Search results for: protein stability prediction

Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation

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Authors: Zaide Montes Ortiz, Jorge Alberto Molina, Alejandro Reyes

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Insects are extremely successful organisms. A sophisticated olfactory system is in part responsible for their survival and reproduction. The detection of volatile organic compounds can positively or negatively affect many behaviors in insects. Compounds such as carbon dioxide (CO2), ammonium, indol, and lactic acid are essential for many species of mosquitoes like Anopheles gambiae in order to locate vertebrate hosts. For instance, in A. gambiae, the olfactory receptor AgOR2 is strongly activated by indol, which accounts for almost 30% of human sweat. On the other hand, in some insects of agricultural importance, the detection and identification of pheromone receptors (PRs) in lepidopteran species has become a promising field for integrated pest management. For example, with the disruption of the pheromone receptor, BmOR1, mediated by transcription activator-like effector nucleases (TALENs), the sensitivity to bombykol was completely removed affecting the pheromone-source searching behavior in male moths. Then, the detection and identification of olfactory receptors in the genomes of insects is fundamental to improve our understanding of the ecological interactions, and to provide alternatives in the integrated pests and vectors management. Hence, the objective of this study is to propose a bioinformatic workflow to enhance the detection and identification of potential olfactory receptors in genomes of relevant insects. Applying Hidden Markov models (Hmms) and different computational tools, potential candidates for pheromone receptors in Tuta absoluta were obtained, as well as potential carbon dioxide receptors in Rhodnius prolixus, the main vector of Chagas disease. This study showed the validity of a bioinformatic workflow with a potential to improve the identification of certain olfactory receptors in different orders of insects.

Keywords: bioinformatic workflow, insects, olfactory receptors, protein prediction

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Authors: B. D. Nkosi, T. F. Mutavhatsindi, J. J. Baloyi, R. Meeske, T. M. Langa, I. M. M. Malebana, M. D. Motiang

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Potato hash (PH), a by-product from food production industry, contains 188.4 g dry matter (DM)/kg and 3.4 g water soluble carbohydrate (WSC)/kg DM, and was mixed with wheat bran (70:30 as is basis) to provide 352 g DM/kg and 315 g WSC/kg DM. The materials were ensiled with or without silage additives in 1.5L anaerobic jars (3 jars/treatment) that were kept at 25-280 C for 3 months. Four types of silages were produced which were: control (no additive, denoted as T1), celluclast enzyme (denoted as T2), emsilage bacterial inoculant (denoted as T3) and silosolve bacterial inoculant (denoted as T4). Three jars per treatment were opened after 3 months of ensiling for the determination of nutritive values, fermentation characteristics and aerobic stability. Aerobic stability was done by exposing silage samples to air for 5 days. The addition of enzyme (T2) was reduced (P<0.05) silage pH, fiber fractions (NDF and ADF) while increasing (P < 0.05) residual WSC and lactic acid (LA) production, compared to other treatments. Silage produced had pH of < 4.0, indications of well-preserved silage. Bacterial inoculation (T3 and T4) improved (P < 0.05) aerobic stability of the silage, as indicated by increased number of hours and lower CO2 production, compared to other treatments. However, the aerobic stability of silage was worsen (P < 0.05) with the addition of an enzyme (T2). Further work to elucidate these effects on nutrient digestion and growth performance on ruminants fed the silage is needed.

Keywords: by-products, digestibility, feeds, inoculation, ruminants, silage

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Authors: Ehsan Mehryaar, Seyed Armin Motahari Tabari

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Without a doubt, soil shear strength is the most important property of the soil. The majority of fatal and catastrophic geological accidents are related to shear strength failure of the soil. Therefore, its prediction is a matter of high importance. However, acquiring the shear strength is usually a cumbersome task that might need complicated laboratory testing. Therefore, prediction of it based on common and easy to get soil properties can simplify the projects substantially. In this paper, A hybrid model based on the classification and regression tree algorithm and logistic regression is proposed where each leaf of the tree is an independent regression model. A database of 189 points for clay soil, including Moisture content, liquid limit, plastic limit, clay content, and shear strength, is collected. The performance of the developed model compared to the existing models and equations using root mean squared error and coefficient of correlation.

Keywords: model tree, CART, logistic regression, soil shear strength

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Authors: Said Boukais, Ali Kezmane, Kahil Amar, Mohand Hamizi, Hannachi Neceur Eddine

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This paper presents an analytical study on the behavior of rectangular reinforced concrete walls with an aspect ratio between one and tow. Several experiments on such walls have been selected to be studied. Database from various experiments were collected and nominal wall strengths have been calculated using formulas, such as those of the ACI (American), NZS (New Zealand), Mexican (NTCC), and Wood equation for shear and strain compatibility analysis for flexure. Subsequently, nominal ultimate wall strengths from the formulas were compared with the ultimate wall strengths from the database. These formulas vary substantially in functional form and do not account for all variables that affect the response of walls. There is substantial scatter in the predicted values of ultimate strength. New semi empirical equation are developed using data from tests of 46 walls with the objective of improving the prediction of ultimate strength of walls with the most possible accuracy and for all failure modes.

Keywords: prediction, ultimate strength, reinforced concrete walls, walls, rectangular walls

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin 1), whose disruption leads to increased drought stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1 is regulated in response to drought stress by alternative splicing.

