Search results for: molecular mechanics.

Authors: Joel Arrais, João E. Pereira, João Fernandes, José Luís Oliveira

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The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires typically the simultaneous study of the obtained dataset with data that is available in several distinct public databases. Nevertheless, developing a centralized access to these distributed databases rises up a set of challenges such as: what is the best integration strategy, how to solve nomenclature clashes, how to solve database overlapping data and how to deal with huge datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be publicly downloaded or remotely access through SOAP web services.

Keywords: Data integration, biological databases

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Authors: Nurhayati Abdullah, Fauziah Sulaiman, Muhamad Azman Miskam, Rahmad Mohd Taib

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Banana pseudo-stem and fruit-bunch-stem are agricultural residues that can be used for conversion to bio-char, biooil, and gases by using thermochemical process. The aim of this work is to characterize banana pseudo-stem and banana fruit-bunch-stem through proximate analysis, elemental analysis, chemical analysis, thermo-gravimetric analysis, and heating calorific value. The ash contents of the banana pseudo-stem and banana fruit-bunch-stem are 11.0 mf wt.% and 20.6 mf wt.%; while the carbon content of banana pseudo-stem and fruit-bunch-stem are 37.9 mf wt.% and 35.58 mf wt.% respectively. The molecular formulas for banana stem and banana fruit-bunch-stem are C24H33NO26 and C19H29NO33 respectively. The measured higher heating values of banana pseudostem and banana fruit-bunch-stem are 15.5MJ/kg and 12.7 MJ/kg respectively. By chemical analysis, the lignin, cellulose, and hemicellulose contents in the samples will also be presented. The feasibility of the banana wastes to be a feedstock for thermochemical process in comparison with other biomass will be discussed in this paper.

Keywords: Banana Waste, Biomass, Renewable Energy, Thermo-chemical Characteristics.

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Authors: M. Nikbakht, N. Choupani

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In this paper delamination phenomenon in Carbon-Epoxy laminated composite material is investigated numerically. Arcan apparatus and specimen is modeled in ABAQUS finite element software for different loading conditions and crack geometries. The influence of variation of crack geometry on interlaminar fracture stress intensity factor and energy release rate for various mixed mode ratios and pure mode I and II was studied. Also, correction factors for this specimen for different crack length ratios were calculated. The finite element results indicate that for loading angles close to pure mode-II loading, a high ratio of mode-II to mode-I fracture is dominant and there is an opposite trend for loading angles close to pure mode-I loading. It confirms that by varying the loading angle of Arcan specimen pure mode-I, pure mode-II and a wide range of mixed-mode loading conditions can be created and tested. Also, numerical results confirm that the increase of the mode- II loading contribution leads to an increase of fracture resistance in the CF/PEI composite (i.e., a reduction in the total strain energy release rate) and the increase of the crack length leads to a reduction of interlaminar fracture resistance in the CF/PEI composite (i.e., an increase in the total interlaminar strain energy release rate).

Keywords: Fracture Mechanics, Mixed Mode, Arcan Specimen, Finite Element.

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Authors: Jin Xu, Albert Y.S. Lam, Victor O.K. Li

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Stock portfolio selection is a classic problem in finance, and it involves deciding how to allocate an institution-s or an individual-s wealth to a number of stocks, with certain investment objectives (return and risk). In this paper, we adopt the classical Markowitz mean-variance model and consider an additional common realistic constraint, namely, the cardinality constraint. Thus, stock portfolio optimization becomes a mixed-integer quadratic programming problem and it is difficult to be solved by exact optimization algorithms. Chemical Reaction Optimization (CRO), which mimics the molecular interactions in a chemical reaction process, is a population-based metaheuristic method. Two different types of CRO, named canonical CRO and Super Molecule-based CRO (S-CRO), are proposed to solve the stock portfolio selection problem. We test both canonical CRO and S-CRO on a benchmark and compare their performance under two criteria: Markowitz efficient frontier (Pareto frontier) and Sharpe ratio. Computational experiments suggest that S-CRO is promising in handling the stock portfolio optimization problem.

