Search results for: molecular imprinted polymers

Authors: Sakshi Piplani, Ajit Kumar

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Valproic acid (VPA) is the first synthetic therapeutic agent used to treat epileptic disorders, which account for affecting nearly 1% world population. Teratogenicity caused by VPA has prompted the search for next generation drug with better efficacy and lower side effects. Recent studies have posed HDAC8 as direct target of VPA that causes the teratogenic effect in foetus. We have employed molecular dynamics (MD) and docking simulations to understand the binding mode of VPA and their analogues onto HDAC8. A total of twenty 3D-structures of human HDAC8 isoforms were selected using BLAST-P search against PDB. Multiple sequence alignment was carried out using ClustalW and PDB-3F07 having least missing and mutated regions was selected for study. The missing residues of loop region were constructed using MODELLER and energy was minimized. A set of 216 structural analogues (>90% identity) of VPA were obtained from Pubchem and ZINC database and their energy was optimized with Chemsketch software using 3-D CHARMM-type force field. Four major neurotransmitters (GABAt, SSADH, α-KGDH, GAD) involved in anticonvulsant activity were docked with VPA and its analogues. Out of 216 analogues, 75 were selected on the basis of lower binding energy and inhibition constant as compared to VPA, thus predicted to have anti-convulsant activity. Selected hHDAC8 structure was then subjected to MD Simulation using licenced version YASARA with AMBER99SB force field. The structure was solvated in rectangular box of TIP3P. The simulation was carried out with periodic boundary conditions and electrostatic interactions and treated with Particle mesh Ewald algorithm. pH of system was set to 7.4, temperature 323K and pressure 1atm respectively. Simulation snapshots were stored every 25ps. The MD simulation was carried out for 20ns and pdb file of HDAC8 structure was saved every 2ns. The structures were analysed using castP and UCSF Chimera and most stabilized structure (20ns) was used for docking study. Molecular docking of 75 selected VPA-analogues with PDB-3F07 was performed using AUTODOCK4.2.6. Lamarckian Genetic Algorithm was used to generate conformations of docked ligand and structure. The docking study revealed that VPA and its analogues have more affinity towards ‘hydrophobic active site channel’, due to its hydrophobic properties and allows VPA and their analogues to take part in van der Waal interactions with TYR24, HIS42, VAL41, TYR20, SER138, TRP137 while TRP137 and SER138 showed hydrogen bonding interaction with VPA-analogues. 14 analogues showed better binding affinity than VPA. ADMET SAR server was used to predict the ADMET properties of selected VPA analogues for predicting their druggability. On the basis of ADMET screening, 09 molecules were selected and are being used for in-vivo evaluation using Danio rerio model.

Keywords: HDAC8, docking, molecular dynamics simulation, valproic acid

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Authors: Yuvraj Singh Dangi, Kamta Prasad Namdeo, Surendra Bodhake

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The purpose of this research was to develop and evaluate mucoadhesive films for buccal administration of itraconazole using film-forming and mucoashesive polymers. Buccal films of chitosan bearing Itraconazole were prepared by solvent casting technique. The films have been evaluated in terms of film weight, thickness, density, surface pH, FTIR, X-ray diffraction analysis, bioadhesion, swelling properties, and in vitro drug release studies. It was found that film formulations of 2 cm2 size having weight in the range of 204 ± 0.76 to 223 ± 2.09 mg and film thickness were in the range of 0.44 ± 0.11 to 0.57 ± 0.19 mm. Density of the films was found to be 0.102 to 0.126 g/ml. Drug content was found to be uniform in the range of 8.23 ± 0.07 to 8.73 ± 0.09 mg/cm2 for formulation A1 to A4. Maximum bioadhesion force was recorded for HPMC buccal films (A2) i.e. 0.57 ± 0.47 as compared to other films. In vitro residence time was in range of 1.7 ± 0.12 to 7.65 ± 0.15 h. The drug release studies show that formulations follow non-fickian diffusion. These mucoadhesive formulations could offer many advantages in comparison to traditional treatments.