Keywords: alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance

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Authors: Abdelhakam A. Noreldien, Sakhr B. Abudarag, Muslim S. Eltoum, Salih O. Osman

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This paper presents an analytical study of Small Unmanned Aerial Vehicle (SUAV) dynamic stability derivatives. Simulating SUAV dynamics and analyzing its behavior at the earliest design stages is too important and more efficient design aspect. The approach suggested in this paper is using the wind tunnel experiment to collect the aerodynamic data and get the dynamic stability derivatives. AutoCAD Software was used to draw the case study (wildlife surveillance SUAV). The SUAV is scaled down to be 0.25% of the real SUAV dimensions and converted to a wind tunnel model. The model was tested in three different speeds for three different attitudes which are; pitch, roll and yaw. The wind tunnel results were then used to determine the case study stability derivative values, and hence it used to calculate the roots of the characteristic equation for both longitudinal and lateral motions. Finally, the characteristic equation roots were found and discussed in all possible cases.

Keywords: model, simulating, SUAV, wind tunnel

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Authors: Salman Akrokayan

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Synthetic cDNA (ScDNA) of granulocyte colony-stimulating factor (G-CSF) was constructed using a DNA synthesizer with the aim to increase its expression level. 5' end of the ScDNA of G-CSF coding region was modified by decreasing the GC content without altering the predicted amino acids sequence. The identity of the resulting protein from ScDNA was confirmed by the highly specific enzyme-linked immunosorbent assay. In conclusion, a synthetic G-CSF cDNA in combination with the recombinant DNA protocol offers a rapid and reliable strategy for synthesizing the target protein. However, the commercial utilization of this methodology requires rigorous validation and quality control.

Keywords: synthetic cDNA, recombinant G-CSF, cloning, gene expression

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Authors: Carlos A. C. G. Neto, Natan C. G. e Silva , Thaís de O. Costa, Luciana R. B. Gonçalves, Maria V. P. Rocha

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β-galactosidases (E.C. 3.2.1.23) are enzymes that have attracted by catalyzing the hydrolysis of lactose and in producing galacto-oligosaccharides by favoring transgalactosylation reactions. These enzymes, when immobilized, can have some enzymatic characteristics substantially improved, and the coating of supports with multifunctional polymers is a promising alternative to enhance the stability of the biocatalysts, among which polyethylenimine (PEI) stands out. PEI has certain properties, such as being a flexible polymer that suits the structure of the enzyme, giving greater stability, especially for multimeric enzymes such as β-galactosidases. Besides that, protects them from environmental variations. The use of chitosan support coated with PEI could improve the catalytic efficiency of β-galactosidase from Kluyveromyces lactis in the transgalactosylation reaction for the production of prebiotics, such as lactulose since this strain is more effective in the hydrolysis reaction. In this context, the aim of the present work was first to develop biocatalysts of β-galactosidase from K. lactis immobilized on chitosan-coated with PEI, determining the immobilization parameters, its operational and thermal stability, and then to apply it in hydrolysis and transgalactolisation reactions to produce lactulose using whey as a substrate. The immobilization of β-galactosidase in chitosan previously functionalized with 0.8% (v/v) glutaraldehyde and then coated with 10% (w/v) PEI solution was evaluated using an enzymatic load of 10 mg protein per gram support. Subsequently, the hydrolysis and transgalactosylation reactions were conducted at 50 °C, 120 RPM for 20 minutes, using whey supplemented with fructose at a ratio of 1:2 lactose/fructose, totaling 200 g/L. Operational stability studies were performed in the same conditions for 10 cycles. Thermal stabilities of biocatalysts were conducted at 50 ºC in 50 mM phosphate buffer, pH 6.6 with 0.1 mM MnCl2. The biocatalyst whose support was coated was named CHI_GLU_PEI_GAL, and the one that was not coated was named CHI_GLU_GAL. The coating of the support with PEI considerably improved the parameters of immobilization. The immobilization yield increased from 56.53% to 97.45%, biocatalyst activity from 38.93 U/g to 95.26 U/g and the efficiency from 3.51% to 6.0% for uncoated and coated support, respectively. The biocatalyst CHI_GLU_PEI_GAL was better than CHI_GLU_GAL in the hydrolysis of lactose and production of lactulose, converting 97.05% of lactose at 5 min of reaction and producing 7.60 g/L lactulose in the same time interval. QUI_GLU_PEI_GAL biocatalyst was stable in the hydrolysis reactions of lactose during the 10 cycles evaluated, converting 73.45% lactose even after the tenth cycle, and in the lactulose production was stable until the fifth cycle evaluated, producing 10.95 g/L lactulose. However, the thermal stability of CHI_GLU_GAL biocatalyst was superior, with a half-life time 6 times higher, probably because the enzyme was immobilized by covalent bonding, which is stronger than adsorption (CHI_GLU_PEI_GAL). Therefore, the strategy of coating the supports with PEI has proven to be effective for the immobilization of β-galactosidase from K. lactis, considerably improving the immobilization parameters, as well as, the catalytic action of the enzyme. Besides that, this process can be economically viable due to the use of an industrial residue as a substrate.

Keywords: β-galactosidase, immobilization, kluyveromyces lactis, lactulose, polyethylenimine, transgalactosylation reaction, whey

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Authors: Pawan Kumar Sharma, J. Stephan Sampath Kumar, S. Anand, Chandana B. L.

