Search results for: cytokine expression

Authors: C. Gunavathi, K. Premalatha

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Tumor classification is a key area of research in the field of bioinformatics. Microarray technology is commonly used in the study of disease diagnosis using gene expression levels. The main drawback of gene expression data is that it contains thousands of genes and a very few samples. Feature selection methods are used to select the informative genes from the microarray. These methods considerably improve the classification accuracy. In the proposed method, Genetic Algorithm (GA) is used for effective feature selection. Informative genes are identified based on the T-Statistics, Signal-to-Noise Ratio (SNR) and F-Test values. The initial candidate solutions of GA are obtained from top-m informative genes. The classification accuracy of k-Nearest Neighbor (kNN) method is used as the fitness function for GA. In this work, kNN and Support Vector Machine (SVM) are used as the classifiers. The experimental results show that the proposed work is suitable for effective feature selection. With the help of the selected genes, GA-kNN method achieves 100% accuracy in 4 datasets and GA-SVM method achieves in 5 out of 10 datasets. The GA with kNN and SVM methods are demonstrated to be an accurate method for microarray based tumor classification.

Keywords: F-Test, Gene Expression, Genetic Algorithm, k- Nearest-Neighbor, Microarray, Signal-to-Noise Ratio, Support Vector Machine, T-statistics, Tumor Classification.

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Authors: Siti Aisya Gany, Swee Ching Tan, Sook Yee Gan

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Diminished antioxidant defense or increased production of reactive oxygen species in the biological system can result in oxidative stress which may lead to various neurodegenerative diseases including Alzheimer’s disease (AD). Microglial activation also contributes to the progression of AD by producing several proinflammatory cytokines, nitric oxide (NO) and prostaglandin E2 (PGE2). Oxidative stress and inflammation have been reported to be possible pathophysiological mechanisms underlying AD. In addition, the cholinergic hypothesis postulates that memory impairment in patient with AD is also associated with the deficit of cholinergic function in the brain. Although a number of drugs have been approved for the treatment of AD, most of these synthetic drugs have diverse side effects and yield relatively modest benefits. Marine algae have great potential in pharmaceutical and biomedical applications as they are valuable sources of bioactive properties such as anticoagulation, antimicrobial, antioxidative, anticancer and anti-inflammatory. Hence, this study aimed to provide an overview of the properties of Malaysian seaweeds (Padina australis, Sargassum polycystum and Caulerpa racemosa) in inhibiting oxidative stress, neuroinflammation and cholinesterase enzymes. These seaweeds significantly exhibited potent DPPH and moderate superoxide anion radical scavenging ability (P<0.05). Hexane and methanol extracts of S. polycystum exhibited the most potent radical scavenging ability with IC50 values of 0.157±0.004mg/ml and 0.849±0.02mg/ml for DPPH and ABTS assays, respectively. Hexane extract of C. racemosa gave the strongest superoxide radical inhibitory effect (IC50 of 0.386±0.01mg/ml). Most seaweed extracts significantly inhibited the production of cytokine (IL-6, IL-1 β, TNFα) and NO in a concentration-dependent manner without causing significant cytotoxicity to the lipopolysaccharide (LPS)-stimulated microglia cells (P<0.05). All extracts suppressed cytokine and NO level by more than 50% at the concentration of 0.4mg/ml. In addition, C. racemosa and S. polycystum also showed anti-acetylcholinesterase activities with the IC50 values ranging from 0.086-0.115 mg/ml. Moreover, C. racemosa and P. australis were also found to be active against butyrylcholinesterase with IC50 values ranging from 0.118- 0.287 mg/ml.

Keywords: Anticholinesterase, antioxidative, neuroinflammation, seaweeds.