Keywords: Stock portfolio selection, Markowitz model, Chemical Reaction Optimization, Sharpe ratio

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Authors: Hyung T. Kwak, Jun Gao, Yao An, Alfred Kleinhammes, Yue Wu

Abstract:

Surface wettability is a crucial factor in oil recovery. In oil industry, the rock wettability involves the interplay between water, oil, and solid surface. Therefore, studying the interplay between adsorptions of water and hydrocarbon molecules on solid surface would be very informative for understanding rock wettability. Here we use the in-situ Nuclear Magnetic Resonance (NMR) gas isotherm technique to study competitive adsorptions of water and isopropanol, an intermediate step from hydrocarbons. This in-situ NMR technique obtains information on thermodynamic properties such as the isotherm, molecular dynamics via spin relaxation measurements, and adsorption kinetics such as how fast the system can reach thermal equilibrium after changes of vapor pressures. Using surfaces of silica glass beads, which can be modified from hydrophilic to hydrophobic, we obtained information on the influence of surface hydrophilicity on the state of surface water via obtained thermodynamic and dynamic properties.

Keywords: Competitive adsorption, nuclear magnetic resonance, wettability.

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Authors: N. Abbas, S. Lagomarsino, S. Cattari

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Examining existing experimental results for shallow rigid foundations subjected to vertical centric load (N), accompanied or not with a bending moment (M), two main non-linear mechanisms governing the cyclic response of the soil-foundation system can be distinguished: foundation uplift and soil yielding. A soil-foundation failure limit, is defined as a domain of resistance in the two dimensional (2D) load space (N, M) inside of which lie all the admissible combinations of loads; these latter correspond to a pure elastic, non-linear elastic or plastic behavior of the soil-foundation system, while the points lying on the failure limit correspond to a combination of loads leading to a failure of the soil-foundation system. In this study, the proposed resistance domain is constructed analytically based on mechanics. Original elastic limit, uplift initiation limit and iso-uplift limits are constructed inside this domain. These limits give a prediction of the mechanisms activated for each combination of loads applied to the foundation. A comparison of the proposed failure limit with experimental tests existing in the literature shows interesting results. Also, the developed uplift initiation limit and iso-uplift curves are confronted with others already proposed in the literature and widely used due to the absence of other alternatives, and remarkable differences are noted, showing evident errors in the past proposals and relevant accuracy for those given in the present work.

Keywords: Foundation uplift, Iso-uplift curves, Resistance domain, Soil yield.

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Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

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To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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Authors: Ibrahim Abdul Razak, Suhana Arshad, Nur Rafikah Razali, Azhar Abdul Rahman, Mohd Sukeri Mohd Yusof

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Theoretical investigations are performed by DFT method of B3LYP/6-31G+(2d,p) and B3LYP/6-311G+(2d,p) basis sets for three carbonyl thiourea compounds, namely N-[(2,6-Diethylphenyl)carbamothioyl]-2,2-diphenylacetamide (Compound I), N-[(3-Ethylphenyl)carbamothioyl]-2,2-diphenylacetamide (Compound II) and 2,2-Diphenyl-N-{[2-(trifluoromethyl)phenyl]carbamothioyl}acetamide (Compound III). Theoretical calculations for bond parameters, harmonic vibration frequencies and isotropic chemical shifts are in good agreement with the experimental results. The calculated molecular vibrations show good correlation values, which are 0.998 and 0.999 with the experimental data. The energy gap for compounds I, II and III calculated at B3LYP/6-31G+(2d,p) basis set are 4.455866117, 4.297495791 and 4.313550514 eV respectively, while for B3LYP/6-311G+(2d,p) basis set the energy gap obtained are 4.453689205 (Compound I), 4.311373603 (Compound II) and 4.315727426 (Compound III) eV.