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Protein is the major component for the success in culture of shrimp and fishes. Apparently, excess dietary protein is undesirable, as it not only enhances the production cost but also leads to water quality deterioration. A field survey was conducted with aqua farmers of Kerala, India, a leading state in coastal aquaculture, to assess the role of protein component in feed that can be efficiently and effectively managed for sustainable aquaculture. The study showed an average feed amount of 13.55 ± 2.16 tonnes per hectare was being used by the farmers of Kerala. The average feed cost percentage of Rs. 57.76 ± 13.46 /kg was invested for an average protein level of 36.26 % ± 0.082 in the feed and Rs.78.95 ± 3.086 per kilogram of feed was being paid by the farmers. Study revealed that replacement of fish meal and fish oil within shrimp aquafeeds with alternative protein, and lipid sources can only be achieved if changes are made in the basic shrimp culturing practices, such as closed farming system through water recycling or zero-water exchange, and by maximizing in-situ, floc and natural food production within the culture system. The upshot of such production systems is that imports of high-quality feed ingredients and aqua feeds can eventually be eliminated, and the utilization of locally available feed ingredients from agricultural by-products can be greatly improved and maximized. The promotion of closed shrimp production systems would also greatly reduce water use and increase shrimp production per unit area but would necessitate the continuous provision of electricity for aeration during production. Alternative energy sources such as solar power might be used, and resource poor farming communities should also explore wind energy for use. The study concluded that farm made feed and closed farming systems are essential for the sustainability and profitability of the aquaculture industry.

Keywords: aqua feeds, floc, fish meal, protein, zero-water exchange

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Authors: Anuar Ishak

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The mixed convection stagnation point flow toward a vertical plate is investigated. The external flow impinges normal to the heated plate and the surface temperature is assumed to vary linearly with the distance from the stagnation point. The governing partial differential equations are transformed into a set of ordinary differential equations, which are then solved numerically using MATLAB routine boundary value problem solver bvp4c. Numerical results show that dual solutions are possible for a certain range of the mixed convection parameter. A stability analysis is performed to determine which solution is linearly stable and physically realizable.

Keywords: dual solutions, heat transfer, mixed convection, stability analysis

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Authors: Kwang Chun, John Kemeny

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Light detection and ranging (LiDAR) has been a prevalent remote-sensing technology applied in the geological fields due to its high precision and ease of use. One of the major applications is to use the detailed geometrical information of underground structures as a basis for the generation of a three-dimensional numerical model that can be used in a geotechnical stability analysis such as FEM or DEM. To date, however, straightforward techniques in reconstructing the numerical model from the scanned data of the underground structures have not been well established or tested. In this paper, we propose a comprehensive approach integrating all the various processes, from LiDAR scanning to finite element numerical analysis. The study focuses on converting LiDAR 3D point clouds of geologic structures containing complex surface geometries into a finite element model. This methodology has been applied to Kartchner Caverns in Arizona, where detailed underground and surface point clouds can be used for the analysis of underground stability. Numerical simulations were performed using the finite element code Abaqus and presented by 3D computing visualization solution, ParaView. The results are useful in studying the stability of all types of underground excavations including underground mining and tunneling.

Keywords: finite element analysis, LiDAR, remote-sensing, scientific visualization, underground stability

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Authors: Sunita Makchuchit, Arunporn Itharat

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Prasaprohyai, a Thai traditional medicine preparation listed in the Thai National List of Essential Medicines, is commonly used for treatment of fever and colds. Prasaprohyai preparation consists of 21 different plants, with Kaempferia galanga (50% w/w) as the main ingredient. The objective of this study was to investigate the anti-allergic activity of the crude extract from Prasaprohyai after accelerated stability test procedure. The method of extract used maceration in 95% ethanol and the crude extract was kept under accelerated condition at 40 ± 2 oC and 75 ± 5% relative humidity (RH) for six months. After six months of storage at 40 oC, the crude sample in various storage times (0, 15, 30, 45, 60, 90, 120, 150 and 180 days) were investigated for anti-allergic activity using IgE-sensitized RBL-2H3 cell lines. The results showed that the stability of crude ethanolic extract from Prasaprohyai under accelerated testing had no significant effect of anti-allergic activity when compared with day 0. The results showed that the ethanolic extract could be stored for two years at room temperature without loss of activity.

Keywords: accelerated stability, anti-allergy, prasaprohyai, RBL-2H3 cell lines

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Authors: Pemika Ketsuwan, Pitt Supaphol, Manit Nithitanakul

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A typical used of ethylene methyl acrylate (EMA) gasket is in the manufacture of optical lens, and often, they are deteriorated rapidly due to high temperature during the process. The objective of this project is to improve the thermal stability of the EMA copolymer gasket by preparing EMA with cellulose and silica composites. Hydroxy propyl methyl cellulose (HPMC) and Carboxy methyl cellulose (CMC) were used in preparing of EMA/cellulose composites and fumed silica (SiO2) was used in preparing EMA/silica composites with different amounts of filler (3, 5, 7, 10, 15 wt.%), using a twin screw extruder at 160 °C and the test specimens were prepared by the injection molding machine. The morphology and dispersion of fillers in the EMA matrix were investigated by field emission scanning electron microscopy (FESEM). The thermal stability of the composite was determined by thermal gravimetric analysis (TGA), and differential scanning calorimeter (DSC). Mechanical properties were evaluated by tensile testing. The developed composites were found to enhance thermal and mechanical properties when compared to that of the EMA copolymer alone.

