Search results for: microarray gene expression

Authors: D. R. Ambika, K. R. Radhika, D. Seshachalam

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Unconstrained authentication is an important component for personal automated systems and human-computer interfaces. Existing solutions mostly use face as the primary object of analysis. The performance of face-based systems is largely determined by the extent of deformation caused in the facial region and amount of useful information available in occluded face images. Periocular region is a useful portion of face with discriminative ability coupled with resistance to deformation. A reliable portion of periocular area is available for occluded images. The present work demonstrates that joint representation of periocular texture and periocular structure provides an effective expression and poses invariant representation. The proposed methodology provides an effective and compact description of periocular texture and shape. The method is tested over four benchmark datasets exhibiting varied acquisition conditions.

Keywords: Periocular authentication, Zernike moments, LBPV, shape and texture fusion.

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Authors: Tzong Yuan Wu, Sheng Kuo Hsieh, Tzyy Rong Jinn

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Fip-gts, an immunomodulatory protein purified from Ganoderma tsugae, has been reported to possess therapeutic effects in the treatment of cancer and autoimmune disease. For medicinal application, a recombinant Fip-gts was successfully expressed and purified in Sf21 insect cells by our previously work. It is important to evaluate the immunomodulatory activity of the rFip-gts. To assess the immunomodulatory potential of rFip-gts, the T lymphocytes of murine splenocytes were used in the present study. Results revealed that rFip-gts induced cellular aggregation formation. Additionally, the expression of IL-2 and IFN-r were up-regulated after the treatment of rFip-gts, and a corresponding increased production of IL-2 and IFN-r in a dose-dependent manner. The results showed that rFip-gts has an immunomodulatory activity in inducing Th1 lymphocytes from murine splenocytes released IL-2 and IFN-γ, thus suggest that rFip-gts may have therapeutic potential in vivo as an immune modulator.

Keywords: Fungal immunomodulatory protein, Ganodermatsugae, Interleukin 2, Interferon γ, Lingzhi.

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Authors: Manduth Ramchander

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Evaluating expressions involving multiplication and division can give rise to the fallacy that brackets can be arbitrarily inserted into expressions involving multiplication and division. The aim of this article was to draw upon mathematical theory to prove that brackets cannot be arbitrarily inserted into expressions involving multiplication and division and in particular in expressions where division precedes multiplication. In doing so, it demonstrates that the notion that two different answers are possible, when evaluating expressions involving multiplication and division, is indeed a false one. Searches conducted in a number of scholarly databases unearthed the rules to be applied when removing brackets from expressions, which revealed that consideration needs to be given to sign changes when brackets are removed. The rule pertaining to expressions involving multiplication and division was then extended upon, in its reverse format, to prove that brackets cannot be arbitrarily inserted into expressions involving multiplication and division. The application of the rule demonstrates that an expression involving multiplication and division can have only one correct answer. It is recommended that both the rule and its reverse be included in the curriculum, preferably at the juncture when manipulation with brackets is introduced.

Keywords: Brackets, multiplication, division, operations, order.

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Authors: Saleh Abu Dabous, Khaled Hamad, Rami Al-Ruzouq

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Bridge condition assessment and rating provide essential information needed for bridge management. This paper reviews bridge inspection and condition rating practices and introduces a defect-based urgency index. The index is estimated at the element-level based on the extent and severity of the different defects typical to the bridge element. The urgency index approach has the following advantages: (1) It facilitates judgment submission, i.e. instead of rating the bridge element with a specific linguistic overall expression (which can be subjective and used differently by different people), the approach is based on assessing the defects; (2) It captures multiple defects that can be present within a deteriorated element; and (3) It reflects how critical the element is through quantifying critical defects and their severity. The approach can be further developed and validated. It is expected to be useful for practical purposes as an early-warning system for critical bridge elements.

Keywords: Condition rating, deterioration, inspection, maintenance.

