Search results for: sterol regulatory element binding proteins

Authors: Sofia G. Meirinho, Luis G. Dias, António M. Peres, Lígia R. Rodrigues

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The emerging development of electrochemical aptasen sors has enabled the easy and fast detection of protein biomarkers in standard and real samples. Biomarkers are produced by body organs or tumours and provide a measure of antigens on cell surfaces. When detected in high amounts in blood, they can be suggestive of tumour activity. These biomarkers are more often used to evaluate treatment effects or to assess the potential for metastatic disease in patients with established disease. Osteopontin (OPN) is a protein found in all body fluids and constitutes a possible biomarker because its overexpression has been related with breast cancer evolution and metastasis. Currently, biomarkers are commonly used for the development of diagnostic methods, allowing the detection of the disease in its initial stages. A previously described RNA aptamer was used in the current work to develop a simple and sensitive electrochemical aptasensor with high affinity for human OPN. The RNA aptamer was biotinylated and immobilized on a gold electrode by avidin-biotin interaction. The electrochemical signal generated from the aptamer–target molecule interaction was monitored electrochemically using cyclic voltammetry in the presence of [Fe (CN) 6]−3/− as a redox probe. The signal observed showed a current decrease due to the binding of OPN. The preliminary results showed that this aptasensor enables the detection of OPN in standard solutions, showing good selectivity towards the target in the presence of others interfering proteins such as bovine OPN and bovine serum albumin. The results gathered in the current work suggest that the proposed electrochemical aptasensor is a simple and sensitive detection tool for human OPN and so, may have future applications in cancer disease monitoring.

Keywords: osteopontin, aptamer, aptasensor, screen-printed electrode, cyclic voltammetry

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Authors: Mariam Mojally, Randa Abdou, Wisal Bokhari, Sultan Sab, Mohammed Dawoud, Amjad Albohy

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Secondary metabolites produced by endophytes are an excellent source of biologically active compounds. In our current study, we evaluated terezine E and 14-hydroxyterezine D for binding to the active site of histone deacetylase (PDB ID: 4CBT) and matrix metalloproteinase 9 (PDB ID: 4H3X) by molecular docking using AutoDock Vina software after having tested their cytotoxic activities on three cell lines (human ductal breast epithelial tumor cells (T47D)-HCC1937), human hepatocarcinoma cell line (HepG2)-HB8065), and human colorectal carcinoma cells (HCT-116)-TCP1006, purchased from ATCC, USA)). Additionally, their antimicrobial activities were investigated, and their minimum inhibitory concentration (MIC) values were determined against P. notatum and S. aureus by the broth microdilution method. Higher cytotoxicity was observed for terezine E against all tested cell lines compared to 14-hydroxyterezine D. Molecular docking results supported the high cytotoxicity of terezine E and showed higher binding affinity with 4CBT with an energy score of 9 kcal/mol. Terezine E showed higher antibacterial and antifungal activities than 14-hydroxyrerezine D: MIC values were 15.45 and 21.73 mg/mL against S. aureus and 8.61 and 11.54 mg/mL against P. notatum, respectively

Keywords: Terezine E, 14-Hydroxyterezine D, cytotoxicity, antimicrobial activity, molecular docking

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Authors: Ernesto Pineda Leon, Dante Tolentino Lopez, Janis Zapata Lopez

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The current paper shows the application of the boundary element method for the analysis of plates under shear stress causing plasticity. In this case, the shear deformation of a plate is considered by means of the Reissner’s theory. The probability of failure of a Reissner’s plate due to a proposed index plastic behavior is calculated taken into account the uncertainty in mechanical and geometrical properties. The problem is developed in two dimensions. The classic plasticity’s theory is applied and a formulation for initial stresses that lead to the boundary integral equations due to plasticity is also used. For the plasticity calculation, the Von Misses criteria is used. To solve the non-linear equations an incremental method is employed. The results show a relatively small failure probability for the ranges of loads between 0.6 and 1.0. However, for values between 1.0 and 2.5, the probability of failure increases significantly. Consequently, for load bigger than 2.5 the plate failure is a safe event. The results are compared to those that were found in the literature and the agreement is good.