Keywords: ethylene methyl acrylate, HPMC, Silica, Thermal stability

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Authors: Massimiliano Biagini, Marco Spinsanti, Gabriella De Angelis, Sara Tomei, Ilaria Ferlenghi, Maria Scarselli, Alessia Biolchi, Alessandro Muzzi, Brunella Brunelli, Silvana Savino, Marzia M. Giuliani, Isabel Delany, Paolo Costantino, Rino Rappuoli, Vega Masignani, Nathalie Norais

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The gram-negative bacterium Neisseria meningitidis serogroup B (MenB) is an exclusively human pathogen representing the major cause of meningitides and severe sepsis in infants and children but also in young adults. This pathogen is usually present in the 30% of healthy population that act as a reservoir, spreading it through saliva and respiratory fluids during coughing, sneezing, kissing. Among surface-exposed protein components of this diplococcus, factor H binding protein is a lipoprotein proved to be a protective antigen used as a component of the recently licensed Bexsero vaccine. fHbp is a highly variable meningococcal protein: to reflect its remarkable sequence variability, it has been classified in three variants (or two subfamilies), and with poor cross-protection among the different variants. Furthermore, the level of fHbp expression varies significantly among strains, and this has also been considered an important factor for predicting MenB strain susceptibility to anti-fHbp antisera. Different methods have been used to assess fHbp expression on meningococcal strains, however, all these methods use anti-fHbp antibodies, and for this reason, the results are affected by the different affinity that antibodies can have to different antigenic variants. To overcome the limitations of an antibody-based quantification, we developed a quantitative Mass Spectrometry (MS) approach. Selected Reaction Monitoring (SRM) recently emerged as a powerful MS tool for detecting and quantifying proteins in complex mixtures. SRM is based on the targeted detection of ProteoTypicPeptides (PTPs), which are unique signatures of a protein that can be easily detected and quantified by MS. This approach, proven to be highly sensitive, quantitatively accurate and highly reproducible, was used to quantify the absolute amount of fHbp antigen in total extracts derived from 105 clinical isolates, evenly distributed among the three main variant groups and selected to be representative of the fHbp circulating subvariants around the world. We extended the study at the genetic level investigating the correlation between the differential level of expression and polymorphisms present within the genes and their promoter sequences. The implications of fHbp expression on the susceptibility of the strain to killing by anti-fHbp antisera are also presented. To date this is the first comprehensive fHbp expression profiling in a large panel of Neisseria meningitidis clinical isolates driven by an antibody-independent MS-based methodology, opening the door to new applications in vaccine coverage prediction and reinforcing the molecular understanding of released vaccines.

Keywords: quantitative mass spectrometry, Neisseria meningitidis, vaccines, bexsero, molecular epidemiology

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Authors: Mona Hejazi, Ali Motie Nasrabadi

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Epilepsy is a persistent neurological disorder that affects more than 50 million people worldwide. Hence, there is a necessity to introduce an efficient prediction model for making a correct diagnosis of the epileptic seizure and accurate prediction of its type. In this study we consider how the Effective Connectivity (EC) patterns obtained from intracranial Electroencephalographic (EEG) recordings reveal information about the dynamics of the epileptic brain and can be used to predict imminent seizures, as this will enable the patients (and caregivers) to take appropriate precautions. We use this definition because we believe that effective connectivity near seizures begin to change, so we can predict seizures according to this feature. Results are reported on the standard Freiburg EEG dataset which contains data from 21 patients suffering from medically intractable focal epilepsy. Six channels of EEG from each patients are considered and effective connectivity using Directed Transfer Function (DTF) and Granger Causality (GC) methods is estimated. We concentrate on effective connectivity standard deviation over time and feature changes in five brain frequency sub-bands (Alpha, Beta, Theta, Delta, and Gamma) are compared. The performance obtained for the proposed scheme in predicting seizures is: average prediction time is 50 minutes before seizure onset, the maximum sensitivity is approximate ~80% and the false positive rate is 0.33 FP/h. DTF method is more acceptable to predict epileptic seizures and generally we can observe that the greater results are in gamma and beta sub-bands. The research of this paper is significantly helpful for clinical applications, especially for the exploitation of online portable devices.

Keywords: effective connectivity, Granger causality, directed transfer function, epilepsy seizure prediction, EEG

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Authors: Sagir M. Yusuf, Chris Baber