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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: Anna Trusek-Holownia, Andrzej Noworyta

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Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'_F = 10991.4 L/g^.h, k'_M = 14.83L/g^.h, k'_S about 10^-1 L/g^.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.

Keywords: Peptide bond hydrolysis, kinetics, enzyme specificity, biologically active peptides.

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Authors: S. Hariharan, P. Muthuchidambaranathan

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In this paper, we consider a multi user multiple input multiple output (MU-MIMO) based cooperative reporting system for cognitive radio network. In the reporting network, the secondary users forward the primary user data to the common fusion center (FC). The FC is equipped with linear equalizers and an energy detector to make the decision about the spectrum. The primary user data are considered to be a digital video broadcasting - terrestrial (DVB-T) signal. The sensing channel and the reporting channel are assumed to be an additive white Gaussian noise and an independent identically distributed Raleigh fading respectively. We analyzed the detection probability of MU-MIMO system with linear equalizers and arrived at the closed form expression for average detection probability. Also the system performance is investigated under various MIMO scenarios through Monte Carlo simulations.

Keywords: Cooperative MU-MIMO, DVB-T, Linear Equalizers.

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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: Yanhua Jin, Won Suk Lee

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The two-dimensional gel electrophoresis method (2-DE) is widely used in Proteomics to separate thousands of proteins in a sample. By comparing the protein expression levels of proteins in a normal sample with those in a diseased one, it is possible to identify a meaningful set of marker proteins for the targeted disease. The major shortcomings of this approach involve inherent noises and irregular geometric distortions of spots observed in 2-DE images. Various experimental conditions can be the major causes of these problems. In the protein analysis of samples, these problems eventually lead to incorrect conclusions. In order to minimize the influence of these problems, this paper proposes a partition based pair extension method that performs spot-matching on a set of gel images multiple times and segregates more reliable mapping results which can improve the accuracy of gel image analysis. The improved accuracy of the proposed method is analyzed through various experiments on real 2-DE images of human liver tissues.

Keywords: Proteomics, spot-matching, two-dimensionalelectrophoresis.

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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: S Hariharan, K Chaitanya, P Muthuchidambaranathan

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The IEEE 802.22 working group aims to drive the Digital Video Broadcasting-Terrestrial (DVB-T) bands for data communication to the rural area without interfering the TV broadcast. In this paper, we arrive at a closed-form expression for average detection probability of Fusion center (FC) with multiple antenna over the κ − μ fading channel model. We consider a centralized cooperative multiple antenna network for reporting. The DVB-T samples forwarded by the secondary user (SU) were combined using Maximum ratio combiner at FC, an energy detection is performed to make the decision. The fading effects of the channel degrades the detection probability of the FC, a generalized independent and identically distributed (IID) κ − μ and an additive white Gaussian noise (AWGN) channel is considered for reporting and sensing respectively. The proposed system performance is verified through simulation results.

Keywords: IEEE 802.22, Cooperative spectrum sensing, Multiple antenna, κ − μ .

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Authors: Giovanni Luca Masala

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A typical definition of the Computer Aided Diagnosis (CAD), found in literature, can be: A diagnosis made by a radiologist using the output of a computerized scheme for automated image analysis as a diagnostic aid. Often it is possible to find the expression Computer Aided Detection (CAD or CADe): this definition emphasizes the intent of CAD to support rather than substitute the human observer in the analysis of radiographic images. In this article we will illustrate the application of CAD systems and the aim of these definitions. Commercially available CAD systems use computerized algorithms for identifying suspicious regions of interest. In this paper are described the general CAD systems as an expert system constituted of the following components: segmentation / detection, feature extraction, and classification / decision making. As example, in this work is shown the realization of a Computer- Aided Detection system that is able to assist the radiologist in identifying types of mammary tumor lesions. Furthermore this prototype of station uses a GRID configuration to work on a large distributed database of digitized mammographic images.