Keywords: boundary element method, failure, plasticity, probability

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Authors: Abdul Matin, Salik Nawaz, Suk-Yul Jung

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Balamuthia mandrillaris is well known to cause fatal Balamuthia amoebic encephalitis (BAE). Amoebic transmission into the central nervous system (CNS), haematogenous spread is thought to be the prime step, followed by blood-brain barrier (BBB) dissemination. Macrophages are considered to be the foremost line of defense and present in excessive numbers during amoebic infections. The aim of the present investigation was to evaluate the effects of macrophages alone or primed with cytokines on the biological characteristics of Balamuthia in vitro. Using human brain microvascular endothelial cells (HBMEC), which constitutes the BBB, we have shown that Balamuthia demonstrated > 90% binding and > 70% cytotoxicity to host cells. However, macrophages further increased amoebic binding and Balamuthia-mediated cell cytotoxicity. Furthermore, macrophages exhibited no amoebicidal effect against Balamuthia. Zymography assay demonstrated that macrophages exhibited no inhibitory effect on proteolytic activity of Balamuthia. Overall, to our best knowledge, we have shown for the first time macrophages has no inhibitory effects on the biological properties of Balamuthia in vitro. This also strengthened the concept that how and why Balamuthia can cause infections in both immuno-competent and immuno-compromised individuals.

Keywords: Balamuthia mandrillaris, macrophages, cytokines, human brain microvascular endothelial cells, Balamuthia amoebic encephalitis

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Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

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The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: C. Juntarasaid, T. Pulngern, S. Chucheepsakul

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A formulation of postbuckling analysis of end supported rods under self-weight has been presented by the variational method. The variational formulation involving the strain energy due to bending and the potential energy of the self-weight, are expressed in terms of the intrinsic coordinates. The variational formulation is accomplished by introducing the Lagrange multiplier technique to impose the boundary conditions. The finite element method is used to derive a system of nonlinear equations resulting from the stationary of the total potential energy and then Newton-Raphson iterative procedure is applied to solve this system of equations. The numerical results demonstrate the postbluckled configurations of end supported rods under self-weight. This finite element method based on variational formulation expressed in term of intrinsic coordinate is highly recommended for postbuckling analysis of end-supported rods under self-weight.

Keywords: postbuckling, finite element method, variational method, intrinsic coordinate

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Authors: Aidan Battison, Neliswa Mama

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Environmental pollution by ionic species has been identified as one of the biggest challenges to the sustainable development of communities. The widespread use of organic and inorganic chemical products and the release of toxic chemical species from industrial waste have resulted in a need for advanced monitoring technologies for environment protection, remediation and restoration. Some of the disadvantages of conventional sensing methods include expensive instrumentation, well-controlled experimental conditions, time-consuming procedures and sometimes complicated sample preparation. On the contrary, the development of fluorescent chemosensors for biological and environmental detection of metal ions has attracted a great deal of attention due to their simplicity, high selectivity, eidetic recognition, rapid response and real-life monitoring. Coumarin derivatives S1 and S2 (Scheme 1) containing 1,2,3-triazole moieties at position -3- have been designed and synthesized from azide and alkyne derivatives by CuAAC “click” reactions for the detection of metal ions. These compounds displayed a strong preference for Fe3+ ions with complexation resulting in fluorescent quenching through photo-induced electron transfer (PET) by the “sphere of action” static quenching model. The tested metal ions included Cd2+, Pb2+, Ag+, Na+, Ca2+, Cr3+, Fe3+, Al3+, Cd2+, Ba2+, Cu2+, Co2+, Hg2+, Zn2+ and Ni2+. The detection limits of S1 and S2 were determined to be 4.1 and 5.1 uM, respectively. Compound S1 displayed the greatest selectivity towards Fe3+ in the presence of competing for metal cations. S1 could also be used for the detection of Fe3+ in a mixture of CH3CN/H¬2¬O. Binding stoichiometry between S1 and Fe3+ was determined by using both Jobs-plot and Benesi-Hildebrand analysis. The binding was shown to occur in a 1:1 ratio between the sensor and a metal cation. Reversibility studies between S1 and Fe3+ were conducted by using EDTA. The binding site of Fe3+ to S1 was determined by using 13 C NMR and Molecular Modelling studies. Complexation was suggested to occur between the lone-pair of electrons from the coumarin-carbonyl and the triazole-carbon double bond.

Keywords: chemosensor, "click" chemistry, coumarin, fluorescence, static quenching, triazole

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Authors: Majid Afkhami, Maryam Ehsanpour

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The present study provides information about the nature of adverse effects on fish and the ecological impact that polycyclic aromatic hydrocarbons (PAHs) pollutant are having in the northern coast of Hormuz Strait. The glucose and cholesterol levels were higher in fish from the St3 than in Walton's mudskipper from other stations however St3 samples had lowest total proteins levels. There was a significant positive correlation between glucose and cholesterol with PAHs concentrations in sediment and tissue samples (P<0.05). However, total proteins had adverse significant correlation with PAHs concentrations (P>0.05). The adverse correlation was seen between length and body weight of fish samples with PAHs concentrations. According to the results of this study, the monitoring of contaminants bioaccumulation in the northern part of Hormuz Strait is necessary, because this will give an indication of the temporal and spatial extent of the process, as well as an assessment of the potential impact on aquatic organisms health.

