Search results for: substance of expression

Authors: Mohamed A. Mahfouz, M. A. Ismail

Abstract:

Biclustering is a very useful data mining technique for identifying patterns where different genes are co-related based on a subset of conditions in gene expression analysis. Association rules mining is an efficient approach to achieve biclustering as in BIMODULE algorithm but it is sensitive to the value given to its input parameters and the discretization procedure used in the preprocessing step, also when noise is present, classical association rules miners discover multiple small fragments of the true bicluster, but miss the true bicluster itself. This paper formally presents a generalized noise tolerant bicluster model, termed as μBicluster. An iterative algorithm termed as BIDENS based on the proposed model is introduced that can discover a set of k possibly overlapping biclusters simultaneously. Our model uses a more flexible method to partition the dimensions to preserve meaningful and significant biclusters. The proposed algorithm allows discovering biclusters that hard to be discovered by BIMODULE. Experimental study on yeast, human gene expression data and several artificial datasets shows that our algorithm offers substantial improvements over several previously proposed biclustering algorithms.

Keywords: Machine learning, biclustering, bi-dimensional clustering, gene expression analysis, data mining.

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Authors: Fawzi Irshaid, Fatiha Dilmi, Khaled Tarawneh, Raji Hadeth, Adnan Jaran, Ahad Al-Khatib

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P16/INK4A is tumor suppressor protein that plays a critical role in cell cycle regulation. Loss of P16 protein expression has been implicated in pathogenesis of many cancers, including lymphoma. Therefore, we sought to investigate if loss of P16 protein expression is associated with lymphoma and/or any specific lymphoma subtypes (Hodgkin-s lymphoma (HL) and nonHodgkin-s lymphoma (NHL)). Fifty-five lymphoma cases consisted of 30 cases of HL and 25 cases of NHL, with an age range of 3 to 78 years, were examined for loss of P16 by immunohistochemical technique using a specific antibody reacting against P16. In total, P16 loss was seen in 33% of all lymphoma cases. P16 loss was identified in 47.7% of HL cases. In contrast, only 16% of NHL showed loss of P16. Loss of P16 was seen in 67% of HL patients with 50 years of age or older, whereas P16 loss was found in only 42% of HL patients with less than 50 years of age. P16 loss in HL is somewhat higher in male (55%) than in female (30%). In subtypes of HL, P16 loss was found exclusively in all cases of lymphocyte depletion, lymphocyte predominance and unclassified cases, whereas P16 loss was seen in 39% of mixed cellularity and 29% of nodular sclerosis cases. In low grade NHL patients, P16 loss was seen in approximately one-third of cases, whereas no or very rare of P16 loss was found in intermediate and high grade cases. P16 loss did not show any correlation with age or gender of NHL patients. In conclusion, the high rate of P16 loss seen in our study suggests that loss of P16 expression plays a critical role in the pathogenesis of lymphoma, particularly with HL.

Keywords: B-cells, immunostaining, P16 protein, Reed-Sternberg cells, tumors.

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Authors: Rezvan Najafi, Korosh Heydari, Massoud Saidijam

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5-FU is a chemotherapeutic agent that has been used in colorectal cancer (CRC) treatment. However, it is usually associated with the acquired resistance, which decreases the therapeutic effects of 5-FU. miR-200c is involved in chemotherapeutic drug resistance, but its mechanism is not fully understood. In this study, the effect of inhibition of miR-200c in sensitivity of HCT-116 CRC cells to 5-FU was evaluated. HCT-116 cells were transfected with LNA-anti- miR-200c for 48 h. mRNA expression of miR-200c was evaluated using quantitative real- time PCR. The protein expression of phosphatase and tensin homolog (PTEN) and E-cadherin were analyzed by western blotting. Annexin V and propidium iodide staining assay were applied for apoptosis detection. The caspase-3 activation was evaluated by an enzymatic assay. The results showed LNA-anti-miR-200c inhibited the expression of PTEN and E-cadherin protein, apoptosis and activation of caspase 3 compared with control cells. In conclusion, these results suggest that miR-200c as a prognostic marker can overcome to 5-FU chemoresistance in CRC.

Keywords: Colorectal cancer, miR-200c, 5-FU resistance, E-cadherin, PTEN.