Keywords: Computer Aided Detection, Computer Aided Diagnosis, mammography, GRID.

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Authors: Hyungkeun Jee, Jooyoung Lee, Dowon Hong

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The most common forensic activity is searching a hard disk for string of data. Nowadays, investigators and analysts are increasingly experiencing large, even terabyte sized data sets when conducting digital investigations. Therefore consecutive searching can take weeks to complete successfully. There are two primary search methods: index-based search and bitwise search. Index-based searching is very fast after the initial indexing but initial indexing takes a long time. In this paper, we discuss a high speed bitwise search model for large-scale digital forensic investigations. We used pattern matching board, which is generally used for network security, to search for string and complex regular expressions. Our results indicate that in many cases, the use of pattern matching board can substantially increase the performance of digital forensic search tools.

Keywords: Digital forensics, search, regular expression.

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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: Kuniyasu Soda

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Surgical trauma seems to facilitate metastatic spread, although the underlying mechanisms are not known. Increased concentrations of polyamines (spermine and spermidine) in the blood seem to have associated with the enhanced malignant potential of cancer cells and decrease in anti-tumor immunity of cancer patients. In addition to de novo synthesis in rapidly growing cells such as normal regenerating cells and cancer cells, cells can take up polyamines from extra-cellular sources. We have shown that increased polyamine concentration results in decreases in cytokine production and expression of adhesion molecules involved in anti-tumor immunity, such as CD11a. And, immune cells in an environment with increased polyamine levels lose anti-tumor immune functions, such as lymphokine activated killer cell (LAK) activities. Because blood polyamine levels are increased in post-surgical patients, polyamine seems to have roles on post-traumatic tumor spread.

Keywords: Immune function, LAK, Polyamine, Surgical trauma.

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Authors: H. Nouri, I. E. Achouri, A. Grimes, H. Ait Said, M. Aissou, Y. Zebboudj

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This paper aims to analysis the behavior of DC corona discharge in wire-to-plate electrostatic precipitators (ESP). Currentvoltage curves are particularly analyzed. Experimental results show that discharge current is strongly affected by the applied voltage. The proposed method of current identification is to use the method of least squares. Least squares problems that of into two categories: linear or ordinary least squares and non-linear least squares, depending on whether or not the residuals are linear in all unknowns. The linear least-squares problem occurs in statistical regression analysis; it has a closed-form solution. A closed-form solution (or closed form expression) is any formula that can be evaluated in a finite number of standard operations. The non-linear problem has no closed-form solution and is usually solved by iterative.

Keywords: Electrostatic precipitator, current-voltage characteristics, Least Squares method, electric field, magnetic field.

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Authors: Hoang Van Ngoc, Nguyen Thu Huong, Nguyen Quang Bau

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Using the quantum kinetic equation for electrons interacting with acoustic phonon, the density of the constant current associated with the drag of charge carriers in cylindrical quantum wire by a linearly polarized electromagnetic wave, a DC electric field and a laser radiation field is calculated. The density of the constant current is studied as a function of the frequency of electromagnetic wave, as well as the frequency of laser field and the basic elements of quantum wire with a parabolic potential. The analytic expression of the constant current density is numerically evaluated and plotted for a specific quantum wires GaAs/AlGaAs to show the dependence of the constant current density on above parameters. All these results of quantum wire compared with bulk semiconductors and superlattices to show the difference.

Keywords: Photon-drag effect, constant current density, quantum wire, parabolic potential.

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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: 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: Ghulam Rasool, Ilka Philippow

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Modernizing legacy applications is the key issue facing IT managers today because there's enormous pressure on organizations to change the way they run their business to meet the new requirements. The importance of software maintenance and reengineering is forever increasing. Understanding the architecture of existing legacy applications is the most critical issue for maintenance and reengineering. The artifacts recovery can be facilitated with different recovery approaches, methods and tools. The existing methods provide static and dynamic set of techniques for extracting architectural information, but are not suitable for all users in different domains. This paper presents a simple and lightweight pattern extraction technique to extract different artifacts from legacy systems using regular expression pattern specifications with multiple language support. We used our custom-built tool DRT to recover artifacts from existing system at different levels of abstractions. In order to evaluate our approach a case study is conducted.

