Search results for: plasma-assisted molecular beam epitaxy

Authors: Hossein Bazmara, Kaamran Raahemifar, Mostafa Sefidgar, Madjid Soltani

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Angiogenesis is formation of new blood vessels from existing vessels. Due to flow of blood in vessels, during angiogenesis, blood flow plays an important role in regulating the angiogenesis process. Multiple mathematical models of angiogenesis have been proposed to simulate the formation of the complicated network of capillaries around a tumor. In this work, a multi-scale model of angiogenesis is developed to show the effect of blood flow on capillaries and network formation. This model spans multiple temporal and spatial scales, i.e. intracellular (molecular), cellular, and extracellular (tissue) scales. In intracellular or molecular scale, the signaling cascade of endothelial cells is obtained. Two main stages in development of a vessel are considered. In the first stage, single sprouts are extended toward the tumor. In this stage, the main regulator of endothelial cells behavior is the signals from extracellular matrix. After anastomosis and formation of closed loops, blood flow starts in the capillaries. In this stage, blood flow induced signals regulate endothelial cells behaviors. In cellular scale, growth and migration of endothelial cells is modeled with a discrete lattice Monte Carlo method called cellular Pott's model (CPM). In extracellular (tissue) scale, diffusion of tumor angiogenic factors in the extracellular matrix, formation of closed loops (anastomosis), and shear stress induced by blood flow is considered. The model is able to simulate the formation of a closed loop and its extension. The results are validated against experimental data. The results show that, without blood flow, the capillaries are not able to maintain their integrity.

Keywords: angiogenesis, endothelial cells, multi-scale model, cellular Pott's model, signaling cascade

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Authors: Shikha Rani, Neeta Sehgal, Vipin Kumar Verma, Om Prakash

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Introduction: Fish is an important protein source for humans and has great economic value. Fish cultures are affected due to various anthropogenic activities that lead to bacterial and viral infections. Aeromonas hydrophila is a fish pathogenic bacterium that causes several aquaculture outbreaks throughout the world and leads to huge mortalities. In this study, plants of no commercial value were used to investigate their immunostimulatory, antioxidant, anti-inflammatory, anti-bacterial, and disease resistance potential in fish against Aeromonas hydrophila, through fish feed fortification. Methods: The plant was dried at room temperature in the shade, dissolved in methanol, and analysed for biological compounds through GC-MS/MS. DPPH, FRAP, Phenolic, and flavonoids were estimated following standardized protocols. In silico molecular docking was also performed to validate its broad-spectrum activities based on binding affinity with specific proteins. Fish were divided into four groups (n=6; total 30 in a group): Group 1, non-challenged fish (fed on a non-supplemented diet); Group 2, fish challenged with bacteria (fed on a non-supplemented diet); Group 3 and 4, fish challenged with bacteria (A. hydrophila) and fed on plant supplemented feed at 2.5% and 5%. Blood was collected from the fish on 0, 7th, 14th, 21st, and 28th days. Serum was separated for glutamic-oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT), alkaline phosphatase assay (ALP), lysozyme activity assay, superoxide dismutase assay (SOD), lipid peroxidation assay (LPO) and molecular parameters (including cytokine levels) were estimated through ELISA. The phagocytic activity of macrophages from the spleen and head kidney, along with quantitative analysis of immune-related genes, were analysed in different tissue samples. The digestive enzymes (Pepsin, Trypsin, and Chymotrypsin) were also measured to evaluate the effect of plant-supplemented feed on freshwater fish. Results and Discussion: GC-MS/MS analysis of a methanolic extract of plant validated the presence of key compounds having antioxidant, anti-inflammatory, anti-bacterial, anti-inflammatory, and immunomodulatory activities along with disease resistance properties. From biochemical investigations like ABTS, DPPH, and FRAP, the amount of total flavonoids, phenols, and promising binding affinities towards different proteins in molecular docking analysis helped us to realize the potential of this plant that can be used for investigation in the supplemented feed of fish. Measurement liver function tests, ALPs, oxidation-antioxidant enzyme concentrations, and immunoglobulin concentrations in the experimental groups (3 and 4) showed significant improvement as compared to the positive control group. The histopathological evaluation of the liver, spleen, and head kidney supports the biochemical findings. The isolated macrophages from the group fed on supplemented feed showed a higher percentage of phagocytosis and a phagocytic index, indicating an enhanced cell-mediated immune response. Significant improvements in digestive enzymes were also observed in fish fed on supplemented feed, even after weekly challenges with bacteria. Hence, the plant-fortified feed can be recommended as a regular feed to enhance fish immunity and disease resistance against the Aeromonas hydrophila infection after confirmation from the field trial.

Keywords: immunostimulation, antipathogen, plant fortified feed, macrophages, GC-MS/MS, in silico molecular docking

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Authors: Ivan Balázs, Jindřich Melcher

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Metal thin-walled members have been widely used in building industry. Usually they are utilized as purlins, girts or ceiling beams. Due to slenderness of thin-walled cross-sections these structural members are prone to stability problems (e.g. flexural buckling, lateral torsional buckling). If buckling is not constructionally prevented their resistance is limited by buckling strength. In practice planar members of roof or wall cladding can be attached to thin-walled members. These elements reduce displacement of thin-walled members and therefore increase their buckling strength. If this effect is taken into static assessment more economical sections of thin-walled members might be utilized and certain savings of material might be achieved. This paper focuses on problem of determination of critical load of steel thin-walled beams with lateral continuous restraint which is crucial for lateral torsional buckling assessment.