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Authors: Yulia Irnidayanti, Win Darmanto, Agus Abadi

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research goal was to determine the expression levels cDNA of brain embrio at gestation days 10 (GD-10). The Electroforesis DNA results showed that GAPDH, Fibronectin1, Ncam1, Tenascin, Vimentin, Neurofilament heavy, Neurofilament medium and Neurofilament low were 447 bp, 462 bp, 293 bp. 416 bp, 327 bp, 301 bp, 398 bp and 289 bp. Result of real-time RT-PCR on brain Embryo at gestation days 10 showed that the expression of copy gen Fibronectin 36 copies, Ncam 21,708 copies; Tenascin 24,505 copies; Vimentin 538,554 copies; Neurofilament heavy 2,419 copies; Neurofilament medium 92,928 copies; Neurofilament low 125,809 copies. Vimentin expressed gene copies is very high compared with other gene copies. This condition are caused by Vimentin, that contribute to proliferate of brain development. The vimentin role to cell proliferation of brain.

Keywords: GAPDH, Fibronectin, Ncam, Tenascin, vimentin, Neurofilamen heavy, Neurofilament medium, Neurofilamen low.

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Authors: V. T. S. Dao, T. G. Etoh, C. Vo Le, H. D. Nguyen, K. Takehara, T. Akino, K. Nishi

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We present an explicit expression to estimate driving voltage attenuation through RC networks representation of an ultrahigh- speed image sensor. Elmore delay metric for a fundamental RC chain is employed as the first-order approximation. By application of dimensional analysis to SPICE simulation data, we found a simple expression that significantly improves the accuracy of the approximation. Estimation error of the resultant expression for uniform RC networks is less than 2%. Similarly, another simple closed-form model to estimate 50 % delay through fundamental RC networks is also derived with sufficient accuracy. The framework of this analysis can be extended to address delay or attenuation issues of other VLSI structures.

Keywords: Dimensional Analysis, Elmore model, RC network, Signal Attenuation, Ultra-High-Speed Image Sensor.

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Authors: Seo Young Kim, Tai Myong Choi

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The main goal of microarray experiments is to quantify the expression of every object on a slide as precisely as possible, with a further goal of clustering the objects. Recently, many studies have discussed clustering issues involving similar patterns of gene expression. This paper presents an application of fuzzy-type methods for clustering DNA microarray data that can be applied to typical comparisons. Clustering and analyses were performed on microarray and simulated data. The results show that fuzzy-possibility c-means clustering substantially improves the findings obtained by others.

Keywords: Clustering, microarray data, Fuzzy-type clustering, Validation

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Authors: Ghada Esheba, Fatimah Alturkistani, Arwa Obaid, Ahdab Bashehab, Moayad Alturkistani

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Introduction: Craniopharyngiomas (CPs) are rare epithelial tumors located mainly in the sellar/parasellar region. CPs have been classified histopathologically, genetically, clinically and prognostically into two distinctive subtypes: adamantinomatous and papillary variants. Aim: To examine the pattern of expression of both the β-catenin and epidermal growth factor receptor (EGFR) in surgically resected samples of adamantinomatous CP, and to asses for the possibility of using anti-EGFR in the management of ACP patients. Materials and methods: β-catenin and EGFR immunostaining was performed on paraffin-embedded tissue sections of 18 ACP cases. Result: 17 out of 18 cases (94%) of ACP exhibited strong nuclear/cytoplasmic expression of β-catenin, 15 (83%) of APC cases were positive for EGFR. Conclusion: Nuclear accumulation of β-catenin is a diagnostic hallmark of ACP. EGFR positivity in most cases of ACP could qualify the use of anti-EGFR therapy. 

Keywords: Craniopharyngioma, adamantinomatous, papillary, epidermal growth factor receptor, B-catenin.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

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The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Sukrit Shankar, Chetana Shanta Patsa, Jaydev Sharma

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Fractional Fourier Transform is a generalization of the classical Fourier Transform. The Fractional Fourier span in general depends on the amplitude and phase functions of the signal and varies with the transform order. However, with the development of the Fractional Fourier filter banks, it is advantageous in some cases to have different transform orders for different filter banks to achieve better decorrelation of the windowed and overlapped time signal. We present an expression that is useful for finding the perturbation in the Fractional Fourier span due to the erroneous transform order and the possible variation in the window shape and length. The expression is based on the dependency of the time-Fractional Fourier span Uncertainty on the amplitude and phase function of the signal. We also show with the help of the developed expression that the perturbation of span has a varying degree of sensitivity for varying degree of transform order and the window coefficients.