Keywords: PAHs, blood metabolic factors, Periophthalmus waltoni, Hormuz Strait

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Authors: M. R. Daneshgar, S. E. Habibi, E. Daneshgar, A. Daneshgar

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In this paper, a two-dimensional method is developed to simulate the fillet welds in a stiffened cylindrical shell, using finite element method. The stiffener material is aluminum 2519. The thermo-elasto-plastic analysis is used to analyze the thermo-mechanical behavior. Due to the high heat flux rate of the welding process, two uncouple thermal and mechanical analysis are carried out instead of performing a single couple thermo-mechanical simulation. In order to investigate the effects of the welding procedures, two different welding techniques are examined. The resulted residual stresses and distortions due to different welding procedures are obtained. Furthermore, this study employed the technique of element birth and death to simulate the weld filler variation with time in fillet welds. The obtained results are in good agreement with the published experimental and three-dimensional numerical simulation results. Therefore, the proposed 2D modeling technique can effectively give the corresponding results of 3D models. Furthermore, by inspection of the obtained residual hoop and transverse stresses and angular distortions, proper welding procedure is suggested.

Keywords: stiffened cylindrical shell, fillet welds, residual stress, angular distortion, finite element method

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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: Mai Abdul Latif, Yuntian Feng

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Applied Element Method (AEM) is a method that was developed to aid in the analysis of the collapse of structures. Current available methods cannot deal with structural collapse accurately; however, AEM can simulate the behavior of a structure from an initial state of no loading until collapse of the structure. The elements in AEM are connected with sets of normal and shear springs along the edges of the elements, that represent the stresses and strains of the element in that region. The elements are rigid, and the material properties are introduced through the spring stiffness. Nonlinear dynamic analysis has been widely modelled using the finite element method for analysis of progressive collapse of structures; however, difficulties in the analysis were found at the presence of excessively deformed elements with cracking or crushing, as well as having a high computational cost, and difficulties on choosing the appropriate material models for analysis. The Applied Element method is developed and coded to significantly improve the accuracy and also reduce the computational costs of the method. The scheme works for both linear elastic, and nonlinear cases, including elasto-plastic materials. This paper will focus on elastic and elasto-plastic material behaviour, where the number of springs required for an accurate analysis is tested. A steel cantilever beam is used as the structural element for the analysis. The first modification of the method is based on the Gaussian Quadrature to distribute the springs. Usually, the springs are equally distributed along the face of the element, but it was found that using Gaussian springs, only up to 2 springs were required for perfectly elastic cases, while with equal springs at least 5 springs were required. The method runs on a Newton-Raphson iteration scheme, and quadratic convergence was obtained. The second modification is based on adapting the number of springs required depending on the elasticity of the material. After the first Newton Raphson iteration, Von Mises stress conditions were used to calculate the stresses in the springs, and the springs are classified as elastic or plastic. Then transition springs, springs located exactly between the elastic and plastic region, are interpolated between regions to strictly identify the elastic and plastic regions in the cross section. Since a rectangular cross-section was analyzed, there were two plastic regions (top and bottom), and one elastic region (middle). The results of the present study show that elasto-plastic cases require only 2 springs for the elastic region, and 2 springs for the plastic region. This showed to improve the computational cost, reducing the minimum number of springs in elasto-plastic cases to only 6 springs. All the work is done using MATLAB and the results will be compared to models of structural elements using the finite element method in ANSYS.

Keywords: applied element method, elasto-plastic, Gaussian springs, nonlinear

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Authors: Jinan Fiaidhi, Sabah Mohammed

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Diagnosing cataract severity is an important factor in deciding to undertake surgery. It is usually conducted by an ophthalmologist or through taking a variety of fundus photography that needs to be examined by the ophthalmologist. This paper carries out an investigation using a Siamese neural net that can be trained with small anchor samples to score cataract severity. The model used in this paper is based on a triplet loss function that takes the ophthalmologist best experience in rating positive and negative anchors to a specific cataract scaling system. This approach that takes the heuristics of the ophthalmologist is generally called the thick data approach, which is a kind of machine learning approach that learn from a few shots. Clinical Relevance: The lens of the eye is mostly made up of water and proteins. A cataract occurs when these proteins at the eye lens start to clump together and block lights causing impair vision. This research aims at employing thick data machine learning techniques to rate the severity of the cataract using Siamese neural network.

