Search results for: protein expression

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: N. Cetinkaya, N. H. Ozdemir

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The aim of the study was to investigate the effect of Saccharomyces cerevisiae (SC) live yeast culture on microbial protein supply to small intestine in Kivircik male yearlings when fed with different ratio of forage and concentrate diets. Four Kivircik male yearlings with permanent rumen canula were used in the experiment. The treatments were allocated to a 4x4 Latin square design. Diet I consisted of 70% alfalfa hay and 30% concentrate, Diet II consisted of 30% alfalfa hay and 70% concentrate, Diet I and II were supplemented with a SC. Daily urine was collected and stored at -20°C until analysis. Calorimetric methods were used for the determination of urinary allantoin and creatinine levels. The estimated microbial N supply to small intestine for Diets I, I+SC, II and II+SC were 2.51, 2.64, 2.95 and 3.43 g N/d respectively. Supplementation of Diets I and II with SC significantly affected the allantoin levels in μmol/W0.75 (p<0.05). Mean creatinine values in μmol/W0.75 and allantoin:creatinine ratios were not significantly different among diets. In conclusion, supplementation with SC live yeast culture had a significant effect on urinary allantoin excretion and microbial protein supply to small intestine in Kivircik yearlings fed with high concentrate Diet II (P<0.05). Hence urinary allantoin excretion may be used as a tool for estimating microbial protein supply in Kivircık yearlings. However, further studies are necessary to understand the metabolism of Saccharomyces cerevisiae live yeast culture with different forage:concentrate ratio in Kıvırcık Yearlings.

Keywords: Allantoin, creatinine, Kivircik yearling, microbial nitrogen, Saccharomyces cerevisiae.

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Authors: Mohamed A. Ahmed, Lydia J. Campbell

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The fortified of soft wheat flour with cowpea flour in bread making was investigated. The Soft wheat flour (SWF) was substituted by cowpea flour at levels of 5, 15 and 20%. The protein content of composite breads ranged from 6.1 – 9.9%. Significant difference was observed in moisture, protein and crude fibre contents of control (wheat bread) and composite bread at 5% addition of cowpea. Water absorption capacities of composite flours increased with increasing levels of cowpea flour in the blend. The specific loaf volume decreased significantly with increased cowpea content of blends. The overall acceptability of the 5% cowpea flour content of composite bread was not significantly different from the control (Soft Wheat-bread) but there is significantly different with increasing the levels of cowpea flour in the blend more than 5%.

Keywords: Cowpea flour, wheat flour, baking properties, sensory quality.

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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: V. R. Ahire, A. Kumar, B. N. Pandey, K. P. Mishra, G. R. Kulkarni

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Radiation therapy is an effective vital strategy used globally in the treatment of cervical cancer. However, radiation efficacy principally depends on the radiosensitivity of the tumor, and not all patient exhibit significant response to irradiation. A radiosensitive tumor is easier to cure than a radioresistant tumor which later advances to local recurrence and metastasis. Herbal polyphenols are gaining attention for exhibiting radiosensitization through various signaling. Current work focuses to study the radiosensitization effect of ellagic acid (EA), on HeLa cells. EA intermediated radiosensitization of HeLa cells was due to the induction γ-H2AX foci formation, G1 phase cell cycle arrest, and loss of reproductive potential, growth inhibition, drop in the mitochondrial membrane potential and protein expression studies that eventually induced apoptosis. Irradiation of HeLa in presence of EA (10 μM) to doses of 2 and 4 Gy γ-radiation produced marked tumor cytotoxicity. EA also demonstrated radio-protective effect on normal cell, NIH3T3 and aided recovery from the radiation damage. Our results advocate EA to be an effective adjuvant for improving cancer radiotherapy as it displays striking tumor cytotoxicity and reduced normal cell damage instigated by irradiation.

Keywords: Apoptotic radiosensitivity, ellagic acid, mitochondrial potential, cell-cycle arrest.