Keywords: Crystallization, DFT studies, Spectroscopic Analysis, Thiourea.

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Authors: K. Santacruz-Gomez, E. Silva-Campa, S. Álvarez-García, V. Mata-Haro, D. Soto-Puebla, M. Pedroza-Montero

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Blood gamma irradiation is the only available method to prevent transfusion associated graft versus host disease (TAGVHD). However, when blood is irradiated, determine blood shelf time is crucial. Non irradiated blood have a self-time from 21 to 35 days when is preserved with anticoagulated solution and stored at 4°C. During their storage, red blood cells (RBC) undergo a series of biochemical, biomechanical and molecular changes involving what is known as storage lesion (SL). SL include loss of structural integrity of RBC, decrease of 2,3-diphosphatidylglyceric acid levels, and increase of both ion potassium concentration and hemoglobin (Hb). On the other hand, Atomic force Microscopy (AFM) represents a versatile tool for a nano-scale high resolution topographic analysis in biological systems. In order to evaluate SL in irradiated and nonirradiated blood, RBC topography and morphometric parameters were obtained from an AFM XE-BIO system. Cell viability was followed using flow cytometry. Our results showed that early markers as nanoscale roughness, allow us to evaluate blood quality since other perspective.

Keywords: AFM, Blood γ-irradiation, roughness, Storage lesion.

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Authors: Phakamas Rachamontree, Theerawut Phusantisampan, Natthakorn Woravutthikul, Peerapong Pornwongthong, Malinee Sriariyanun

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A total of 115 yeast strains isolated from local cassava processing wastes were measured for crude protein content. Among these strains, the strain MSY-2 possessed the highest protein concentration (>3.5 mg protein/mL). By using molecular identification tools, it was identified to be a strain of Pichia kudriavzevii based on similarity of D1/D2 domain of 26S rDNA region. In this study, to optimize the protein production by MSY-2 strain, Response Surface Methodology (RSM) was applied. The tested parameters were the carbon content, nitrogen content, and incubation time. Here, the value of regression coefficient (R2) = 0.7194 could be explained by the model which is high to support the significance of the model. Under the optimal condition, the protein content was produced up to 3.77 g per L of the culture and MSY-2 strain contains 66.8 g protein per 100 g of cell dry weight. These results revealed the plausibility of applying the novel strain of yeast in single-cell protein production.

Keywords: Single cell protein, response surface methodology, yeast, cassava processing waste.

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Authors: Mohammad A. Bani-Khaled

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In this work we use the Discrete Proper Orthogonal Decomposition transform to characterize the properties of coupled dynamics in thin-walled beams by exploiting numerical simulations obtained from finite element simulations. The outcomes of the will improve our understanding of the linear and nonlinear coupled behavior of thin-walled beams structures. Thin-walled beams have widespread usage in modern engineering application in both large scale structures (aeronautical structures), as well as in nano-structures (nano-tubes). Therefore, detailed knowledge in regard to the properties of coupled vibrations and buckling in these structures are of great interest in the research community. Due to the geometric complexity in the overall structure and in particular in the cross-sections it is necessary to involve computational mechanics to numerically simulate the dynamics. In using numerical computational techniques, it is not necessary to over simplify a model in order to solve the equations of motions. Computational dynamics methods produce databases of controlled resolution in time and space. These numerical databases contain information on the properties of the coupled dynamics. In order to extract the system dynamic properties and strength of coupling among the various fields of the motion, processing techniques are required. Time- Proper Orthogonal Decomposition transform is a powerful tool for processing databases for the dynamics. It will be used to study the coupled dynamics of thin-walled basic structures. These structures are ideal to form a basis for a systematic study of coupled dynamics in structures of complex geometry.

Keywords: Coupled dynamics, geometric complexity, Proper Orthogonal Decomposition (POD), thin walled beams.