Keywords: Artifacts recovery, Pattern matching, Reverseengineering, Program understanding, Regular expressions, Sourcecode analysis.

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Authors: Robert Niese, Ayoub Al-Hamadi, Bernd Michaelis

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In modern human computer interaction systems (HCI), emotion recognition is becoming an imperative characteristic. The quest for effective and reliable emotion recognition in HCI has resulted in a need for better face detection, feature extraction and classification. In this paper we present results of feature space analysis after briefly explaining our fully automatic vision based emotion recognition method. We demonstrate the compactness of the feature space and show how the 2d/3d based method achieves superior features for the purpose of emotion classification. Also it is exposed that through feature normalization a widely person independent feature space is created. As a consequence, the classifier architecture has only a minor influence on the classification result. This is particularly elucidated with the help of confusion matrices. For this purpose advanced classification algorithms, such as Support Vector Machines and Artificial Neural Networks are employed, as well as the simple k- Nearest Neighbor classifier.

Keywords: Facial expression analysis, Feature extraction, Image processing, Pattern Recognition, Application.

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Authors: So Jeong Nam, Seung Woo Lee, Jai-Kyung Lee

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With the globalized production and logistics environment, the need for reducing the product development interval and lead time, having a faster response to orders, conforming to quality standards, fair tracking, and boosting information exchanging activities with customers and partners, and coping with changes in the management environment, manufacturers are in dire need of an information management system in their manufacturing environments. There are lots of information systems that have been designed to manage the condition or operation of equipment in the field but existing systems have a decentralized architecture, which is not unified. Also, these systems cannot effectively handle the status data extraction process upon encountering a problem related to protocols or changes in the equipment or the setting. In this regard, this paper will introduce a system for processing and saving the status info of production equipment, which uses standard representation formats, to enable flexible responses to and support for variables in the field equipment. This system can be used for a variety of manufacturing and equipment settings and is capable of interacting with higher-tier systems such as MES.

Keywords: DAS, Equipment Status, Regular Expression

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Authors: A. Derardja, L. Baroura, M. Brioua

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The nanotechnology based on epitaxial systems includes single or arranged misfit dislocations. In general, whatever is the type of dislocation or the geometry of the array formed by the dislocations; it is important for experimental studies to know exactly the stress distribution for which there is no analytical expression [1, 2]. This work, using a numerical analysis, deals with relaxation of epitaxial layers having at their interface a periodic network of edge misfit dislocations. The stress distribution is estimated by using isotropic elasticity. The results show that the thickness of the two sheets is a crucial parameter in the stress distributions and then in the profile of the two sheets. A comparative study between the case of single dislocation and the case of parallel network shows that the layers relaxed better when the interface is covered by a parallel arrangement of misfit. Consequently, a single dislocation at the interface produces an important stress field which can be reduced by inserting a parallel network of dislocations with suitable periodicity.

Keywords: Parallel array of misfit, interface, isotropic elasticity, single crystalline substrates, coherent interface

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Authors: R. Moosazadeh

Abstract:

Among the Ottomans, dress was one of the means of expression of the society to which an individual was belonged, and as much as the cloth of the dress, its color reflected the individual's class. Those cloths, and the type and color of the dresses that were worn in the court, were forbidden to ordinary people. In addition, whatever the person's position was, his/her clothes were changed according to that special time and position. The clothes that were worn on trips and ceremonies were different from ordinary clothes in everyday life. At the time of the Ottoman Empire and the old Turkey, the miniature forms, and historical manuscripts were an indicator of the time of that day, and each of them is used as a document from the history of that time for today. The method used in this study is descriptive-analytical and the data collection procedure has been done through library. In this article, the cloth, shape and form of the Kaftan is considered. Firstly, a summary of the history and an explanation of this style of dressing and the importance of it at that time are considered. Finally, by the completion of this research, some of the findings of this research are mentioned, such as the distinctive features of this style and the process of updating it to use it in the present era.