Keywords: beam, buckling, numerical analysis, stability, steel

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Authors: Mohammad Faheem, M. Tabish Rehman, Mohd Danishuddin, Asad U. Khan

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The worldwide dissemination of CTX-M type β-lactamases is a threat to human health. Previously, we have reported the spread of blaCTX-M-15 gene in different clinical strains of Enterobacteriaceae from the hospital settings of Aligarh in north India. In view of the varying resistance pattern against cephalosporins and other β-lactam antibiotics, we intended to understand the correlation between MICs and catalytic activity of CTX-M-15. In this study, steady-state kinetic parameters and MICs were determined on E. coli DH5α transformed with blaCTX-M-15 gene that was cloned from Enterobacter cloacae (EC-15) strain of clinical background. The effect of conventional β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) on CTX-M-15 was also studied. We have found that tazobactam is the best among these inhibitors against CTX-M-15. The inhibition characteristic of tazobactam is defined by its very low IC50 value (6 nM), high affinity (Ki = 0.017 µM) and better acylation efficiency (k+2/K9 = 0.44 µM-1s-1). It forms an acyl-enzyme covalent complex, which is quite stable (k+3 = 0.0057 s-1). Since increasing resistance has been reported against conventional b-lactam antibiotic-inhibitor combinations, we aspire to design a non-b-lactam core containing b-lactamase inhibitor. For this, we screened ZINC database and performed molecular docking to identify a potential non-β-lactam based inhibitor (ZINC03787097). The MICs of cephalosporin antibiotics in combination with this inhibitor gave promising results. Steady-state kinetics and molecular docking studies showed that ZINC03787097 is a reversible inhibitor which binds non-covalently to the active site of the enzyme through hydrogen bonds and hydrophobic interactions. Though, it’s IC50 (180 nM) is much higher than tazobactam, it has good affinity for CTX-M-15 (Ki = 0.388 µM). This study concludes that ZINC03787097 compound can be used as seed molecule to design more efficient non-b-lactam containing b-lactamase inhibitor that could evade pre-existing bacterial resistance mechanisms.

Keywords: ESBL, non-b-lactam-b-lactamase inhibitor, bioinformatics, biomedicine

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Authors: Yunzhe Tong, Jun Fan, Bin Wang

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The vibroacoustic behavior of an immersed infinite cylindrical shell with periodic lengthwise ribs has been studied in this paper. The motions of the shell are described by the Donnell equations. Each lengthwise rib is modeled as an elastic beam. The motions of the bulkheads are decomposed into the longitudinal motions and flexural motions. The analytical expressions of the shell motions can be obtained through circumferential mode expansion, Fourier Transform and periodic boundary condition in the circumferential direction. Furthermore, the far-field radiated pressure has been obtained using the stationary phase. The analysis of wavenumber domain shows that periodic lengthwise stiffeners in the circumferential direction can produce flexural Bloch waves. The dominant feature in far-field pressure amplitude is the resonance of the supersonic components of the flexural Bloch waves in the circumferential direction.

Keywords: flexural Bloch wave, stiffened shell, vibroacoustics, wavenumber analysis

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Authors: Tahani Hallek, Dhaou Akrout, Riadh Ahmadi, Mabrouk Montacer

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The present work is an organic geochemical study of the Fahdene Formation outcrops at the Mahjouba region belonging to the Eastern part of the Kalaat Senan structure in northwestern Tunisia (the Kef-Tedjerouine area). The analytical study of the organic content of the samples collected, allowed us to point out that the Formation in question is characterized by an average to good oil potential. This fossilized organic matter has a mixed origin (type II and III), as indicated by the relatively high values of hydrogen index. This origin is confirmed by the C29 Steranes abundance and also by tricyclic terpanes C19/(C19+C23) and tetracyclic terpanes C24/(C24+C23) ratios, that suggest a marine environment of deposit with high plants contribution. We have demonstrated that the heterogeneity of organic matter between the marine aspect, confirmed by the presence of foraminifera, and the continental contribution, is the result of an episodic anomaly in relation to the sequential stratigraphy. Given that the study area is defined as an outer platform forming a transition zone between a stable continental domain to the south and a deep basin to the north, we have explained the continental contribution by successive forced regressions, having blocked the albian transgression, allowing the installation of the lowstand system tracts. This aspect is represented by the incised valleys filling, in direct contact with the pelagic and deep sea facies. Consequently, the Fahdene Formation, in the Kef-Tedjerouine area, consists of transgressive system tracts (TST) brutally truncated by extras of continental progradation; resulting in a mixed influence deposition having retained a heterogeneous organic material.

Keywords: molecular geochemistry, biomarkers, forced regression, deposit environment, mixed origin, Northern Tunisia

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Authors: Md Abdullah Al Mashud, M. Tariquzzaman, M. Jahangir Alam, Tapan Kumar Godder, M. Mahbubur Rahman

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This paper presents a Monte Carlo (MC) method-based dose distributions on lung tumor for 6 MV photon beam to improve the dosimetric accuracy for cancer treatment. The polystyrene which is tissue equivalent material to the lung tumor density is used in this research. In the empirical calculations, TRS-398 formalism of IAEA has been used, and the setup was made according to the ICRU recommendations. The research outcomes were compared with the state-of-the-art experimental results. From the experimental results, it is observed that the proposed based approach provides more accurate results and improves the accuracy than the existing approaches. The average %variation between measured and TPS simulated values was obtained 1.337±0.531, which shows a substantial improvement comparing with the state-of-the-art technology.

Keywords: lung tumour, Monte Carlo, polystyrene, Elekta synergy, Monaco planning system

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Authors: Sami Ayad, Mengshan Lee

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The Sustainable Development Goals (SDGs) were designed to be the best possible blueprint to achieve peace, prosperity, and overall, a better and more sustainable future for the Earth and all its people, and such a blueprint is needed more than ever. The SDGs face many hurdles that will prevent them from becoming a reality, one of such hurdles, arguably, is the chemical pollution and unintended chemical impacts generated through the production of various goods and resources that we consume. Chemical Alternatives Assessment has proven to be a viable solution for chemical pollution management in terms of filtering out hazardous chemicals for a greener alternative. However, the current substitution practice lacks crucial quantitative datasets (exposures and life cycle impacts) to ensure no unintended trade-offs occur in the substitution process. A Chemical Life Cycle Alternative Assessment (CLiCAA) framework is proposed as a reliable and replicable alternative to Life Cycle Based Alternative Assessment (LCAA) as it integrates chemical molecular structure analysis and Chemical Life Cycle Collaborative (CLiCC) web-based tool to fill in data gaps that the former frameworks suffer from. The CLiCAA framework consists of a four filtering layers, the first two being mandatory, with the final two being optional assessment and data extrapolation steps. Each layer includes relevant impact categories of each chemical, ranging from human to environmental impacts, that will be assessed and aggregated into unique scores for overall comparable results, with little to no data. A feasibility study will demonstrate the efficiency and accuracy of CLiCAA whilst bridging both cancer potency and exposure limit data, hoping to provide the necessary categorical impact information for every firm possible, especially those disadvantaged in terms of research and resource management.