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Authors: Zeynep R. Ege, Aydin Akan, Faik N. Oktar, Betul Karademir, Oguzhan Gunduz

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Early detection of cancer could save human life and quality in insidious cases by advanced biomedical imaging techniques. Designing targeted detection system is necessary in order to protect of healthy cells. Electrospun nanofibers are efficient and targetable nanocarriers which have important properties such as nanometric diameter, mechanical properties, elasticity, porosity and surface area to volume ratio. In the present study, indocyanine green (ICG) organic dye was stabilized and encapsulated in polymer matrix which polyethylene oxide (PEO) and chitosan (CHI) multilayer nanofibers via co-axial electrospinning method at one step. The co-axial electrospun nanofibers were characterized as morphological (SEM), molecular (FT-IR), and entrapment efficiency of Indocyanine Green (ICG) (confocal imaging). Controlled release profile of PEO/CHI/ICG nanofiber was also evaluated up to 40 hours.

Keywords: Chitosan, coaxial electrospinning, controlled releasing, indocyanine green, nanoprobe, polyethylene oxide.

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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Authors: Mehdi Shamshiri, Mahmud Ashrafizaadeh

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The significant effects of the interactions between the system boundaries and the near wall molecules in miniaturized gaseous devices lead to the formation of the Knudsen layer in which the Navier-Stokes-Fourier (NSF) equations fail to predict the correct associated phenomena. In this paper, the well-known lattice Boltzmann method (LBM) is employed to simulate the fluid flow and heat transfer processes in rarefied gaseous micro media. Persuaded by the problematic deficiency of the LBM in capturing the Knudsen layer phenomena, present study tends to concentrate on the effective molecular mean free path concept the main essence of which is to compensate the incapability of this mesoscopic method in dealing with the momentum and energy transport within the above mentioned kinetic boundary layer. The results show qualitative and quantitative accuracy comparable to the solutions of the linearized Boltzmann equation or the DSMC data for the Knudsen numbers of O (1) .

Keywords: Fluid flow and Heat transfer, Knudsen layer, Lattice Boltzmann method (LBM), Micro-scale numerical simulation, Transition regime.

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Authors: Andrej Golowin, Viktor Denk, Axel Riepe

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Solid fan blades and discs in aero engines are subjected to high combined low and high cycle fatigue loads especially around the contact areas between blade and disc. Therefore, special coatings (e.g. dry film lubricant) and surface treatments (e.g. shot peening or laser shock peening) are applied to increase the strength with respect to combined cyclic fatigue and fretting fatigue, but also to improve damage tolerance capability. The traditional deterministic damage tolerance assessment based on fracture mechanics analysis, which treats service damage as an initial crack, often gives overly conservative results especially in the presence of vibratory stresses. A probabilistic damage tolerance methodology using crack initiation data has been developed for fan discs exposed to relatively high vibratory stresses in cross- and tail-wind conditions at certain resonance speeds for limited time periods. This Monte-Carlo based method uses a damage databank from similar designs, measured vibration levels at typical aircraft operations and wind conditions and experimental crack initiation data derived from testing of artificially damaged specimens with representative surface treatment under combined fatigue conditions. The proposed methodology leads to a more realistic prediction of the minimum damage tolerance life for the most critical locations applicable to modern fan disc designs.

Keywords: Damage tolerance, Monte-Carlo method, fan blade and disc, laser shock peening.

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Authors: Binnur Sagbas

Abstract:

Artificial joint replacements such as total knee and total hip prosthesis have been applied to the patients who affected by osteoarthritis. Although different material combinations are used for these joints, biopolymers are most commonly preferred materials especially for acetabular cup and tibial component of hip and knee joints respectively. The main limitation that shortens the service life of these prostheses is wear. Wear is complicated phenomena and it must be considered with friction and lubrication. In this study, micro wave (MW) induced argon+oxygen plasma surface modification were applied on ultra-high molecular weight polyethylene (UHMWPE) and vitamin E blended UHMWPE (VE-UHMWPE) biopolymer surfaces to improve surface wettability and wear resistance of the surfaces. Contact angel measurement method was used for determination of wettability. Ball-on-disc wear test was applied under 25% bovine serum lubrication conditions. The results show that surface wettability and wear resistance of both material samples were increased by plasma surface modification.

