Search results for: turbulent and molecular diffusion

Authors: Bianca Schweiger, Lucile Bahnweg, Barbara Palm, Ute Steinfeld

Abstract:

The occurrence and removal of trace organic contaminants in the aquatic environment has become a focus of environmental concern. For the selective removal of carbamazepine from loaded waters molecularly imprinted polymers (MIPs) were synthesized with carbamazepine as template. Parameters varied were the type of monomer, crosslinker, and porogen, the ratio of starting materials, and the synthesis temperature. Best results were obtained with a template to crosslinker ratio of 1:20, toluene as porogen, and methacrylic acid (MAA) as monomer. MIPs were then capable to recover carbamazepine by 93% from a 10-5 M landfill leachate solution containing also caffeine and salicylic acid. By comparison, carbamazepine recoveries of 75% were achieved using a nonimprinted polymer (NIP) synthesized under the same conditions, but without template. In landfill leachate containing solutions carbamazepine was adsorbed by 93-96% compared with an uptake of 73% by activated carbon. The best solvent for desorption was acetonitrile, with which the amount of solvent necessary and dilution with water was tested. Selected MIPs were tested for their reusability and showed good results for at least five cycles. Adsorption isotherms were prepared with carbamazepine solutions in the concentration range of 0.01 M to 5*10-6 M. The heterogeneity index showed a more homogenous binding site distribution.

Keywords: Carbamazepine, landfill leachate, removal, reuse

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Authors: Yahia I. Mohamed, Ahmed I. Marzouk, Mohamed A. Yacout

Abstract:

Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100% of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was identified as two fragments, 1- Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2- Predicted: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86 % of similarity.

Keywords: Olea europaea, fingerprinting, Diacylglycerol acyltransferase type- 2 (DGAT2).

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Authors: Fabian Horn, Reinhard Guthke

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In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Jonmichael A. Weaver, David A. Miller

Abstract:

Ultra High Molecular Weight Polyethylene (UHMWPE) presents several distinct advantages as a material with a high strength to weight ratio, durability, and neutron stability. Understanding the change in the mechanical performance of UHMWPE due to environmental exposure is key to safety for future applications. Dyneema® HB-210, a 15 µm diameter UHMWPE multi-filament fiber laid up in a polyurethane matrix in [0/ 90]2, with a thickness of 0.17 mm is compared to the same fiber and orientation system, HB-212, with a rubber-based matrix under UV aging conditions. UV aging tests according to ASTM-G154 were performed on both HB-210 and HB-212 to interrogate the change in mechanical properties, as measured through dynamic mechanical analysis and imaged using a scanning electron microscope. These results showed a decrease in both the storage modulus and loss modulus of the aged material compared to the unaged, even though the tan δ slightly increased. Material degradation occurred at a higher rate in Dyneema® HB-212 compared to HB-210. The HB-210 was characterized for the effects of 100 hours of UV aging via dynamic mechanical analysis. Scanning electron microscope images were taken of the HB-210 and HB-212 to identify the primary damage mechanisms in the matrix. Embrittlement and matrix spall were the products of prolonged UV exposure and erosion, resulting in decreased mechanical properties.

Keywords: Composite materials, material characterization, UV aging, UHMWPE.

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Authors: Rupinder Bakshi, Geeta Walia, Anita Gupta

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Urinary Tract Infections are considered as one of the most common bacterial infections with an estimated annual global incidence of 150 million. Antimicrobial drug resistance is one of the major threats due to wide spread usage of uncontrolled antibiotics. In this study, a total number of 9149 urine samples were collected from R.H Patiala and processed in the Department of Microbiology G. M. C Patiala (January 2013 to December 2013). Urine samples were inoculated on MacConkey’s and blood agar plates and incubated at 370C for 24 hrs. The organisms were identified by colony characters, Gram’s staining, and biochemical reactions. Antimicrobial susceptibility of the isolates was determined against various antimicrobial agents (Hi – Media Mumbai India) by Kirby Bauer DISK diffusion method on Muller Hinton agar plates. Maximum patients were in the age group of 21-30 yrs followed by 31-40 yrs. Males (34%) are less prone to urinary tract infections than females (66%). Culture was positive in 25% of the samples. Escherichia coli was the most common isolate 60.3% followed by Klebsiella pneumoniae 13.5%, Proteus spp. 9% and Staphylococcus aureus 7.6%. Most of the urinary isolates were sensitive to, carbepenems, Aztreonam, Amikacin, and Piperacillin + Tazobactum. All the isolates showed a good sensitivity towards Nitrofurantoin (82%). ESBL production was found to be 70.6% in Escherichia coli and 29.4% in Klebsiella pneumonia. Susceptibility of ESBL producers to Imipenem, Nitrofurantoin and Amikacin were found to be 100%, 76%, and 75% respectively. Uropathogens are increasingly showing resistance to many antibiotics making empiric management of outpatient UTIs challenging. Ampicillin, Cotrimoxazole and Ciprofloxacin should not be used in empiric treatment. Nitrofurantoin could be used in lower urinary tract infection. Knowledge of uropathogens and their antimicrobial susceptibility pattern in a geographical region will help in appropriate and judicious antibiotic usage in a health care setup.

