Search results for: metabolic interactions.

Authors: Eleftheria Tzamali, Panayiota Poirazi, Ioannis G. Tollis, Martin Reczko

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Stable bacterial polymorphism on a single limiting resource may appear if between the evolved strains metabolic interactions take place that allow the exchange of essential nutrients [8]. Towards an attempt to predict the possible outcome of longrunning evolution experiments, a network based on the metabolic capabilities of homogeneous populations of every single gene knockout strain (nodes) of the bacterium E. coli is reconstructed. Potential metabolic interactions (edges) are allowed only between strains of different metabolic capabilities. Bacterial communities are determined by finding cliques in this network. Growth of the emerged hypothetical bacterial communities is simulated by extending the metabolic flux balance analysis model of Varma et al [2] to embody heterogeneous cell population growth in a mutual environment. Results from aerobic growth on 10 different carbon sources are presented. The upper bounds of the diversity that can emerge from single-cloned populations of E. coli such as the number of strains that appears to metabolically differ from most strains (highly connected nodes), the maximum clique size as well as the number of all the possible communities are determined. Certain single gene deletions are identified to consistently participate in our hypothetical bacterial communities under most environmental conditions implying a pattern of growth-condition- invariant strains with similar metabolic effects. Moreover, evaluation of all the hypothetical bacterial communities under growth on pyruvate reveals heterogeneous populations that can exhibit superior growth performance when compared to the performance of the homogeneous wild-type population.

Keywords: Bacterial polymorphism, clique identification, dynamic FBA, evolution, metabolic interactions.

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Authors: Feng-Sheng Wang, Wu-Hsiung Wu, Kai-Cheng Hsu

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The optimization of biological systems, which is a branch of metabolic engineering, has generated a lot of industrial and academic interest for a long time. In the last decade, metabolic engineering approaches based on mathematical optimizations have been used extensively for the analysis and manipulation of metabolic networks. In practical optimization of metabolic reaction networks, designers have to manage the nature of uncertainty resulting from qualitative characters of metabolic reactions, e.g., the possibility of enzyme effects. A deterministic approach does not give an adequate representation for metabolic reaction networks with uncertain characters. Fuzzy optimization formulations can be applied to cope with this problem. A fuzzy multi-objective optimization problem can be introduced for finding the optimal engineering interventions on metabolic network systems considering the resilience phenomenon and cell viability constraints. The accuracy of optimization results depends heavily on the development of essential kinetic models of metabolic networks. Kinetic models can quantitatively capture the experimentally observed regulation data of metabolic systems and are often used to find the optimal manipulation of external inputs. To address the issues of optimizing the regulatory structure of metabolic networks, it is necessary to consider qualitative effects, e.g., the resilience phenomena and cell viability constraints. Combining the qualitative and quantitative descriptions for metabolic networks makes it possible to design a viable strain and accurately predict the maximum possible flux rates of desired products. Considering the resilience phenomena in metabolic networks can improve the predictions of gene intervention and maximum synthesis rates in metabolic engineering. Two case studies will present in the conference to illustrate the phenomena.

Keywords: Fuzzy multi-objective optimization problem, kinetic model, metabolic engineering.

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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Authors: Valentina L. Kouznetsova, Jonathan W. Wang, Igor F. Tsigelny

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Metabolomics has become a rising field of research for various diseases, particularly cancer. Increases or decreases in metabolite concentrations in the human body are indicative of various cancers. Further elucidation of metabolic pathways and their significance in cancer research may greatly spur medicinal discovery. We analyzed the metabolomics profiles of lung cancer. Thirty-three metabolites were selected as significant. These metabolites are involved in 37 metabolic pathways delivered by MetaboAnalyst software. The top pathways are glyoxylate and dicarboxylate pathway (its hubs are formic acid and glyoxylic acid) along with Citrate cycle pathway followed by Taurine and hypotaurine pathway (the hubs in the latter are taurine and sulfoacetaldehyde) and Glycine, serine, and threonine pathway (the hubs are glycine and L-serine). We studied interactions of the metabolites with the proteins involved in cancer-related signaling networks, and developed an approach to metabolomics biomarker use in cancer diagnostics. Our analysis showed that a significant part of lung-cancer-related metabolites interacts with main cancer-related signaling pathways present in this network: PI3K–mTOR–AKT pathway, RAS–RAF–ERK1/2 pathway, and NFKB pathway. These results can be employed for use of metabolomics profiles in elucidation of the related cancer proteins signaling networks.