Keywords: Artificial joints, plasma surface modification, UHMWPE, vitamin E, wear.

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Authors: Suman Bala, Sunil Kamboj, Vipin Saini

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Quantitative Structure Activity Relationship (QSAR) analysis has been developed to relate antifungal activity of novel substituted 1,3,4-oxadiazole against Candida albicans and Aspergillus niger using computer assisted multiple regression analysis. The study has shown the better relationship between antifungal activities with respect to various descriptors established by multiple regression analysis. The analysis has shown statistically significant correlation with R² values 0.932 and 0.782 against Candida albicans and Aspergillus niger respectively. These derivatives were further subjected to molecular docking studies to investigate the interactions between the target compounds and amino acid residues present in the active site of glucosamine-6-phosphate synthase. All the synthesized compounds have better docking score as compared to standard fluconazole. Our results could be used for the further design as well as development of optimal and potential antifungal agents.

Keywords: 1, 3, 4-Oxadiazole, QSAR, Multiple linear regression, Docking, Glucosamine-6-Phosphate Synthase.

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Authors: Pravin S. Bodke, Shradha S. Binani, Ravi V. Joat

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Science and technology of ultrasonic is widely used in recent years for industrial and medicinal application. The acoustical properties of 2-mercapto substituted pyrimidines viz.,2- Mercapto-4- (2’,4’ –dichloro phenyl) – 6-(2’ – hydroxyl -4’ –methyl-5’ – chlorophenyl) pyrimidine and 2 –Mercapto – 4-(4’ –chloro phenyl) – 6-(2’ – hydroxyl -4’ –methyl-5’ –chlorophenyl) pyrimidine have been investigated from the ultrasonic velocity and density measurements at different concentration and different % in dioxane-water mixture at 305K. The adiabatic compressibility (βs), acoustic impedance (Z), intermolecular free length (Lf), apparent molar volume(ϕv) and relative association (RA) values have been calculated from the experimental data of velocity and density measurement at concentration range of 0.01- 0.000625 mol/lit and 70%,75% and 80% dioxane water mixture. These above parameters are used to discuss the structural and molecular interactions.

Keywords: Acoustical parameters, Density, Dioxane-water mixture, Ultrasonic velocity.

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Authors: M. Hashemi, R. Madani, N. Razmi

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M. paratuberculosis is a slow growing mycobactin dependent mycobacterial species known to be the causative agent of Johne’s disease in all species of domestic ruminants worldwide. JD is characterized by gradual weight loss; decreased milk production. Excretion of the organism may occur for prolonged periods (1 to 2.5 years) before the onset of clinical disease. In recent years researchers focus on identification a specific antigen of MAP to use in diagnosis test and preparation of effective vaccine. In this paper, for production of polyclonal antibody against proteins of Mycobacterium avium paratuberculosis cell well a rabbit immunization at a certain time period with antigen. After immunization of the animal, rabbit was bleeded for producing enriched serum. Antibodies were purification with ion exchange chromatography. For exact measurement of interaction, western blotting test was used that this study demonstrated sharp bands appears in nitrocellulose paper and specific bands were 50 and 150 KD molecular weight. These were indicating immunodominant proteins.

Keywords: Paratuberculosis, Immunodominant, Western blotting, Ion exchange choromatography.