Keywords: biovariability, buccal patches, itraconazole, Mucoadhesion

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Authors: R. R. Ali, W. A. W. A. Rahman, R. M. Kasmani, H. Hasbullah, N. Ibrahim, A. N. Sadikin, U. A. Asli

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In this study, tapioca starch which acts as natural polymer was added in the blend in order to produce biodegradable product. Low density polyethylene (LDPE) and tapioca starch blends were prepared by extrusion and the test sample by injection moulding process. Ethylene vinyl acetate (EVA) acts as compatibilizer while glycerol as processing aid was added in the blend. The blends were characterized by using melt flow index (MFI), fourier transform infrared (FTIR) and the effects of water absorption to the sample. As the starch content increased, MFI of the blend was decreased. Tensile testing were conducted shows the tensile strength and elongation at break decreased while the modulus increased as the starch increased. For the biodegradation, soil burial test was conducted and the loss in weight was studied as the starch content increased. Morphology studies were conducted in order to show the distribution between LDPE and starch.

Keywords: biopolymers, degradable polymers, starch based polyethylene, injection moulding

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Authors: Othman S. Alsheraida, Sherif El-Gamal

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Fiber Reinforced Polymers (FRP) is a composite material with exceptional properties that are capable of replacing conventional steel reinforcement in reinforced and pre-stressed concrete structures. However, the main obstacle for their wide use in the pre-stressed concrete application is the anchorage system. Due to the weakness of FRP in the transverse direction, the pre-stressing capacity of FRP bars is limited. This paper investigates the modification of the conventional wedge anchorage system to be used for stressing of FRP bars in pre-stressed applications. Epoxy adhesive material with glass FRP (GFRP) bars and conventional steel wedge were used in this paper. The GFRP bars are encased with epoxy at the anchor zone and the wedge system was used in the pull-out test. The results showed a loading capacity of 47.6 kN which is 69% of the bar ultimate capacity. Additionally, nylon wedge was made with the same dimensions of the steel wedge and tested for GFRP bars without epoxy layer. The nylon wedge showed a loading capacity of 19.7 kN which is only 28.5% of the ultimate bar capacity.

Keywords: anchorage, concrete, epoxy, frp, pre-stressed

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Authors: Athena Nguyen, Rojin Belganeh

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Detecting and identifying differences in like polymer materials are key factors in failure and deformulation analysis, and reverse engineering. Pyrolysis-GC/MS is an easy solid sample introduction technique which expands the application areas of gas chromatography and mass spectrometry. The Micro furnace pyrolyzer is directly interfaced with the GC injector preventing any potential of cold spot, carryover, and cross contamination. In this presentation, the analysis of the differences in three polystyrene samples is demonstrated. Although the three samples look very similar by Evolve gas analysis (EGA) and Flash pyrolysis, there are indications of small levels of other materials. By performing Thermal desorption-GC/MS, the additive compounds between samples show the differences. EGA, flash pyrolysis, and thermal desorption analysis are the different modes of operations of the micro-furnace pyrolyzer enabling users to perform multiple analytical techniques.

Keywords: Gas chromatography/Mass spectrometry, pyrolysis, pyrolyzer, thermal desorption-GC/MS

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Authors: Foteini Zagklavara, Peter Jimack, Nikil Kapur, Ozz Querin, Harvey Thompson