Keywords: Urinary Tract Infection, UTI, antibiotic susceptibility pattern, ESBL.

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Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: Ekin Kıpçak, Sinan Kutluay, Mesut Akgün

Abstract:

Recently, a growing interest has emerged on the development of new and efficient energy sources, due to the inevitable extinction of the nonrenewable energy reserves. One of these alternative sources which has a great potential and sustainability to meet up the energy demand is biomass energy. This significant energy source can be utilized with various energy conversion technologies, one of which is biomass gasification in supercritical water. Water, being the most important solvent in nature, has very important characteristics as a reaction solvent under supercritical circumstances. At temperatures above its critical point (374.8oC and 22.1 MPa), water becomes more acidic and its diffusivity increases. Working with water at high temperatures increases the thermal reaction rate, which in consequence leads to a better dissolving of the organic matters and a fast reaction with oxygen. Hence, supercritical water offers a control mechanism depending on solubility, excellent transport properties based on its high diffusion ability and new reaction possibilities for hydrolysis or oxidation. In this study the gasification of a real biomass, namely olive mill wastewater (OMW), in supercritical water is investigated with the use of Pt/Al2O3 and Ni/Al2O3 catalysts. OMW is a by-product obtained during olive oil production, which has a complex nature characterized by a high content of organic compounds and polyphenols. These properties impose OMW a significant pollution potential, but at the same time, the high content of organics makes OMW a desirable biomass candidate for energy production. All of the catalytic gasification experiments were made with five different reaction temperatures (400, 450, 500, 550 and 600°C), under a constant pressure of 25 MPa. For the experiments conducted with Ni/Al2O3 catalyst, the effect of five reaction times (30, 60, 90, 120 and 150 s) was investigated. However, procuring that similar gasification efficiencies could be obtained at shorter times, the experiments were made by using different reaction times (10, 15, 20, 25 and 30 s) for the case of Pt/Al2O3 catalyst. Through these experiments, the effects of temperature, time and catalyst type on the gasification yields and treatment efficiencies were investigated.

Keywords: Catalyst, Gasification, Olive mill wastewater, Supercritical water.

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Authors: Xiaowei Zhang, Min Xu, Saeid Habibi, Fengjun Yan, Ryan Ahmed

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Recently, Electric Vehicles (EVs) have received extensive consideration since they offer a more sustainable and greener transportation alternative compared to fossil-fuel propelled vehicles. Lithium-Ion (Li-ion) batteries are increasingly being deployed in EVs because of their high energy density, high cell-level voltage, and low rate of self-discharge. Since Li-ion batteries represent the most expensive component in the EV powertrain, accurate monitoring and control strategies must be executed to ensure their prolonged lifespan. The Battery Management System (BMS) has to accurately estimate parameters such as the battery State-of-Charge (SOC), State-of-Health (SOH), and Remaining Useful Life (RUL). In order for the BMS to estimate these parameters, an accurate and control-oriented battery model has to work collaboratively with a robust state and parameter estimation strategy. Since battery physical parameters, such as the internal resistance and diffusion coefficient change depending on the battery state-of-life (SOL), the BMS has to be adaptive to accommodate for this change. In this paper, an extensive battery aging study has been conducted over 12-months period on 5.4 Ah, 3.7 V Lithium polymer cells. Instead of using fixed charging/discharging aging cycles at fixed C-rate, a set of real-world driving scenarios have been used to age the cells. The test has been interrupted every 5% capacity degradation by a set of reference performance tests to assess the battery degradation and track model parameters. As battery ages, the combined model parameters are optimized and tracked in an offline mode over the entire batteries lifespan. Based on the optimized model, a state and parameter estimation strategy based on the Extended Kalman Filter (EKF) and the relatively new Smooth Variable Structure Filter (SVSF) have been applied to estimate the SOC at various states of life.