Keywords: Kaftan, cloth, Ottoman, Turkey.

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Authors: Rosnani Hasham, Hyun Kyung Choi, Chang Seo Park

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Ficus deltoidea from the Moraceae family is a popular medicinal herb in Malaysia. It possesses strong antioxidant and antiinflammatory properties. In the present study, the anti-inflammatory effects of F. deltoidea extract on UVB-irradiated HaCaT Keratinocytes were investigated. HaCaT Keratinocytes were UVBirradiated (12.5 mJ/cm3) and were treated with 0.05, 0.08 or 0.1% of F. deltoidea extract. Cell viability following UVB irradiation was significantly higher in the groups treated with the F. deltoidea extract at doses of 0.05, 0.08 or 0.1% than in control group with UVB irradiation only. Tumor necrosis factor-α (TNF-α), interleukin-1α (IL-1α), interleukin-6 (IL-6) and cyclooxygenase (COX-2) play primary roles in the inflammation process upon UV irradiation and are known to be stimulated by UVB irradiation. Treatment with the F. deltoidea extract dramatically inhibited the UV-induced TNF-α, IL-1α, IL-6, and COX-2 expression. These results suggest that the F. deltoidea extract inhibits the production of pro-inflammatory cytokines and may be an effective protective agent for the treatment of skin diseases.

Keywords: Ficus deltoidea, anti-inflammatory activity, cytokines, COX-2.

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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: Saimir Heta, Ilma Robo, Nevila Alliu, Tea Meta

Abstract:

Background: Plasma levels of inflammatory markers are the expression of the infectious wastes of existing periodontitis, as well as of existing inflammation everywhere in the body. Materials and Methods: The study consists of the clinical part of the measurement of inflammatory markers of 23 patients diagnosed with chronic periodontitis and the recording of parental periodontal parameters of patient periodontal status: hemorrhage index and probe values, before and 7-10 days after non-surgical periodontal treatment. Results: The level of fibrinogen drops according to the categorization of disease progression, active and passive, with the biggest % (18%-30%) at the fluctuation 10-20 mg/d. Fluctuations in fibrinogen level according to the age of patients in the range 0-10 mg/dL under 40 years and over 40 years was 13%-26%, in the range 10-20 mg/dL was 26%-22%, in the 20-40 mg/dL was 9%-4%. Conclusions: Non-surgical periodontal treatment significantly reduces the level of non-inflammatory markers in the blood. Oral health significantly reduces the potential source for periodontal bacteria, with the potential of promoting thromboembolism, through interaction between thrombocytes.

Keywords: Chronic periodontitis, atherosclerosis, risk factor, inflammatory markers.

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Authors: Abdallah S. Abdallah, Mohamad A bou El-Nasr, A. Lynn Abbott

Abstract:

This paper presents a new color face image database for benchmarking of automatic face detection algorithms and human skin segmentation techniques. It is named the VT-AAST image database, and is divided into four parts. Part one is a set of 286 color photographs that include a total of 1027 faces in the original format given by our digital cameras, offering a wide range of difference in orientation, pose, environment, illumination, facial expression and race. Part two contains the same set in a different file format. The third part is a set of corresponding image files that contain human colored skin regions resulting from a manual segmentation procedure. The fourth part of the database has the same regions converted into grayscale. The database is available on-line for noncommercial use. In this paper, descriptions of the database development, organization, format as well as information needed for benchmarking of algorithms are depicted in detail.

Keywords: Image database, color image analysis, facedetection, skin segmentation.

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