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Authors: Kasra Afsahi, Maryam Soheilifar

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Cerebrovascular accident (CVA) is a neurological side effect of COVID-19 disease wit high rate in pandemics. Effect of COVID-19 disease on disorder is unclear. In this cohort, patients with COVID-19 disease were assessed. 60 CVA cases were assessed in a referral hospital in 2020. The major factor was mortality and the cases were those with and without death. The groups were compared for all features about mortality in the patients with COVID-19 and CVA. Totally 23 out of 60 cases (38.3%) were expired. In univariate analysis there was significant association for death by ischemic heart disease (P = 0.015), high-severity stroke (P = 0.012), high C-reactive protein (CRP) (P = 0.001), high ESR (P = 0.009), pleural effusion (P = 0.005), pericardial effusion (P = 0.027), cardiomegaly (P = 0.005), ground glass opacity (P = 0.001), and consolidation (P = 0.001). Among these factors, there was significant association only for CRP (P = 0.001) and consolidation (P = 0.003) in multivariate analysis. Mortality in the cases with COVID-19-related CVA is one-third and it has relationship to elevated CRP and finding the consolidation in the computerized tomography scan of the lungs.

Keywords: COVID-19, stroke, prognosis, C-reactive protein, CRP.

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Authors: M. Nosik, I. Rymanova, N. Adamovich, S. Sevostyanihin, K. Ryzhov, Y. Kuimova, A. Kravtchenko, N. Sergeeva, A. Sobkin

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HIV and Tuberculosis (TB) infections each speed the other's progress. HIV-infection increases the risk of TB disease. At the same time, TB infection is associated with clinical progression of HIV-infection. HIV+TB co-infected patients are also at higher risk of acquiring new opportunistic infections. An important feature of disease progression and clinical outcome is the innate and acquired immune responses. HIV and TB, however, have a spectrum of dysfunctions of the immune response. As cytokines play a crucial role in the immunopathology of both infections, it is important to study immune interactions in patients with dual infection HIV+TB. Plasma levels of proinflammatory cytokines IL-2, IFN-γ and immunoregulating cytokines IL-4, IL-10 were evaluated in 75 patients with dual infection HIV+TB, 58 patients with HIV monoinfection and 50 patients with TB monoinfection who were previously naïve for HAART. The decreased levels of IL-2, IFN-γ, IL-4 and IL-10 were observed in patients with dual infection HIV+TB in comparison with patients who had only HIV or TB which means the profound suppression of Th1 and Th2 cytokine secretion. Thus, those cytokines could possibly serve as immunological markers of progression of HIV-infection in patients with TB.

Keywords: HIV, Tuberculosis, TB, HIV associated with TB, Th1/ Th2 cytokine expression.

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Authors: P. M. Ikonić, T. A. Tasić, L. S. Petrović, S. B. Škaljac, M. R. Jokanović, V. M. Tomović, B. V. Šojić, N. R. Džinić, A. M. Torbica, B. B. Ikonić

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The aim of the study was to determine how different ripening processes (traditional vs. industrial) influenced the proteolysis in traditional Serbian dry-fermented sausage Petrovská klobása. The obtained results indicated more intensive pH decline (0.7 units after 9 days) in industrially ripened products (I), what had a positive impact on drying process and proteolytic changes in these samples. Thus, moisture content in I sausages was lower at each sampling time, amounting 24.7% at the end of production period (90 days). Likewise, the process of proteolysis was more pronounced in I samples, resulting in higher contents of non-protein nitrogen (NPN) and free amino acids nitrogen (FAAN), as well as in faster and more intensive degradation of myosin (≈220 kDa), actin (≈45 kDa) and other polypeptides during processing. Consequently, the appearance and accumulation of several protein fragments were registered.

Keywords: Dry-fermented sausage, Petrovská klobása, proteolysis, ripening process.

