Search results for: Interacting Proteins

Authors: Ilze Beitane

Abstract:

The influence of flakes from biologically activated hull-less barley grain and malt extract on chemical composition of yoghurt was studied. Pasteurized milk, freeze-dried yoghurt culture YF-L811 (Chr. Hansen, Denmark), flakes from biologically activated hull-less barley grain (Latvia) and malt extract (Ilgezeem, Latvia) were used for experiments. Yoghurt samples with and without flakes from biologically activated hull-less barley grain and malt extract were analyzed for content of total solids, total proteins, fats, amino acids and riboflavin. The addition of flakes from biologically activated hull-less barley grain and malt extract allowed increase of nutritional value of yoghurt samples. There was obtained the increase of total proteins (p>0.05) and the decrease of fat (p>0.05). The presence of flakes from biologically activated hull-less barley grain and malt extract in yoghurt samples provided significant increase of amino acids amount (p<0.05) and riboflavin concentration (p<0.05).

Keywords: Chemical composition, hull-less barley grain, malt extract, yoghurt.

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

Abstract:

Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase–pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed-specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: Kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization.

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Authors: Berardina De Carolis, Giovanni Cozzolongo

Abstract:

In this paper, we present C@sa, a multiagent system aiming at modeling, controlling and simulating the behavior of an intelligent house. The developed system aims at providing to architects, designers and psychologists a simulation and control tool for understanding which is the impact of embedded and pervasive technology on people daily life. In this vision, the house is seen as an environment made up of independent and distributed devices, controlled by agents, interacting to support user's goals and tasks.

Keywords: Ambient intelligence, agent-based systems, influence diagrams.

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Authors: A. F. Ali, D. M. Shawky

Abstract:

Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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

Abstract:

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: Arun Kumar V.A., Keshav Mohan

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Adenylate kinase (AK) catalyse the phosphotransferase reaction plays an important role in cellular energy homeostasis. The inhibitors of bacterial AK are useful in the treatment of several bacterial infections. To the novel inhibitors of AK, docking studies performed by using the 3D structure of Bacillus stearothermophilus adenylate kinase from protein data bank (IZIP). 46 Quinoxaline analogues were docked in 1ZIP and selected the highly interacting compounds based on their binding energies, for further studies

Keywords: Kinase, quinoxaline, homeostasis, inhibitor, nucleotide.

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Authors: Boonsrimuang P., Numsomran A., Kangwanrat S.

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The typical coupled-tanks process that is TITO plant has the difficulty in controller design because changing of system dynamics and interacting of process. This paper presents design methodology of auto-adjustable PI controller using MRAC technique. The proposed method can adjust the controller parameters in response to changes in plant and disturbance real time by referring to the reference model that specifies properties of the desired control system.

Keywords: PI controller, MRAC, Couple-tanks process

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Authors: Aouachria Mekki

Abstract:

We consider a spin-1/2 particle interacting with a time-dependent magnetic field using path integral formalism. The propagator is first of all written in the standard form replacing the spin by two fermionic oscillators via the Schwinger model. The propagator is then exactly determined, thanks to a simple transformation, and the transition probability is deduced.

Keywords: Path integral, formalism, Propagator.

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Authors: Weifeng Pan

Abstract:

Complex networks have been intensively studied across many fields, especially in Internet technology, biological engineering, and nonlinear science. Software is built up out of many interacting components at various levels of granularity, such as functions, classes, and packages, representing another important class of complex networks. It can also be studied using complex network theory. Over the last decade, many papers on the interdisciplinary research between software engineering and complex networks have been published. It provides a different dimension to our understanding of software and also is very useful for the design and development of software systems. This paper will explore how to use the complex network theory to analyze software structure, and briefly review the main advances in corresponding aspects.

Keywords: Metrics, measurement, complex networks, software.

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Authors: Thomas M. Prinz Wilhelm R. Rossak, Kai Gebhardt

Abstract:

A straightforward and intuitive combination of single simulations into an aggregated master-simulation is not trivial. There are lots of problems, which trigger-specific difficulties during the modeling and execution of such a simulation. In this paper we identify these problems and aim to solve them by mapping the task to the field of multi agent systems. The solution is a new meta-model named AGENTMAP, which is able to mitigate most of the problems and to support intuitive modeling at the same time. This meta-model will be introduced and explained on basis of an example from the e-commerce domain.

