Search results for: Gene expression profiling

Authors: C. Kridtayopas, W. Danvilai, P. Sopannarath, A. Kayan, W. Loongyai

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Both Betong chicken (KU Line) and Thai Native chickens were the high quality of the meat and low carcass fat compared to broiler chickens. The objective of this study was to determine the growth performance, carcass characteristic, meat quality and association of polymorphism in the ApoVLDL-II gene with fat accumulation in the female broiler, Thai Native and Betong (KU line) chickens at 4-14 weeks. The chickens were used and reared under the same environment and management (100 chicks per breed). The results showed that body weight (BW) of broiler chickens was significantly higher than Thai Native and Betong (KU line) chickens (P < 0.01) through all the experiment. At 4-8 weeks of age, feed conversion ratio (FCR) of broiler chickens was significantly better than Thai Native and Betong (KU line) chickens (P < 0.01), then increased at week 8-14. The percentage of breast, abdominal fat and subcutaneous fat of broiler chickens was significantly greater than Thai Native and Betong (KU line) chickens (P < 0.01). However, Thai Native chickens showed the highest percentage of liver (P < 0.01) when compared to other breeds. In addition, the percentage of wing of Thai Native and Betong (KU line) chickens were significantly (P < 0.01) higher than broiler chickens. Meat quality was also determined and found that, pH of breast meat left from slaughter 45 minutes (pH45) and 24 hours (pH24) of broiler was significantly higher than Thai Native and Betong (KU line) (P < 0.01) whereas the percentage of drip loss, thawing loss, cooking loss and shear force was not significantly different between breeds. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to genotype the polymorphism in the ApoVLDL-II gene in the broiler, Thai Native and Betong (KU line) chickens. The results found that, the polymorphism in the ApoVLDL-II gene at VLDL6 loci was not associated with fat accumulation in those studied population.

Keywords: ApoVLDL-II Gene, Betong (KU line) chickens, broiler chickens, carcass characteristic, growth performance, meat quality, Thai Native Chickens.

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Authors: Ekaterina Y. Lukianova-Hleb, Dmitri O. Lapotko

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Cell processing techniques for gene and cell therapies use several separate procedures for gene transfer and cell separation or elimination, because no current technology can offer simultaneous multi-functional processing of specific cell sub-sets in heterogeneous cell systems. Using our novel on-demand nonstationary intracellular events instead of permanent materials, plasmonic nanobubbles, generated with a short laser pulse only in target cells, we achieved simultaneous multifunctional cell-specific processing with the rate up to 50 million cells per minute.

Keywords: Delivery, cell separation, graft, laser, plasmonic nanobubble, cell therapy, gold nanoparticle.

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

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We introduce a new interactive 3D simulator 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). Using state-of-the-art computer animation technology we have modeled and rigged a physiologically accurate 3D model of the eyes, eyelids, and eyebrow regions and we have 'optimized' it for use with an interactive and web deliverable platform. In addition, we have realized 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 simulator of eye motion and ocular expression is, to our knowledge, the most advanced/realistic available so far for applications in character animation and medical pedagogy.

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

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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: Atnaf Tiruneh Mulugeta, Mohammed Ali Hussein, Zelleke Habtamu

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Thirty six genotypes (8 parents and 28 F1 diallel crosses) were grown in randomized complete block design during 2006 at Mandura, North western Ethiopia. The experiment was executed to study the inheritance of two primary yield component traits: number of seeds per pod and 1000 seed weight. Statistical significant difference was observed between genotypes, parents, and crosses for these traits. The mean square due to GCA was significant for the two traits. However, SCA mean square was significant only for number of seeds per pod. Thus both additive and non-additive types of gene actions were important in the inheritance of number of seeds per pod. Significant b1 component was obtained for this trait. The b2 and b3 components, however, were not significant, suggesting the absence of gene asymmetry. From Wr/Vr graph, inheritance of seeds per pod was governed by partial dominance with additive gene action.

Keywords: Diallel crosses, General combining ability, Phaseolus vulgaris L., Specific combining ability

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Authors: P. S. Seboletswe, Z. Mkhize, L. M. Katata-Seru

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Protorhus longifolia is known as a medicinal plant that has been used traditionally to treat various ailments such as hemiplegic paralysis, blood clotting related diseases, diarrhoea, heartburn, etc. The study reports a High-Performance Thin Layer Chromatography (HPTLC) fingerprint profile of Protorhus longifolia methanolic extract and its qualitative analysis of gallic acid, rutin, and quercetin. HPTLC analysis was achieved using CAMAG HPTLC system equipped with CAMAG automatic TLC sampler 4, CAMAG Automatic Developing Chamber 2 (ADC2), CAMAG visualizer 2, CAMAG Thin Layer Chromatography (TLC) scanner and visionCATS CAMAG HPTLC software. Mobile phase comprising toluene, ethyl acetate, formic acid (21:15:3) was used for qualitative analysis of gallic acid and revealed eight peaks while the mobile phase containing ethyl acetate, water, glacial acetic acid, formic acid (100:26:11:11) for qualitative analysis of rutin and quercetin revealed six peaks. HPTLC sillica gel 60 F254 glass plates (10 × 10) were used as the stationary phase. Gallic acid was detected at the R_f = 0.35; while rutin and quercetin were not evident in the extract. Further studies will be performed to quantify gallic acid in Protorhus longifolia leaves and also identify other biomarkers.

Keywords: Biomarkers, fingerprint profiling, gallic acid, HPTLC, Protorhus longifolia.