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Authors: Seyeon Park, Mi Jang

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

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

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Authors: Simon Brown

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Glomerular filtration rate (GFR) is a measure of kidney function. It is usually estimated from serum concentrations of cystatin C or creatinine although there has been considerable debate in the literature about (i) the best equation to use and (ii) the variability in the correlation between the concentrations of creatinine and cystatin C. The equations for GFR can be written in a general form and from these I calculate the error of the GFR estimates associated with analyte measurement error. These show that the error of the GFR estimates is such that it is not possible to distinguish between the equations over much of the concentration range of either analyte. The general forms of the equations are also used to derive an expression for the concentration of cystatin C as a function of the concentration of creatinine. This equation shows that these analyte concentrations are not linearly related. Clinical reports of cystatin C and creatinine concentration are consistent with the expression derived.

Keywords: creatinine, cystatin C, error analysis, glomerularfiltration rate, measurement error.

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Authors: Praseeda Lekshmi.V, Dr.M.Sasikumar

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Facial recognition and expression analysis is rapidly becoming an area of intense interest in computer science and humancomputer interaction design communities. The most expressive way humans display emotions is through facial expressions. In this paper skin and non-skin pixels were separated. Face regions were extracted from the detected skin regions. Facial expressions are analyzed from facial images by applying Gabor wavelet transform (GWT) and Discrete Cosine Transform (DCT) on face images. Radial Basis Function (RBF) Network is used to identify the person and to classify the facial expressions. Our method reliably works even with faces, which carry heavy expressions.

Keywords: Face Recognition, Radial Basis Function, Gabor Wavelet Transform, Discrete Cosine Transform

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Authors: Neelima Gupta, Seema Aggarwal

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

Keywords: Biclustering, mutual information.

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Authors: Tze Sian Pui, Tushar Bansal, Patthara Kongsuphol, Sunil K. Arya

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We present a label-free biosensor based on electrochemical impedance spectroscopy for the detection of proinflammatory cytokine Tumor Necrosis Factor (TNF-α). Secretion of TNF-α has been correlated to the onset of various diseases including rheumatoid arthritis, Crohn-s disease etc. Gold electrodes were patterned on a silicon substrate and self assembled monolayer of dithiobis-succinimidyl propionate was used to develop the biosensor which achieved a detection limit of ~57fM. A linear relationship was also observed between increasing TNF-α concentrations and chargetransfer resistance within a dynamic range of 1pg/ml – 1ng/ml.

Keywords: Tumor necrosis factor, electrochemical impedance spectroscopy, label free, self assembled monolayer

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Authors: Elyse Sili, Jean Pascal Cambronne

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In aircraft applications, according to the nature of electrical equipment its location may be in unpressurized area or very close to the engine; thus, the environmental conditions may change from atmospheric pressure to less than 100 mbar, and the temperature may be higher than the ambient one as in most real working conditions of electrical equipment. Then, the classical Paschen curve has to be replotted since these parameters may affect the discharge ignition voltage. In this paper, we firstly investigate the domain of validity of two corrective expressions on the Paschen-s law found in the literature, in case of changing the air environment and known as Peek and Dunbar corrections. Results show that these corrections are no longer valid for combined variation of temperature and pressure. After that, a new empirical expression for breakdown voltage is proposed and is validated in the case of combined variations of temperature and pressure.

Keywords: Gas breakdown, gas density, Paschen curve, temperature effects

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Authors: Jing Lei, Yoram Vodovotz, Timothy R. Billiar

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To identify an endothelial cell-specific promoter suitable for vascular-specific targeting, we tested five promoters in vitro--Tie2SE, Tie2LE, ICAM2, Flt-1 and vWF--for promoter activity and specificity in endothelial cells, smooth muscle cells and non-vascular resident cells as well as tissues. These promoters, except for vWF, exhibited good endothelial activity and specificity in vitro. In a syngenic heart transplantation model, the ICAM2 promoter was variably functional in coronary endothelial cells of donor hearts. Thus, the ICAM2, Flt-1, Tie2SE and Tie2LE promoters hold promise for endothelial-specific targeting, but in vitro expression may not predict in vivo expression.

Keywords: vascular-specific targeting, endothelial cell-specificpromoter, endothelial specificity.