Keywords: Multi Agent System, Agent-based Simulation, Distributed Systems, Meta-models.

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Authors: N. Veerasamy, JPH Eloff

Abstract:

Network warfare is an emerging concept that focuses on the network and computer based forms through which information is attacked and defended. Various computer and network security concepts thus play a role in network warfare. Due the intricacy of the various interacting components, a model to better understand the complexity in a network warfare environment would be beneficial. Non-quantitative modeling is a useful method to better characterize the field due to the rich ideas that can be generated based on the use of secular associations, chronological origins, linked concepts, categorizations and context specifications. This paper proposes the use of non-quantitative methods through a morphological analysis to better explore and define the influential conditions in a network warfare environment.

Keywords: Morphological, non-quantitative, network warfare.

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Authors: Larbi Omar, Elberrichi Zakaria

Abstract:

Many research works are carried out on the analysis of traces in a digital learning environment. These studies produce large volumes of usage tracks from the various actions performed by a user. However, to exploit these data, compare and improve performance, several issues are raised. To remedy this, several works deal with this problem seen recently. This research studied a series of questions about format and description of the data to be shared. Our goal is to share thoughts on these issues by presenting our experience in the analysis of trace-based log files, comparing several approaches used in automatic classification applied to e-learning platforms. Finally, the obtained results are discussed.

Keywords: Classification, , e-learning platform, log file, Trace.

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Authors: Ching-Wei Tsai, Chih-I Liu, Ruoh-Chyu Ruaana

Abstract:

A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.

Keywords: Protein Oriented immobilization, Molecular docking, ligand design, surface modification.

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Authors: Piercarlo Dondi, Luca Lombardi, Marco Porta

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In the last years numerous applications of Human- Computer Interaction have exploited the capabilities of Time-of- Flight cameras for achieving more and more comfortable and precise interactions. In particular, gesture recognition is one of the most active fields. This work presents a new method for interacting with a virtual object in a 3D space. Our approach is based on the fusion of depth data, supplied by a ToF camera, with color information, supplied by a HD webcam. The hand detection procedure does not require any learning phase and is able to concurrently manage gestures of two hands. The system is robust to the presence in the scene of other objects or people, thanks to the use of the Kalman filter for maintaining the tracking of the hands.

Keywords: Gesture recognition, human-computer interaction, Time-of-Flight camera.

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Authors: C. Temaneh Nyah

Abstract:

The analysis of electromagnetic environment using deterministic mathematical models is characterized by the impossibility of analyzing a large number of interacting network stations with a priori unknown parameters, and this is characteristic, for example, of mobile wireless communication networks. One of the tasks of the tools used in designing, planning and optimization of mobile wireless network is to carry out simulation of electromagnetic environment based on mathematical modelling methods, including computer experiment, and to estimate its effect on radio communication devices. This paper proposes the development of a statistical model of electromagnetic environment of a mobile wireless communication network by describing the parameters and factors affecting it including the propagation channel and their statistical models.

Keywords: Electromagnetic Environment, Statistical model, Wireless communication network.

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Authors: Eduard Kuriščák, Jiří Chludil

Abstract:

We created the tool, which combines the powerful GENESIS (GEneral NEural SImulation System) simulation language with the up-to-date visualisation and internet techniques. Our solution resides in the connection between the simulation output from GENESIS, which is converted to the data-structure suitable for WWW browsers and VRML (Virtual Reality Modelling Language) viewers. The selected GENESIS simulations are once exported into the VRML code, and stored in our neurovisualisation portal (webserver). There, the loaded models, demonstrating mainly the spread of electrical signal (action potentials, postsynaptic potentials) along the neuronal membrane (axon, dendritic tree, neuron) could be displayed in the client-s VRML viewer, without interacting with original GENESIS environment. This enables the visualisation of basic neurophysiological phenomena designed for GENESIS simulator on the independent OS (operation system).

Keywords: GENESIS, neurosimulation, VRML, Java3D.