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Authors: Mustafa Salman, Nurcan Cetinkaya, Zehra Selcuk, Bugra Genc

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The objectives of the present study were to estimate the microbial-N flow to the small intestine and to predict the digestible organic matter intake (DOMI) in grazing Karayaka sheep based on urinary excretion of purine derivatives (xanthine, hypoxanthine, uric acid, and allantoin) by the use of spot urine sampling under field conditions. In the trial, 10 Karayaka sheep from 2 to 3 years of age were used. The animals were grazed in a pasture for ten months and fed with concentrate and vetch plus oat hay for the other two months (January and February) indoors. Highly significant linear and cubic relationships (P<0.001) were found among months for purine derivatives index, purine derivatives excretion, purine derivatives absorption, microbial-N and DOMI. Through urine sampling and the determination of levels of excreted urinary PD and Purine Derivatives / Creatinine ratio (PDC index), microbial-N values were estimated and they indicated that the protein nutrition of the sheep was insufficient.

In conclusion, the prediction of protein nutrition of sheep under the field conditions may be possible with the use of spot urine sampling, urinary excreted PD and PDC index. The mean purine derivative levels in spot urine samples from sheep were highest in June, July and October. Protein nutrition of pastured sheep may be affected by weather changes, including rainfall. Spot urine sampling may useful in modeling the feed consumption of pasturing sheep. However, further studies are required under different field conditions with different breeds of sheep to develop spot urine sampling as a model.

Keywords: Karayaka sheep, spot sampling, urinary purine derivatives, PDC index, microbial-N, feed intake.

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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: Laima Silina, Ilze Gramatina, Lija Dukalska, Liga Skudra, Tatjana Rakcejeva, Dace Klava, Anita Blija

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The objective of the present study was to determine quality parameters changes of red wine marinade marinated venison during storage. Beef as a control was analysed. Protein, fat, moisture and pH content dynamics as well microbiological quality was analyzed. The meat pieces were marinated in red wine marinade at 4±2ºC temperature for 48±1h. Marinated meat was placed in polypropylene trays, hermetically sealed with high barrier polymer film Multibarrier 60 under modified atmosphere (CO₂ 40%+N₂ 60%) without and with oxygen absorber sachets, as a control packaging in air ambiance packed marinated venison and beef was used. Meat samples were analyzed after 0, 4, 7, 11 and 14 days of storage. During the storage of meat, protein and moisture content significantly (p<0.05) decreased, pH and colony forming units significantly (p<0.05) increased, fat content does not change in all treatments irrespective of the packaging method.

Keywords: Marinating, modified atmosphere, quality, venison.

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Authors: P.Varzakas

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In this paper, an accurate theoretical analysis for the achievable average channel capacity (in the Shannon sense) per user of a hybrid cellular direct-sequence/fast frequency hopping code-division multiple-access (DS/FFH-CDMA) system operating in a Rayleigh fading environment is presented. The analysis covers the downlink operation and leads to the derivation of an exact mathematical expression between the normalized average channel capacity available to each system-s user, under simultaneous optimal power and rate adaptation and the system-s parameters, as the number of hops per bit, the processing gain applied, the number of users per cell and the received signal-tonoise power ratio over the signal bandwidth. Finally, numerical results are presented to illustrate the proposed mathematical analysis.

Keywords: Shannon capacity, adaptive systems, code-division multiple access, fading channels.

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Authors: Jiří Pavelka

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The study is based on the assumption that media products are appropriate subjects for the exploration of social and cultural identities as a keystone of value orientations of their authors, producers and target audiences. The research object of the study is the title page of the book cover of a professional publication that serves as a medium of marketing, scientific and intercultural communication, which is the result of semiotic and intercultural transfer. The study aims to answer the question whether the book cover is an expression of conceptualization and tool for social identity construction. It attempts to determine what value orientations and what concepts of social and cultural identities are hidden in the narrative structures of the book cover of the Czech translation of the book by G. Ritzer The McDonaldization of Society (1993), issued after the fall of the iron curtain in 1996 in the Czech Republic.