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Authors: Emine Tirali

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This article provides a conceptual framework of the freedom of media and its correlation with democracy. In a democracy, media should serve the publics’ right to know and reflect human rights violations and offer options for meaningful political choices and effective participation in civic affairs. On that point, the 2013 events at Gezi Park in Turkey are a good empirical example to be discussed. During the events, when self-censorship was broadly employed by mainstream Turkish media, social media filled the important role of providing information to the public. New technologies have made information into a fundamental tool for change and growth, and as a consequence, societies worldwide have merged into a single, interdependent, and autonomous organism. For this reason, violations of human rights can no longer be considered domestic issues, but rather global ones. Only global political action is an adequate response. Democracy depends on people shaping the society they live in, and in order to accomplish this, they need to express themselves. Freedom of expression is therefore necessary in order to understand diversity and differing perspectives, which in turn are necessary to resolve conflicts among people. Moreover, freedom of information is integral to freedom of expression. In this context, the international rules and laws regarding freedom of expression and freedom of information – indispensable for a free and independent media – are examined. These were put in place by international institutions such as the United Nations, UNESCO, the Council of Europe, and the European Union, which have aimed to build a free, democratic, and pluralist world committed to human rights and the rule of law. The methods of international human rights institutions depend on effective and frequent employment of mass media to relay human rights violations to the public. Therefore, in this study, the relationship between mass media and democracy, the process of how mass media forms public opinion, the problems of mass media, the neo-liberal theory of mass media, and the use of mass media by NGOs will be evaluated.

Keywords: Freedom of expression, democracy, public opinion, self-censorship.

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Authors: Tiancheng Lan

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E10A is a kind of replication-defective adenovirus which carries the human endostatin gene to inhibit the growth of tumors. Kringle 5(K5) has almost the same function as angiostatin to also inhibit the growth of tumors since they are all the byproduct of the proteolytic cleavage of plasminogen. Tumor size increasing can be suppressed because both of the endostatin and K5 can restrain the angiogenesis process. Therefore, in order to improve the treatment effect on tumor, 2A peptide is used to construct a fusion gene carrying both E10A and K5. Using 2A peptide is an ideal strategy when a fusion gene is expressed because it can avoid many problems during the expression of more than one kind of protein. The overlap extension PCR is also used to connect 2A peptide with E10A and K5. The final construction of fusion gene E10A-2A-K5 can provide a possible new method of the anti-angiogenesis treatment with a better expression performance.

Keywords: E10A, Kringle 5, 2A peptide, overlap extension PCR.

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Authors: Rafael Tedrus Bento

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The analysis of proportionality as a test is raised as a basic foundation for the achievement of Fundamental Rights. We used legal dogmatics and empirical analysis to seek the expected results, from the reading of the RV Oakes trial by the Supreme Court of Canada. In cases involving freedom of expression, two tests are used to resolve disputes. The first examines whether, in fact, the case can be characterized as a violation of freedom of expression; the second assesses whether this violation can be justified by the reasonable limit clause. This test was defined in the RV Oakes trial by the Supreme Court of Canada, concluding with the Oakes Test, used worldwide as a proportionality test. Resulting is a proportionality between the effects of the limiting measure and the objective - the more serious the harmful effects of a measure, the more important the objective must be.

Keywords: Oakes, proportionality. fundamental rights, Canadian Charter of Rights and Freedoms.

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Authors: Kobra Nalbandi, Bahram Baghban Kohnehrouz, Khalil Alami Saeed