Keywords: Cancer, metabolites, metabolic pathway, signaling pathway.

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Authors: Y. Hong, H. Y. Hu, A. Sakoda, M. Sagehashi

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In this study, inhibition of Microcystis aeruginosa by antialgal alleochemical gramine, was studied by analyzing algal metabolic activity (represented by esterase and total dehydrogenase activities) and cell ultrastructure (showing morphological and ultrastructure alterations using transmission electron microscopy and DNA ladder analysis). After gramine exposure, esterase and total dehydrogenase activities were increased firstly but decreased later. In contrast with the controls, the cells exposed to gramine showed apparent ultrastructure alterations with thylakoids in breakage, phycobilins in decrease, lipid and cyanophycin granules abundant firstly but dissolved afterwards, DNA in fragementation. The occurrence of increase of metabolic activity and specific granules reflected that the resistance of cellular response to gramine was initiated. DNA fragementation associated with the increase of metabolic activity and specific granules hinted that gramine caused M. aeruginosa cells to initiate some morphotype of programmed cell death.

Keywords: Allelochemical, gramine, metabolic activity, Microcystis aeruginosa, ultrastructure.

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Authors: Orkide Donma, Mustafa M. Donma

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Basal metabolic rate is questioned as a risk factor for weight gain. The relations between basal metabolic rate and body composition have not been cleared yet. The impact of fat mass on basal metabolic rate is also uncertain. Within this context, indices based upon total body mass as well as total body fat mass are available. In this study, the aim is to investigate the potential clinical utility of these indices in the adult population. 287 individuals, aged from 18 to 79 years, were included into the scope of the study. Based upon body mass index values, 10 underweight, 88 normal, 88 overweight, 81 obese, and 20 morbid obese individuals participated. Anthropometric measurements including height (m), and weight (kg) were performed. Body mass index, diagnostic obesity notation model assessment index I, diagnostic obesity notation model assessment index II, basal metabolic rate-to-weight ratio were calculated. Total body fat mass (kg), fat percent (%), basal metabolic rate, metabolic age, visceral adiposity, fat mass of upper as well as lower extremities and trunk, obesity degree were measured by TANITA body composition monitor using bioelectrical impedance analysis technology. Statistical evaluations were performed by statistical package (SPSS) for Windows Version 16.0. Scatterplots of individual measurements for the parameters concerning correlations were drawn. Linear regression lines were displayed. The statistical significance degree was accepted as p < 0.05. The strong correlations between body mass index and diagnostic obesity notation model assessment index I as well as diagnostic obesity notation model assessment index II were obtained (p < 0.001). A much stronger correlation was detected between basal metabolic rate and diagnostic obesity notation model assessment index I in comparison with that calculated for basal metabolic rate and body mass index (p < 0.001). Upon consideration of the associations between basal metabolic rate-to-weight ratio and these three indices, the best association was observed between basal metabolic rate-to-weight and diagnostic obesity notation model assessment index II. In a similar manner, this index was highly correlated with fat percent (p < 0.001). Being independent of the indices, a strong correlation was found between fat percent and basal metabolic rate-to-weight ratio (p < 0.001). Visceral adiposity was much strongly correlated with metabolic age when compared to that with chronological age (p < 0.001). In conclusion, all three indices were associated with metabolic age, but not with chronological age. Diagnostic obesity notation model assessment index II values were highly correlated with body mass index values throughout all ranges starting with underweight going towards morbid obesity. This index is the best in terms of its association with basal metabolic rate-to-weight ratio, which can be interpreted as basal metabolic rate unit.

Keywords: Basal metabolic rate, body mass index, children, diagnostic obesity notation model assessment index, obesity.

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

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Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning.