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In this paper, we describe how to achieve knowledge understanding and prediction (Situation Awareness (SA)) for multiple-agents conducting searching activity using Bayesian inferential reasoning and learning. Bayesian Belief Network was used to monitor agents' knowledge about their environment, and cases are recorded for the network training using expectation-maximisation or gradient descent algorithm. The well trained network will be used for decision making and environmental situation prediction. Forest fire searching by multiple UAVs was the use case. UAVs are tasked to explore a forest and find a fire for urgent actions by the fire wardens. The paper focused on two problems: (i) effective agents’ path planning strategy and (ii) knowledge understanding and prediction (SA). The path planning problem by inspiring animal mode of foraging using Lévy distribution augmented with Bayesian reasoning was fully described in this paper. Results proof that the Lévy flight strategy performs better than the previous fixed-pattern (e.g., parallel sweeps) approaches in terms of energy and time utilisation. We also introduced a waypoint assessment strategy called k-previous waypoints assessment. It improves the performance of the ordinary levy flight by saving agent’s resources and mission time through redundant search avoidance. The agents (UAVs) are to report their mission knowledge at the central server for interpretation and prediction purposes. Bayesian reasoning and learning were used for the SA and results proof effectiveness in different environments scenario in terms of prediction and effective knowledge representation. The prediction accuracy was measured using learning error rate, logarithm loss, and Brier score and the result proves that little agents mission that can be used for prediction within the same or different environment. Finally, we described a situation-based knowledge visualization and prediction technique for heterogeneous multi-UAV mission. While this paper proves linkage of Bayesian reasoning and learning with SA and effective searching strategy, future works is focusing on simplifying the architecture.

Keywords: Levy flight, distributed constraint optimization problem, multi-agent system, multi-robot coordination, autonomous system, swarm intelligence

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Authors: Natalia Caldeira De Carvalho, Tassia Batista Pessato, Luis Gustavo R. Fernandes, Ricardo L. Zollner, Flavia Maria Netto

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Protein hydrolysates are ingredients of enteral diets and hypoallergenic formulas. Enzymatic hydrolysis is the most commonly used method for reducing the antigenicity of milk protein. The antigenicity and physicochemical characteristics of the protein hydrolysates depend on the reaction parameters. Among them, pH has been pointed out as of the major importance. Hydrolysis reaction in laboratory scale is commonly carried out under controlled pH (pH-stat). However, from the industrial point of view, controlling pH during hydrolysis reaction may be infeasible. This study evaluated the impact of pH control on the physicochemical properties and antigenicity of the hydrolysates of whey proteins with Alcalase. Whey protein isolate (WPI) solutions containing 3 and 7 % protein (w/v) were hydrolyzed with Alcalase 50 and 100 U g-1 protein at 60°C for 180 min. The reactions were carried out under controlled and uncontrolled pH conditions. Hydrolyses performed under controlled pH (pH-stat) were initially adjusted and maintained at pH 8.5. Hydrolyses carried out without pH control were initially adjusted to pH 8.5. Degree of hydrolysis (DH) was determined by OPA method, peptides profile was evaluated by HPLC-RP, and molecular mass distribution by SDS-PAGE/Tricine. The residual α-lactalbumin (α-La) and β-lactoglobulin (β-Lg) concentrations were determined using commercial ELISA kits. The specific IgE and IgG binding capacity of hydrolysates was evaluated by ELISA technique, using polyclonal antibodies obtained by immunization of female BALB/c mice with α-La, β-Lg and BSA. In hydrolysis under uncontrolled pH, the pH dropped from 8.5 to 7.0 during the first 15 min, remaining constant throughout the process. No significant difference was observed between the DH of the hydrolysates obtained under controlled and uncontrolled pH conditions. Although all hydrolysates showed hydrophilic character and low molecular mass peptides, hydrolysates obtained with and without pH control exhibited different chromatographic profiles. Hydrolysis under uncontrolled pH released, predominantly, peptides between 3.5 and 6.5 kDa, while hydrolysis under controlled pH released peptides smaller than 3.5 kDa. Hydrolysis with Alcalase under all conditions studied decreased by 99.9% the α-La and β-Lg concentrations in the hydrolysates detected by commercial kits. In general, β-Lg concentrations detected in the hydrolysates obtained under uncontrolled pH were significantly higher (p<0.05) than those detected in hydrolysates produced with pH control. The anti-α-La and anti-β-Lg IgE and IgG responses to all hydrolysates decreased significantly compared to WPI. Levels of specific IgE and IgG to the hydrolysates were below 25 and 12 ng ml-1, respectively. Despite the differences in peptide composition and α-La and β-Lg concentrations, no significant difference was found between IgE and IgG binding capacity of hydrolysates obtained with or without pH control. These results highlight the impact of pH on the hydrolysates characteristics and their concentrations of antigenic protein. Divergence between the antigen detection by commercial ELISA kits and specific IgE and IgG binding response was found in this study. This result shows that lower protein detection does not imply in lower protein antigenicity. Thus, the use of commercial kits for allergen contamination analysis should be cautious.

Keywords: allergy, enzymatic hydrolysis, milk protein, pH conditions, physicochemical characteristics

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Authors: Rehab Abdulmajed, Amr Hamada, Ahmed Elsaid, Hisashi Hayakawa, Ayman Mahrous

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Solar emissions have a high impact on the Earth’s magnetic field, and the prediction of solar events is of high interest. Various techniques have been used in the prediction of solar wind using mathematical models, MHD models, and neural network (NN) models. This study investigates the coronal hole (CH) derived high-speed streams (HSSs) and their correlation to the CH area and create a neural network model to predict the HSSs. Two different algorithms were used to compare different models to find a model that best simulates the HSSs. A dataset of CH synoptic maps through Carrington rotations 1601 to 2185 along with Omni-data set solar wind speed averaged over the Carrington rotations is used, which covers Solar cycles (sc) 21, 22, 23, and most of 24.

