the strength of the correlation of miRNA and its target mRNA expression level for nine tissue types are computed, which serve as an indicator for suggesting miRNAs could play a role in human cancer. The database is freely accessible at http://ppi.bioinfo.asia.edu.tw/mirna_target/index.html.

Keywords: MicroRNA, miRNA expression profile, mRNAexpression profile, cancer genes, oncogene, tumor suppressor gene

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Authors: Hanina M. N., Hairul Shahril M., Ismatul Nurul Asyikin I., Abdul Jalil A. K., Salina M. R., Maryam M. R., Rosfarizan M.

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The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.

Keywords: Bacillus subtilis ATCC21332, Streptomycin Sulfate, extracellular proteins.

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility including albumin, globulin, glutenin and prolamin or gliadin. Gliadins are major components of the storage proteins in wheat endosperm. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, in terms of coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected for this study. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 93% of the accessions carried allele 210 bp, and only 8% did not any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: Diploied wheat, gliadin, Triticum boeoticum, Triticum urartu.

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Authors: Ergin Kosa, Ali Göksenli

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Erosion and abrasion are wear mechanisms reducing the lifetime of machine elements like valves, pump and pipe systems. Both wear mechanisms are acting at the same time, causing a “Synergy” effect, which leads to a rapid damage of the surface. Different parameters are effective on erosive abrasive wear rate. In this study effect of particle impact angle on wear rate and wear mechanism of ductile and brittle materials was investigated. A new slurry pot was designed for experimental investigation. As abrasive particle, silica sand was used. Particle size was ranking between 200- 500 μm. All tests were carried out in a sand-water mixture of 20% concentration for four hours. Impact velocities of the particles were 4.76 m/s. As ductile material steel St 37 with Vickers Hardness Number (VHN) of 245 and quenched St 37 with 510 VHN was used as brittle material. After wear tests, morphology of the eroded surfaces were investigated for better understanding of the wear mechanisms acting at different impact angles by using Scanning Electron Microscope. The results indicated that wear rate of ductile material was higher than brittle material. Maximum wear rate was observed by ductile material at a particle impact angle of 300 and decreased further by an increase in attack angle. Maximum wear rate by brittle materials was by impact angle of 450 and decreased further up to 900. Ploughing was the dominant wear mechanism by ductile material. Microcracks on the surface were detected by ductile materials, which are nucleation centers for crater formation. Number of craters decreased and depth of craters increased by ductile materials by attack angle higher than 300. Deformation wear mechanism was observed by brittle materials. Number and depth of pits decreased by brittle materials by impact angles higher than 450. At the end it is concluded that wear rate could not be directly related to impact angle of particles due to the different reaction of ductile and brittle materials.

Keywords: Erosive wear, particle impact angle, silica sand, wear rate, ductile-brittle material.

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Authors: C. Ardil

Abstract:

This paper aims to select the best military attack helicopter to purchase by the Armed Forces and provide greater reconnaissance and offensive combat capability in military operations. For this purpose, a multiple criteria decision analysis method integrated with the variance weight procedure was applied to the military attack helicopter selection problem. A real military aviation case problem is conducted to support the Armed Forces decision-making process and contributes to the better performance of the Armed Forces. Application of the methodology resulted in ranking lists for ordering and prioritizing attack helicopters, providing transparency and simplicity to the decision-making process. Nine military attack helicopter models were analyzed in the light of strategic, tactical, and operational criteria, considering attack helicopters. The selected military attack helicopter would be used for fire support and reconnaissance activities required by the Armed Forces operation. This study makes a valuable contribution to the problem of military attack helicopter selection, as it represents a state-of-the-art application of the MCDMA method to contribute to the solution of a real problem of the Armed Forces. The methodology presented in this paper can be used to solve real problems of a wide variety, especially strategic, tactical and operational, and is, therefore, a very useful method for decision making.