Keywords: Fractional Fourier Transform, Perturbation, Fractional Fourier span, amplitude, phase, transform order, filterbanks.

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Authors: Sanjaykumar R. Patel, Parth R. Kayastha

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α-lactose monohydrate is widely used in the pharmaceutical industries as an inactive substance that acts as a vehicle or a medium for a drug or other active substance. It is a byproduct of dairy industries, and the recovery of lactose from whey not only boosts the improvement of the economics of whey utilization but also causes a reduction in pollution as lactose recovery can reduce the BOD of whey by more than 80%. In the present study, levels of process parameters were kept as initial lactose concentration (30-50% w/w), sonication amplitude (20-40%), sonication time (2-6 hours), and crystallization temperature (10-20 ^oC) for the recovery of lactose in ultrasound assisted cooling crystallization. In comparison with cooling crystallization, the use of ultrasound enhanced the lactose recovery by 39.17% (w/w). The parameters were optimized for the lactose recovery using Taguchi Method. The optimum conditions found were initial lactose concentration at level 3 (50% w/w), amplitude of sonication at level 2 (40%), the sonication time at level 3 (6 hours), and crystallization temperature at level 1 (10 °C). The maximum recovery was found to be 85.85% at the optimum conditions. Sonication time and the initial lactose concentration were found to be significant parameters for the lactose recovery.

Keywords: Crystallization, Taguchi method, ultrasound, lactose.

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Authors: Hong Ding, Fatiha Benslimane, Isra Marei, Chris R. Triggle

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Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

Keywords: store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction

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Authors: Prasad Senadheera, Younousse Saidi, Frans JM Maathuis

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Rice seed expression (cDNA) library in the Lambda Zap 11® phage constructed from the developing grain 10-20 days after flowering was transformed into yeast for functional complementation assays in three salt sensitive yeast mutants S. cerevisiae strain CY162, G19 and Axt3K. Transformed cells of G19 and Axt3K with pYES vector with cDNA inserts showed enhance tolerance than those with empty pYes vector. Sequencing of the cDNA inserts revealed that they encode for the putative proteins with the sequence homologous to rice putative protein PROLM24 (Os06g31070), a prolamin precursor. Expression of this cDNA did not affect yeast growth in absence of salt. Axt3k and G19 strains expressing the PROLM24 were able to grow upto 400 mM and 600 mM of NaCl respectively. Similarly, Axt3k mutant with PROLM24 expression showed comparatively higher growth rate in the medium with excess LiCl (50 mM). The observation that expression of PROLM24 rescued the salt sensitive phenotypes of G19 and Axt3k indicates the existence of a regulatory system that ameliorates the effect of salt stress in the transformed yeast mutants. However, the exact function of the cDNA sequence, which shows partial sequence homology to yeast UTR1 is not clear. Although UTR1 involved in ferrous uptake and iron homeostasis in yeast cells, there is no evidence to prove its role in Na+ homeostasis in yeast cells. Absence of transmembrane regions in Os06g31070 protein indicates that salt tolerance is achieved not through the direct functional complementation of the mutant genes but through an alternative mechanism.

Keywords: Rice seed expression, salt stress, prolamin, salinitytolerance, Oryza sativa

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Authors: M. Mikusova

Abstract:

Thanks to the interdisciplinary nature of crises, the position of researchers in that field is rather difficult. Very often the traditional methods of research cannot be applied there. The article is aimed at the changes in crises research. It describes the substance of individual changes and emphasizes the shift in research approaches to the crisis.