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Authors: L. V. Ignatova, Y. V. Brazhnikova, T. D. Mukasheva, A. A. Omirbekova, R. Zh. Berzhanova, R. K. Sydykbekova, T. A. Karpenyuk, A. V. Goncharova

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The comparative analysis of different taxonomic groups of microorganisms isolated from dark chernozem soils under different agricultures (alfalfa, melilot, sainfoin, soybean, rapeseed) at Almaty region of Kazakhstan was conducted. It was shown that the greatest number of micromycetes was typical to the soil planted with alfalfa and canola. Species diversity of micromycetes markedly decreases as it approaches the surface of the root, so that the species composition in the rhizosphere is much more uniform than in the virgin soil. Promising strains of microscopic fungi and yeast with plant growth-promoting activity to agricultures were selected. Among the selected fungi there are representatives of Penicillium bilaiae, Trichoderma koningii, Fusarium equiseti, Aspergillus ustus. The highest rates of growth and development of seedlings of plants observed under the influence of yeasts Aureobasidium pullulans, Rhodotorula mucilaginosa, Metschnikovia pulcherrima. Using molecular - genetic techniques confirmation of the identification results of selected micromycetes was conducted.

Keywords: Agricultures, biodiversity, micromycetes, plant growth-promoting microorganisms.

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Authors: Juliana V. Pereira, Adriana S. M. Batista, Jefferson P. Nascimento, Clascídia A. Furtado, Luiz O. Faria

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The combination of the properties of graphene oxide (OG) and PVDF homopolymer makes their combined composite materials as multifunctional systems with great potential. Knowledge of the molecular structure is essential for better use. In this work, the degradation of PVDF polymer exposed to gamma irradiation in oxygen atmosphere in high dose rate has been studied and compared to degradation of PVDF/OG composites. The samples were irradiated with a Co-60 source at constant dose rate, with doses ranging from 100 kGy to 1,000 kGy. In FTIR data shown that the formation of oxidation products was at the both samples with formation of carbonyl and hydroxyl groups amongst the most prevalent products in the pure PVDF samples. In the other hand, the composites samples exhibit less presence of degradation products with predominant formation of carbonyl groups, these results also seen in the UV-Vis analysis. The results show that the samples of composites may have greater resistance to the irradiation process, since they have less degradation products than pure PVDF samples seen by spectroscopic techniques.

Keywords: Gamma irradiation, PVDF, PVDF/OG composites, spectroscopic techniques.

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Authors: Puntipar Sonthiphand, Tawan Limpiyakorn

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In this study, communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrifying activated sludge (NAS) prepared by enriching sludge from a municipal wastewater treatment plant in three continuous-flow reactors receiving an inorganic medium containing different ammonium concentrations of 2, 10, and 30 mM NH4 +-N (NAS2, NAS10, and NAS30, respectively) were investigated using molecular analysis. Results suggested that almost all AOA clones from NAS2, NAS10, and NAS30 fell into the same AOA cluster and AOA communities in NAS2 and NAS10 were more diverse than those of NAS30. In contrast to AOA, AOB communities obviously shifted from the seed sludge to enriched NASs and in each enriched NAS, communities of AOB varied particularly. The seed sludge contained members of N. communis cluster and N. oligotropha cluster. After it was enriched under various ammonium loads, members of N. communis cluster disappeared from all enriched NASs. AOB with high affinity to ammonia presented in NAS 2, AOB with low affinity to ammonia presented in NAS 30, and both types of AOB survived in NAS 10. These demonstrated that ammonium load significantly influenced AOB communities, but not AOA communities in enriched NASs.

Keywords: ammonia-oxidizing bacteria, ammonia-oxidizingarchaea, nitrifying activated sludge.