Keywords: thick data analytics, siamese neural network, triplet-loss model, few shot learning

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Authors: A. Armin, R. Fotouhi, W. Szyszkowski

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In this paper a 3-D finite element (FE) investigation of soil-blade interaction is described. The effects of blade’s shape and rake angle are examined both numerically and experimentally. The soil is considered as an elastic-plastic granular material with non-associated Drucker-Prager material model. Contact elements with different properties are used to mimic soil-blade sliding and soil-soil cutting phenomena. A separation criterion is presented and a procedure to evaluate the forces acting on the blade is given and discussed in detail. Experimental results were derived from tests using soil bin facility and instruments at the University of Saskatchewan. During motion of the blade, load cells collect data and send them to a computer. The measured forces using load cells had noisy signals which are needed to be filtered. The FE results are compared with experimental results for verification. This technique can be used in blade shape optimization and design of more complicated blade’s shape.

Keywords: finite element analysis, experimental results, blade force, soil-blade contact modeling

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Authors: Libo Jiang, Huan Li, Rongling Wu

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Ordinary differentiation equations (ODE) have proven to be powerful for reconstructing precise and informative gene regulatory networks (GRNs) from dynamic gene expression data. However, joint modeling and analysis of all genes, essential for the systematical characterization of genetic interactions, are challenging due to high dimensionality and a complex pattern of genetic regulation including activation, repression, and antitermination. Here, we address these challenges by unifying variable selection and game theory through ODE. Each gene within a GRN is co-expressed with its partner genes in a way like a game of multiple players, each of which tends to choose an optimal strategy to maximize its “fitness” across the whole network. Based on this unifying theory, we designed and conducted a real experiment to infer salt tolerance-related GRNs for Euphrates poplar, a hero tree that can grow in the saline desert. The pattern and magnitude of interactions between several hub genes within these GRNs were found to determine the capacity of Euphrates poplar to resist to saline stress.

Keywords: gene regulatory network, ordinary differential equation, game theory, LASSO, saline resistance

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Authors: Alexander A. Tokmakov

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Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

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Authors: Taylan Ozturk, Osama Maklad

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This study examines the aerodynamic and flow properties of a multi-element airfoil using computational fluid dynamics (CFD) research. This computational analysis aims to optimize slat design concerning lift-drag coefficients and to determine the ideal gap size between the main airfoil and the front flap. It examines the influence of varying angles of attack and the effects of varied Reynolds numbers. A NACA 2412 airfoil, equipped with custom-designed front and rear flaps, was modeled in SolidWorks and simulated in ANSYS Fluent utilizing the k-ω SST turbulence model. This study quantifies lift and drag coefficients, turbulent kinetic energy, and vorticity magnitude across various configurations. The results clearly indicate that the slat-optimized design geometry featuring a 4 mm gap provides the best performance regarding both lift and drag, with maximum efficiency achieved at a 4-degree angle of attack. Furthermore, the results indicate the initiation of stall conditions beyond 20 degrees and demonstrate how an increase in Reynolds numbers influences flow separation and turbulence patterns. In addition, the maximum L/D ratio which is 36.18 achieved. These findings enhance the comprehension of multi-element airfoil behavior, directly impacting aircraft design and operation, particularly in high-lift situations.

Keywords: multi-element airfoil, CFD simulation, aerodynamic characteristics, Reynolds number analysis

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Authors: Hamioud Saida, Khalfallah Salah

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In this study, a spectral element method is employed to predict the free vibration of a Euler-Bernoulli beam resting on a Winkler foundation with elastically restrained ends. The formulation of the dynamic stiffness matrix has been established by solving the differential equation of motion, which was transformed to frequency domain. Non-dimensional natural frequencies and shape modes are obtained by solving the partial differential equations, numerically. Numerical comparisons and examples are performed to show the effectiveness of the SEM and to investigate the effects of various parameters, such as the springs at the boundaries and the elastic foundation parameter on the vibration frequencies. The obtained results demonstrate that the present method can also be applied to solve the more general problem of the dynamic analysis of structures with higher order precision.