Keywords: aircraft selection, military attack helicopter selection, attack helicopter fleet planning, MCDMA, multiple criteria analysis, multiple criteria decision making analysis, distance function measure

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Authors: C. Ardil, A. M. Pashaev, R.A. Sadiqov, P. Abdullayev

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In this paper, multiple criteria decision making analysis technique, is presented for ranking and selection of a set of determined alternatives - fighter aircraft - which are associated with a set of decision factors. In fighter aircraft design, conflicting decision criteria, disciplines, and technologies are always involved in the design process. Multiple criteria decision making analysis techniques can be helpful to effectively deal with such situations and make wise design decisions. Multiple criteria decision making analysis theory is a systematic mathematical approach for dealing with problems which contain uncertainties in decision making. The feasibility and contributions of applying the multiple criteria decision making analysis technique in fighter aircraft selection analysis is explored. In this study, an integrated framework incorporating multiple criteria decision making analysis technique in fighter aircraft analysis is established using entropy objective weighting method. An improved integrated multiple criteria decision making analysis method is utilized to aggregate the multiple decision criteria into one composite figure of merit, which serves as an objective function in the decision process. Therefore, it is demonstrated that the suitable multiple criteria decision making analysis method with decision solution provides an effective objective function for the decision making analysis. Considering that the inherent uncertainties and the weighting factors have crucial decision impacts on the fighter aircraft evaluation, seven fighter aircraft models for the multiple design criteria in terms of the weighting factors are constructed. The proposed multiple criteria decision making analysis model is based on integrated entropy index procedure, and additive multiple criteria decision making analysis theory. Hence, the applicability of proposed technique for fighter aircraft selection problem is considered. The constructed multiple criteria decision making analysis model can provide efficient decision analysis approach for uncertainty assessment of the decision problem. Consequently, the fighter aircraft alternatives are ranked based their final evaluation scores, and sensitivity analysis is conducted.

Keywords: Fighter Aircraft, Fighter Aircraft Selection, Multiple Criteria Decision Making, Multiple Criteria Decision Making Analysis, MCDMA

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Authors: Fabio Fabris, Alex A. Freitas

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Hierarchical classification is a special type of classification task where the class labels are organised into a hierarchy, with more generic class labels being ancestors of more specific ones. Meta-learning for classification-algorithm recommendation consists of recommending to the user a classification algorithm, from a pool of candidate algorithms, for a dataset, based on the past performance of the candidate algorithms in other datasets. Meta-learning is normally used in conventional, non-hierarchical classification. By contrast, this paper proposes a meta-learning approach for more challenging task of hierarchical classification, and evaluates it in a large number of bioinformatics datasets. Hierarchical classification is especially relevant for bioinformatics problems, as protein and gene functions tend to be organised into a hierarchy of class labels. This work proposes meta-learning approach for recommending the best hierarchical classification algorithm to a hierarchical classification dataset. This work’s contributions are: 1) proposing an algorithm for splitting hierarchical datasets into new datasets to increase the number of meta-instances, 2) proposing meta-features for hierarchical classification, and 3) interpreting decision-tree meta-models for hierarchical classification algorithm recommendation.

Keywords: Algorithm recommendation, meta-learning, bioinformatics, hierarchical classification.

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Authors: Patricia M. Boechler, Heather M. Gautreau

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In this research study, postsecondary students completed an information learning task in an avatar-based 3D virtual learning environment. Three factors were of interest in relation to learning; 1) the influence of collaborative vs. independent conditions, 2) the influence of the spatial arrangement of the virtual environment (linear, random and clustered), and 3) the relationship of individual differences such as spatial skill, general computer experience and video game experience to learning. Students completed pretest measures of prior computer experience and prior spatial skill. Following the premeasure administration, students were given instruction to move through the virtual environment and study all the material within 10 information stations. In the collaborative condition, students proceeded in randomly assigned pairs, while in the independent condition they proceeded alone. After this learning phase, all students individually completed a multiple choice test to determine information retention. The overall results indicated that students in pairs did not perform any better or worse than independent students. As far as individual differences, only spatial ability predicted the performance of students. General computer experience and video game experience did not. Taking a closer look at the pairs and spatial ability, comparisons were made on pairs high/matched spatial ability, pairs low/matched spatial ability and pairs that were mismatched on spatial ability. The results showed that both high/matched pairs and mismatched pairs outperformed low/matched pairs. That is, if a pair had even one individual with strong spatial ability they would perform better than pairs with only low spatial ability individuals. This suggests that, in virtual environments, the specific individuals that are paired together are important for performance outcomes. The paper also includes a discussion of trends within the data that have implications for virtual environment education.

Keywords: Avatar-based, virtual environment, paired learning, individual differences.