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

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Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: M. Petchsangsai, N. Wonglertnirant, T. Rojanarata, P. Opanasopit, T. Ngawhirunpat

Abstract:

The objective of the present study was to evaluate the potential of hollow microneedles for enhancing the transdermal delivery of Bovine Serum Albumin (MW~66,000 Da)-Fluorescein Isothiocyanate (BSA-FITC) conjugate, a hydrophilic large molecular compound. Moreover, the effect of different formulations was evaluated. The series of binary mixtures composed of propylene glycol (PG) and pH 7.4 phosphate buffer solution (PBS) was prepared and used as a medium for BSA-FITC. The results showed that there was no permeation of BSA-FITC solution across the neonatal porcine skin without using hollow microneedles, whereas the cumulative amount of BSA-FITC released at 8 h through the neonatal porcine skin was about 60-70% when using hollow microneedles. Furthermore, the results demonstrated that the higher volume of PG in binary mixtures injected, the lower cumulative amount of BSA-FITC released and release rate of BSA-FITC from skin. These release profiles of BSA-FITC in binary mixtures were expressed by Fick-s law of diffusion. These results suggest the utilization of hollow microneedle to enhance transdermal delivery of protein and provide useful information for designing an effective hollow microneedle system.

Keywords: Hydrophilic macromolecules, Microneedles, Propylene glycol, Transdermal drug delivery

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Authors: J. Carlos Kuri, Varun Vij, Raymond J. Turner, Orly Yadid-Pecht

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Celiac disease (CD) is an immune system disorder that is related to eating gluten. As gluten-free (GF) diet has become a concern of many people for health reasons, a gold standard had to be nominated. Enzyme-linked immunosorbent assay (ELISA) has taken the seat of this role. However, multiple limitations were discovered, and with that, the desire for an alternative method now exists. Nucleic acid based aptamers have become of great interest due to their selectivity, specificity, simplicity, and rapid-testing advantages. However, fluorescence-based aptasensors have been tagged as unstable, but lifespan details are rarely stated. In this work, the lifespan stability of a fluorescence-based aptasensor is shown over a 8-week long study displaying the accuracy of the sensor and false negatives. This study follows 22 different samples, including GF and gluten-rich (GR) and soy sauce products, off-the-shelf products, and reference material from laboratories; giving a total of 836 tests. The analysis shows an accuracy of correctly classifying GF and GR products of 96.30% and 100%, respectively, when the protocol is augmented with molecular sieves. The overall accuracy remains around 94% within the first 4 weeks and then decays to 63%.

Keywords: Aptasensor, PEG, rGO, FAM, RM, ELISA.

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Authors: H. M. Haytham, E. A. Azza, E.S. Mohamed, E. G. Nesreen

Abstract:

Thoracotomy is a great surgery that has serious pulmonary complications, so purpose of this study was to determine the response of diaphragmatic excursion to inspiratory muscle trainer post thoracotomy. Thirty patients of both sexes (16 men and 14 women) with age ranged from 20 to 40 years old had done thoracotomy participated in this study. The practical work was done in cardiothoracic department, Kasr-El-Aini hospital at faculty of medicine for individuals 3 days Post operatively. Patients were assigned into two groups: group A (study group) included 15 patients (8 men and 7 women) who received inspiratory muscle training by using inspiratory muscle trainer for 20 minutes and routine chest physiotherapy (deep breathing, cough and early ambulation) twice daily, 3 days per week for one month. Group B (control group) included 15 patients (8 men and 7 women) who received the routine chest physiotherapy only (deep breathing, cough and early ambulation) twice daily, 3 days per week for one month. Ultrasonography was used to evaluate the changes in diaphragmatic excursion before and after training program. Statistical analysis revealed a significant increase in diaphragmatic excursion in the study group (59.52%) more than control group (18.66%) after using inspiratory muscle trainer post operatively in patients post thoracotomy. It was concluded that the inspiratory muscle training device increases diaphragmatic excursion in patients post thoracotomy through improving inspiratory muscle strength and improving mechanics of breathing and using of inspiratory muscle trainer as a method of physical therapy rehabilitation to reduce post-operative pulmonary complications post thoracotomy.

Keywords: Diaphragmatic excursion, inspiratory muscle trainer, ultrasonography, thoracotomy.