Keywords: chemical alternative assessment, LCA, LCAA, CLiCC, CLiCAA, chemical substitution framework, cancer potency data, chemical molecular structure analysis

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Authors: Merouane Salhi, Mohamed Roudane, Abdelkader Kirad

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In this work, we present a new form of characteristics method, which is a technique for solving partial differential equations. Typically, it applies to first-order equations; the aim of this method is to reduce a partial differential equation to a family of ordinary differential equations along which the solution can be integrated from some initial data. This latter developed under the real gas theory, because when the thermal and the caloric imperfections of a gas increases, the specific heat and their ratio do not remain constant anymore and start to vary with the gas parameters. The gas doesn’t stay perfect. Its state equation change and it becomes for a real gas. The presented equations of the characteristics remain valid whatever area or field of study. Here we need have inserted the developed Prandtl Meyer function in the mathematical system to find a new model when the effect of stagnation pressure is taken into account. In this case, the effects of molecular size and intermolecular attraction forces intervene to correct the state equation, the thermodynamic parameters and the value of Prandtl Meyer function. However, with the assumptions that Berthelot’s state equation accounts for molecular size and intermolecular force effects, expressions are developed for analyzing the supersonic flow for thermally and calorically imperfect gas. The supersonic parameters depend directly on the stagnation parameters of the combustion chamber. The resolution has been made by the finite differences method using the corrector predictor algorithm. As results, the developed mathematical model used to design 2D minimum length nozzles under effect of the stagnation parameters of fluid flow. A comparison for air with the perfect gas PG and high temperature models on the one hand and our results by the real gas theory on the other of nozzles shapes and characteristics are made.

Keywords: numerical methods, nozzles design, real gas, stagnation parameters, supersonic expansion, the characteristics method

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Authors: Audrey Ngambia, Ondrej Masek, Valentina Erastova

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Biochar is an amorphous carbon-rich material generated from the pyrolysis of biomass with multifarious properties and functionality. Biochar has shown proven applications in the treatment of flue gas and organic and inorganic pollutants in soil and water/wastewater as a result of its multiple surface functional groups and porous structures. These properties have also shown potential in energy storage and carbon capture. The availability of diverse sources of biomass to produce biochar has increased interest in it as a sustainable and environmentally friendly material. The properties and porous structures of biochar vary depending on the type of biomass and high heat treatment temperature (HHT). Biochars produced at HHT between 400°C – 800°C generally have lower H/C and O/C ratios, higher porosities, larger pore sizes and higher surface areas with temperature. While all is known experimentally, there is little knowledge on the porous role structure and functional groups play on processes occurring at the atomistic scale, which are extremely important for the optimization of biochar for application, especially in the adsorption of gases. Atomistic simulations methods have shown the potential to generate such amorphous materials; however, most of the models available are composed of only carbon atoms or graphitic sheets, which are very dense or with simple slit pores, all of which ignore the important role of heteroatoms such as O, N, S and pore morphologies. Hence, developing realistic models that integrate these parameters are important to understand their role in governing adsorption mechanisms that will aid in guiding the design and optimization of biochar materials for target applications. In this work, molecular dynamics simulations in the isobaric ensemble are used to generate realistic biochar models taking into account experimentally determined H/C, O/C, N/C, aromaticity, micropore size range, micropore volumes and true densities of biochars. A pore generation approach was developed using virtual atoms, which is a Lennard-Jones sphere of varying van der Waals radius and softness. Its interaction via a soft-core potential with the biochar matrix allows the creation of pores with rough surfaces while varying the van der Waals radius parameters gives control to the pore-size distribution. We focused on microporosity, creating average pore sizes of 0.5 - 2 nm in diameter and pore volumes in the range of 0.05 – 1 cm3/g, which corresponds to experimental gas adsorption micropore sizes of amorphous porous biochars. Realistic biochar models with surface functionalities, micropore size distribution and pore morphologies were developed, and they could aid in the study of adsorption processes in confined micropores.

Keywords: biochar, heteroatoms, micropore size, molecular dynamics simulations, surface functional groups, virtual atoms

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Authors: Neha Thakur, Pravin S. More

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The interaction of CO, H2 and LPG with Cu-dosed SnO2 catalysts was studied by means of Fourier transform infrared spectroscopy (FTIR). With increasing Cu loading, pronounced and progressive red shifts of the C–O stretching frequency associated with molecular CO adsorbed on the Cu/SnO2 component were observed. This decrease in n(CO) correlates with enhancement of CO dissociation at higher temperatures on Cu promoted SnO2 catalysts under conditions, where clean Cu is almost ineffective. In the conclusion, the capability of our technique is discussed, and a technique for enhancing the sensitivity in our technique is proposed.