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Authors: Liu-Chao Qiu

Abstract:

The damage caused by surge waves generated in water bodies by flow-like landslides can be very high in terms of human lives and economic losses. The complicated phenomena occurred in this highly unsteady process are difficult to model because three interacting phases: air, water and sediment are involved. The problem therefore is challenging since the effects of non-Newtonian fluid describing the rheology of the flow-like landslides, multi-phase flow and free surface have to be included in the simulation. In this work, the commercial computational fluid dynamics (CFD) package FLUENT is used to model the surge waves due to flow-like landslides. The comparison between the numerical results and experimental data reported in the literature confirms the accuracy of the method.

Keywords: Flow-like landslide, surge wave, VOF, non-Newtonian fluids, multi-phase flows, free surface flow.

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Authors: Maysam Mard-Soltani, Mohamad Javad Rasaee, Saeed Khalili, Abdol Karim Sheikhi, Mehdi Hedayati

Abstract:

Production of specific antibody responses against hTSH is a cumbersome process due to the high identity between the hTSH and the other members of the glycoprotein hormone family (FSH, LH and HCG) and the high identity between the human hTSH and host animals for antibody production. Therefore, two polyclonal antibodies were purified against two recombinant proteins. Four possible ELISA tests were designed based on these antibodies. These ELISA tests were checked against hTSH and other glycoprotein hormones, and their sensitivity and specificity were assessed. Bioinformatics tools were used to analyze the immunological properties. After the immunogen region selection from hTSH protein, c terminal of B hTSH was selected and applied. Two recombinant genes, with these cut pieces (first: two repeats of C terminal of B hTSH, second: tetanous toxin+B hTSH C terminal), were designed and sub-cloned into the pET32a expression vector. Standard methods were used for protein expression, purification, and verification. Thereafter, immunizations of the white New Zealand rabbits were performed and the serums of them were used for antibody titration, purification and characterization. Then, four ELISA tests based on two antibodies were employed to assess the hTSH and other glycoprotein hormones. The results of these assessments were compared with standard amounts. The obtained results indicated that the desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. The raised antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum. Among the four designed tests, the test in which the antibody against first protein was used as capture antibody, and the antibody against second protein was used as detector antibody did not show any hook effect up to 50 miu/l. Both proteins have the ability to induce highly sensitive and specific antibody responses against the hTSH. One of the antibody combinations of these antibodies has the highest sensitivity and specificity in hTSH detection.

Keywords: hTSH, bioinformatics, protein expression, cross reactivity.

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Authors: Mella Ismelina Farma Rahayu

Abstract:

Environmental problems could not be separated from unethical human perspectives and behaviors toward the environment. There is a fundamental error in the philosophy of people’s perspective about human and nature and their relationship with the environment, which in turn will create an inappropriate behavior in relation to the environment. The aim of this study is to investigate and to understand the ethics of the environment in the context of humans interacting with the environment by using the hermeneutic approach. The related theories and concepts collected from literature review are used as data, which were analyzed by using interpretation, critical evaluation, internal coherence, comparisons, and heuristic techniques. As a result of this study, there will be a picture related to the interaction of human and environment in the perspective of environmental ethics, as well as the problems of the value of ecological justice in the interaction of humans and environment. We suggest that the interaction between humans and environment need to be based on environmental ethics, in a spirit of mutual respect between humans and the natural world.

Keywords: The environment, environmental ethics, the interaction, value.

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Authors: A. R. Tavakolpour-Saleh, A. R. Setoodeh, E. Ansari

Abstract:

This paper presents modeling and control of a highly nonlinear system including, non-interacting two spherical tanks using iterative learning control (ILC). Consequently, the objective of the paper is to control the liquid levels in the nonlinear tanks. First, a proportional-integral-derivative (PID) controller is applied to the plant model as a suitable benchmark for comparison. Then, dynamic responses of the control system corresponding to different step inputs are investigated. It is found that the conventional PID control is not able to fulfill the design criteria such as desired time constant. Consequently, an iterative learning controller is proposed to accurately control the coupled nonlinear tanks system. The simulation results clearly demonstrate the superiority of the presented ILC approach over the conventional PID controller to cope with the nonlinearities presented in the dynamic system.

Keywords: Iterative learning control, spherical tanks, nonlinear system.