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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: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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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: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: Gypsies, HK1, HSMN-Russe, rare disease.

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Authors: Wiriya Loongyai, Kiettisak Promphet, Nilubol Kangsukul, Ratchawat Noppha

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Polymerase chain reaction (PCR) assay and conventional microbiological methods were used to detect bacterial contamination of egg shells and egg content in different commercial housing systems, open house system and evaporative cooling system. A PCR assay was developed for direct detection using a set of primers specific for the invasion by A gene (invA) of Salmonella spp. PCR detected the presence of Salmonella in 2 samples of shell egg from the evaporative cooling system, while conventional cultural methods detected no Salmonella from the same samples.

Keywords: egg content, egg shell, invA gene, PCR, Salmonellaspp.

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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: Archana Panchapakesan Iyer, Taha Abdullah Kumosani

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Many high-risk pathogens that cause disease in humans are transmitted through various food items. Food-borne disease constitutes a major public health problem. Assessment of the quality and safety of foods is important in human health. Rapid and easy detection of pathogenic organisms will facilitate precautionary measures to maintain healthy food. The Polymerase Chain Reaction (PCR) is a handy tool for rapid detection of low numbers of bacteria. We have designed gene specific primers for most common food borne pathogens such as Staphylococci, Salmonella and E.coli. Bacteria were isolated from food samples of various food outlets and identified using gene specific PCRs. We identified Staphylococci, Salmonella and E.coli O157 using gene specific primers by rapid and direct PCR technique in various food samples. This study helps us in getting a complete picture of the various pathogens that threaten to cause and spread food borne diseases and it would also enable establishment of a routine procedure and methodology for rapid identification of food borne bacteria using the rapid technique of direct PCR. This study will also enable us to judge the efficiency of present food safety steps taken by food manufacturers and exporters.

Keywords: food borne pathogens, PCR, food safety, rapiddetection.

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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: 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: Fabian Horn, Reinhard Guthke

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In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Rosarin Rujananon, Poonsuk Prasertsan, Amornrat Phongdara, Tanate Panrat, Jibin Sun, Sugima Rappert, An-Ping Zeng

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In this study, a synthetic pathway was created by assembling genes from Clostridium butyricum and Escherichia coli in different combinations. Among the genes were dhaB1 and dhaB2 from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt) and its activator (GDHtAc), respectively, involved in the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene from E.coli BL21 was also included which codes for an NADPHdependent 1,3-propanediol oxidoreductase isoenzyme (PDORI) reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling analysis indicated that the conformation of fusion protein of YQHD and DHAB1 was favorable for direct molecular channeling of the intermediate 3-HPA. According to the simulation results, the yqhD and dhaB1 gene were assembled in the upstream of dhaB2 to express a fusion protein, yielding the recombinant strain E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing the recombinant enzymes simultaneously but in a non-fusion mode. This is the first report using a gene fusion approach to enhance the biological conversion of glycerol to the value added compound 1,3- PD.

Keywords: Recombinant E.coli, 1, 3-propanediol, glycerol, fusion protein.

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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: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

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A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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

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

Keywords: MicroRNA, mRNA, plant, superoxide dismutase.

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

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

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

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Authors: Seung Pil Pack

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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

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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: Bezuidt O., Lima-Mendez G., Reva O. N.

Abstract:

SeqWord Gene Island Sniffer, a new program for the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial genomes and further analyzed by sequence similarity and the functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome. php). The developed computer program and the database provide the information valuable for further investigation of the distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.

Keywords: mobile genetic elements, virulence, bacterial genomes

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Authors: Tahani Aljohani, Jialin Yu, Alexandra. I. Cristea

Abstract:

The more an educational system knows about a learner, the more personalised interaction it can provide, which leads to better learning. However, asking a learner directly is potentially disruptive, and often ignored by learners. Especially in the booming realm of MOOC Massive Online Learning platforms, only a very low percentage of users disclose demographic information about themselves. Thus, in this paper, we aim to predict learners’ demographic characteristics, by proposing an approach using linguistically motivated Deep Learning Architectures for Learner Profiling, particularly targeting gender prediction on a FutureLearn MOOC platform. Additionally, we tackle here the difficult problem of predicting the gender of learners based on their comments only – which are often available across MOOCs. The most common current approaches to text classification use the Long Short-Term Memory (LSTM) model, considering sentences as sequences. However, human language also has structures. In this research, rather than considering sentences as plain sequences, we hypothesise that higher semantic - and syntactic level sentence processing based on linguistics will render a richer representation. We thus evaluate, the traditional LSTM versus other bleeding edge models, which take into account syntactic structure, such as tree-structured LSTM, Stack-augmented Parser-Interpreter Neural Network (SPINN) and the Structure-Aware Tag Augmented model (SATA). Additionally, we explore using different word-level encoding functions. We have implemented these methods on Our MOOC dataset, which is the most performant one comparing with a public dataset on sentiment analysis that is further used as a cross-examining for the models' results.

Keywords: Deep learning, data mining, gender predication, MOOCs.

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Authors: Abtehal Y. Anaas, Mohd. Nazmi Bin Abd. Manap

Abstract:

Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p<0.05), whereas there were similar in the rates of cooking loss. The study confirms some previous results that the markers CAPN1 C7198A and G9950A were not significantly associated with the variation in meat tenderness in chickens. Therefore, further study is needed to confirm the functional molecular mechanism of these SNPs and evaluate their associations in different chicken populations.

Keywords: CAPNl, chicken, meat tenderness, meat quality, SNPs.

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

Abstract:

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

Abstract:

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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