Keywords: crisis, change, research

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Authors: Yungeng Xie, Cong Liu, Yi Liu, Xuanao Wan

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The study aims to explore microblog users’ emotion expression and sharing behaviors on the Chinese microblog (Weibo). The first theme of study analyzed whether microblog emotions impact readers’ message sharing behaviors, specifically, how the strength of emotion (positive and negative) in microblog messages facilitate/inhibit readers’ sharing behaviors. The second theme compared the differences among the three types of microblog users (i.e., verified enterprise users, verified individual users and unverified users) in terms of their profiles and microblog behaviors. A total of 7114 microblog messages about 24 hot public events in China were sampled from Sina Weibo. The first study results show that strength of negative emotions that microblog messages carry significantly increase the possibility of the message being shared. The second study results indicate that there are significant differences across the three types of users in terms of their emotion expression and its influence on microblog behaviors.

Keywords: Microblog, emotion expression, information diffusion.

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Authors: Kittiwann Nimkerdphol, Masahiro Nakagawa

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Biological reactions of individuals of a testing animal to toxic substance are unique and can be used as an indication of the existing of toxic substance. However, to distinguish such phenomenon need a very complicate system and even more complicate to analyze data in 3 dimensional. In this paper, a system to evaluate in vitro biological activities to acute toxicity of stochastic self-affine non-stationary signal of 3D goldfish swimming by using fractal analysis is introduced. Regular digital camcorders are utilized by proposed algorithm 3DCCPC to effectively capture and construct 3D movements of the fish. A Critical Exponent Method (CEM) has been adopted as a fractal estimator. The hypothesis was that the swimming of goldfish to acute toxic would show the fractal property which related to the toxic concentration. The experimental results supported the hypothesis by showing that the swimming of goldfish under the different toxic concentration has fractal properties. It also shows that the fractal dimension of the swimming related to the pH value of FD Ôëê 0.26pH + 0.05. With the proposed system, the fish is allowed to swim freely in all direction to react to the toxic. In addition, the trajectories are precisely evaluated by fractal analysis with critical exponent method and hence the results exhibit with much higher degree of confidence.

Keywords: 3D locomotion, bioassay, critical exponent method, CEM, fractal analysis, goldfish.

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Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

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Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: Ahmad R. Naghsh-Nilchi, Mohammad Roshanzamir

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One of the popular methods for recognition of facial expressions such as happiness, sadness and surprise is based on deformation of facial features. Motion vectors which show these deformations can be specified by the optical flow. In this method, for detecting emotions, the resulted set of motion vectors are compared with standard deformation template that caused by facial expressions. In this paper, a new method is introduced to compute the quantity of likeness in order to make decision based on the importance of obtained vectors from an optical flow approach. For finding the vectors, one of the efficient optical flow method developed by Gautama and VanHulle[17] is used. The suggested method has been examined over Cohn-Kanade AU-Coded Facial Expression Database, one of the most comprehensive collections of test images available. The experimental results show that our method could correctly recognize the facial expressions in 94% of case studies. The results also show that only a few number of image frames (three frames) are sufficient to detect facial expressions with rate of success of about 83.3%. This is a significant improvement over the available methods.

Keywords: Facial expression, Facial features, Optical flow, Motion vectors.

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Authors: Seung Pil Pack

Abstract:

Carbonic anhydrases (CAs) has been focused as biological catalysis for CO2 sequestration process because it can catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized sequence of α type-CA cloned from Duneliala species. (DsCAopt) was constructed, expressed, and characterized. The expression level in E. coli BL21(DE3) was better for codon-optimized DsCAopt than intact sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH 7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt enzyme can catalyze well the conversion of CO2 to CaCO3, as the calcite form.

Keywords: Carbonic anhydrase, Codon-optimization, Duneliala species, CO2 sequestration

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Authors: Md. Zahangir Alom, Mei-Lan Piao, Md. Ashraful Alam, Nam Kim, Jae-Hyeung Park

Abstract:

A new approach for facial expressions recognition based on face context and adaptively weighted sub-pattern PCA (Aw-SpPCA) has been presented in this paper. The facial region and others part of the body have been segmented from the complex environment based on skin color model. An algorithm has been proposed to accurate detection of face region from the segmented image based on constant ratio of height and width of face (δ= 1.618). The paper also discusses on new concept to detect the eye and mouth position. The desired part of the face has been cropped to analysis the expression of a person. Unlike PCA based on a whole image pattern, Aw-SpPCA operates directly on its sub patterns partitioned from an original whole pattern and separately extracts features from them. Aw-SpPCA can adaptively compute the contributions of each part and a classification task in order to enhance the robustness to both expression and illumination variations. Experiments on single standard face with five types of facial expression database shows that the proposed method is competitive.