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The invention and development of the Polymerase Chain Reaction (PCR) technology have revolutionised molecular biology and molecular diagnostics. There is an urgent need to optimise their performance of those devices while reducing the total construction and operation costs. The present study proposes a CFD-enabled optimisation methodology for continuous flow (CF) PCR devices with serpentine-channel structure, which enables the trade-offs between competing objectives of DNA amplification efficiency and pressure drop to be explored. This is achieved by using a surrogate-enabled optimisation approach accounting for the geometrical features of a CF μPCR device by performing a series of simulations at a relatively small number of Design of Experiments (DoE) points, with the use of COMSOL Multiphysics 5.4. The values of the objectives are extracted from the CFD solutions, and response surfaces created using the polyharmonic splines and neural networks. After creating the respective response surfaces, genetic algorithm, and a multi-level coordinate search optimisation function are used to locate the optimum design parameters. Both optimisation methods produced similar results for both the neural network and the polyharmonic spline response surfaces. The results indicate that there is the possibility of improving the DNA efficiency by ∼2% in one PCR cycle when doubling the width of the microchannel to 400 μm while maintaining the height at the value of the original design (50μm). Moreover, the increase in the width of the serpentine microchannel is combined with a decrease in its total length in order to obtain the same residence times in all the simulations, resulting in a smaller total substrate volume (32.94% decrease). A multi-objective optimisation is also performed with the use of a Pareto Front plot. Such knowledge will enable designers to maximise the amount of DNA amplified or to minimise the time taken throughout thermal cycling in such devices.

Keywords: PCR, optimisation, microfluidics, COMSOL

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Authors: J. H. O. Nascimento, F. R. Oliveira, K. K. O. S. Silva, J. Neves, V. Teixeira, J. Carneiro

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These the aliphatic polyesters such as Polylactic Acid (PLA) in the form of fibers, nanofibers or plastic films, generally possess chemically inert surfaces, free porosity, and surface free energy (ΔG) lesser than 32 mN/m. It is therefore considered a low surface energy material, consequently has a low work of adhesion. For this reason, the products manufactured using these polymers are often subjected to surface treatments in order to change its physic-chemical surface, improving their wettability and the Work of Adhesion (WA). Plasma Radio Frequency low pressure (RF) treatment was performed in order to improve the Work of Adhesion (WA) on PLA fibers. Different parameters, such as, power, ratio of working gas (Argon/Oxygen) and treatment time were used to optimize the plasma conditions to modify the PLA surface properties. With plasma treatment, a significant increase in the work of adhesion on PLA fiber surface was observed. The analysis performed by XPS showed an increase in polar functional groups and the SEM and AFM image revealed a considerable increase in roughness.

Keywords: RF plasma, surface modification, PLA fabric, atomic force macroscopic, Nanotechnology

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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: 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: 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: 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: Fernando G. Torres, Omar P. Troncoso

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Quercetin is a naturally occurring polyphenol found in many vegetables, such as onion, with antioxidant properties. It is a dietary component with a documented role in reducing different human cancers. However, its low bioavailability, poor water solubility, and chemical instability limit its applications. Different nano-delivery systems such as nanoparticles, micelles, and nanohydrogels have been studied in order to improve the bioavailability of quercetin. Nanoparticles based on natural polymers such as starch have the advantage of being biocompatible, biodegradable, and non-toxic. In this study, quercetin was loaded into starch nanoparticles using a nanoprecipitation method. Different routes, using sodium tripolyphosphate and Tween® 80 as tensioactive agents, were tested in order to obtain an optimized starch-based nano-delivery system. The characterization of the nanoparticles loaded with quercetin was assessed by Fourier Transform Infrared Spectroscopy, Dynamic Light Scattering, Zeta potential, and Differential scanning calorimetry. UV-vis spectrophotometry was used to evaluate the loading efficiency and capacity of the samples. The results showed that starch-based systems could be successfully used for the nano-delivery of quercetin.

Keywords: starch nanoparticles, nanoprecipitation, quercetin, biomedical applications

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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: Saad Ahmed, Sanjeev Khannaa

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Glass fiber reinforced polymers are widely used in structural systems as load-bearing elements at both high and low temperatures. This investigation presents the evaluation of glass fiber reinforced unsaturated polyurethane under harsh conditions of changing temperature and moisture content. This study Explores how these parameters affect the optical properties of the polymer matrix and the composite. Using the hand layup method, the polyurethane resin was modified by E-glass fibers (15 vol. %) to manufacture fiber-reinforced composite. This work includes the preparation of glass-like polyurethane resin sheets and estimates all light transmittance properties at high and very low temperatures and wet conditions. All-optical properties were retested to evaluate the level of improvement or failure. The results found that when comprising reinforced composite fiber to the unreinforced specimens, the reinforced composite shows a fair optical property at high temperatures and good performance at low temperatures.