Keywords: Social and cultural identity, book cover, marketing communication, semiotic and intercultural transfer, narrative structure, the McDonaldisation of Society.

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Authors: Irina Spaka, Rita Birkenfelde, Svetlana Kozireva, Jevgenija Osmjana, Madara Upmane, ElenaKashuba, Irina Kholodnyuk Holodnuka

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Epstein-Barr virus (EBV) is implicated in the pathogenesis of the endemic Burkitt-s lymphoma (BL). The EBVpositive BL-derived cell lines initially maintain the original tumor phenotype of EBV infection (latency I, LatI), but most of them drift toward a lymphoblast phenotype of EBV latency III (LatIII) during in vitro culturing. The aim of the present work was to characterize the B-cell subsets in EBV-positive BL cell lines and to verify whether a particular cell subset correlates with the type of EBV infection. The phenotype analysis of two EBV-negative and eleven EBV-positive (three of LatI and eight of LatIII) BL cell lines was performed by polychromatic flow cytomery, based on expression pattern of CD19, CD10, CD38, CD27, and CD5 markers. Two cell subsets, CD19+CD10+ and CD19+CD10-, were defined in LatIII BL cell lines. In both subsets, the CD27 and CD5 cell surface expression was detected in a proportion of the cells.

Keywords: B-cell subsets, Burkitt's lymphoma cell lines, EBV latency, phenotype profiles.

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Authors: O. Aluko, M. R. Brai, A. O. Adelore

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Healthy snack (cookie) was produced from corn flour and moringa seed flour blends. The samples were mixed in various proportions and analysed for proximate composition and functional characteristics. The healthy snack (cookies) was evaluated for sensory parameters of Colour, Crispness, Taste, Aroma and Overall Acceptability. The proximate analysis of the flour obtained from different proportion showed that proximate composition increased with increase in substitution level of moringa seed flour especially with protein, fat and crude fibre. The protein contents of samples range from 1.75 to 6.58, fat from 0.60 to 6.80, while fibre from 0.85 to 2.06. There was no significance difference in the functional properties of the blend when compared with 100% corn flour. Sensory evaluation results shows a significant difference in Colour, Taste, Crispness, Aroma and Overall Acceptability of healthy snack (cookies) sample from different blends at 5% significance level.

Keywords: Healthy snack, moringa.

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Authors: A. E. O. Malau-Aduli, B. W. B. Holman, P. A. Lane

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Our objectives were to evaluate the effects of sire breed, type of protein supplement, level of supplementation and sex on wool spinning fineness (SF), its correlations with other wool characteristics and prediction accuracy in F1 Merino crossbred lambs. Texel, Coopworth, White Suffolk, East Friesian and Dorset rams were mated with 500 purebred Merino dams at a ratio of 1:100 in separate paddocks within a single management system. The F1 progeny were raised on ryegrass pasture until weaning, before forty lambs were randomly allocated to treatments in a 5 x 2 x 2 x 2 factorial experimental design representing 5 sire breeds, 2 supplementary feeds (canola or lupins), 2 levels of supplementation (1% or 2% of liveweight) and sex (wethers or ewes). Lambs were supplemented for six weeks after an initial three weeks of adjustment, wool sampled at the commencement and conclusion of the feeding trial and analyzed for SF, mean fibre diameter (FD), coefficient of variation (CV), standard deviation, comfort factor (CF), fibre curvature (CURV), and clean fleece yield. Data were analyzed using mixed linear model procedures with sire fitted as a random effect, and sire breed, sex, supplementary feed type, level of supplementation and their second-order interactions as fixed effects. Sire breed (P<0.001), sex (P<0.004), sire breed x level of supplementation (P<0.004), and sire breed x sex (P<0.019) interactions significantly influenced SF. SF ranged from 22.7 ± 0.2μm in White Suffolk-sired lambs to 25.1 ± 0.2μm in East Friesian crossbred lambs. Ewes had higher SF than wethers. There were significant (P<0.001) correlations between SF and FD (0.93), CV (0.40), CF (-0.94) and CURV (-0.12). Its strong relationship with other wool quality traits enabled accurate predictions explaining up to about 93% of the observed variation. The interactions between sire breed genetics and nutrition will have an impact on the choices that dual-purpose sheep producers make when selecting sire breeds and protein supplementary feed levels to achieve optimal wool spinning fineness at the farmgate level. This will facilitate selective breeding programs being able to better account for SF and its interactions with other wool characteristics.