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Authors: K. Prachumrak, T. Kanchanapornchai

Abstract:

This research simulates one of the natural phenomena, the ocean wave. Our goal is to be able to simulate the ocean wave at real-time rate with the water surface interacting with objects. The wave in this research is calm and smooth caused by the force of the wind above the ocean surface. In order to make the simulation of the wave real-time, the implementation of the GPU and the multithreading techniques are used here. Based on the fact that the new generation CPUs, for personal computers, have multi cores, they are useful for the multithread. This technique utilizes more than one core at a time. This simulation is programmed by C language with OpenGL. To make the simulation of the wave look more realistic, we applied an OpenGL technique called cube mapping (environmental mapping) to make water surface reflective and more realistic.

Keywords: Interactive wave, ocean wave, wind effect, multithread

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Authors: Imran Sarwar Bajwa, Rafaqut Kazmi, Shahzad Mumtaz, M. Abbas Choudhary, M. Shahid Naweed

Abstract:

Business Process Management (BPM) helps in optimizing the business processes inside an enterprise. But BPM architecture does not provide any help for extending the enterprise. Modern business environments and rapidly changing technologies are asking for brisk changes in the business processes. Service Oriented Architecture (SOA) can help in enabling the success of enterprise-wide BPM. SOA supports agility in software development that is directly related to achieve loose coupling of interacting software agents. Agility is a premium concern of the current software designing architectures. Together, BPM and SOA provide a perfect combination for enterprise computing. SOA provides the capabilities for services to be combined together and to support and create an agile, flexible enterprise. But there are still many questions to answer; BPM is better or SOA? and what is the future track of BPM and SOA? This paper tries to answer some of these important questions.

Keywords: Information Systems, BPM, SOA, Process management, IT management.

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Authors: Hossein Sahoolizadeh, Mahdi Rahimi, Hamid Dehghani

Abstract:

We introduce an algorithm based on the morphological shared-weight neural network. Being nonlinear and translation-invariant, the MSNN can be used to create better generalization during face recognition. Feature extraction is performed on grayscale images using hit-miss transforms that are independent of gray-level shifts. The output is then learned by interacting with the classification process. The feature extraction and classification networks are trained together, allowing the MSNN to simultaneously learn feature extraction and classification for a face. For evaluation, we test for robustness under variations in gray levels and noise while varying the network-s configuration to optimize recognition efficiency and processing time. Results show that the MSNN performs better for grayscale image pattern classification than ordinary neural networks.

Keywords: Face recognition, Neural Networks, Multi-layer Perceptron, masking.

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Authors: Iryna Atamaniuk, Hannah Boysen, Nils Wieczorek, Natalia Politaeva, Iuliia Bazarnova, Kerstin Kuchta

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Over the last decade due to climate change and a strategy of natural resources preservation, the interest for the aquatic biomass has dramatically increased. Along with mitigation of the environmental pressure and connection of waste streams (including CO₂ and heat emissions), microalgae bioeconomy can supply food, feed, as well as the pharmaceutical and power industry with number of value-added products. Furthermore, in comparison to conventional biomass, microalgae can be cultivated in wide range of conditions without compromising food and feed production, thus addressing issues associated with negative social and the environmental impacts. This paper presents the state-of-the art technology for microalgae bioeconomy from cultivation process to production of valuable components and by-streams. Microalgae Chlorella sorokiniana were cultivated in the pilot-scale innovation concept in Hamburg (Germany) using different systems such as race way pond (5000 L) and flat panel reactors (8 x 180 L). In order to achieve the optimum growth conditions along with suitable cellular composition for the further extraction of the value-added components, process parameters such as light intensity, temperature and pH are continuously being monitored. On the other hand, metabolic needs in nutrients were provided by addition of micro- and macro-nutrients into a medium to ensure autotrophic growth conditions of microalgae. The cultivation was further followed by downstream process and extraction of lipids, proteins and saccharides. Lipids extraction is conducted in repeated-batch semi-automatic mode using hot extraction method according to Randall. As solvents hexane and ethanol are used at different ratio of 9:1 and 1:9, respectively. Depending on cell disruption method along with solvents ratio, the total lipids content showed significant variations between 8.1% and 13.9 %. The highest percentage of extracted biomass was reached with a sample pretreated with microwave digestion using 90% of hexane and 10% of ethanol as solvents. Proteins content in microalgae was determined by two different methods, namely: Total Kejadahl Nitrogen (TKN), which further was converted to protein content, as well as Bradford method using Brilliant Blue G-250 dye. Obtained results, showed a good correlation between both methods with protein content being in the range of 39.8–47.1%. Characterization of neutral and acid saccharides from microalgae was conducted by phenol-sulfuric acid method at two wavelengths of 480 nm and 490 nm. The average concentration of neutral and acid saccharides under the optimal cultivation conditions was 19.5% and 26.1%, respectively. Subsequently, biomass residues are used as substrate for anaerobic digestion on the laboratory-scale. The methane concentration, which was measured on the daily bases, showed some variations for different samples after extraction steps but was in the range between 48% and 55%. CO₂ which is formed during the fermentation process and after the combustion in the Combined Heat and Power unit can potentially be used within the cultivation process as a carbon source for the photoautotrophic synthesis of biomass.