Keywords: FTIR, spectroscopic, dissociation, n(CO)

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Authors: Steffen Illig, Alexander S. Eggeman, Alessandro Troisi, Stephen G. Yeates, John E. Anthony, Henning Sirringhaus

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Large-amplitude intermolecular vibrations in combination with complex shaped transfer integrals generate a thermally fluctuating energetic landscape. The resulting dynamic disorder and its intrinsic presence in organic semiconductors is one of the most fundamental differences to their inorganic counterparts. Dynamic disorder is believed to govern many of the unique electrical and optical properties of organic systems. However, the low energy nature of these vibrations makes it difficult to access them experimentally and because of this we still lack clear molecular design rules to control and reduce dynamic disorder. Applying a novel technique based on electron diffraction we encountered strong intermolecular, thermal vibrations in every single organic material we studied (14 up to date), indicating that a large degree of dynamic disorder is a universal phenomenon in organic crystals. In this paper a new molecular design strategy will be presented to avoid dynamic disorder. We found that small molecules that have their side chains attached to the long axis of their conjugated core have been found to be less likely to suffer from dynamic disorder effects. In particular, we demonstrate that 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene (C8-BTBT) and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene (C10DNTT) exhibit strongly reduced thermal vibrations in comparison to other molecules and relate their outstanding performance to their lower dynamic disorder. We rationalize the low degree of dynamic disorder in C8-BTBT and C10-DNTT with a better encapsulation of the conjugated cores in the crystal structure which helps reduce large amplitude thermal motions. The work presented in this paper provides a general strategy for the design of new classes of very high mobility organic semiconductors with low dynamic disorder.

Keywords: charge transport, C8-BTBT, C10-DNTT, dynamic disorder, organic semiconductors, thermal vibrations

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Authors: Daniel Y. Abebe, Sijeong Jeong, Jaehyouk Choi

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The use of eccentrically braced frame (EBF) is increasing day by day as EBF possesses high elastic stiffness, stable inelastic response under cyclic lateral loading, and excellent ductility and energy dissipation capacity. The ductility and energy dissipation capacity of EBF depends on the active link beams. Recently, there are two types EBFs; these are conventional EBFs and EBFs with replaceable links. The conventional EBF has a disadvantage during maintenance in post-earthquake. The concept of removable active link beam in EBF is developed to overcome the limitation of the conventional EBF in post-earthquake. In this study, a replaceable link with reduced web section is introduced and design equations are suggested. In addition, nonlinear finite element analysis was conducted in order to evaluate the proposed links.

Keywords: EBFs, replaceable link, earthquake disaster, reduced section

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Authors: A. C. Kumbharkhane

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Time domain dielectric relaxation microwave spectroscopy (TDRMS) is a term used to describe a technique of observing the time dependant response of a sample after application of time dependant electromagnetic field. A TDRMS probes the interaction of a macroscopic sample with a time dependent electrical field. The resulting complex permittivity spectrum, characterizes amplitude (voltage) and time scale of the charge-density fluctuations within the sample. These fluctuations may arise from the reorientation of the permanent dipole moments of individual molecules or from the rotation of dipolar moieties in flexible molecules, like polymers. The time scale of these fluctuations depends on the sample and its relative relaxation mechanism. Relaxation times range from some picoseconds in low viscosity liquids to hours in glasses, Therefore the TDRS technique covers an extensive dynamical process. The corresponding frequencies range from 10-4 Hz to 1012 Hz. This inherent ability to monitor the cooperative motion of molecular ensemble distinguishes dielectric relaxation from methods like NMR or Raman spectroscopy, which yield information on the motions of individual molecules. Recently, we have developed and established the TDR technique in laboratory that provides information regarding dielectric permittivity in the frequency range 10 MHz to 30 GHz. The TDR method involves the generation of step pulse with rise time of 20 pico-seconds in a coaxial line system and monitoring the change in pulse shape after reflection from the sample placed at the end of the coaxial line. There is a great interest to study the dielectric relaxation behaviour in liquid systems to understand the role of hydrogen bond in liquid system. The intermolecular interaction through hydrogen bonds in molecular liquids results in peculiar dynamical properties. The dynamics of hydrogen-bonded liquids have been studied. The theoretical model to explain the experimental results will be discussed.

Keywords: microwave, time domain reflectometry (TDR), dielectric measurement, relaxation time

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Authors: Mohd Ali Abbas Zaidi, Meenu Sachdeva, Jonaki Sen

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In the vertebrate embryo, the forebrain anlagen develops from the anterior-most region of the neural tube which is the precursor of the central nervous system (CNS). The roof plate located at the dorsal midline region of the forebrain anlagen, acts as a source of several secreted molecules involved in patterning and morphogenesis of the forebrain. One such key morphogenetic event is the invagination of the forebrain roof plate which results in separation of the single forebrain vesicle into two cerebral hemispheres. Retinoic acid (RA) signaling plays a key role in this process. Blocking RA signaling at the dorsal forebrain midline inhibits dorsal invagination and results in the absence of certain key features of this region, such as thinning of the neuroepithelium and a lowering of cell proliferation. At present we are investigating the possibility of other signaling pathways acting in concert with RA signaling to regulate this process. We have focused on BMP signaling, which we found to be active in a mutually exclusive domain to that of RA signaling within the roof plate. We have also observed that there is a change in BMP signaling activity on modulation of RA signaling indicating an antagonistic relationship between the two. Moreover, constitutive activation of BMP signaling seems to completely inhibit thinning and partially affect invagination, leaving the lowering of cell proliferation in the midline unaffected. We are employing in-silico modeling as well as molecular manipulations to investigate the relative contribution if any, of regional differences in rates of cell proliferation and thinning of the neuroepithelium towards the process of invagination. We have found expression of certain cell adhesion molecules in forebrain roof-plate whose mRNA localization across the thickness of neuroepithelium is influenced by Bmp and RA signaling, giving regional rigidity to roof plate and assisting invagination. We also found expression of certain cytoskeleton modifiers in a localized small domains in invaginating forebrain roof plate suggesting that midline invagination is under control of many factors.