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Authors: Baharak Khoshkholgh-Sima, Soroush Sardari, Jalal Izadi Mobarakeh, Ramezan Ali Khavari-Nejad

Abstract:

There is an urgent need to develop novel Mycobacterium tuberculosis (Mtb) drugs that are active against drug resistant bacteria but, more importantly, kill persistent bacteria. Our study structured based on integrated analysis of metabolic pathways, small molecule screening and similarity Search in PubChem Database. Metabolic analysis approaches based on Unified weighted used for potent target selection. Our results suggest that pantothenate synthetase (panC) and and 3-methyl-2-oxobutanoate hydroxymethyl transferase (panB) as a appropriate drug targets. In our study, we used pantothenate synthetase because of existence inhibitors. We have reported the discovery of new antitubercular compounds through ligand based approaches using computational tools.

Keywords: In Silico, Ligand-based Virtual Screening, Metabolic Pathways, Mycobacterium tuberculosis

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Authors: R. Bendib, A. Khelassi

Abstract:

In this paper we will consider the most known ratios control schemes ((L/D, V/B),(L/D,V/F), Ryskamp-s, and (D/(L+D),V/B)) for binary distillation column and we compare them in the basis of interactions and disturbance propagation. The models for these configurations are deuced using mathematical transformations taking the energy balance structure (LV) as a base model. The dynamic relative magnitude criterion (DRMC) is used to assess the interactions. The results show that the introduction of ratios in controlling the column tends to minimize the degree of interactions between the loops.

Keywords: Distillation, interaction, DRMC, configurations.

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Authors: Vladyslav Povoroznyuk, Larysa Martynyuk, Iryna Syzonenko, Liliya Martynyuk

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Osteoporosis is one of the important problems in postmenopausal women due to an increased risk of sudden and unexpected fractures. This study is aimed to determine the connection between bone mineral density (BMD) and trabecular bone score (TBS) in Ukrainian women suffering from metabolic syndrome. Participating in the study, 566 menopausal women aged 50-79 year-old were examined and divided into two groups: Group A included 336 women with no obesity (BMI ≤ 29.9 kg/m²), and Group B – 230 women with metabolic syndrome (diagnosis according to IDF criteria, 2005). Dual-energy X-ray absorptiometry was used for measuring of lumbar spine (L1-L4), femoral neck, total body and forearm BMD and bone quality indexes (last according to Med-Imaps installation). Data were analyzed using Statistical Package 6.0. A significant increase of lumbar spine (L1-L4), femoral neck, total body and ultradistal radius BMD was found in women with metabolic syndrome compared to those without obesity (p < 0.001) both in their totality and in groups of 50-59 years, 60-69 years, and 70-79 years. TBS was significantly higher in non-obese women compared to metabolic syndrome patients of 50-59 years and in the general sample (p < 0.05). Analysis showed significant positive correlation between body mass index (BMI) and BMD at all levels. Significant negative correlation between BMI and TBS (L1-L4) was established. Despite the fact that BMD indexes were significantly higher in women with metabolic syndrome, the frequency of vertebral and non-vertebral fractures did not differ significantly in the groups of patients.

Keywords: Bone mineral density, trabecular bone score, metabolic syndrome, fracture.

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Authors: Philippe Fauquet-Alekhine

Abstract:

For professions of high risk industries, simulation training has always been thought in terms of high degree of fidelity regarding the real operational situation. Due to the recent progress, this way of training is changing, modifying the human-computer and software interactions: the interactions between trainees during simulation training session tend to become virtual, transforming the social-based embodiness (the way subjects integrate social skills for interpersonal relationship with co-workers). On the basis of the analysis of eight different profession trainings, a categorization of interactions has help to produce an analytical tool, the social interactions table. This tool may be very valuable to point out the changes of social interactions when the training sessions are skipping from a high fidelity simulator to a virtual simulator. In this case, it helps the designers of professional training to analyze and to assess the consequences of the potential lack the social-based embodiness.

Keywords: Interface, interaction, simulator, virtual training.