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The low level of foreign genes expression in transgenic plants is a key factor that limits plant genetic engineering. Because of the critical regulatory activity of the promoters on gene transcription, they are studied extensively to improve the efficiency of the plant transgenic system. The strong constitutive promoters, such as CaMV 35S promoter and Ubiqutin 1 maize are usually used in plant biotechnology research. However the expression level of the foreign genes in all tissues is often undesirable. But using a strong seed-specific promoter to limit gene expression in the seed solves such problems. The purpose of this study is to isolate one of the seed specific promoters of Hordeum vulgare. So one of the common varieties of Hordeum vulgare in Iran was selected and their genomes extracted then the D-Hordein promoter amplified using the specific designed primers. Then the amplified fragment of the insert cloned in an appropriate vector and then transformed to E. coli. At last for the final admission of accuracy the cloned fragments sent for sequencing. Sequencing analysis showed that the cloned fragment DHPcontained motifs; like TATA box, CAAT-box, CCGTCC-box, AMYBOX1 and E-box etc., which constituted the seed-specific promoter activity. The results were compared with sequences existing in data banks. D-Hordein promoters of Alger has 99% similarity at 100 % coverage. The results also showed that D-Hordein promoter of barley and HMW promoter of wheat are too similar.

Keywords: Barley, Seed specific promoter, Hordein.

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Authors: Olga A. Berillo, Gaukhar K. Baidildinova, Аnatoliy Т. Ivashchenko

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Tumour suppressors are key participants in the prevention of cancer. Regulation of their expression through miRNAs is important for comprehensive translation inhibition of tumour suppressors and elucidation of carcinogenesis mechanisms. We studies the possibility of 1521 miRNAs to bind with 873 mRNAs of human tumour suppressors using RNAHybrid 2.1 and ERNAhybrid programmes. Only 978 miRNAs were found to be translational regulators of 812 mRNAs, and 61 mRNAs did not have any miRNA binding sites. Additionally, 45.9% of all miRNA binding sites were located in coding sequences (CDSs), 33.8% were located in 3' untranslated region (UTR), and 20.3% were located in the 5'UTR. MiRNAs binding with more than 50 target mRNAs and mRNAs binding with several miRNAs were selected. Hsa-miR-5096 had 15 perfectly complementary binding sites with mRNAs of 14 tumour suppressors. These newly indentified miRNA binding sites can be used in the development of medicines (anti-sense therapies) for cancer treatment.

Keywords: Exonic miRNA, intergenic miRNA, intronic miRNA, tumor suppressor.

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Authors: Olga V. Lebedinskaya, Irina N. Kabanovskaya, Anna S. Lasareva, Nelly K. Akhmatova, Anatoliy P. Godovalov, Andrey V. Horinko, Mikhail V. Kiselevsky

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The nature, prevalence, cellular composition of leukocyte infiltrates and immunohistochemical characteristics of their constituent cells in the liver of patients with chronic viral hepatitis B and C were investigated. It was found that the area of distribution and cellular composition of infiltrates depended on the virus type and process activity. The expediency of immunohistochemical study using leukocyte infiltrates from liver biopsies of patients with viral hepatitis aimed at clarifying diagnosis, making prognosis, and choice of optimal treatment with elements of immune correction is emphasized.

Keywords: Viral hepatitis, leukocyte infiltration, immunohistochemical characteristics, immunosupression.

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Authors: Ksheeraj Sai Vepuri, Nada Attar

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We as humans use words with accompanying visual and facial cues to communicate effectively. Classifying facial emotion using computer vision methodologies has been an active research area in the computer vision field. In this paper, we propose a simple method for facial expression recognition that enhances accuracy. We tested our method on the FER-2013 dataset that contains static images. Instead of using Histogram equalization to preprocess the dataset, we used Unsharp Mask to emphasize texture and details and sharpened the edges. We also used ImageDataGenerator from Keras library for data augmentation. Then we used Convolutional Neural Networks (CNN) model to classify the images into 7 different facial expressions, yielding an accuracy of 69.46% on the test set. Our results show that using image preprocessing such as the sharpening technique for a CNN model can improve the performance, even when the CNN model is relatively simple.

Keywords: Facial expression recognition, image pre-processing, deep learning, CNN.