Keywords: Merino crossbred sheep, protein supplementation, sire breed, wool quality, wool spinning fineness

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Authors: Trinh Trong Chuong

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At present, it is very common to find renewable energy resources, especially wind power, connected to distribution systems. The impact of this wind power on voltage distribution levels has been addressed in the literature. The majority of this works deals with the determination of the maximum active and reactive power that is possible to be connected on a system load bus, until the voltage at that bus reaches the voltage collapse point. It is done by the traditional methods of PV curves reported in many references. Theoretical expression of maximum power limited by voltage stability transfer through a grid is formulated using an exact representation of distribution line with ABCD parameters. The expression is used to plot PV curves at various power factors of a radial system. Limited values of reactive power can be obtained. This paper presents a method to study the relationship between the active power and voltage (PV) at the load bus to identify the voltage stability limit. It is a foundation to build a permitted working operation region in complying with the voltage stability limit at the point of common coupling (PCC) connected wind farm.

Keywords: Wind generator, Voltage stability, grid connected

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Authors: Junki Miyamoto, Mariko Kiyomi, Yuuki Nagashio, Takuya Suzuki, Soichi Tanabe

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Anti-allergic effects of royal jelly were evaluated in a human-like mouse model of atopic dermatitis. NC/Nga mice were cutaneously applied with royal jelly for 6 weeks. Royal jelly-treated mice exhibited lower levels of serum total immunoglobulin E in comparison with controls. We found that the treatment decreased (11% to the control) expression of mRNA for aquaporin-3, which is involved in the modulation of epidermal hydration. Microarray analysis revealed more than 10-fold changes in the expression of several genes, such as transglutaminase 2, repetin, and keratins. In normal human epidermal keratinocytes, royal jelly extract suppressed interleukin-8 elevation induced by TNF-α and interferon-γ, suggesting direct anti-inflammatory activity in keratinocytes. Collectively, topical application of royal jelly may be useful for amelioration of lesions and inflammation in atopic dermatitis.

Keywords: Aquaporin 3, immunoglobulin E, NC/Nga, royal jelly.

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Authors: S. B. Fasoyiro, K. A. Arowora

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Pigeon pea (Cajanus cajan) blanched for 20min was dehulled and milled into flour. The flour was incorporated into dried whole fermented maize (Ogi) at five levels. The resultant products were analyzed for chemical and pasting properties. The fortified Ogi samples were also assessed for sensory attributes: appearance, color, flavor, mouth feel and overall acceptability. The protein content in the whole Ogi fortified samples was in the range of 11.2-16.6% and crude fibre 3.22-3.46%. Fortified whole Ogi with pigeon pea at 30%, 40% and 50% of inclusion with pigeon pea flour has higher protein, crude fibre and ash content. Varying range of pasting quality was recorded for the blends, pasting temperature for fortified Obi was in the range of 45.3-49.50C and peak time 5.05-5.210C. The sensory acceptability of the whole Ogi fortified blends prepared into gruel has higher acceptability for various qualities in comparison with the traditional Ogi gruel.

Keywords: Maize Ogi, pigeon pea, chemical, pasting, sensory properties.

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Authors: Razvan Bocu, Dr Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents the latest authors- achievements regarding the analysis of the networks of proteins (interactome networks), by computing more efficiently the betweenness centrality measure. The paper introduces the concept of betweenness centrality, and then describes how betweenness computation can help the interactome net- work analysis. Current sequential implementations for the between- ness computation do not perform satisfactory in terms of execution times. The paper-s main contribution is centered towards introducing a speedup technique for the betweenness computation, based on modified shortest path algorithms for sparse graphs. Three optimized generic algorithms for betweenness computation are described and implemented, and their performance tested against real biological data, which is part of the IntAct dataset.