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Authors: S. Bag, S. Ramaiah, P. Anitha, K. M. Kumar, P. Lavanya, V. Sivasakhthi, A. Anbarasu

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Gene networks present a graphical view at the level of gene activities and genetic functions and help us to understand complex interactions in a meaningful manner. In the present study, we have analyzed the gene interaction of PPAR-γ (peroxisome proliferator-activated receptor gamma) by search tool for retrieval of interacting genes. We find PPAR-γ is highly networked by genetic interactions with 10 genes: RXRA (retinoid X receptor, alpha), PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), NCOA1 (nuclear receptor coactivator 1), NR0B2 (nuclear receptor subfamily 0, group B, member 2), HDAC3 (histone deacetylase 3), MED1 (mediator complex subunit 1), INS (insulin), NCOR2 (nuclear receptor co-repressor 2), PAX8 (paired box 8), ADIPOQ (adiponectin) and it augurs well for the fact that obesity and several other metabolic disorders are inter related.

Keywords: Gene networks, NCOA1, PPARγ, PPARGC1A, RXRA.

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Authors: Ines Hamdi, Mohamed Ben Ahmed

Abstract:

The understanding of the system level of biological behavior and phenomenon variously needs some elements such as gene sequence, protein structure, gene functions and metabolic pathways. Challenging problems are representing, learning and reasoning about these biochemical reactions, gene and protein structure, genotype and relation between the phenotype, and expression system on those interactions. The goal of our work is to understand the behaviors of the interactions networks and to model their evolution in time and in space. We propose in this study an ontological meta-model for the knowledge representation of the genetic regulatory networks. Ontology in artificial intelligence means the fundamental categories and relations that provide a framework for knowledge models. Domain ontology's are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. The interest of our model is to represent the spatial, temporal and spatio-temporal knowledge. We validated our propositions in the genetic regulatory network of the Aarbidosis thaliana flower

Keywords: Ontological model, spatio-temporal modeling, Genetic Regulatory Networks (GRNs), knowledge representation.

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Authors: Yi Chao Huang, Yu Ling Liao, Chiu Shuang Lin

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A data cutting and sorting method (DCSM) is proposed to optimize the performance of data mining. DCSM reduces the calculation time by getting rid of redundant data during the data mining process. In addition, DCSM minimizes the computational units by splitting the database and by sorting data with support counts. In the process of searching for the relationship between metabolic syndrome and lifestyles with the health examination database of an electronics manufacturing company, DCSM demonstrates higher search efficiency than the traditional Apriori algorithm in tests with different support counts.

Keywords: Data mining, Data cutting and sorting method, Apriori algorithm, Metabolic syndrome

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Authors: P. Pasomboon, P. Chumnanpuen, T. E-kobon

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Hyaluronic acid (HA) consists of linear heteropolysaccharides repeat of D-glucuronic acid and N-acetyl-D-glucosamine. HA has various useful properties to maintain skin elasticity and moisture, reduce inflammation, and lubricate the movement of various body parts without causing immunogenic allergy. HA can be found in several animal tissues as well as in the capsule component of some bacteria including Pasteurella multocida. This study aimed to modify a genome-scale metabolic model of Escherichia coli using computational simulation and flux analysis methods to predict HA productivity under different carbon sources and nitrogen supplement by the addition of two enzymes (GLMU2 and HYAD) from P. multocida to improve the HA production under the specified amount of carbon sources and nitrogen supplements. Result revealed that threonine and aspartate supplement raised the HA production by 12.186%. Our analyses proposed the genome-scale metabolic model is useful for improving the HA production and narrows the number of conditions to be tested further.

Keywords: Pasteurella multocida, Escherichia coli, hyaluronic acid, genome-scale metabolic model, bioinformatics.

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Authors: Vladyslav Povoroznyuk, Larysa Martynyuk, Iryna Syzonenko, Liliya Martynyuk

Abstract:

Medical, social, and economic relevance of osteoporosis is caused by reducing quality of life, increasing disability and mortality of the patients as a result of fractures due to the low-energy trauma. This study is aimed to examine the associations of metabolic syndrome components, bone mineral density (BMD) and trabecular bone score (TBS) in menopausal women with non-vertebral fractures. 1161 menopausal women aged 50-79 year-old were examined and divided into three groups: A included 419 women with increased body weight (BMI - 25.0-29.9 kg/m²), B – 442 females with obesity (BMI >29.9 kg/m²)i and C – 300 women with metabolic syndrome (diagnosis according to IDF criteria, 2005). BMD of lumbar spine (L1-L4), femoral neck, total body and forearm was investigated with usage of dual-energy X-ray absorptiometry. The bone quality indexes were measured according to Med-Imaps installation. All analyses were performed using Statistical Package 6.0. BMD of lumbar spine (L1-L4), femoral neck, total body, and ultradistal radius was significant higher in women with obesity and metabolic syndrome compared to the pre-obese ones (p<0.001). TBS was significantly higher in women with increased body weight compared to obese and metabolic syndrome patients. Analysis showed significant positive correlation between waist circumference, triglycerides level and BMD of lumbar spine and femur. Significant negative association between serum HDL level and BMD of investigated sites was established. The TBS (L1-L4) indexes positively correlated with HDL (high-density lipoprotein) level. Despite the fact that BMD indexes were better in women with metabolic syndrome, the frequency of non-vertebral fractures was significantly higher in this group of patients.

Keywords: Bone mineral density, trabecular bone score, metabolic syndrome, fracture.

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

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Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: A.-C. Bennis, F. Dumas, F. Ardhuin, B. Blanke

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The mechanics of rip currents are complex, involving interactions between waves, currents, water levels and the bathymetry, that present particular challenges for numerical models. Here, the effects of a grid-spacing dependent horizontal mixing on the wave-current interactions are studied. Near the shore, wave rays diverge from channels towards bar crests because of refraction by topography and currents, in a way that depends on the rip current intensity which is itself modulated by the horizontal mixing. At low resolution with the grid-spacing dependent horizontal mixing, the wave motion is the same for both coupling modes because the wave deviation by the currents is weak. In high resolution case, however, classical results are found with the stabilizing effect of the flow by feedback of waves on currents. Lastly, wave-current interactions and the horizontal mixing strongly affect the intensity of the three-dimensional rip velocity.

Keywords: Numerical modeling, Rip currents, Turbulence modeling, Wave-current interactions.

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Authors: S. J. Higgs, E. Van Eck, K. Heynis, S. H. Broadberry

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Engagement with non-human animals is a rapidly-growing field of study within the animal science and social science sectors, with human-interactions occurring in many forms; interactions, encounters and animal-assisted therapy. To our knowledge, there has been a wide array of research published on domestic and livestock human-animal interactions, however, there appear to be fewer publications relating to zoo animals and the effect these interactions have on the animal, human and establishment. The aim of this study was to identify if there were any perceivable benefits from the human-animal interaction for the cheetah, the human and the establishment. Behaviour data were collected before, during and after the interaction on the behaviour of the cheetah and the human participants to highlight any trends with nine interactions conducted. All 35 participants were asked to fill in a questionnaire prior to the interaction and immediately after to ascertain if their perceptions changed following an interaction with the cheetah. An online questionnaire was also distributed for three months to gain an understanding of the perceptions of human-animal interactions from members of the public, gaining 229 responses. Both questionnaires contained qualitative and quantitative questions to allow for specific definitive answers to be analysed, but also expansion on the participants perceived perception of human-animal interactions. In conclusion, it was found that participants’ perceptions of human-animal interactions saw a positive change, with 64% of participants altering their opinion and viewing the interaction as beneficial for the cheetah (reduction in stress assumed behaviours) following participation in a 15-minute interaction. However, it was noted that many participants felt the interaction lacked educational values and therefore this is an area in which zoological establishments can work to further improve upon. The results highlighted many positive benefits for the human, animal and establishment, however, the study does indicate further areas for research in order to promote positive perceptions of human-animal interactions and to further increase the welfare of the animal during these interactions, with recommendations to create and regulate legislation.

Keywords: Acinonyx jubatus, encounters, human-animal interactions, perceptions, zoological establishments.

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Authors: A. T. Nakysh, A. S. Idrisov, S. A. Baidurin

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This work presents the results of a study the incidence of metabolic syndrome (MetS) in women with impaired reproductive function (IRF) according to the data of Astana, Kazakhstan. The anthropometric, biochemical and instrumental studies were conducted among 515 women, of which 53 patients with MetS according to IDF criteria, 2006, were selected. The frequency of occurrence of the IRF, due to MetS is 10.3% of cases according to the data of Astana. In women of childbearing age with IRF and the MetS, blood pressure (BP), indicators of carbohydrate and lipid metabolism were significantly higher and the level of high density lipoprotein (HDL) significantly lower compared to the same in women with the IRF without MetS. The hyperandrogenism, the hyperestrogenemia, the hyperprolactinemia and the hypoprogesteronemia were found in the patients with MetS and IRF, indicating the impact of MetS on the development of the polycystic ovary syndrome in 28% of cases and hyperplastic processes of the myometrium in 20% of cases.