Keywords: bone morphogenetic signaling, cytoskeleton, cell adhesion molecules, forebrain roof plate, retinoic acid signaling

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Authors: Mohammad Moeini, Mehrdad Ghyabi, Kiarash Mohtasham Dolatshahi

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This paper investigates seismic soil-pile interaction using the Beam on Nonlinear Winkler Foundation (BNWF) approach. Three soil types are considered to cover all the possible responses, as well as nonlinear site response analysis using finite element method in OpenSees platform. Excitations at each elevation that are output of the site response analysis are used as the input excitation to the soil pile system implementing multi-support excitation method. Spectral intensities of acceleration show that the extent of the response in sand is more severe than that of clay, in addition, increasing the PGA of ground strong motion will affect the sandy soil more, in comparison with clayey medium, which is an indicator of the sensitivity of soil-pile systems in sandy soil.

Keywords: BNWF method, multi-support excitation, nonlinear site response analysis, seismic soil-pile interaction

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Authors: Ekaterina A. Savchenko, Elena N. Velichko, Evgenii T. Aksenov

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The development of pathological processes, such as cardiovascular and oncological diseases, are accompanied by changes in molecular parameters in cells, tissues, and serum. The study of the behavior of protein molecules in solutions is of primarily importance for diagnosis of such diseases. Various physical and chemical methods are used to study molecular systems. With the advent of the laser and advances in electronics, optical methods, such as scanning electron microscopy, sedimentation analysis, nephelometry, static and dynamic light scattering, have become the most universal, informative and accurate tools for estimating the parameters of nanoscale objects. The electrophoretic light scattering is the most effective technique. It has a high potential in the study of biological solutions and their properties. This technique allows one to investigate the processes of aggregation and dissociation of different macromolecules and obtain information on their shapes, sizes and molecular weights. Electrophoretic light scattering is an analytical method for registration of the motion of microscopic particles under the influence of an electric field by means of quasi-elastic light scattering in a homogeneous solution with a subsequent registration of the spectral or correlation characteristics of the light scattered from a moving object. We modified the technique by using the regime of total internal reflection with the aim of increasing its sensitivity and reducing the volume of the sample to be investigated, which opens the prospects of automating simultaneous multiparameter measurements. In addition, the method of total internal reflection allows one to study biological fluids on the level of single molecules, which also makes it possible to increase the sensitivity and the informativeness of the results because the data obtained from an individual molecule is not averaged over an ensemble, which is important in the study of bimolecular fluids. To our best knowledge the study of electrophoretic light scattering in the regime of total internal reflection is proposed for the first time, latex microspheres 1 μm in size were used as test objects. In this study, the total internal reflection regime was realized on a quartz prism where the free electrophoresis regime was set. A semiconductor laser with a wavelength of 655 nm was used as a radiation source, and the light scattering signal was registered by a pin-diode. Then the signal from a photodetector was transmitted to a digital oscilloscope and to a computer. The autocorrelation functions and the fast Fourier transform in the regime of Brownian motion and under the action of the field were calculated to obtain the parameters of the object investigated. The main result of the study was the dependence of the autocorrelation function on the concentration of microspheres and the applied field magnitude. The effect of heating became more pronounced with increasing sample concentrations and electric field. The results obtained in our study demonstrated the applicability of the method for the examination of liquid solutions, including biological fluids.

Keywords: light scattering, electrophoretic light scattering, electrophoresis, total internal reflection

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Authors: Djamal Atlaoui, Youcef Bouafia

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This work deals with the experimental study of the mechanical behavior, by shear tests (fracture shear), elements of concrete beams reinforced with fibers in chips. These fibers come from the machining waste of the steel parts. The shear tests are carried out on prismatic specimens of dimensions 10 x 20 x 120 cm³. The fibers are characterized by mechanical resistance and tearing. The optimal composition of the concrete was determined by the workability test. Two fiber contents are selected for this study (W = 0.6% and W = 0.8%) and a BT control concrete (W = 0%) of the same composition as the matrix is developed to serve as a reference with a sand-to-gravel ratio (S/G) of concrete matrix equal to 1. The comparison of the different results obtained shows that the chips fibers confer a significant ductility to the material after cracking of the concrete. Also, the fibers used limit diagonal cracks in shear and improve strength and rigidity.

Keywords: characterization, chips fibers, cracking mode, ductility, undulation, shear

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Authors: Yong Chen

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To understand the detailed molecular mechanisms of memory formation in engram cells is one of the most fundamental questions in neuroscience. Recent single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) techniques have allowed us to explore the sparsely activated engram ensembles, enabling access to the molecular mechanisms that underlie experience-dependent memory formation and consolidation. However, the absence of specific and powerful computational methods to detect memory-related genes (modules) and their regulatory relationships in the sc/snRNA-seq datasets has strictly limited the analysis of underlying mechanisms and memory coding principles in mammalian brains. Here, we present a deep-learning method named SCENTBOX, to detect memory-related gene modules and causal regulatory relationships among themfromsc/snRNA-seq datasets. SCENTBOX first constructs codifferential expression gene network (CEGN) from case versus control sc/snRNA-seq datasets. It then detects the highly correlated modules of differential expression genes (DEGs) in CEGN. The deep network embedding and attention-based convolutional neural network strategies are employed to precisely detect regulatory relationships among DEG genes in a module. We applied them on scRNA-seq datasets of TRAP; Ai14 mouse neurons with fear memory and detected not only known memory-related genes, but also the modules and potential causal regulations. Our results provided novel regulations within an interesting module, including Arc, Bdnf, Creb, Dusp1, Rgs4, and Btg2. Overall, our methods provide a general computational tool for processing sc/snRNA-seq data from case versus control studie and a systematic investigation of fear-memory-related gene modules.