Keywords: elastically supported Euler-Bernoulli beam, free-vibration, spectral element method, Winkler foundation

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Authors: Pavel Borodkin, Nikolay Khrennikov, Azamat Gazetdinov

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The problem of ensuring of VVER type reactor equipment integrity is now most actual in connection with justification of safety of the NPP Units and extension of their service life to 60 years and more. First of all, it concerns old units with VVER-440 and VVER-1000. The justification of the VVER equipment integrity depends on the reliability of estimation of the degree of the equipment damage. One of the mandatory requirements, providing the reliability of such estimation, and also evaluation of VVER equipment lifetime, is the monitoring of equipment radiation loading parameters. In this connection, there is a problem of justification of such normative parameters, used for an estimation of the pressure vessel metal embrittlement, as the fluence and fluence rate (FR) of fast neutrons above 0.5 MeV. From the point of view of regulatory practice, a comparison of displacement per atom (DPA) and fast neutron fluence (FNF) above 0.5 MeV has a practical concern. In accordance with the Russian regulatory rules, neutron fluence F(E > 0.5 MeV) is a radiation exposure parameter used in steel embrittlement prediction under neutron irradiation. However, the DPA parameter is a more physically legitimate quantity of neutron damage of Fe based materials. If DPA distribution in reactor structures is more conservative as neutron fluence, this case should attract the attention of the regulatory authority. The purpose of this work was to show what radiation load parameters (fluence, DPA) on all VVER equipment should be under control, and give the reasonable estimations of such parameters in the volume of all equipment. The second task is to give the conservative estimation of each parameter including its uncertainty. Results of recently received investigations allow to test the conservatism of calculational predictions, and, as it has been shown in the paper, combination of ex-vessel measured data with calculated ones allows to assess unpredicted uncertainties which are results of specific unique features of individual equipment for VVER reactor. Some results of calculational-experimental investigations are presented in this paper.

Keywords: equipment integrity, fluence, displacement per atom, nuclear power plant, neutron activation measurements, neutron transport calculations

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

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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: Mohanad Talal Alfach

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This paper concerns the seismic behaviour of soil-piles-bridge reinforced by additional micropiles. The analysis carried out by three-dimensional finite element modelling using the FE software ABAQUS. The soil behaviour is assumed to be elastic with Rayleigh damping, while the micropiles are modeled as 3D elastic beam elements. The bridge deck slab was represented by a concentrated mass at the top of the pier column. The interaction between the added micropiles and the existing piles as well as the performance of the retrofitted soil-pile-superstructure system were investigated for different configurations of additional micropiles (number, position, inclination). Numerical simulation results show that additional micropiles constitute an efficient retrofitting solution. Analysis of results also shows that spacing between existing piles and retrofitting micropiles has little effect; while it is observed a substantial improvement (in case of weak piles/micropiles - soil interface) with reducing the inclination angle of retrofitting micropiles.

Keywords: retrofitting, seismic, finite element, micropiles, elastic

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Authors: Hamid Hossein Khezri, Afsaneh Javdani-Mallak

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Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Cannabidiol (CBD) is one of the members of cannabinoid compounds found in cannabis. CBD and Cannabinol (CBN), as the other extract of plant Cannabis, were able to reduce myofascial pain in rats with immunosuppressive and anti-inflammatory activities. In this study, we accomplished protein-protein BLAST and the sequence was found to be for Gamma-aminobutyric acid receptor subunit alpha-1 (GBRA1) chain A and its 3D structure was subsequently downloaded from Protein Data Bank. The structures of the ligands cannabinol and cannabidiol were obtained from PubChem. After a necessary process of the obtained files, AutoDock Vina was used to performing molecular docking. Docking between the ligands and GBRA1 chain A revealed that cannabinol has a higher affinity to GBRA1 (binding energy = -7.5 kcal/mol) compared to cannabidiol (binding energy = -6.5 kcal/mol). Furthermore, cannabinol seems to be able to interact with 10 residues of the protein, out of which 3 are in the neurotransmitter-gated ion-channel transmembrane domain of GBRA1, whereas cannabidiol interacts with two other residues. Although the results of this project do not indicate the activating /or inhibitory capability of the studied compounds, it suggests that cannabinol can act as a relatively strong ligand for GBRA1.

Keywords: protein-ligand docking, cannabinol, cannabidiol, GBRA1

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Authors: Razieh Karimi Aghcheh, Christian Kubicek, Joseph Strauss, Gerhard Braus