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Authors: Ali Hamadi Dicko, Nicolas Tong-Yette, Benjamin Gilles, François Faure, Olivier Palombi

Abstract:

A novel hybrid model of the lumbar spine, allowing fast static and dynamic simulations of the disc pressure and the spine mobility, is introduced in this work. Our contribution is to combine rigid bodies, deformable finite elements, articular constraints, and springs into a unique model of the spine. Each vertebra is represented by a rigid body controlling a surface mesh to model contacts on the facet joints and the spinous process. The discs are modeled using a heterogeneous tetrahedral finite element model. The facet joints are represented as elastic joints with six degrees of freedom, while the ligaments are modeled using non-linear one-dimensional elastic elements. The challenge we tackle is to make these different models efficiently interact while respecting the principles of Anatomy and Mechanics. The mobility, the intradiscal pressure, the facet joint force and the instantaneous center of rotation of the lumbar spine are validated against the experimental and theoretical results of the literature on flexion, extension, lateral bending as well as axial rotation. Our hybrid model greatly simplifies the modeling task and dramatically accelerates the simulation of pressure within the discs, as well as the evaluation of the range of motion and the instantaneous centers of rotation, without penalizing precision. These results suggest that for some types of biomechanical simulations, simplified models allow far easier modeling and faster simulations compared to usual full-FEM approaches without any loss of accuracy.

Keywords: Hybrid, modeling, fast simulation, lumbar spine.

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Authors: A. H. Abdol Rahim, Alhassan Salami Tijani

Abstract:

Hydrogen produced by means of polymer electrolyte membrane electrolyzer (PEME) is one of the most promising methods due to clean and renewable energy source. In the process, some energy loss due to mass transfer through a PEM is caused by diffusion, electro-osmotic drag, and the pressure difference between the cathode channel and anode channel. In PEME, water molecules and ionic particles transferred between the electrodes from anode to cathode, Extensive mixing of the hydrogen and oxygen at anode channel due to gases cross-over must be avoided. In recent times the consciousness of safety issue in high pressure PEME where the oxygen mix with hydrogen at anode channel could create, explosive conditions have generated a lot of concern. In this paper, the steady state and simulation analysis of gases crossover in PEME on the temperature and pressure effect are presented. The simulations have been analysis in MATLAB based on the well-known Fick’s Law of molecular diffusion. The simulation results indicated that as temperature increases, there is a significant decrease in operating voltage.

Keywords: Diffusion, gases cross-over, steady state.

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Authors: Md. Shafiqul Islam, Abdullah Khan, Sharon Kao-Walter, Li Jian

Abstract:

Shear testing is one of the most complex testing areas where available methods and specimen geometries are different from each other. Therefore, a modified shear test specimen (MSTS) combining the simple uniaxial test with a zone of interest (ZOI) is tested which gives almost the pure shear. In this study, material parameters of polypropylene (PP) and high density polyethylene (HDPE) are first measured by tensile tests with a dogbone shaped specimen. These parameters are then used as an input for the finite element analysis. Secondly, a specially designed specimen (MSTS) is used to perform the shear stress tests in a tensile testing machine to get the results in terms of forces and extension, crack initiation etc. Scanning Electron Microscopy (SEM) is also performed on the shear fracture surface to find material behavior. These experiments are then simulated by finite element method and compared with the experimental results in order to confirm the simulation model. Shear stress state is inspected to find the usability of the proposed shear specimen. Finally, a geometry correction factor can be established for these two materials in this specific loading and geometry with notch using Linear Elastic Fracture Mechanics (LEFM). By these results, strain energy of shear failure and stress intensity factor (SIF) of shear of these two polymers are discussed in the special application of the screw cap opening of the medical or food packages with a temper evidence safety solution.

Keywords: Shear test specimen, Stress intensity factor, Finite Element simulation, Scanning electron microscopy, Screw cap opening.

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