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Authors: Charles Chikwendu Okpala, Christopher Chukwutoo Ihueze

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As a technique that reduces variation in a product by lessening the sensitivity of the design to sources of variation, rather than by controlling their sources, Taguchi Robust Design entails the designing of ideal goods, by developing a product that has minimal variance in its characteristics and also meets the desired exact performance. This paper examined the concept of the manufacturing approach and its application to brake pad product of an automotive parts manufacturing company. Although the firm claimed that only defects, excess inventory, and over-production were the few wastes that grossly affect their productivity and profitability, a careful study and analysis of their manufacturing processes with the application of Single Minute Exchange of Dies (SMED) tool showed that the waste of waiting is the fourth waste that bedevils the firm. The selection of the Taguchi L9 orthogonal array which is based on the four parameters and the three levels of variation for each parameter revealed that with a range of 2.17, that waiting is the major waste that the company must reduce in order to continue to be viable. Also, to enhance the company’s throughput and profitability, the wastes of over-production, excess inventory, and defects with ranges of 2.01, 1.46, and 0.82, ranking second, third, and fourth respectively must also be reduced to the barest minimum. After proposing -33.84 as the highest optimum Signal-to-Noise ratio to be maintained for the waste of waiting, the paper advocated for the adoption of all the tools and techniques of Lean Production System (LPS), and Continuous Improvement (CI), and concluded by recommending SMED in order to drastically reduce set up time which leads to unnecessary waiting.

Keywords: Taguchi Robust Design, signal to noise ratio, Single Minute Exchange of Dies, lean production system, waste.

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Authors: C. Ardil

Abstract:

In this paper, the comparison of composite programming and compromise programming for the aircraft selection problem is discussed using the multiple criteria decision analysis method. The decision making process requires the prior definition and fulfillment of certain factors, especially when it comes to complex areas such as aircraft selection problems. The proposed technique gives more efficient results by extending the composite programming and compromise programming, which are widely used in modeling multiple criteria decisions. The proposed model is applied to a practical decision problem for evaluating and selecting aircraft problems.A selection of aircraft was made based on the proposed approach developed in the field of multiple criteria decision making. The model presented is solved by using the following methods: composite programming, and compromise programming. The importance values of the weight coefficients of the criteria are calculated using the mean weight method. The evaluation and ranking of aircraft are carried out using the composite programming and compromise programming methods. In order to determine the stability of the model and the ability to apply the developed composite programming and compromise programming approach, the paper analyzes its sensitivity, which involves changing the value of the coefficient λ and q in the first part. The second part of the sensitivity analysis relates to the application of different multiple criteria decision making methods, composite programming and compromise programming. In addition, in the third part of the sensitivity analysis, the Spearman correlation coefficient of the ranks obtained was calculated which confirms the applicability of all the proposed approaches.

Keywords: composite programming, compromise programming, additive weighted model, multiplicative weighted model, multiple criteria decision making analysis, MCDMA, aircraft selection

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

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In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

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Authors: Zhen Cheng, Xinyu Dai, Shujian Huang, Jiajun Chen

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Recently, explanatory natural language inference has attracted much attention for the interpretability of logic relationship prediction, which is also known as explanation generation for Natural Language Inference (NLI). Existing explanation generators based on discriminative Encoder-Decoder architecture have achieved noticeable results. However, we find that these discriminative generators usually generate explanations with correct evidence but incorrect logic semantic. It is due to that logic information is implicitly encoded in the premise-hypothesis pairs and difficult to model. Actually, logic information identically exists between premise-hypothesis pair and explanation. And it is easy to extract logic information that is explicitly contained in the target explanation. Hence we assume that there exists a latent space of logic information while generating explanations. Specifically, we propose a generative model called Variational Explanation Generator (VariationalEG) with a latent variable to model this space. Training with the guide of explicit logic information in target explanations, latent variable in VariationalEG could capture the implicit logic information in premise-hypothesis pairs effectively. Additionally, to tackle the problem of posterior collapse while training VariaztionalEG, we propose a simple yet effective approach called Logic Supervision on the latent variable to force it to encode logic information. Experiments on explanation generation benchmark—explanation-Stanford Natural Language Inference (e-SNLI) demonstrate that the proposed VariationalEG achieves significant improvement compared to previous studies and yields a state-of-the-art result. Furthermore, we perform the analysis of generated explanations to demonstrate the effect of the latent variable.

Keywords: Natural Language Inference, explanation generation, variational auto-encoder, generative model.