Keywords: sc/snRNA-seq, memory formation, deep learning, gene module, causal inference

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Authors: Tz-Bang Du, Cheng-Han Hsieh, Li-Ping Ju, Hung-Jie Liou

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Polyether amines synthesize by secondary hydroxyl polyether diol play an important role in epoxy hardener. The low molecular weight product is used in low viscosity and high transparent polyamine product for the logo, ground cover, especially for wind turbine blade, while the high molecular weight products are used in advanced agricultures such as a high-speed railway. High-pressure reductive amination process is required for producing these amines. In the condition of higher than 150 atm pressure and 200 degrees Celsius temperature, supercritical ammonia is used as a reactant and also a solvent. It would be a great challenge to select a catalyst support for such high-temperature alkaline circumstance. In this study, we have established a six-autoclave-type (SAT) high-pressure reactor for amination catalyst screening, which six experiment conditions with different temperature and pressure could be examined at the same time. We synthesized copper-nickel catalyst on different shaped alumina catalyst support and evaluated the catalyst activity for high-pressure reductive amination of polypropylene glycol (PPG) by SAT reactor. Ball type gamma alumina, ball type activated alumina and pellet type gamma alumina catalyst supports are evaluated in this study. Gamma alumina supports have shown better activity on PPG reductive amination than activated alumina support. In addition, the catalysts are evaluated in fixed bed reactor. The diamine product was successfully synthesized via this catalyst and the strength of the catalysts is measured. The crush strength of blank supports is about 13.5 lb for both gamma alumina and activated alumina. The strength increases to 20.3 lb after synthesized to be copper-nickel catalyst. After test in the fixed bed high-pressure reductive amination process for 100 hours, the crush strength of the used catalyst is 3.7 lb for activated alumina support, 12.0 lb for gamma alumina support. The gamma alumina is better than activated alumina to use as catalyst support in high-pressure reductive amination process.

Keywords: high pressure reductive amination, copper nickel catalyst, polyether amine, alumina

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Authors: Mitsuhiro Hirai, Satoshi Ajito, Nobutaka Shimizu, Noriyuki Igarashi, Hiroki Iwase, Shinichi Takata

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Sugars and polyols are known to be bioprotectants preventing such as protein denaturation and enzyme deactivation and widely used as a nontoxic additive in various industrial and medical products. The mechanism of their protective actions has been explained by specific bindings between biological components and additives, changes in solvent viscosities, and surface tension and free energy changes upon transfer of those components into additive solutions. On the other hand, some organisms having tolerances against extreme environment produce stress proteins and/or accumulate sugars in cells, which is called cryptobiosis. In particular, trehalose has been drawing attention relevant to cryptobiosis under external stress such as high or low temperature, drying, osmotic pressure, and so on. The function of cryptobiosis by trehalose has been explained relevant to the restriction of the intra-and/or-inter-molecular movement by vitrification or from the replacement of water molecule by trehalose. Previous results suggest that the structure and interaction between sugar and water are a key determinant for understanding cryptobiosis. Recently, we have shown direct evidence that the protein hydration (solvation) and structural stability against chemical and thermal denaturation significantly depend on sugar species and glycerol. Sugar and glycerol molecules tend to be preferentially or weakly excluded from the protein surface and preserved the native protein hydration shell. Due to the protective action of the protein hydration shell by those molecules, the protein structure is stabilized against chemical (guanidinium chloride) and thermal denaturation. The protective action depends on sugar species. To understand the above trend and difference in detail, it is essentially important to clarify the characteristics of solutions containing those additives. In this study, by using wide-angle X-ray scattering technique covering a wide spatial region (~3-120 Å), we have clarified structures of sugar solutions with the concentration from 5% w/w to 65% w/w. The sugars measured in the present study were monosaccharides (glucose, fructose, mannose) and disaccharides (sucrose, trehalose, maltose). Due to observed scattering data with a wide spatial resolution, we have succeeded in obtaining information on the internal structure of individual sugar molecules and on the correlation between them. Every sugar gradually shortened the average inter-molecular distance as the concentration increased. The inter-molecular interaction between sugar molecules was essentially showed an exclusive tendency for every sugar, which appeared as the presence of a repulsive correlation hole. This trend was more weakly seen for trehalose compared to other sugars. The intermolecular distance and spread of individual molecule clearly showed the dependence of sugar species. We will discuss the relation between the characteristic of sugar solution and its protective action of biological materials.

Keywords: hydration, protein, sugar, X-ray scattering

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Authors: M. Cardenas-Garcia, P. P. Gonzalez-Perez

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Intercellular communication is a necessary condition for cellular functions and it allows a group of cells to survive as a population. Throughout this interaction, the cells work in a coordinated and collaborative way which facilitates their survival. In the case of cancerous cells, these take advantage of intercellular communication to preserve their malignancy, since through these physical unions they can send signs of malignancy. The Wnt/β-catenin signaling pathway plays an important role in the formation of intercellular communications, being also involved in a large number of cellular processes such as proliferation, differentiation, adhesion, cell survival, and cell death. The modeling and simulation of cellular signaling systems have found valuable support in a wide range of modeling approaches, which cover a wide spectrum ranging from mathematical models; e.g., ordinary differential equations, statistical methods, and numerical methods– to computational models; e.g., process algebra for modeling behavior and variation in molecular systems. Based on these models, different simulation tools have been developed from mathematical ones to computational ones. Regarding cellular and molecular processes in cancer, its study has also found a valuable support in different simulation tools that, covering a spectrum as mentioned above, have allowed the in silico experimentation of this phenomenon at the cellular and molecular level. In this work, we simulate and explore the complex interaction patterns of intercellular communication in cancer cells using the Cellulat bioinformatics tool, a computational simulation tool developed by us and motivated by two key elements: 1) a biochemically inspired model of self-organizing coordination in tuple spaces, and 2) the Gillespie’s algorithm, a stochastic simulation algorithm typically used to mimic systems of chemical/biochemical reactions in an efficient and accurate way. The main idea behind the Cellulat simulation tool is to provide an in silico experimentation environment that complements and guides in vitro experimentation in intra and intercellular signaling networks. Unlike most of the cell signaling simulation tools, such as E-Cell, BetaWB and Cell Illustrator which provides abstractions to model only intracellular behavior, Cellulat is appropriate for modeling both intracellular signaling and intercellular communication, providing the abstractions required to model –and as a result, simulate– the interaction mechanisms that involve two or more cells, that is essential in the scenario discussed in this work. During the development of this work we made evident the application of our computational simulation tool (Cellulat) for the modeling and simulation of intercellular communication between normal and cancerous cells, and in this way, propose key molecules that may prevent the arrival of malignant signals to the cells that surround the tumor cells. In this manner, we could identify the significant role that has the Wnt/β-catenin signaling pathway in cellular communication, and therefore, in the dissemination of cancer cells. We verified, using in silico experiments, how the inhibition of this signaling pathway prevents that the cells that surround a cancerous cell are transformed.