Keywords: Dyslipidemia, insulin resistance, metabolic syndrome, reproductive disorders, obesity.

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Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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Authors: A. Khelassi, R. Bendib

Abstract:

The paper considers the effect of feed plate location on the interactions in a seven plate binary distillation column. The mathematical model of the distillation column is deduced based on the equations of mass and energy balances for each stage, detailed model for both reboiler and condenser, and heat transfer equations. The Dynamic Relative Magnitude Criterion, DRMC is used to assess the interactions in different feed plate locations for a seven plate (Benzene-Toluene) binary distillation column ( the feed plate is originally at stage 4). The results show that whenever we go far from the optimum feed plate position, the level of interaction augments.

Keywords: Distillation column, assessment of interactions, feedplate location, DRMC.

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Authors: Orkide Donma, Mustafa M. Donma

Abstract:

Chronologic age (CA) of individuals is closely related to obesity and generally affects the magnitude of obesity parameters. On the other hand, close association between basal metabolic rate (BMR) and metabolic age (MA) is also a matter of concern. It is suggested that MA higher than CA is the indicator of the need to improve the metabolic rate. In this study, the aim was to assess some commonly used obesity parameters, such as obesity degree, visceral adiposity, BMR, BMR-to-weight ratio, in several groups with varying differences between MA and CA values. The study comprises adults, whose ages vary between 18 and 79 years. Four groups were constituted. Group 1, 2, 3 and 4 were composed of 55, 33, 76 and 47 adults, respectively. The individuals exhibiting -1, 0 and +1 for their MA-CA values were involved in Group 1, which was considered as the control group. Those, whose MA-CA values varying between -5 and -10 participated in Group 2. Those, whose MAs above their real ages were divided into two groups [Group 3 (MA-CA; from +5 to + 10) and Group 4 (MA-CA; from +11 to + 12)]. Body mass index (BMI) values were calculated. TANITA body composition monitor using bioelectrical impedance analysis technology was used to obtain values for obesity degree, visceral adiposity, BMR and BMR-to-weight ratio. The compiled data were evaluated statistically using a statistical package program; SPSS. Mean ± SD values were determined. Correlation analyses were performed. The statistical significance degree was accepted as p < 0.05. The increase in BMR was positively correlated with obesity degree. MAs and CAs of the groups were 39.9 ± 16.8 vs 39.9 ± 16.7 years for Group 1, 45.0 ± 15.3 vs 51.4 ± 15.7 years for Group 2, 47.2 ± 12.7 vs 40.0 ± 12.7 years for Group 3, and 53.6 ± 14.8 vs 42 ± 14.8 years for Group 4. BMI values of the groups were 24.3 ± 3.6 kg/m², 23.2 ± 1.7 kg/m², 30.3 ± 3.8 kg/m², and 40.1 ± 5.1 kg/m² for Group 1, 2, 3 and 4, respectively. Values obtained for BMR were 1599 ± 328 kcal in Group 1, 1463 ± 198 kcal in Group 2, 1652 ± 350 kcal in Group 3, and 1890 ± 360 kcal in Group 4. A correlation was observed between BMR and MA-CA values in Group 1. No correlation was detected in other groups. On the other hand, statistically significant correlations between MA-CA values and obesity degree, BMI as well as BMR/weight were found in Group 3 and in Group 4. It was concluded that upon consideration of these findings in terms of MA-CA values, BMR-to-weight ratio was found to be much more useful indicator of the severe increase in obesity development than BMR. Also, the lack of associations between MA and BMR as well as BMR-to-weight ratio emphasize the importance of consideration of MA-CA values rather than MA.