Keywords: Aw-SpPC, Expressoin Recognition, Face context, Face Detection, PCA

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Authors: R. Sutjiati, Rubianto, I. B. Narmada, I. K. Sudiana, R. P. Rahayu

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The prevalence of post-treatment relapse in orthodontics in the community is high enough; therefore, relapses in orthodontic treatment must be prevented well. The aim of this study is to experimentally test the inhibition of relapse of orthodontics tooth movement in NaF of expression TGF-β1, Runx2, alkaline phosphatase (ALP) and microscopic of woven bone. The research method used was experimental laboratory research involving 30 rats, which were divided into three groups. Group A: rats were not given orthodontic tooth movement and without NaF. Group B: rats were given orthodontic tooth movement and without 11.5 ppm by topical application. Group C: rats were given orthodontic tooth movement and 11.75 ppm by topical application. Orthodontic tooth movement was conducted by applying ligature wires of 0.02 mm in diameter on the molar-1 (M-1) of left permanent maxilla and left insisivus of maxilla. Immunohistochemical examination was conducted to calculate the number of osteoblast to determine TGF β1, Runx2, ALP and haematoxylin to determine woven bone on day 7 and day 14. Results: It was shown that administrations of Natrium Fluoride topical application proved effective to increase the expression of TGF-β1, Runx2, ALP and to increase woven bone in the tension area greater than administration without natrium fluoride topical application (p < 0.05), except the expression of ALP on day 7 and day 14 which was significant. The results of the study show that NaF significantly increases the expressions of TGF-β1, Runx2, ALP and woven bone. The expression of the variables enhanced on day 7 compared on that on day 14, except ALP. Thus, it can be said that the acceleration of woven bone occurs on day 7.

Keywords: TGF-β1, Runx2, ALP, woven bone, natrium fluoride.

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Authors: Taeung Yoon, Dahae Chong, Sangho Ahn, Seokho Yoon

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In a chirp spread spectrum (CSS) system, the overlap technique is used for increasing bit rate. More overlaps can offer higher data throughput; however, they may cause more intersymbol interference (ISI) at the same time, resulting in serious bit error rate (BER) performance degradation. In this paper, we perform the BER analysis and derive a closed form BER expression for the overlap-based CSS system. The derived BER expression includes the number of overlaps as a parameter, and thus, would be very useful in determining the number of overlaps for a specified BER. The numerical results demonstrate that the BER derived in a closed form closely agrees with the simulated BER.

Keywords: CSS, DM, chirp, overlap.

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Authors: Luminiţa Duţică

Abstract:

For the music composer Myriam Marbe the musical time and memory represent 2 (complementary) phenomena with conclusive impact on the settlement of new musical ontologies. Summarizing the most important achievements of the contemporary techniques of composition, her vision on the microform presented in The Concert for Daniel Kientzy, saxophone and orchestra transcends the linear and unidirectional time in favour of a flexible, multivectorial speech with spiral developments, where the sound substance is auto(re)generated by analogy with the fundamental processes of the memory. The conceptual model is of an archetypal essence, the music composer being concerned with identifying the mechanisms of the creation process, especially of those specific to the collective creation (of oral tradition). Hence the spontaneity of expression, improvisation tint, free rhythm, micro-interval intonation, coloristictimbral universe dominated by multiphonics and unique sound effects, hence the atmosphere of ritual, however purged by the primary connotations and reprojected into a wonderful spectacular space. The Concert is a work of artistic maturity and enforces respect, among others, by the timbral diversity of the three species of saxophone required by the music composer (baritone, sopranino and alt), in Part III Daniel Kientzy shows the performance of playing two saxophones concomitantly. The score of the music composer Myriam Marbe contains a deeply spiritualized music, full or archetypal symbols, a music whose drama suggests a real cinematographic movement.

Keywords: Archetype, chronogenesis, concert, multiphonics.