Keywords: Lithium-Ion batteries, genetic algorithm optimization, battery aging test, and parameter identification.

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Authors: Eda Gök

Abstract:

Peridynamics is a new modeling concept of non-local interactions for solid structures. The formulations of Peridynamic (PD) theory are based on integral equations rather than differential equations. Through, undefined equations of associated problems are avoided. PD theory might be defined as continuum version of molecular dynamics. The medium is usually modeled with mass particles bonded together. Particles interact with each other directly across finite distances through central forces named as bonds. The main assumption of this theory is that the body is composed of material points which interact with other material points within a finite distance. Although, PD theory developed for discontinuities, it gives good results for structures which have no discontinuities. In this paper, displacement control of the isotropic plate under the effect of tensile and bending loading has been investigated by means of PD theory. A MATLAB code is generated to create PD bonds and corresponding surface correction factors. Using generated MATLAB code the geometry of the specimen is generated, and the code is implemented in Finite Element Software. The results obtained from non-local continuum theory are compared with the Finite Element Analysis results and analytical solution. The results show good agreement.

Keywords: Flexural loading, non-local continuum mechanics, Peridynamic theory, solid structures, tensile loading.

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Authors: Francis William S, Imtiaz Ahmed Choudhury, Ananda Kumar Eriki, A. John Rajan

Abstract:

Diesel Engines emit complex mixtures of inorganic and organic compounds in the form of both solid and vapour phase particles. Most of the particulates released are ultrafine nanoparticles which are detrimental to human health and can easily enter the body by respiration. The emissions standards on particulate matter release from diesel engines are constantly upgraded within the European Union and with future regulations based on the particles numbers released instead of merely mass, the need for effective aftertreatment devices will increase. Standard particulate filters in the form of wall flow filters can have problems with high soot accumulation, producing a large exhaust backpressure. A potential solution would be to combine the standard filter with a flow through filter to reduce the load on the wall flow filter. In this paper soot particle trapping has been simulated in different continuous flow filters of monolithic structure including the use of promoters, at laminar flow conditions. An Euler Lagrange model, the discrete phase model in Ansys used with user defined functions for forces acting on particles. A method to quickly screen trapping of 5 nm and 10 nm particles in different catalysts designs with tracers was also developed. Simulations of square duct monoliths with promoters show that the strength of the vortices produced are not enough to give a high amount of particle deposition on the catalyst walls. The smallest particles in the simulations, 5 and 10 nm particles were trapped to a higher extent, than larger particles up to 1000 nm, in all studied geometries with the predominant deposition mechanism being Brownian diffusion. The comparison of the different filters designed with a wall flow filter does show that the options for altering a design of a flow through filter, without imposing a too large pressure drop penalty are good.

Keywords: Diesel Engine trap, thermophoresis, Exhaust pipe, PM-Simulation modeling.

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Authors: Maurizio Dapor, Isabel Abril, Pablo de Vera, Rafael Garcia-Molina

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The ionization yield of ion tracks in polymers and bio-molecular systems reaches a maximum, known as the Bragg peak, close to the end of the ion trajectories. Along the path of the ions through the materials, many electrons are generated, which produce a cascade of further ionizations and, consequently, a shower of secondary electrons. Among these, very low energy secondary electrons can produce damage in the biomolecules by dissociative electron attachment. This work deals with the calculation of the energy distribution of electrons produced by protons in a sample of polymethylmethacrylate (PMMA), a material that is used as a phantom for living tissues in hadron therapy. PMMA is also of relevance for microelectronics in CMOS technologies and as a photoresist mask in electron beam lithography. We present a Monte Carlo code that, starting from a realistic description of the energy distribution of the electrons ejected by protons moving through PMMA, simulates the entire cascade of generated secondary electrons. By following in detail the motion of all these electrons, we find the radial distribution of the energy that they deposit in PMMA for several initial proton energies characteristic of the Bragg peak.

Keywords: Monte Carlo method, secondary electrons, energetic ions, ion-beam cancer therapy, ionization cross section, polymethylmethacrylate, proton beams, secondary electrons, radial energy distribution.