Keywords: artificial neural network, coronal hole area, feed-forward neural network models, solar high speed streams

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Authors: I. Sani, A. Abdulhamid, F. Bello, Isah M. Fakai

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This research has focused on the application of green fluorescent protein (GFP) as a new technique for direct monitoring of fermentation processes involving cultured bacteria. To use GFP as a sensor for pH and oxygen, percentage ratio of red fluorescence to green (% R/G) was evaluated. Assessing the magnitude of the % R/G ratio in relation to low or high pH and oxygen concentration, the bacterial strains were cultivated under aerobic and anaerobic conditions. SCC1 strains of E. coli were grown in a 5 L laboratory fermenter, and during the fermentation, the pH and temperature were controlled at 7.0 and 370C respectively. Dissolved oxygen tension (DOT) was controlled between 15-100% by changing the agitation speed between 20-500 rpm respectively. Effect of reducing the DOT level from 100% to 15% was observed after 4.5 h fermentation. There was a growth arrest as indicated by the decrease in the OD650 at this time (4.5-5 h). The relative fluorescence (green) intensity was decreased from about 460 to 420 RFU. However, %R/G ratio was significantly increased from about 0.1% to about 0.25% when the DOT level was decreased to 15%. But when the DOT was changed to 100%, a little increase in the RF and decrease in the %R/G ratio were observed. Therefore, GFP can effectively detect and indicate any change in pH and oxygen level during fermentation processes.

Keywords: Escherichia coli SCC1, fermentation process, green fluorescent protein, red fluorescence

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Authors: Mohammed Alasel, Michael Keusgen

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Gold is a noble metal; in its nano-scale level (e.g. spherical nanoparticles), the conduction electrons are triggered to collectively oscillate with a resonant frequency when certain wavelengths of electromagnetic radiation interact with its surface; this phenomenon is known as surface plasmon resonance (SPR). SPR is responsible for giving the gold nanoparticles its intense red color depending mainly on its size, shape and distance between nanoparticles. A decreased distance between gold nanoparticles results in aggregation of them causing a change in color from red to blue. This aggregation enables gold nanoparticles to serve as a sensitive biosensoric indicator. In the proposed work, gold nanoparticles were modified with two proteins: i) Borrelia antigen, variable lipoprotein surface-exposed protein (VlsE), and ii) protein A. VlsE antigen induces a strong antibody response against Lyme disease and can be detected from early to late phase during the disease in humans infected with Borrelia. In addition, it shows low cross-reaction with the other non-pathogenic Borrelia strains. The high specificity of VlsE antigen to anti-Borrelia antibodies, combined simultaneously with the high specificity of protein A to the Fc region of all IgG human antibodies, was utilized to develop a rapid test for serological point of care diagnosis of borreliosis in human serum. Only in the presence of anti-Borrelia antibodies in the serum probe, an aggregation of gold nanoparticles can be observed, which is visible by a concentration-dependent colour shift from red (low IgG) to blue (high IgG). Experiments showed it is clearly possible to distinguish between positive and negative sera samples using a simple suspension of the two-protein modified gold nanoparticles in a very short time (30 minutes). The proposed work showed the potential of using such modified gold nanoparticles generally for serological diagnosis. Improved specificity and reduced assay time can be archived in applying increased salt concentrations combined with decreased pH values (pH 5).

Keywords: gold nanoparticles, gold aggregation, serological diagnosis, protein A, lyme borreliosis

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Authors: Kübra Aktaş, Nihat Akin

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Tarhana is a traditional Turkish fermented food. It is widely consumed as soup and includes many different ingredients such as wheat flour, various vegetables, and spices, yoghurt, bakery yeast. It can also be enriched by adding other ingredients. Thus, its nutritional properties can be enhanced. In this study, tarhana was supplemented with two different types of brans (rice bran and corn bran) and WPC (whey protein concentrate powder) to improve its nutritional and functional properties. Some chemical properties of tarhana containing two different brans and their levels (0, 5, 10 and 15%) and WPC (0, 5, 10%) were investigated. The results indicated that addition of WPC increased ash content in tarhanas which were fortified with rice and corn bran. The highest antioxidant and phenolic content values were obtained with addition of rice bran in tarhana formulation. Compared to tarhana with corn bran, rice bran addition gave higher oil content values. The cellulose content of tarhana samples was determined between 0.75% and 2.74% and corn bran showed an improving effect on cellulose contents of samples. In terms of protein content, addition of WPC into the tarhana raised protein content for the samples.

Keywords: corn, rice, tarhana, whey

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Authors: Katerina H. Takova, Ivan N. Minkov, Gergana G. Zahmanova