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Authors: Ahmad Ali Shahid, Muhammad Shakil Shaukat, Kamran Shehzad Bajwa, Abdul Qayyum Rao, Tayyab Husnain

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Agriculture is the backbone of economy of Pakistan and cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat severe problems of insect and weed, combination of three genes namely Cry1Ac, Cry2A and EPSPS genes was transferred in locally cultivated cotton variety MNH-786 with the use of Agrobacterium mediated genetic transformation. The present study focused on the molecular screening of transgenic cotton plants at T3 generation in order to confirm integration and expression of all three genes (Cry1Ac, Cry2A and EPSP synthase) into the cotton genome. Initially, glyphosate spray assay was used for screening of transgenic cotton plants containing EPSP synthase gene at T3 generation. Transgenic cotton plants which were healthy and showed no damage on leaves were selected after 07 days of spray. For molecular analysis of transgenic cotton plants in the laboratory, the genomic DNA of these transgenic cotton plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty (Cry1Ac gene), ten out of twenty (Cry2A gene) and all twenty (EPSP synthase gene) were produced positive amplification. On the base of PCR amplification, ten transgenic plant samples were subjected to protein expression analysis through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the mRNA expression levels of Cry1Ac and EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes at T3 generation.

Keywords: Agriculture, Cotton, Transformation, Cry Genes, ELISA and PCR.

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Authors: M R Asadi, G Torkaman, M Hedayati

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We evaluated the effect of sensory (direct current (DC), 600μA) and motor (monophasic current, pulse duration 300μs, 100 Hz, 2.5-3mA) intensities of cathodal electrical stimulation (ES) current to release VEGF and biomechanical properties of wound. 54 male Sprague-dawley rats were randomly assigned into one control and two experimental groups. A full thickness skin incision was made on animals- dorsal region. The experimental groups received ES for 1h/day and every other day. VEGF expression was measured in skin on the 7th day after surgical incision and tensile strength was measured on 21st day. On the 7th day, the values of skin VEGF in the sensory group were significantly greater than those of the other groups (p < 0.05). Sensory and Motor intensity stimulation, can not improve the biomechanical properties of the repaired wounds. It seems the mechanical environment induced by sensory and motor intensity of electrical stimulation, could not simulate the role of normal daily stress and strain to maturation of collagen fibers and their cross links. Further work is needed to determine the relationship between VEGF expression after ES and its effect on tensile strength of healed wound.

Keywords: Biomechanical properties Direct current, Monophasic current, Skin, VEGF

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Authors: Ankit Agrawal, Ankush Mittal

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A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial and challenging problems in Bioinformatics. Most work done so far either assumes that there is no time delay in gene regulation or there is a constant time delay. We here propose a Dynamic Time- Lagged Correlation Based Method (DTCBM) to learn the gene networks, which uses time-lagged correlation to find the potential gene interactions, and then uses a post-processing stage to remove false gene interactions to common parents, and finally uses dynamic correlation thresholds for each gene to construct the gene network. DTCBM finds correlation between gene expression signals shifted in time, and therefore takes into consideration the multi time delay relationships among the genes. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae gene expression data and comparison with other methods indicate that it has a better performance.

Keywords: Activators, correlation, dynamic time-lagged correlation based method, inhibitors, multi-time delay gene network.

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Authors: Tzyy Rong Jinn, Nguyen Tiep Khac, Tzong Yuan Wu

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Highly pathogenic avian influenza (HPAI) H5N1 viruses have created demand for a cost-effective vaccine to prevent a pandemic of the disease. Here, we report that Trichoplusia ni (T. ni) larvae can act as a cost-effective bioreactor to produce recombinant HA5 (rH5HA) proteins as an potential effective vaccine for chickens. To facilitate the recombinant virus identification, virus titer determination and access the infected larvae, we employed the internal ribosome entry site (IRES) derived from Perina nuda virus (PnV, belongs to insect picorna like Iflavirus genus) to construct a bi-cistronic baculovirus expression vector that can express the rH5HA protein and enhanced green fluorescent protein (EGFP) simultaneously. Western blot analysis revealed that the 70 kDa rH5HA protein and partially cleaved products (40 kDa H5HA1) were generated in T. ni larvae infected with recombinant baculovirus carrying the H5HA gene. These data suggest that the baculovirus-larvae recombinant protein expression system could be a cost-effective platform for H5N1 vaccine production.