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Authors: Ahmed O. Apampa, Yinusa A. Jimoh

Abstract:

The paper examines the mechanism of pozzolan-soil reactions, using a recent study on the chemical stabilization of a Class A-2-7 (3) lateritic soil, with corn cob ash (CCA) as case study. The objectives are to establish a nexus between cation exchange capacity of the soil, the alkaline forming compounds in CCA and percentage CCA addition to soil beyond which no more improvement in strength properties can be achieved; and to propose feasible chemical reactions to explain the chemical stabilization of the lateritic soil with CCA alone. The lateritic soil, as well as CCA of pozzolanic quality Class C were separately analysed for their metallic oxide composition using the X-Ray Fluorescence technique. The cation exchange capacity (CEC) of the soil and the CCA were computed theoretically using the percentage composition of the base cations Ca²⁺, Mg²⁺ K⁺ and Na²⁺ as 1.48 meq/100 g and 61.67 meq/100 g respectively, thus indicating a ratio of 0.024 or 2.4%. This figure, taken as the theoretical amount required to just fill up the exchangeable sites of the clay molecules, compares well with the laboratory observation of 1.5% for the optimum level of CCA addition to lateritic soil. The paper went on to present chemical reaction equations between the alkaline earth metals in the CCA and the silica in the lateritic soil to form silicates, thereby proposing an extension of the theory of mechanism of soil stabilization to cover chemical stabilization with pozzolanic ash only. The paper concluded by recommending further research on the molecular structure of soils stabilized with pozzolanic waste ash alone, with a view to confirming the chemical equations advanced in the study.

Keywords: Cation exchange capacity, corn cob ash, lateritic soil, soil stabilization.

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Authors: Ekin Kıpçak, Mesut Akgün

Abstract:

Recently, a growing interest has emerged on the development of new and efficient energy sources, due to the inevitable extinction of the nonrenewable energy reserves. One of these alternative sources which have a great potential and sustainability to meet up the energy demand is biomass energy. This significant energy source can be utilized with various energy conversion technologies, one of which is biomass gasification in supercritical water.

Water, being the most important solvent in nature, has very important characteristics as a reaction solvent under supercritical circumstances. At temperatures above its critical point (374.8^oC and 22.1MPa), water becomes more acidic and its diffusivity increases. Working with water at high temperatures increases the thermal reaction rate, which in consequence leads to a better dissolving of the organic matters and a fast reaction with oxygen. Hence, supercritical water offers a control mechanism depending on solubility, excellent transport properties based on its high diffusion ability and new reaction possibilities for hydrolysis or oxidation.

In this study the gasification of a real biomass, namely olive mill wastewater (OMW), in supercritical water conditions is investigated with the use of Ru/Al₂O₃ catalyst. OMW is a by-product obtained during olive oil production, which has a complex nature characterized by a high content of organic compounds and polyphenols. These properties impose OMW a significant pollution potential, but at the same time, the high content of organics makes OMW a desirable biomass candidate for energy production.

The catalytic gasification experiments were made with five different reaction temperatures (400, 450, 500, 550 and 600°C) and five reaction times (30, 60, 90, 120 and 150s), under a constant pressure of 25MPa. Through these experiments, the effects of reaction temperature and time on the gasification yield, gaseous product composition and OMW treatment efficiency were investigated.

Keywords: Catalyst, Gasification, Olive mill wastewater, Ru/Al2O3, Supercritical water.

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Authors: H. Djaara, M. Yahia, H. Bousselsela, N Khelif, A. Zidani, S. Benbia.

Abstract:

Von Willebrand-s disease is the most common inherited bleeding disorder in humans, it caused by qualitative abnormalities of the von Willebrand factor (vWF). Our objective is to determine the prevalence of this disease at part of the Algerian population in the East and the South by a biological diagnosis based on specific biological tests (automated platelet count, the bleeding time (TS), the time of cephalin + activator (TCA), measure of the prothrombin rate (TP), vWF rate and factor VIII rate, Molecular electrophoresis of vWF multimers in agarose gel in the presence of SDS). Four patients of type III or severe Willebrand-s disease were found on 200 suspect cases. All cases are showed a deficit in vWF rate (< 5%), and factor VIII (P<0, 0001), and lengthening very significantly high of the TCA (P<0, 0001) and of the bleeding time (P<0,0001), with a normal blood platelet rate (P=0,7433) and a normal prothrombin rate (P=0,5808), an absence of all the multimers of vWF in plasma patients. The severe Willebrand-s disease is not only one pathology of primary haemostasis, but it can be accompanied by coagulation-s anomaly due to deficit in factor VIII. At this studied population, von Willebrand-s disease is less frequent (2%) than other hemorrhagic syndromes identified by the differential diagnosis like the thrombocytopenia (36%).

Keywords: Von Willebrand's disease, differential diagnosis, von Willebrand factor, factor VIII, biological diagnosis, thrombocytopenia.