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Molecular farming is the production of recombinant proteins in plants with the aim to use the protein as a purified product, crude extract or directly in the planta. Plants gain more attention as expression systems compared to other ones due to the cost effective production of pharmaceutically important proteins, appropriate post-translational modifications, assembly of complex proteins, absence of human pathogens to name a few. In addition, transient expression in plant leaves enables production of recombinant proteins within few weeks. Hepatitis E virus (HEV) is a causative agent of acute hepatitis. HEV causes epidemics in developing countries and is primarily transmitted through the fecal-oral route. Presently, all efforts for development of Hepatitis E vaccine are focused on the Open Read Frame 2 (ORF2) capsid protein as it contains epitopes that can induce neutralizing antibodies. For our purpose, we used the CMPV-based vector-pEAQ-HT for transient expression of HEV ORF2 in Nicotiana benthamina. Different molecular analysis (Western blot and ELISA) showed that HEV ORF2 capsid protein was expressed in plant tissue in high-yield up to 1g/kg of fresh leaf tissue. Electron microscopy showed that the capsid protein spontaneously assembled in low abundance virus-like particles (VLPs), which are highly immunogenic structures and suitable for vaccine development. The expressed protein was recognized by both human and swine HEV positive sera and can be used as a diagnostic reagent for the detection of HEV infection. Production of HEV capsid protein in plants is a promising technology for further HEV vaccine investigations. Here, we reported for a rapid high-yield transient expression of a recombinant protein in plants suitable for vaccine production as well as a diagnostic reagent. Acknowledgments -The authors’ research on HEV is supported with grants from the Project PlantaSYST under the Widening Program, H2020 as well as under the UK Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Grant ‘Understanding and Exploiting Plant and Microbial Secondary Metabolism’ (BB/J004596/1). The authors want to thank Prof. George Lomonossoff (JIC, Norwich, UK) for his contribution.

Keywords: hepatitis E virus, plant molecular farming, transient expression, vaccines

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Authors: N. Zeinalzadeh, Mahdi Sadeghi

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Enterotoxigenic Escherichia coli (ETEC) is the most common cause of non-inflammatory diarrhea in the developing countries, resulting in approximately 20% of all diarrheal episodes in children in these areas. ST is one of the most important virulence factors and CFA/I is one of the frequent colonization factors that help to process of ETEC infection. ST and CfaB (CFA/I subunit) are among vaccine candidates against ETEC. So, ST because of its small size is not a good immunogenic in the natural form. However to increase its immunogenic potential, here we explored candidate positions for ST insertion in CfaB sequence. After bioinformatics analysis, one of the candidate positions was selected and the chimeric gene (cfaB*st) sequence was synthesized and expressed in E. coli BL21 (DE3). The chimeric recombinant protein was purified with Ni-NTA columns and characterized with western blot analysis. The residue 74-75 of CfaB sequence could be a good candidate position for ST and other epitopes insertion.

Keywords: bioinformatics, CFA/I, enterotoxigenic E. coli, ST toxoid

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Authors: Kongrat Nokkaew

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This article assessed the surface erosion and stability of cut and fill slope in the excavation of the detention basin, Kalasin Province, Thailand. The large excavation project was built to enlarge detention basin for relieving repeated flooding and drought which usually happen in this area. However, at the end of the 1st rainstorm season, severely erosions slope failures were widespread observed. After investigation, the severity of erosions and slope failure were classified into five level from sheet erosion (Level 1), rill erosion (Level 2, 3), gully erosion (Level 4), and slope failure (Level 5) for proposing slope remediation. The preliminary investigation showed that lack of runoff control were the major factors of the surface erosions while insufficient compacted of the fill slope leaded to slopes failures. The slope stability of four selected slope failure was back calculated by using Simplified Bishop with Seep-W. The result show that factor of safety of slope located on non-plasticity sand was less than one, representing instability of the embankment slope. Such analysis agreed well with the failures observed in the field.

Keywords: surface erosion, slope stability, detention basin, cut and fill

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Authors: Muhammad Arifur Rahman, Talukdar M. Waliullah, Takashi Ushimaru

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Nucleophagy selectively degrades nuclear materials, especially nucleolus after nutrient starvation or inactivation of TORC1 kinase in budding yeast. Budding yeast phosphatidate (PA) phosphatase Pah1 that converts PA to diacylglycerol is essential for partitioning of lipid precursors between membrane and storage that is crucial for many aspects of cell growth and development. Pah1 is required for nuclear/ER membrane biogenesis and vacuole function, but whether Pah1 and its activator Nem1/Spo7 protein phosphatase complex are involved in autophagy is largely unknown. Loss of Pah1 causes expansion of the nucleus and fragmentation of the vacuole. Here we show that Pah1 is required for bulk autophagy and nucleophagy after TORC1 inactivation. Loss of Pah1 impaired nucleophagy severely and bulk autophagy to a lesser extent. Loss of the Pah1 activator Nem1-Spo7 protein phosphatase exhibited similar features.

Keywords: autophagy, Nem1/Spo7 phosphatase, Pah1, nucleophagy, TORC1

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Authors: Brahim-Fares Zaidi, Malika Boudraa, Sid-Ahmed Selouani

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Our work aims to improve our Automatic Recognition System for Dysarthria Speech (ARSDS) based on the Hidden Models of Markov (HMM) and the Hidden Markov Model Toolkit (HTK) to help people who are sick. With pronunciation problems, we applied two techniques of speech parameterization based on Mel Frequency Cepstral Coefficients (MFCC's) and Perceptual Linear Prediction (PLP's) and concatenated them with JITTER and SHIMMER coefficients in order to increase the recognition rate of a dysarthria speech. For our tests, we used the NEMOURS database that represents speakers with dysarthria and normal speakers.