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Authors: Nicoletta Adamo-Villani, Gerardo Beni, Jeremy White

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We introduce, a new interactive 3D simulation system of ocular motion and expressions suitable for: (1) character animation applications to game design, film production, HCI (Human Computer Interface), conversational animated agents, and virtual reality; (2) medical applications (ophthalmic neurological and muscular pathologies: research and education); and (3) real time simulation of unconscious cognitive and emotional responses (for use, e.g., in psychological research). The system is comprised of: (1) a physiologically accurate parameterized 3D model of the eyes, eyelids, and eyebrow regions; and (2) a prototype device for realtime control of eye motions and expressions, including unconsciously produced expressions, for application as in (1), (2), and (3) above. The 3D eye simulation system, created using state-of-the-art computer animation technology and 'optimized' for use with an interactive and web deliverable platform, is, to our knowledge, the most advanced/realistic available so far for applications to character animation and medical pedagogy.

Keywords: 3D animation, HCI, medical simulation, ocularmotion and expression.

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Authors: Anjali Haloi, Debabrata Das

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Silver nanoparticles inhibit a wide variety of microorganisms. The mechanism of inhibition is not entirely known although it is recognized to be concentration dependent and associated with the disruption of membrane permeability. Data on differential gene expression as a response to nanoparticles could provide insights into the mechanism of this inhibitory effect. Silver nanoparticles were synthesized in yeast growth media using a modification of the Creighton method and characterized with UV-Vis spectrophotometry, transmission electron microscopy (TEM), and X-ray diffraction (XRD). In yeasts grown in the presence of silver nanoparticles, we observed that at concentrations below the minimum inhibitory concentration (MIC) of 48.51 µg/ml, the total RNA content was steady while the cellular protein content declined rapidly. The analysis of the expression levels of KRR1 and PWP2, two important genes involved in rRNA maturation in yeasts, showed up to 258 and 42-fold decreases, respectively, compared to that of control samples. Whether silver nanoparticles have an adverse effect on ribosome assembly and function could be an area of further investigation.

Keywords: Ag NP, yeast, qRT-PCR, KRR1, PWP2.

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Authors: Urska Cvek, Marjan Trutschl, Randolph Stone II, Zanobia Syed, John L. Clifford, Anita L. Sabichi

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Expression data analysis is based mostly on the statistical approaches that are indispensable for the study of biological systems. Large amounts of multidimensional data resulting from the high-throughput technologies are not completely served by biostatistical techniques and are usually complemented with visual, knowledge discovery and other computational tools. In many cases, in biological systems we only speculate on the processes that are causing the changes, and it is the visual explorative analysis of data during which a hypothesis is formed. We would like to show the usability of multidimensional visualization tools and promote their use in life sciences. We survey and show some of the multidimensional visualization tools in the process of data exploration, such as parallel coordinates and radviz and we extend them by combining them with the self-organizing map algorithm. We use a time course data set of transitional cell carcinoma of the bladder in our examples. Analysis of data with these tools has the potential to uncover additional relationships and non-trivial structures.

Keywords: microarrays, visualization, parallel coordinates, radviz, self-organizing maps.

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Authors: T. Bovornvirakit, K. Viravaidya

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Acute kidney injury (AKI) is a new worldwide public health problem. A diagnosis of this disease using creatinine is still a problem in clinical practice. Therefore, a measurement of biomarkers responsible for AKI has received much attention in the past couple years. Cytokine interleukin-18 (IL-18) was reported as one of the early biomarkers for AKI. The most commonly used method to detect this biomarker is an immunoassay. This study used a planar platform to perform an immunoassay using fluorescence for detection. In this study, anti-IL-18 antibody was immobilized onto a microscope slide using a covalent binding method. Make-up samples were diluted at the concentration between 10 to 1000 pg/ml to create a calibration curve. The precision of the system was determined using a coefficient of variability (CV), which was found to be less than 10%. The performance of this immunoassay system was compared with the measurement from ELISA.