Keywords: Betweenness centrality, interactome networks, protein-protein interactions, sub-communities, sparse networks, speedup tech-nique, IntAct.

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Authors: Sang-Ho Baik

Abstract:

D-erythro-cyclohexylserine (D chiral unnatural β-hydroxy amino acid expected for the synthesis of drug for AIDS treatment. To develop a continuous bioconversion system with whole cell biocatalyst of D-threonine aldolase (D genes for the D-erythro-CHS production, D-threonine aldolase gene was amplified from Ensifer arboris 100383 by direct PCR amplication using two degenerated oligonucleotide primers designed based on genomic sequence of Shinorhizobium meliloti Sequence analysis of the cloned DNA fragment revealed one open-reading frame of 1059 bp and 386 amino acids. This putative D-TA gene was cloned into NdeI and EcoRI (pEnsi His-tag sequence or BamHI (pEnsi-DTA[2]) sequence of the pET21(a) vector. The expression level of the cloned gene was extremely overexpressed by E. coli BL21(DE3) transformed with pEnsi-DTA[1] compared to E. coli BL21(DE3) transformed with pEnsi-DTA[2]. When the cells expressing the wild used for D-TA enzyme activity, 12 mM glycine was successfully detected in HPLC analysis. Moreover, the whole cells harbouring the recombinant D-TA was able to synthesize D-erythro of 0.6 mg/ml in a batch reaction.

Keywords: About four key words or phrases in alphabetical order, separated by commas.

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Authors: Razvan Bocu, Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents a new technique that allows for an accurate analysis of the human interactome network. It is basically a two-step analysis process that involves, at first, the detection of each protein-s absolute importance through the betweenness centrality computation. Then, the second step determines the functionallyrelated communities of proteins. For this purpose, we use a community detection technique that is based on the edge betweenness calculation. The new technique was thoroughly tested on real biological data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its experimental usefulness, the novel technique is also computationally effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented and a possible optimization solution for cancer drugs design is suggested.

Keywords: Betweenness centrality, interactome networks, proteinprotein interactions, protein communities, cancer.

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Authors: Rameswar Debnath, Haruhisa Takahashi

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An evolutionary method whose selection and recombination operations are based on generalization error-bounds of support vector machine (SVM) can select a subset of potentially informative genes for SVM classifier very efficiently [7]. In this paper, we will use the derivative of error-bound (first-order criteria) to select and recombine gene features in the evolutionary process, and compare the performance of the derivative of error-bound with the error-bound itself (zero-order) in the evolutionary process. We also investigate several error-bounds and their derivatives to compare the performance, and find the best criteria for gene selection and classification. We use 7 cancer-related human gene expression datasets to evaluate the performance of the zero-order and first-order criteria of error-bounds. Though both criteria have the same strategy in theoretically, experimental results demonstrate the best criterion for microarray gene expression data.

Keywords: support vector machine, generalization error-bound, feature selection, evolutionary algorithm, microarray data

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

Abstract:

Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: Gnanaprakash K, Madhusudhana Chetty C, Ramkanth S, Alagusundaram M, Tiruvengadarajan VS, Angala Parameswari S, Mohamed Saleem TS

Abstract:

Carbon tetrachloride (CCl4) is a well-known hepatotoxin and exposure to this chemical is known to induce oxidative stress and causes liver injury by the formation of free radicals. Flacourtia indica commonly known as 'Baichi' has been reported as an effective remedy for the treatment of a variety of diseases. The objective of this study was to investigate the hepatoprotective activity of aqueous extract of leaves of Flacourtia indica against CCl4 induced hepatotoxicity. Animals were pretreated with the aqueous extract of Flacourtia indica (250 & 500 mg/kg body weight) for one week and then challenged with CCl4 (1.5 ml/kg bw) in olive oil (1:1, v/v) on 7th day. Serum marker enzymes (ALP, AST, ALT, Total Protein & Total Bilirubin) and TBARS level (Marker for oxidative stress) were estimated in all the study groups. Alteration in the levels of biochemical markers of hepatic damage like AST, ALT, ALP, Total Protein, Total Bilirubin and lipid peroxides (TBARS) were tested in both CCl4 treated and extract treated groups. CCl4 has enhanced the AST, ALT, ALP and the Lipid peroxides (TBARS) in liver. Treatment of aqueous extract of Flacourtia indica leaves (250 & 500 mg/kg) exhibited a significant protective effect by altering the serum levels of AST, ALT, ALP, Total Protein, Total Bilirubin and liver TBARS. These biochemical observations were supported by histopathological study of liver sections. From this preliminary study it has been concluded that the aqueous extract of the leaves of Flacourtia indica protects liver against oxidative damages and could be used as an effective protector against CCl4 induced hepatic damage. Our findings suggested that Flacourtia indica possessed good hepatoprotective activity

Keywords: Carbon Tetrachloride, Flacourtia indica, Hepatoprotective activity, Oxidative stress

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Authors: V. Viliene, V. Sasyte, A. Raceviciute-Stupeliene, R. Gruzauskas

Abstract:

In horse nutrition, the most suitable cereal for their rations composition could be defined as oats and barley. Oats have high nutritive value because it provides more protein, fiber, iron and zinc than other whole grains, has good taste, and an activity of stimulating metabolic changes in the body. Another cereal – barley is very similar to oats as a feed except for some characteristics that affect how it is used; however, barley is lower in fiber than oats and is classified as a "heavy" feed. The value of oats and barley grain, first of all is dependent on its composition. Near-infrared spectroscopy (NIRS) has long been considered and used as a significant method in component and quality analysis and as an emerging technology for authenticity applications for cereal quality control. This paper presents the chemical and amino acid composition of different varieties of barley and oats, also digestible energy of different cereals for horses. Ten different spring barley (n = 5) and oats (n = 5) varieties, grown in one location in Lithuania, were assayed for their chemical composition (dry matter, crude protein, crude fat, crude ash, crude fiber, starch) and amino acids content, digestible amino acids and amino acids digestibility. Also, the grains digestible energy for horses was calculated. The oats and barley samples reflectance spectra were measured by means of NIRS using Foss-Tecator DS2500 equipment. The chemical components: fat, crude protein, starch and fiber differed statistically (P<0.05) between the oats and barley varieties. The highest total amino acid content between oats was determined in variety Flamingsprofi (4.56 g/kg) and the lowest – variety Circle (3.57 g/kg), and between barley - respectively in varieties Publican (3.50 g/kg) and Sebastian (3.11 g/kg). The different varieties of oats digestible amino acid content varied from 3.11 g/kg to 4.07 g/kg; barley different varieties varied from 2.59 g/kg to 2.94 g/kg. The average amino acids digestibility of oats varied from 74.4% (Liz) to 95.6% (Fen) and in barley - from 75.8 % (Tre) to 89.6% (Fen). The amount of digestible energy in the analyzed varieties of oats and barley was an average compound 13.74 MJ/kg DM and 14.85 MJ/kg DM, respectively. An analysis of the results showed that different varieties of oats compared with barley are preferable for horse nutrition according to the crude fat, crude fiber, ash and separate amino acids content, but the analyzed barley varieties dominated the higher amounts of crude protein, the digestible Liz amount and higher DE content, and thus, could be recommended for making feed formulation for horses combining oats and barley, taking into account the chemical composition of using cereal varieties.

Keywords: Barley, digestive energy, horses, nutritional value, oats.

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

Abstract:

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

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

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Authors: Abu Salim Mustafa

Abstract:

Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: Mycobacterium tuberculosis, Rv3873, peptides, vaccine

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