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Authors: Kulaya Wimolwat, Panlop Chakravitthamrong, Neti Waranuch

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Background: Seborrheic dermatitis is a common chronic skin condition affecting the face, scalp, chest, and trunk. The cause of seborrheic dermatitis is still unknown. Sebum production, lipid composition, hormone levels, and Malassezia species have been suggested as important factors in the development of seborrheic dermatitis. Curcuma aeruginosa Roxb. extract-containing cream with anti-inflammatory and anti-androgenic properties may be beneficial for treating mild to moderate facial seborrheic dermatitis. Objectives: We evaluated the efficacy and safety of 2% C. aeruginosa Roxb. extract-containing cream in the treatment of mild to moderate seborrheic dermatitis. Methods: This was a prospective, open-label, and non-comparative study. Ten adult patients clinically diagnosed with mild to moderate seborrheic dermatitis were enrolled in a four-week study. The 2% C. aeruginosa Roxb. cream was applied twice daily to a lesional area on the face for four weeks. The Scoring Index (SI) ranking system on days 14 and 28 was compared with that at baseline to determine the efficacy of treatment. The adverse events (burning sensation and erythema) were evaluated on days 14 and 28 to determine the safety of the treatment. Results: Significant improvement was observed in the reduction of the mean SI at day 14 (2.9) and 28 (1.4) compared to that at baseline (4.9). An adverse reaction was observed on day 14 (mild erythema 20% and mild burning sensation 10%) and was resolved by the end of the study. Conclusion: This open-label pilot study has shown that there was a significant improvement in the severity in these seborrheic patients and most reported they were satisfied with it. Reported adverse events were all mild.

Keywords: Anti-androgenic, antifungals, anti-inflammatory, Curcuma aeruginosa, seborrheic dermatitis, efficacy, safety.

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Authors: N. Tsvetkova, R. Harizanov A. Ivanova, I. Rainova, N. Yancheva-Petrova, D. Strashimirov, R. Enikova, M. Videnova, E. Kaneva, I. Kaftandjiev, V. Levterova, I. Simeonovski, N. Yanev, G. Hinkov

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The Pneumocystis jirovecii (P. jirovecii) and protozoan of the genera Acanthamoeba, Cryptosporidium, and Toxoplasma gondii are opportunistic pathogens that can cause life-threatening infections in immunocompromised patients. Aim of the study was to evaluate the coinfection rate with opportunistic protozoal agents among Bulgarian patients diagnosed with P. jirovecii pneumonia. 38 pulmonary samples were collected from 38 patients (28 HIV-infected) with P. jirovecii infection. P. jirovecii DNA was detected by real-time PCR targeting the large mitochondrial subunit ribosomal RNA gene. Acanthamoeba was determined by genus-specific conventional PCR assay. Real-time PCR for the detection of a Toxoplasma gondii and Cryptosporidium DNA fragment was used. Pneumocystis DNA was detected in all 38 specimens; 28 (73.7%) were from HIV-infected patients. Three (10,7%) of them were coinfected with T. gondii and 1 (3.6%) with Cryptosporidium. In the group of non-HIV-infected (n = 10), Cryptosporidium DNA was detected in an infant (10%). Acanthamoeba DNA was not found in the tested samples. The current study showed a relatively low rate of coinfections of Cryptosporidium spp./T. gondii and P. jirovecii in the Bulgarian patients studied.

Keywords: Coinfection, opportunistic protozoal agents, Pneumocystis jirovecii, pulmonary infections.

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Authors: Guyue Zhu, Liangping Hong

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Chinese overall urban design faces a large number of problems such as the neglect of urban characteristics, generalization of content, and difficulty in implementation. Focusing on these issues, this paper proposes the main points of shaping urban characteristics in overall urban design: focuses on core problems in city function and scale, landscape pattern, historical culture, social resources and modern city style and digs the urban characteristic genes. Then, we put forward “core problem location and characteristic gene enhancement” as a kind of overall urban design technical method. Firstly, based on the main problems in urban space as a whole, for the operability goal, the method extracts the key genes and integrates into the multi-dimension system in a targeted manner. Secondly, hierarchical management and guidance system is established which may be in line with administrative management. Finally, by converting the results, action plan is drawn up that can be dynamically implemented. Based on the above idea and method, a practical exploration has been performed in the case of Xiangyang central city.

Keywords: City characteristics, overall urban design, planning implementation, Xiangyang central city.