Keywords: hidden Markov model toolkit (HTK), hidden models of Markov (HMM), Mel-frequency cepstral coefficients (MFCC), perceptual linear prediction (PLP’s)

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Authors: Nijole Savickiene, Antonella Di Sotto, Gabriela Mazzanti, Rasa Starselskyte, Silvia Di Giacomo, Annabella Vitalone

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Plant lectins are non-enzymic and non-immune origin proteins that specifically recognize and bind to various sugar structures and possess the activity to agglutinate cells and/or precipitate polysaccharides and glycoconjugates. The emerging evidences showed that plant lectins contribute not only to tumour cell recognition but also to cell adhesion and localization, to signal transduction, to mitogenic cytotoxicity and apoptosis. Among chitin-binding lectins, the Urtica dioica agglutinin (UDA), which is a complex of different isoforms, has been poorly studied for its biological activity. In this context and according to the increasing interest for lectins as novel antitumor drugs, present paper aimed at evaluating the potential antimutagenic activity of a lectin-like glycoprotein-enriched fraction from aerial part of Urtica dioica L. Aim: to evaluate the potential chemopreventive properties of a protein - lectin fraction from the aerial part of Urtica dioica. Materials and methods: Protein – lectin fraction has been tested for the antimutagenic activity in bacteria (50–800 mg/plate; Ames test by the preincubation method) and for the cytotoxicity on human hepatoma HepG2 cells (0.06–2 mg/mL; 24 and 48 h incubation). Results: Protein – lectin fraction from stinging nettle was not cytotoxic on HepG2 cells up to 2 mg/mL; conversely, it exhibited a strong antimutagenic activity against the mutagen 2-aminoanthracene (2AA) in all strains tested (maximum inhibition of 56.78 and 61% in TA98, TA100, and WP2uvrA strains, respectively, at 800 mg/plate). Discussion and conclusions: Protein – lectin fraction from Urtica dioica L. possesses antimutagenic and radical scavenging properties. Being 2AA a pro-carcinogenic agent, we hypothesize that the antimutagenicity of it can be due to the inhibition of CYP450-isoenzymes, involved in the mutagen bioactivation.

Keywords: lectins, antimutagenicity, chemoprevention, Urtica dioica

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Authors: Paschal A. Ochang, Emmanuel C. Oji

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The Duffing’s Equation is a second order system that is very important because they are fundamental to the behaviour of higher order systems and they have applications in almost all fields of science and engineering. In the biological area, it is useful in plant stem dependence and natural frequency and model of the Brain Crash Analysis (BCA). In Engineering, it is useful in the study of Damping indoor construction and Traffic lights and to the meteorologist it is used in the prediction of weather conditions. However, most Problems in real life that occur are non-linear in nature and may not have analytical solutions except approximations or simulations, so trying to find an exact explicit solution may in general be complicated and sometimes impossible. Therefore we aim to find out if it is possible to obtain one analytical fixed point to the non-linear ordinary equation using fixed point analytical method. We started by exposing the scope of the Duffing’s equation and other related works on it. With a major focus on the fixed point and fixed point iterative scheme, we tried different iterative schemes on the Duffing’s Equation. We were able to identify that one can only see the fixed points to a Damped Duffing’s Equation and not to the Undamped Duffing’s Equation. This is because the cubic nonlinearity term is the determining factor to the Duffing’s Equation. We finally came to the results where we identified the stability of an equation that is damped, forced and second order in nature. Generally, in this research, we approximate the solution of Duffing’s Equation by converting it to a system of First and Second Order Ordinary Differential Equation and using Fixed Point Iterative approach. This approach shows that for different versions of Duffing’s Equations (damped), we find fixed points, therefore the order of computations and running time of applied software in all fields using the Duffing’s equation will be reduced.

Keywords: damping, Duffing's equation, fixed point analysis, second order differential, stability analysis

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Authors: Tzan-Chain Lee

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Seeds are non-leaves green tissues. Photosynthesis begins with light absorption by chlorophyll and then the energy transfer between two pigment-protein complexes (PPC). Most studies of photosynthesis and PPC expression were focused on leaves; however, during seeds’ development were rare. Developed seeds from beginning pod (stage R3) to dried seed (stage R8), and the dried seed after sowing for 1-4 day, were analyzed for their chlorophyll contents. Thornber and MARS gel systems analysis compositions of PPC. Chlorophyll fluorescence was used to detect maximal photosynthetic efficiency (Fv/Fm). During soybean and black soybean seeds development (stages R3-R6), Fv/Fm up to 0.8, and then down-regulated after full seed (stage R7). In dried seed (stage R8), the two plant seeds lost photosynthetic activity (Fv/Fm=0), but chlorophyll degradation only occurred in soybean after full seed. After seeds sowing for 4 days, chlorophyll drastically increased in soybean seeds, and Fv/Fm recovered to 0.8 in the two seeds. In PPC, the two soybean seeds contained all PPC during seeds development (stages R3-R6), including CPI, CPII, A1, AB1, AB2, and AB3. However, many proteins A1, AB1, AB2, and CPI were totally missing in the two dried seeds (stage R8). The deficiency of these proteins in dried seeds might be caused by the incomplete photosynthetic activity. After seeds germination and seedling exposed to light for 4 days, all PPC were recovered, suggesting that completed PPC took place in the two soybean seeds. This study showed the reversibility of photosynthetic activity and pigment-protein complexes during soybean and black soybean seeds development.

Keywords: light-harvesting complex, pigment–protein complexes, soybean cotyledon, grana development

Procedia PDF Downloads 149