Keywords: unsaturated polyurethane, extreme temperatures, light transmittance, haze number

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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: 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: 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: 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: Ta-Huang Sun, Ming-Hao Hsieh, Min-Chuan Wang, Der-Jun Jan

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Electrochromism refers to the persistent and reversible change of optical properties by an applied voltage pulse. There are many transition metal oxides exhibiting electrochromism, e.g. oxides of W, Ni, Ir, V, Ti, Co and Mo. Organic materials especially some conducting polymers such as poly(aniline), poly(3, 4-propylene- dioxythiophene) also received much attention for electrochromic (EC) applications. Electrochromic materials attract considerable interest because of their potential applications, such as information displays, smart windows, variable reflectance mirrors, and variable-emittance thermal radiators. In this study, the EC characteristics are investigated on an all-solid-state EC device composed of a-WO₃ and Ni(OH)₂ with a Ta₂O₅ protective layer which is prepared by magnetron sputtering. It is found that the transmittance modulation increases with decreasing the film thickness of Ta₂O₅. On the other hand, the transmittance modulation is 57% as the Ni(OH)₂/ITO is prepared by the linear-sweep potential cycling of the sputter-deposited Ta₂O₅/NiO/ITO in a 0.5 M LiClO₄+H₂O electrolyte. However, when Ni(OH)₂/ITO is prepared by a 0.01 M HCl electrolyte, the transmittance modulation of EC device can be improved to 61%.

Keywords: electrochromic device, tungsten oxide, nickel, Ta₂O₅

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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: Dwarakanadha Reddy Peram, D. Swarnalatha, C. Gopinath

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The main aim of this research work was to design and development characterization of Pioglitazone transdermal drug delivery system by using various polymers such as Olibanum with different concentration by solvent evaporation technique. The prepared formulations were evaluated for different physicochemical characteristics like thickness, folding endurance, drug content, percentage moisture absorption, percentage moisture loss, percentage elongation break test and weight uniformity. The diffusion studies were performed by using modified Franz diffusion cells. The result of dissolution studies shows that formulation, F3 (Olibanum with 50 mg) showed maximum release of 99.95 % in 12hrs, whereas F1 (Olibanum and EC backing membrane) showed minimum release of 93.65% in 12 hr. Based on the drug release and physicochemical values obtained the formulation F3 is considered as an optimized formulation which shows higher percentage of drug release of 99.95 % in 12 hr. The developed transdermal patches increase the therapeutic efficacy and reduced toxic effect of pioglitazone.

Keywords: pioglitazone, olibanum, transdermal drug delivery system, drug release percantage

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Authors: Jazlah Majeed Sulaiman, Lakshmi P.

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Concrete slabs are considered to be very ductile structural members. Openings in reinforced slabs are necessary so as to install the mechanical, electrical and pumping (MEP) conduits and ducts. However, these openings reduce the load-carrying capacity, stiffness, energy, and ductility of the slabs. To resolve the undesirable effects of openings in the slab behavior, it is significant to achieve the desired strength against the loads acting on it. The use of Basalt Fiber Reinforcement Polymers (BFRP) as reinforcement has become a valid sustainable option as they produce less greenhouse gases, resist corrosion and have higher tensile strength. In this paper, five slab models are analyzed using non-linear static analysis in ANSYS Workbench to study the effect of openings on slabs reinforced with basalt bars. A parametric numerical study on the loading condition and the shape and size of the opening is conducted, and their load and displacement values are compared. One of the models is validated experimentally.

Keywords: concrete slabs, openings, BFRP, sustainable, corrosion resistant, non-linear static analysis, ANSYS

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