Keywords: cancer cells, in silico approach, intercellular communication, key molecules, modeling and simulation

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Authors: Eirini Konstanta, Cedric Gouedard, Aggeliki Delimitsou, Stefania Patera, Samuel Murray

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Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy.

Keywords: calibrator, CNV, gene copy number, VAF

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Authors: Vadanasundari Vedarethinam, Kun Qian

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The metabolic analysis is more distal over proteomics and genomics engaging in clinics and needs rationally distinct techniques, designed materials, and device for clinical diagnosis. Conventional techniques such as spectroscopic techniques, biochemical analyzers, and electrochemical have been used for metabolic diagnosis. Currently, there are four major challenges including (I) long-term process in sample pretreatment; (II) difficulties in direct metabolic analysis of biosamples due to complexity (III) low molecular weight metabolite detection with accuracy and (IV) construction of diagnostic tools by materials and device-based platforms for real case application in biomedical applications. Development of chips with nanomaterial is promising to address these critical issues. Mass spectroscopy (MS) has displayed high sensitivity and accuracy, throughput, reproducibility, and resolution for molecular analysis. Particularly laser desorption/ ionization mass spectrometry (LDI MS) combined with devices affords desirable speed for mass measurement in seconds and high sensitivity with low cost towards large scale uses. We developed a plasmonic chip for clinical metabolic fingerprinting as a hot carrier in LDI MS by series of chips with gold nanoshells on the surface through controlled particle synthesis, dip-coating, and gold sputtering for mass production. We integrated the optimized chip with microarrays for laboratory automation and nanoscaled experiments, which afforded direct high-performance metabolic fingerprinting by LDI MS using 500 nL of serum, urine, cerebrospinal fluids (CSF) and exosomes. Further, we demonstrated on-chip direct in-vitro metabolic diagnosis of early-stage lung cancer patients using serum and exosomes without any pretreatment or purifications. To our best knowledge, this work initiates a bionanotechnology based platform for advanced metabolic analysis toward large-scale diagnostic use.

Keywords: plasmonic chip, metabolic fingerprinting, LDI MS, in-vitro diagnostics

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Authors: Dilesh Indorkar

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The aromatic, six membered ring containing three nitrogen atoms are known as triazines. Three triazines are theoretically possible, 1,3,5-triazine, 1,2,4-triazine and 1,2,3-triazine[1]. The 1,3,5-triazines are amongst the oldest known organic compounds. Originally they were called the symmetric triazines. Usuelly abbreviated to s- or sys triazines. The numbering follows the usual convention of beginning at the hetero atom as shown for the parent compound 1,3,5-triazine (I). The triazine rings, each contain 6 pi electrons which fill three bonding molecular orbital there are also three pairs of non bonding electrons in each molecule which are responsible for basic properties of the compounds.

Keywords: s-triazine, thiazoline, isoxazoline, benzoxazine heterocyclic

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Authors: Arturo Galván, Jatziri Y. Moreno-Martínez, Israel Enrique Herrera Díaz, José Ramón Gasca Tirado

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In recent years, one of the methods most used for the construction of tunnels in soft soil is the shield-driven tunneling. The advantage of this construction technique is that it allows excavating the tunnel while at the same time a primary lining is placed, which consists of precast segments. There are joints between segments, also called longitudinal joints, and joints between rings (called as circumferential joints). This is the reason because of this type of constructions cannot be considered as a continuous structure. The effect of these joints influences in the rigidity of the segmental lining and therefore in its structural response. A parametric study was performed to take into account the effect of different parameters in the structural response of typical segmental tunnels built in soft soil by using non-linear numerical models based on Finite Element Method by means of the software package ANSYS v. 11.0. In the first part of this study, two types of numerical models were performed. In the first one, the segments were modeled by using beam elements based on Timoshenko beam theory whilst the segment joints were modeled by using inelastic rotational springs considering the constitutive moment-rotation relation proposed by Gladwell. In this way, the mechanical behavior of longitudinal joints was simulated. On the other hand for simulating the mechanical behavior of circumferential joints elastic springs were considered. As well as, the stability given by the soil was modeled by means of elastic-linear springs. In the second type of models, the segments were modeled by means of three-dimensional solid elements and the joints with contact elements. In these models, the zone of the joints is modeled as a discontinuous (increasing the computational effort) therefore a discrete model is obtained. With these contact elements the mechanical behavior of joints is simulated considering that when the joint is closed, there is transmission of compressive and shear stresses but not of tensile stresses and when the joint is opened, there is no transmission of stresses. This type of models can detect changes in the geometry because of the relative movement of the elements that form the joints. A comparison between the numerical results with two types of models was carried out. In this way, the hypothesis considered in the simplified models were validated. In addition, the numerical models were calibrated with (Lab-based) experimental results obtained from the literature of a typical tunnel built in Europe. In the second part of this work, a parametric study was performed by using the simplified models due to less used computational effort compared to complex models. In the parametric study, the effect of material properties, the geometry of the tunnel, the arrangement of the longitudinal joints and the coupling of the rings were studied. Finally, it was concluded that the mechanical behavior of segment and ring joints and the arrangement of the segment joints affect the global behavior of the lining. As well as, the effect of the coupling between rings modifies the structural capacity of the lining.