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Filamentous fungi are of considerable economic and social significance for human health, nutrition and in white biotechnology. These organisms are dominant producers of a range of primary metabolites such as citric acid, microbial lipids (biodiesel) and higher unsaturated fatty acids (HUFAs). In particular, they produce also important but structurally complex secondary metabolites with enormous therapeutic applications in pharmaceutical industry, for example: cephalosporin, penicillin, taxol, zeranol and ergot alkaloids. Several fungal secondary metabolites, which are significantly relevant to human health do not only include antibiotics, but also e.g. lovastatin, a well-known antihypercholesterolemic agent produced by Aspergillus. terreus, or aflatoxin, a carcinogen produced by A. flavus. In addition to their roles for human health and agriculture, some fungi are industrially and commercially important: Species of the ascomycete genus Hypocrea spp. (teleomorph of Trichoderma) have been demonstrated as efficient producer of highly active cellulolytic enzymes. This trait makes them effective in disrupting and depolymerization of lignocellulosic materials and thus applicable tools in number of biotechnological areas as diverse as clothes-washing detergent, animal feed, and pulp and fuel productions. Fungal LaeA/LAE1 (Loss of aflR Expression A) homologs their gene products act at the interphase between secondary metabolisms, cellulase production and development. Lack of the corresponding genes results in significant physiological changes including loss of secondary metabolite and lignocellulose degrading enzymes production. At the molecular level, the encoded proteins are presumably methyltransferases or demethylases which act directly or indirectly at heterochromatin and interact with velvet domain proteins. Velvet proteins bind to DNA and affect expression of secondary metabolites (SMs) genes and cellulases. The dynamic interplay between LaeA/LAE1, velvet proteins and additional interaction partners is the key for an understanding of the coordination of metabolic and morphological functions of fungi and is required for a biotechnological control of the formation of desired bioactive products. Aspergilli and Trichoderma represent different biotechnologically significant species with significant differences in the LaeA/LAE1-Velvet protein machinery and their target proteins. We, therefore, performed a comparative study of the interaction partners of this machinery and the dynamics of the various protein-protein interactions using our robust proteomic and mass spectrometry techniques. This enhances our knowledge about the fungal coordination of secondary metabolism, cellulase production and development and thereby will certainly improve recombinant fungal strain construction for the production of industrial secondary metabolite or lignocellulose hydrolytic enzymes.

Keywords: cellulases, LaeA/1, proteomics, secondary metabolites

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Authors: Zuzana Tatarkova, Ivana Pilchova, Michal Cibulka, Martin Kolisek, Peter Racay, Peter Kaplan

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Introduction: Normal functioning of mitochondria is crucial for cardiac performance. Mitochondria undergo mitophagy and biogenesis, and mitochondrial proteins are subject to extensive post-translational modifications. The state of mitochondrial homeostasis reflects overall cellular fitness and longevity. Perturbed mitochondria produce less ATP, release greater amounts of reactive molecules, and are more prone to apoptosis. Therefore mitochondrial turnover is an integral aspect of quality control in which dysfunctional mitochondria are selectively eliminated through mitophagy. Currently, the progressive deterioration of physiological functions is seen as accumulation of modified/damaged proteins with limiting regenerative ability and disturbance of such affected protein-protein communication throughout aging in myocardial cells. Methodologies: For our study was used immunohistochemistry, biochemical methods: spectrophotometry, western blotting, immunodetection as well as more sophisticated 2D electrophoresis and mass spectrometry for evaluation protein-protein interactions and specific post-translational modification. Results and Discussion: Mitochondrial stress response to reactive species was evaluated as electron transport chain (ETC) complexes, redox-active molecules, and their possible communication. Protein-protein interactions revealed a strong linkage between age and ETC protein subunits. Redox state was strongly affected in senescent mitochondria with shift in favor of more pro-oxidizing condition within cardiomyocytes. Acute myocardial ischemia and ischemia-reperfusion (IR) injury affected ETC complexes I, II and IV with no change in complex III. Ischemia induced decrease in total antioxidant capacity, MnSOD, GSH and catalase activity with recovery in some extent during reperfusion. While MnSOD protein content was higher in IR group, activity returned to 95% of control. Nitric oxide is one of the biological molecules that can out compete MnSOD for superoxide and produce peroxynitrite. This process is faster than dismutation and led to the 10-fold higher production of nitrotyrosine after IR injury in adult with higher protection in senescent ones. 2D protein profiling revealed 140 mitochondrial proteins, 12 of them with significant changes after IR injury and 36 individual nitrotyrosine-modified proteins further identified by mass spectrometry. Linking these two groups, 5 proteins were altered after IR as well as nitrated, but only one showed massive nitration per lowering content of protein after IR injury in adult. Conclusions: Senescent cells have greater proportion of protein content, which might be modulated by several post-translational modifications. If these protein modifications are connected to functional consequences and protein-protein interactions are revealed, link may lead to the solution. Assume all together, dysfunctional proteostasis can play a causative role and restoration of protein homeostasis machinery is protective against aging and possibly age-related disorders. This work was supported by the project VEGA 1/0018/18 and by project 'Competence Center for Research and Development in the field of Diagnostics and Therapy of Oncological diseases', ITMS: 26220220153, co-financed from EU sources.