Keywords: Bioeconomy, lipids, microalgae, proteins, saccharides.

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Authors: F. Habib, A. Shokoohi

Abstract:

Urban problems are problems of organized complexity. Thus, many models and scientific methods to resolve urban problems are failed. This study is concerned with proposing of a fuzzy system driven approach for classification and solving urban problems. The proposed study investigated mainly the selection of the inputs and outputs of urban systems for classification of urban problems. In this research, five categories of urban problems, respect to fuzzy system approach had been recognized: control, polytely, optimizing, open and decision making problems. Grounded Theory techniques were then applied to analyze the data and develop new solving method for each category. The findings indicate that the fuzzy system methods are powerful processes and analytic tools for helping planners to resolve urban complex problems. These tools can be successful where as others have failed because both incorporate or address uncertainty and risk; complexity and systems interacting with other systems.

Keywords: Classification, complexity, Fuzzy theory, urban problems.

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: Globular protein, modulating function, white noise, winding probability.

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Authors: O. P. Misra, Preety Kalra

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It is well recognized that the green house gases such as Chlorofluoro Carbon (CFC), CH4, CO2 etc. are responsible directly or indirectly for the increase in the average global temperature of the Earth. The presence of CFC is responsible for the depletion of ozone concentration in the atmosphere due to which the heat accompanied with the sun rays are less absorbed causing increase in the atmospheric temperature of the Earth. The gases like CH4 and CO2 are also responsible for the increase in the atmospheric temperature. The increase in the temperature level directly or indirectly affects the dynamics of interacting species systems. Therefore, in this paper a mathematical model is proposed and analysed using stability theory to asses the effects of increasing temperature due to greenhouse gases on the survival or extinction of populations in a prey-predator system. A threshold value in terms of a stress parameter is obtained which determines the extinction or existence of populations in the underlying system.

Keywords: Equilibria, Green house gases, Model, Populations, Stability.

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Authors: Dhanashree Nansaheb Kharde, Justus Selwyn

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These days customer satisfaction plays vital role in any business. When customer searches for a product, significantly a junk of irrelevant information is what is given, leading to customer dissatisfaction. To provide exactly relevant information on the searched product, we are proposing a model of KaaS (Knowledge as a Service), which pre-processes the information using decision making paradigm using Multi-agents. Information obtained from various sources is taken to derive knowledge and they are linked to Cloud to capture new idea. The main focus of this work is to acquire relevant information (knowledge) related to product, then convert this knowledge into a service for customer satisfaction and deploy on cloud. For achieving these objectives we are have opted to use multi agents. They are communicating and interacting with each other, manipulate information, provide knowledge, to take decisions. The paper discusses about KaaS as an intelligent approach for Knowledge acquisition.

Keywords: Knowledge acquisition, multi-agents, intelligent user interface, ontology, intelligent agent.

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Authors: Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira, Marta A. S. Perez, Irina S. Moreira, António J. M.Ribeiro, Ana R. A. P. Neves, Maria J. Ramos, Pedro A. Fernandes

Abstract:

In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.

Keywords: Enzyme, Molecular Dynamics, Protein, Quantum Mechanics.

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