Keywords: numerical models, parametric study, segmental tunnels, structural response

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Authors: Mizam Doğan

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In service life; structures can be damaged if they are subjected to dead and live loads which are greater than design values. For preventing this case; possible loads must be correctly calculated, structure must be designed according to determined loads, and structure must not be used out of its function. If loading case of the structure changes when its function changes; it must be reinforced for continuing it is new function. Reinforcement is a process that is made by increasing the existing strengths of structural system elements of the structure as reinforced concrete walls, beams, and slabs. Reinforcement can be done by casting reinforced concrete, placing steel and fiber structural elements. In this paper, reinforcing of columns and slabs of a structure of which function is changed is studied step by step. This reinforcement is made for increasing vertical and lateral load carrying capacity of the building. Not for repairing damaged structural system.

Keywords: strengthening, RC slabs, seismic load, steel beam, structural irregularity

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Authors: Sruthi Ramagiri, Rajeev T.

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Free radical damage has been entailed as the major culprit in the ischemic stroke contributing for oxidative damage. Recent investigations on Hydroxy Safflower Yellow A (HSYA) suggested its role in cerebral ischemia and various neurodegenerative disorders with unidentified molecular mechanisms. The current study was designed to investigate putative therapeutic role and possible molecular mechanisms of HSYA administration during the onset of reperfusion in cerebral ischemia-reperfusion (I/R) injury in cerebral stroke. Cerebral stroke was achieved by focal ischemic model. HSYA (10 mg/kg) was injected intravenously via the tail vein 5 minutes before reperfusion. Losses of sensorimotor abilities were evaluated by neurological scoring, spontaneous locomotor activity, and rotarod performance. Extent of oxidative stress was evaluated by biochemical parameters i.e., malondialdehyde (MDA), Glutathione (GSH), Super Oxide Dismutase (SOD) and catalase levels. The infarct volume of brain was assessed by 2,3,5-triphenyl tetrazolium chloride (TTC) staining technique. Increased cerebral injury (I/R) was evidenced by motor impairment, increased infarct volume and elevation of MDA levels along with significant reduction in antioxidant i.e.,MDA levels along with significant reduction in antioxidant i.e., GSH, SOD and catalase levels when compared to sham control. However, post conditioning with HSYA (10 mg/kg, i.v.) at the onset of reperfusion has significantly ameliorated sensorimotor abilities, attenuated MDA levels and reduced the infarct volume as compared with vehicle treated I/R injury group. Moreover, HSYA treatments improved antioxidant enzyme levels as compared with vehicle treated I/R-injury group. In conclusion, it may be suggested that HSYA post conditioning could be novel therapeutic approach against I/R injury in cerebral stroke possibly through its anti-oxidant mechanism.

Keywords: HSYA, Ischemia reperfusion injury, oxidative stress, stroke

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Authors: Ben Otange, Wolfgang Parak, Florian Schulz, Michael Alexander Rubhausen

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The feasibility of extending the usage of molecular imprinting technique in complex biomolecules is demonstrated in this research. This technique is promising in diverse applications in areas such as drug delivery, diagnosis of diseases, catalysts, and impurities detection as well as treatment of various complications. While molecularly imprinted polymers MIP remain robust in the synthesis of molecules with remarkable binding sites that have high affinities to specific molecules of interest, extending the usage to complex biomolecules remains futile. This work reports on the successful synthesis of MIP from complex proteins: BSA, Transferrin, and MUC1. We show in this research that despite the heterogeneous binding sites and higher conformational flexibility of the chosen proteins, relying on their respective epitopes and motifs rather than the whole template produces highly sensitive and selective MIPs for specific molecular binding. Introduction: Proteins are vital in most biological processes, ranging from cell structure and structural integrity to complex functions such as transport and immunity in biological systems. Unlike other imprinting templates, proteins have heterogeneous binding sites in their complex long-chain structure, which makes their imprinting to be marred by challenges. In addressing this challenge, our attention is inclined toward the targeted delivery, which will use molecular imprinting on the particle surface so that these particles may recognize overexpressed proteins on the target cells. Our goal is thus to make surfaces of nanoparticles that specifically bind to the target cells. Results and Discussions: Using epitopes of BSA and MUC1 proteins and motifs with conserved receptors of transferrin as the respective templates for MIPs, significant improvement in the MIP sensitivity to the binding of complex protein templates was noted. Through the Fluorescence Correlation Spectroscopy FCS measurements on the size of protein corona after incubation of the synthesized nanoparticles with proteins, we noted a high affinity of MIPs to the binding of their respective complex proteins. In addition, quantitative analysis of hard corona using SDS-PAGE showed that only a specific protein was strongly bound on the respective MIPs when incubated with similar concentrations of the protein mixture. Conclusion: Our findings have shown that the merits of MIPs can be extended to complex molecules of higher biomolecular mass. As such, the unique merits of the technique, including high sensitivity and selectivity, relative ease of synthesis, production of materials with higher physical robustness, and higher stability, can be extended to more templates that were previously not suitable candidates despite their abundance and usage within the body.

Keywords: molecularly imprinted polymers, specific binding, drug delivery, high biomolecular mass-templates

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Authors: Yasmin Z. Murad, Haneen M. Abdl-Jabbar

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An experimental program is conducted in this research to investigate the influence of basalt fibers and steel fibers on the flexural behavior of RC beams. Reinforced concrete beams are constructed using steel fiber concrete and basalt fiber concrete. Steel and basalt fibers are included in a percentage of 15% and 2.5% of the total cement weight, respectively. Test results have shown that basalt fibers have increased the load carrying capacity of the beams up to 30% and the maximum deflection to almost 2.4 times that measured in the control specimen. It has also shown that steel fibers have increased the load carrying capacity of the beams up to 47% and the ultimate deflection is almost duplicated compared to the control beam. Steel and basalt fibers have increased the ductility of the reinforced concrete beams.

Keywords: basalt fiber, steel fiber, reinforced concrete beams, flexural behavior

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