Keywords: Avian Influenza, baculovirus, hemagglutinin, Trichoplusia ni larvae

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Authors: S. M. M. Syairah, M. H. Rajikin, A-R. Sharaniza

Abstract:

Several embryonic cellular mechanism including cell cycle, growth and apoptosis are regulated by phosphatidylinositol-3- kinase (PI3K)/Akt signaling pathway. The goal of present study is to determine the effects of annatto (Bixa orellana)-derived δ-tocotrienol (δ-TCT) on the regulations of PI3K/Akt genes in murine morula. Twenty four 6-8 week old (23-25g) female balb/c mice were randomly divided into four groups (G1-G4; n=6). Those groups were subjected to the following treatments for 7 consecutive days: G1 (control) received tocopherol stripped corn oil, G2 was given 60 mg/kg/day of δ-TCT mixture (contains 90% delta & 10% gamma isomers), G3 was given 60 mg/kg/day of pure δ-TCT (>98% purity) and G4 received 60 mg/kg/day α-TOC. On Day 8, females were superovulated with 5 IU Pregnant Mare’s Serum Gonadotropin (PMSG) for 48 hours followed with 5 IU human Chorionic Gonadotropin (hCG) before mated with males at the ratio of 1:1. Females were sacrificed by cervical dislocation for embryo collection 48 hours post-coitum. About fifty morulas from each group were used in the gene expression analyses using Affymetrix QuantiGene Plex 2.0 Assay. Present data showed a significant increase (p<0.05) in the average number (mean + SEM) of morula produced in G2 (27.32 + 0.23), G3 (25.42 + 0.21) and G4 (27.21 + 0.34) compared to control group (G1 – 14.61 + 0.25). This is parallel with the high expression of PDK1 gene with increase of 2.75-fold (G2), 3.07-fold (G3) and 3.59-fold (G4) compared to G1. From the present data, it can be concluded that supplementation with δ-TCT(s) and α-TOC induced high expression of PDK1 in G2-G4 which enhanced the PI3K/Akt signaling activity, resulting in the increased number of morula.

Keywords: Embryonic development, morula, nicotine, vitamin E.

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

Abstract:

Gastric Cancer (GC) has high morbidity and fatality rate in various countries. It is still one of the most frequent and deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes are highly expressed in the normal stomach epithelium and play important roles in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age. They were investigated with gene expression analysis and mutation screening by monitoring RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of gastrokines inactivation. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age, or cancer type of patients. Reduced of gastrokine genes seem to occur at the initial steps of gastric cancer development.

Keywords: Diagnostic biomarker, gastric cancer, nucleotide sequencing, semi-quantitative RT-PCR.

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Authors: U. Kairov, T. Karpenyuk, E. Ramanculov, A. Zinovyev

Abstract:

The most common result of analysis of highthroughput data in molecular biology represents a global list of genes, ranked accordingly to a certain score. The score can be a measure of differential expression. Recent work proposed a new method for selecting a number of genes in a ranked gene list from microarray gene expression data such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. Here we present calculation results of relative connectivity of genes from META-OFTEN network and tentative biological interpretation of the most reproducible signal. The relative connectivity and inbetweenness values of genes from META-OFTEN network were estimated.

Keywords: Microarray, META-OFTEN, gene network.

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Authors: Nelly К. Akhmatova, Оlga V. Lebedinskaya, Stanislav G. Markushin, Elvin А. Akhmatov, Lidiya A. Geiderova, Еlena А. Lebedinskaya, Vera M. Axenova, Аnatoliy P. Godovalov

Abstract:

The study of cytokine expression in mice under the influence of inactivated poliovirus and Imovaks polio vaccine in combination with derivatives of chitosan shows various kinds of processes. There is a significant increase in IL-12 in the serum of immunized animals, which should stimulate the production of IFN-γ NK-cells and T-cells and polarize the immune response to Th1 type. Thus, the derivatives of chitosan can promote cell component of the immune response, providing a full antiviral immunity.

Keywords: Poliovirus, chitosan, cytokine expression, antiviral immunity.

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