Keywords: Basal metabolic rate, chronologic age, metabolic age, obesity degree.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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Authors: Sh. Khoshemehry, M. J. Pourvaghar, M. E. Bahram

Abstract:

In modern life, daily physical activity is relatively reduced, which is why the incidence of some diseases associated with overweight and obesity, such as hypertension, diabetes and other chronic illnesses, even in young people are observed. Obesity and overweight is one of the most common metabolic disorders in industrialized countries and in developing countries. One consequence of pathological obesity is cardiovascular disease and metabolic syndrome. In the past, it was believed that adipose tissue was ineffective and served only for storing triglycerides. In this review article, it was tried to refer to the esteemed scientific sources about physical activity and responses of leptin.

Keywords: Disease, leptin, obesity, physical activity.

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Authors: Jonas Mayer, Kai-Frederic Seitz, Thorben Kuprat

Abstract:

In today’s competitive environment production’s logistic objectives such as ‘delivery reliability’ and ‘delivery time’ and distribution’s logistic objectives such as ‘service level’ and ‘delivery delay’ are attributed great importance. Especially for small and mid-sized enterprises (SME) attaining these objectives pose a key challenge. Within this context, one of the difficulties is that interactions between departments within the enterprise and their specific objectives are insufficiently taken into account and aligned. Interdepartmental independencies along with contradicting targets set within the different departments result in enterprises having sub-optimal logistic performance capability. This paper presents a research project which will systematically describe the interactions between departments and convert them into a quantifiable form.

Keywords: Department-specific actuating and control variables, interdepartmental interactions, cybernetic model, logistic objectives.

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Authors: Daniel C. S. Lim, Eric Y. M. Yeo, W. Y. Tan

Abstract:

This paper presents an overview of how calcium interacts with the various essential nutrients within an environment of cellular and hormonal interactions for the purpose of increasing bioavailability to the human body. One example of such interactions can be illustrated with calcium homeostasis. This paper gives an in-depth discussion on the possible interactive permutations with various nutrients and factors leading to the promotion of calcium bioavailability to the body. The review hopes to provide further insights into how calcium supplement formulations can be improved to better influence its bioavailability in the human body.

Keywords: Bioavailability, environment of cellular and hormonal interactions, combinative nutrition, nutrient synergy.

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Authors: Vilma Zydziunaite, Vaida Jurgile

Abstract:

The concept of teacher leadership refers to professional actors (employees and leaders) who can exercise control over or influence their work and its environment. The particular interest of the current research is gaining an understanding of how teachers experience leadership through educational interactions with students in a classroom. The aim of the research is to identify how teachers experience leadership in their everyday professional life through educational interactions with students in a classroom. Research questions are focused on essences of teacher leadership what are experienced by school teachers. The lifeworld research was performed in the study. 24 teachers participated in qualitative research. Data were collected via semi-structured interviews and analysed by using phenomenological analysis. Findings highlight aspects of teacher leadership through educational interactions with students in a classroom through the contribution to learning and teaching, authenticity, influence, empowerment, respect, equality, acknowledgement, resentment.

Keywords: Classroom, educational interaction, lifeworld research, teacher leadership.

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Authors: S. Yamini Sudha, Ashok Khanna

Abstract:

Owing to the stringent environmental legislations, CO2 capture and sequestration is one of the viable solutions to reduce the CO2 emissions from various sources. In this context, Ionic liquids (ILs) are being investigated as suitable absorption media for CO2 capture. Due to their non-evaporative, non-toxic, and non-corrosive nature, these ILs have the potential to replace the existing solvents like aqueous amine solutions for CO2 separation technologies. Thus, the present work aims at studying the important aspects such as the interactions of CO2 molecule with different anions (F-, Br-, Cl-, NO3 -, BF4 -, PF6 -, Tf2N-, and CF3SO3 -) that are commonly used in ILs through molecular modeling. In this, the minimum energy structures have been obtained using Ab initio based calculations at MP2 (Moller-Plesset perturbation) level. Results revealed various degrees of distortion of CO2 molecule (from its linearity) with the anions studied, most likely due to the Lewis acid-base interactions between CO2 and anion. Furthermore, binding energies for the anion-CO2 complexes were also calculated. The implication of anion-CO2 interactions to the solubility of CO2 in ionic liquids is also discussed.

Keywords: CO2, Ionic liquids, capture, molecular modeling, sequestration.

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