Keywords: aging heart, mitochondria, proteomics, redox state

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Authors: D. K. Lee, S. M. Shin, J. H. Lee

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Topology optimization technique utilizes constant element densities as design parameters. Finally, optimal distribution contours of the material densities between voids (0) and solids (1) in design domain represent the determination of topology. It means that regions with element density values become occupied by solids in design domain, while there are only void phases in regions where no density values exist. Therefore the void regions of topology optimization results provide design information to decide appropriate depositions of web-opening in structure. Contrary to the basic objective of the topology optimization technique which is to obtain optimal topology of structures, this present study proposes a new idea that topology optimization results can be also utilized for decision of proper web-opening’s position. Numerical examples of linear elastostatic structures demonstrate efficiency of methodological design processes using topology optimization in order to determinate the proper deposition of web-openings.

Keywords: topology optimization, web-opening, structure, element density, material

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Authors: Ji Hye Im, Nguyen T. T. Phuong, Keon Wook Kang

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Estrogens are important for the development and growth of estrogen receptor (ER)-positive breast cancer, for which anti-estrogen therapy is one of the most effective treatments. However, its efficacy can be limited by either de novo or acquired resistance. Aromatase is a key enzyme for the biosynthesis of estrogens, and inhibition of this enzyme leads to profound hypoestrogenism. Here, we found that the basal expression and activity of aromatase were significantly increased in tamoxifen (TAM)-resistant human breast cancer (TAMR-MCF-7) cells compared to control MCF-7 cells. We further revealed that aromatase immunoreactivity in tumor tissues was increased in recurrence group after TAM therapy compared to non-recurrence group after TAM therapy. Phosphorylation of Akt, extracellular signal-regulated kinase (ERK), and p38 kinase were all increased in TAMR-MCF-7 cells. Inhibition of phosphoinositide 3-kinase (PI3K) suppressed the transactivation of the aromatase gene and its enzyme activity. Furthermore, we have also shown that PI3K/Akt-dependent cAMP-response element binding protein (CREB) activation was required for the enhanced expression of aromatase in TAMR-MCF-7 cells. Our findings suggest that aromatase expression is up-regulated in TAM-resistant breast cancer via PI3K/Akt-dependent CREB activation.

Keywords: TAMR-MCF-7, CREB, estrogen receptor, aromatase

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Authors: Azhar Jabareen, Mahmoud Huleihel

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BRCA-1 is a multifunctional tumor suppressor, whose expression is activated by the estrogen (E2)-liganded ERα receptor. The activated ERα is a transcriptional factor which activates various genes either by direct binding to the DNA at E2-responsive elements (EREs) and indirectly associated with a range of alternative non-ERE elements. Interference with BRCA-1 expression and/or functions leads to high risk of breast or/and ovarian cancer. Our lab investigated the involvement of Human T-cell leukemia Virus Type 1 (HTLV-1) in breast cancer, since HTLV-1 Tax was found to strongly inhibit BRCA-1 expression. In addition, long exposure of 12-O-tetradecanoylphorbol-13-acetate (TPA), which is one of the stress-inducing agents activated the HTLV-1 promoter. So here the involvement of TPA in breast cancer had been examined by testing the effect of TPA on BRCA-1 and ERE expression. The results showed that TPA activated both BRCA-1 and ERE expression. In the 12 hours TPA activated the tow promoters more than others time, and after 24 hours the level of the tow promoters was decreased. Tax inhibited BRCA-1 expression but did not succeed to inhibit the effect of TPA. Then the activation of the two promoters was not through ERα pathway because TPA had no effect on ERα binding to the two promoters of the BRCA-1 and ERE. Also, the activation was not via nuclear factor kappa B (NF-κB) pathway because when the inhibitory of NF-κB had been added to the TPA, it still activated the tow promoters. However, it seems that 53BP1 may be involved in TPA activation of these promoters because ectopic high expression of 53BP1 significantly reduced the TPA activity. In addition, in the presence of Bisindolylmaleimide-I (BI)- the inhibitor of Protein Kinase C (PKC)- there was no activation for the two promoters, so the PKC is agonized BRCA-1 and ERE activation.