Keywords: Acute kidney injury, Acute renal failure, Antibody immobilization, Interleukin-18

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Authors: Chengming Li, Yong Yin, Peipei Guo, Xiaoli Liu

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Without taking account of the attribute richness of POI (point of interest) data and spatial distribution limited by roads, a POI generalization method considering both attribute information and spatial distribution has been proposed against the existing point generalization algorithm merely focusing on overall information of point groups. Hierarchical characteristic of urban POI information expression has been firstly analyzed to point out the measurement feature of the corresponding hierarchy. On this basis, an urban POI generalizing strategy has been put forward: POIs urban road network have been divided into three distribution pattern; corresponding generalization methods have been proposed according to the characteristic of POI data in different distribution patterns. Experimental results showed that the method taking into account both attribute information and spatial distribution characteristics of POI can better implement urban POI generalization in the mapping presentation.

Keywords: POI, Road network, spatial information expression, selection method, distribution pattern.

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Authors: G. Theonas, D. Hobbs, D. Rigas

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The scope of this research was to study the relation between the facial expressions of three lecturers in a real academic lecture theatre and the reactions of the students to those expressions. The first experiment aimed to investigate the effectiveness of a virtual lecturer-s expressions on the students- learning outcome in a virtual pedagogical environment. The second experiment studied the effectiveness of a single facial expression, i.e. the smile, on the students- performance. Both experiments involved virtual lectures, with virtual lecturers teaching real students. The results suggest that the students performed better by 86%, in the lectures where the lecturer performed facial expressions compared to the results of the lectures that did not use facial expressions. However, when simple or basic information was used, the facial expressions of the virtual lecturer had no substantial effect on the students- learning outcome. Finally, the appropriate use of smiles increased the interest of the students and consequently their performance.

Keywords: emotion, facial expression, smile, virtual educational environment, virtual learning, virtual lecturer.

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Authors: Fang Ye, Han Yu, Yibing Li

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Radio interference is one of the major concerns in using the global positioning system (GPS) for civilian and military applications. Interference signals are produced not only through all electronic systems but also illegal jammers. Among different types of interferences, continuous wave (CW) interference has strong adverse impacts on the quality of the received signal. In this paper, we make more detailed analysis for CW interference effects on GPS signal quality. Based on the C/A code spectrum lines, the influence of CW interference on the acquisition performance of GPS receivers is further analysed. This influence is supported by simulation results using GPS software receiver. As the most important user parameter of GPS receivers, the mathematical expression of bit error probability is also derived in the presence of CW interference, and the expression is consistent with the Monte Carlo simulation results. The research on CW interference provides some theoretical gist and new thoughts on monitoring the radio noise environment and improving the anti-jamming ability of GPS receivers.

Keywords: GPS, CW interference, acquisition performance, bit error probability, Monte Carlo.

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Authors: Frank Emmert-Streib, Matthias Dehmer

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Inferring the network structure from time series data is a hard problem, especially if the time series is short and noisy. DNA microarray is a technology allowing to monitor the mRNA concentration of thousands of genes simultaneously that produces data of these characteristics. In this study we try to investigate the influence of the experimental design on the quality of the result. More precisely, we investigate the influence of two different types of random single gene perturbations on the inference of genetic networks from time series data. To obtain an objective quality measure for this influence we simulate gene expression values with a biologically plausible model of a known network structure. Within this framework we study the influence of single gene knock-outs in opposite to linearly controlled expression for single genes on the quality of the infered network structure.

Keywords: Dynamic Bayesian networks, microarray data, structure learning, Markov chain Monte Carlo.

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Authors: M. Anidha, K. Premalatha

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Feature Selection is significant in order to perform constructive classification in the area of cancer diagnosis. However, a large number of features compared to the number of samples makes the task of classification computationally very hard and prone to errors in microarray gene expression datasets. In this paper, we present an innovative method for selecting highly informative gene subsets of gene expression data that effectively classifies the cancer data into tumorous and non-tumorous. The hybrid gene selection technique comprises of combined Mutual Information and Fisher score to select informative genes. The gene selection is validated by classification using Support Vector Machine (SVM) which is a supervised learning algorithm capable of solving complex classification problems. The results obtained from improved Mutual Information and F-Score with SVM as a classifier has produced efficient results.