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Authors: Zelmina Lubovac, Björn Olsson, Jonas Gamalielsson

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This paper describes a novel approach for deriving modules from protein-protein interaction networks, which combines functional information with topological properties of the network. This approach is based on weighted clustering coefficient, which uses weights representing the functional similarities between the proteins. These weights are calculated according to the semantic similarity between the proteins, which is based on their Gene Ontology terms. We recently proposed an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The rational underlying this approach is that each module can be reduced to a set of triangles (protein triplets connected to each other). Here, we propose considering semantic similarity weights of all triangle-forming edges between proteins. We also apply varying semantic similarity thresholds between neighbours of each node that are not neighbours to each other (and hereby do not form a triangle), to derive new potential triangles to include in module-defining procedure. The results show an improvement of pure topological approach, in terms of number of predicted modules that match known complexes.

Keywords: Modules, systems biology, protein interactionnetworks, yeast.

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Authors: Mohammadjavad Mehrabanpour, Maryam Ranjbar Bushehri, Dorsa Mehrabanpour

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Respiratory diseases are the most important problems in the country’s poultry industry, particularly when it comes to broiler flocks. Ornithobacterium rhinotracheale (ORT) is a species that causes poor performance in growth rate, egg production, and mortality. This pathogen causes a respiratory infection including pulmonary alveolar inflammation, and pneumonia of birds throughout the world. Newcastle disease (ND) is a highly contagious disease in poultry, and also, it causes considerable losses to the poultry industry. The aim of this study was to evaluate the simultaneous occurrence of ORT and ND and NDV isolation by inoculation in embryonated eggs and confirmed by RT-PCR in broiler chicken flocks in Fars province. In this study, 318 blood and 85 tissue samples (brain, trachea, liver, and cecal tonsils) were collected from 15 broiler chicken farms. Survey serum antibody titers against ORT by using a commercial enzyme-linked immunosorbent assay (ELISA) kit performed. Evaluation of antibody titer against ND virus is performed by hemagglutination inhibition test. Virus isolation with chick embryo eggs 9-11 and RT-PCR method were carried out. A total of 318 serum samples, 135 samples (42.5%) were positive for antibodies to ORT and titer of HI antibodies against NDV in 122 serum samples (38/4%) were 7-10 (log2) and 61 serum samples (19/2%) had occurrence antibody titer against Newcastle virus and ORT. Results of the present study indicated that 20 tissue samples were positive in embryonated egg and in rapid hemagglutination (HA) test. HI test with specific ND positive serum confirmed that 6 of 20 samples. PCR confirmed that all six samples were positive and PCR products of samples indicated 535-base pair fragments in electrophrosis. Due to the great economic importance of these two diseases in the poultry industry, it is necessary to design and implement a comprehensive plan for prevention and control of these diseases.

Keywords: ELISA, Newcastle disease, Ornithobacterium rhinotracheale, seroprevalence.

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Authors: Semanur Soyyiğit Kaya, Ercan Eren

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Energy has a prominent role for development of nations. Countries which have energy resources also have strategic power in the international trade of energy since it is essential for all stages of production in the economy. Thus, it is important for countries to analyze the weaknesses and strength of the system. On the other side, international trade is one of the fields that are analyzed as a complex network via network analysis. Complex network is one of the tools to analyze complex systems with heterogeneous agents and interaction between them. A complex network consists of nodes and the interactions between these nodes. Total properties which emerge as a result of these interactions are distinct from the sum of small parts (more or less) in complex systems. Thus, standard approaches to international trade are superficial to analyze these systems. Network analysis provides a new approach to analyze international trade as a network. In this network, countries constitute nodes and trade relations (export or import) constitute edges. It becomes possible to analyze international trade network in terms of high degree indicators which are specific to complex networks such as connectivity, clustering, assortativity/disassortativity, centrality, etc. In this analysis, international trade of crude oil and coal which are types of fossil fuel has been analyzed from 2005 to 2014 via network analysis. First, it has been analyzed in terms of some topological parameters such as density, transitivity, clustering etc. Afterwards, fitness to Pareto distribution has been analyzed via Kolmogorov-Smirnov test. Finally, weighted HITS algorithm has been applied to the data as a centrality measure to determine the real prominence of countries in these trade networks. Weighted HITS algorithm is a strong tool to analyze the network by ranking countries with regards to prominence of their trade partners. We have calculated both an export centrality and an import centrality by applying w-HITS algorithm to the data. As a result, impacts of the trading countries have been presented in terms of high-degree indicators.

Keywords: Complex network approach, fossil fuel, international trade, network theory.

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