Keywords: BRCA-1, ERE, HTLV-1, TPA

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Authors: Isil Gazioglu, Abdulselam Ertas

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Aflatoxins (AFs) are secondary toxic metabolites of Aspergillus flavus and A. parasiticus. AFs can be absorbed through the skin. Potent carcinogens like AFs should be completely absent from cosmetics, this can be achieved by careful quality control of the raw plant materials. Regulatory limits for aflatoxins have been established in many countries, and reliable testing methodology is needed to implement and enforce the regulatory limits. In this study, ten medicinal plant samples (Bundelia tournefortti, Capsella bursa-pastoris, Carduus tenuiflorus, Cardaria draba, Malva neglecta, Malvella sharardiana, Melissa officinalis, Sideritis libanotica, Stakys thirkei, Thymus nummularius) were investigated for aflatoxin (AF) contaminations by employing an HPLC assay for the determination of AFB1, B2, G1 and G2. The samples were extracted with 70% (v/v) methanol in water before further cleaned up with an immunoaffinity column and followed by the detection of AFs by using an electrochemically post-column derivatization with Kobra-Cell and fluorescence detector. The extraction procedure was optimized in order to obtain the best recovery. The method was successfully carried out with all medicinal plant samples. The results revealed that five (50%) of samples were contaminated with AFs. The association between particular samples and the AF contaminated could not be determined due to the low frequency of positive samples.

Keywords: aflatoxin B1, HPLC-FLD, KOBRA-Cell, mycotoxin

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Authors: Mahmoud Lot

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In this article, we will discuss the solution of elliptic optimal control problem. First, by using the nite element method, we obtain the discrete form of the problem. The obtained discrete problem is actually a large scale constrained optimization problem. Solving this optimization problem with traditional methods is difficult and requires a lot of CPU time and memory. But split Bergman method converts the constrained problem to an unconstrained, and hence it saves time and memory requirement. Then we use the split Bregman method for solving this problem, and examples show the speed and accuracy of split Bregman methods for solving these types of problems. We also use the SQP method for solving the examples and compare with the split Bregman method.

Keywords: Split Bregman Method, optimal control with elliptic partial differential equation constraint, finite element method

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Authors: William Thomas Worster

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This paper will highlight the failure of international adjudication to prevent a state from evading an order of provisional measures by simply issuing a diplomatic assurance to the court. This practice changes the positions of the litigants as equals before a court, prevents the court from inquiring into the reliability of the political pledge as it would with assurances from a state to an individual, and diminishes the court’s ability to control its own proceedings in the face of concerns over sovereignty. Both the European Court of Human Rights (ECtHR) and International Court of Justice (ICJ) will entertain these kinds of unilateral pledges, but they consider them differently when the declaration is made between states or between a state and an individual, and when made directly to the court. In short, diplomatic assurances issued between states or to individuals are usually considered not to be legally binding and are essentially questions of fact, but unilateral assurances issued directly to an international court are questions of law, and usually legally binding. At the same time, orders for provisional measures are now understood also to be legally binding, yet international courts will sometimes permit a state to substitute an assurance in place of an order for provisional measures. This emerging practice has brought the nature of a state as a sovereign capable of creating legal obligations into the forum of adjudication where the parties should have equality of arms and permitted states to create legal obligations that escape inquiry into the reliability of the outcome. While most recent practice has occurred at the ICJ in state-to-state litigation, there is some practice potentially extending the practice to human rights courts. Especially where the litigants are factually unequal – a state and an individual – this practice is problematic since states could more easily overcome factual failings in their pledges and evade the control of the court. Consider, for example, the potential for evading non-refoulement obligations by extending the current diplomatic assurances practice from the state-to-state context to the state-to-court context. The dual nature of assurances, as both legal and factual instruments, should be considered as addressed to distinct questions, each with its own considerations, and that we need to be more demanding about their precise legal and factual effects.

Keywords: unilateral, diplomacy, assurances, undertakings, provisional measures, interim measures

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Authors: Hyunwoo Song, Jeong-Min Lee, Yongseok Kim, Junghan Yun, Jungin Byun, Jae-Mean Koo, Chang-Sung Seok

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To avoid the damage of gas turbine blade from high-temperature, thermal barrier coating (TBC) is applied on the blade. However, it is damaged by thermal fatigue during the operation of gas turbine, and this damage lead to delamination of TBC between top coat and bond coat. The blade can be damaged after the failure of TBC, so durability evaluation of TBC should be performed. The durability of thermal barrier coating was decreased according to the increase of temperature, because thermal stress according to increase of temperature. Also, the curvature can be affect to durability of TBC, because the stress is determined by the shape of the TBC. Therefore, the effect of temperature and curvature on the stress should be evaluated. In this study, finite element analysis according to temperature and curvature were performed in the same condition of Kim et al. Finally, the stress was evaluated from the finite element analysis results according to temperature and curvature.

Keywords: curvature, finite element analysis, thermal barrier coating, thermal fatigue, temperature

Procedia PDF Downloads 566