Keywords: Gene selection, mutual information, Fisher score, classification, SVM.

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Authors: J. Franková, V. Pivodová, F. Růžička, J. Ulrichová

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An implant elicits a biological response in the surrounding tissue which determines the acceptance and long-term function of the implant. Dental implants have become one of the main therapy methods in clinic after teeth lose. A successful implant is in contact with bone and soft tissue represent by fibroblasts. In our study we focused on the interaction between six different chemically and physically modified titanium implants (Tis-MALP, Tis-O, Tis- OA, Tis-OPAAE, Tis-OZ, Tis-OPAE) with alveolar fibroblasts as well as with five type of microorganisms (S. epidermis, S.mutans, S. gordonii, S. intermedius, C.albicans). The analysis of microorganism adhesion was determined by CFU (colony forming unite) and biofilm formation. The presence of α3β1 and vinculin expression on alveolar fibroblasts was demonstrated using phospho specific cell based ELISA (PACE). Alveolar fibroblasts have the highest expression of these proteins on Tis-OPAAE and Tis-OPAE. It corresponds with results from bacterial adhesion and biofilm formation and it was related to the lowest production of collagen I by alveolar fibroblasts on Tis-OPAAE titanium disc.

Keywords: titanium disc, alveolar fibroblasts, microorganisms, adhesion

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

Abstract:

Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: E. N. Sathishkumar, K. Thangavel, T. Chandrasekhar

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Feature selection is a process to select features which are more informative. It is one of the important steps in knowledge discovery. The problem is that all genes are not important in gene expression data. Some of the genes may be redundant, and others may be irrelevant and noisy. Here a novel approach is proposed Hybrid K-Mean-Quick Reduct (KMQR) algorithm for gene selection from gene expression data. In this study, the entire dataset is divided into clusters by applying K-Means algorithm. Each cluster contains similar genes. The high class discriminated genes has been selected based on their degree of dependence by applying Quick Reduct algorithm to all the clusters. Average Correlation Value (ACV) is calculated for the high class discriminated genes. The clusters which have the ACV value as 1 is determined as significant clusters, whose classification accuracy will be equal or high when comparing to the accuracy of the entire dataset. The proposed algorithm is evaluated using WEKA classifiers and compared. The proposed work shows that the high classification accuracy.

Keywords: Clustering, Gene Selection, K-Mean-Quick Reduct, Rough Sets.

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Authors: Sadegh Lotfieblisofla, Arash Khodabakhshi

Abstract:

Tissue plasminogen activator (tPA) as a serine protease plays an important role in the fibrinolytic system and the dissolution of fibrin clots in human body. The production of this drug in plants such as tobacco could reduce its production costs. In this study, expression of tPA gene and protein targeting to different plant cell compartments, using various signal peptides has been investigated. For high level of expression, Kozak sequence was used after CaMV35S in the beginning of the gene. In order to design the final construction, Extensin, KDEL (amino acid sequence including Lys-Asp-Glu-Leu) and SP (γ-zein signal peptide coding sequence) were used as leader signals to conduct this protein into apoplast, endoplasmic reticulum and cytosol spaces, respectively. Cloned human tPA gene under the CaMV (Cauliflower mosaic virus) 35S promoter and NOS (Nopaline Synthase) terminator into pBI121 plasmid was transferred into tobacco explants by Agrobacterium tumefaciens strain LBA₄₄₀₄. The presence and copy number of genes in transgenic tobacco was proved by Southern blotting. Enzymatic activity of the rt-PA protein in transgenic plants compared to non-transgenic plants was confirmed by Zymography assay. The presence and amount of rt-PA recombinant protein in plants was estimated by ELISA analysis on crude protein extract of transgenic tobacco using a specific antibody. The yield of recombinant tPA in transgenic tobacco for SP, KDEL, Extensin signals were counted 0.50, 0.68, 0.69 microgram per milligram of total soluble proteins.

Keywords: Recombinant tissue plasminogen activator, plant cell comportment, leader signals, transgenic tobacco.

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