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Authors: Chen-Fu Wang, Lin-Ya Kung

Abstract:

For traditional painting materials, the artisan used to combine the pigments with different binders to create colors. As time goes by, the materials used for painting evolved from natural to chemical materials. The vast variety of ingredients used in chemical materials has complicated restoration work; it makes conservation work more difficult. Conservation work also becomes harder when the materials cannot be easily identified; therefore, it is essential that we take a more scientific approach to assist in conservation work. Paintings materials are high molecular weight polymer, and their analysis is very complicated as well other contamination such as smoke and dirt can also interfere with the analysis of the material. The current methods of composition analysis of painting materials include Fourier transform infrared spectroscopy (FT-IR), mass spectrometer, Raman spectroscopy, X-ray diffraction spectroscopy (XRD), each of which has its own limitation. In this study, FT-IR was used to analyze the components of the paint coating. We have taken the most commonly seen materials as samples and deteriorated it. The aged information was then used for the database to exam the temple painting materials. By observing the FT-IR changes over time, we can tell all of the painting materials will be deteriorated by the UV light, but only the speed of its degradation had some difference. From the deterioration experiment, the acrylic resin resists better than the others. After collecting the painting materials aging information on FT-IR, we performed some test on the paintings on the temples. It was found that most of the artisan used tune-oil for painting materials, and some other paintings used chemical materials. This method is now working successfully on identifying the painting materials. However, the method is destructive and high cost. In the future, we will work on the how to know the painting materials more efficiently.

Keywords: Temple painting, painting material, conservation, FT-IR.

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Authors: S. M. Anisuzzaman, Sariah Abang, Awang Bono, D. Krishnaiah, N. M. Ismail, G. B. Sandrison

Abstract:

Wax and asphaltene are high molecular weighted compounds that contribute to the stability of crude oil at a dispersed state. Transportation of crude oil along pipelines from the oil rig to the refineries causes fluctuation of temperature which will lead to the coagulation of wax and flocculation of asphaltenes. This paper focuses on the prevention of wax and asphaltene precipitate deposition on the inner surface of the pipelines by using a wax inhibitor and an asphaltene dispersant. The novelty of this prevention method is the combination of three substances; a wax inhibitor dissolved in a wax inhibitor solvent and an asphaltene solvent, namely, ethylene-vinyl acetate (EVA) copolymer dissolved in methylcyclohexane (MCH) and toluene (TOL) to inhibit the precipitation and deposition of wax and asphaltene. The objective of this paper was to optimize the percentage composition of each component in this inhibitor which can maximize the viscosity reduction of crude oil. The optimization was divided into two stages which are the laboratory experimental stage in which the viscosity of crude oil samples containing inhibitor of different component compositions is tested at decreasing temperatures and the data optimization stage using response surface methodology (RSM) to design an optimizing model. The results of experiment proved that the combination of 50% EVA + 25% MCH + 25% TOL gave a maximum viscosity reduction of 67% while the RSM model proved that the combination of 57% EVA + 20.5% MCH + 22.5% TOL gave a maximum viscosity reduction of up to 61%.

Keywords: Asphaltene, ethylene-vinyl acetate, methylcyclohexane, toluene, wax.

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Authors: N. H. Abd Raof, H. Abu Hassan, S.K. Mohd Bakhori, S. S. Ng, Z. Hassan

Abstract:

Quaternary InxAlyGa1-x-yN semiconductors have attracted much research interest because the use of this quaternary offer the great flexibility in tailoring their band gap profile while maintaining their lattice-matching and structural integrity. The structural and optical properties of InxAlyGa1-x-yN alloys grown by molecular beam epitaxy (MBE) is presented. The structural quality of InxAlyGa1-x-yN layers was characterized using high-resolution X-ray diffraction (HRXRD). The results confirm that the InxAlyGa1-x-yN films had wurtzite structure and without phase separation. As the In composition increases, the Bragg angle of the (0002) InxAlyGa1-x-yN peak gradually decreases, indicating the increase in the lattice constant c of the alloys. FWHM of (0002) InxAlyGa1-x-yN decreases with increasing In composition from 0 to 0.04, that could indicate the decrease of quality of the samples due to point defects leading to non-uniformity of the epilayers. UV-VIS spectroscopy have been used to study the energy band gap of InxAlyGa1-x-yN. As the indium (In) compositions increases, the energy band gap decreases. However, for InxAlyGa1-x-yN with In composition of 0.1, the band gap shows a sudden increase in energy. This is probably due to local alloy compositional fluctuations in the epilayer. The bowing parameter which appears also to be very sensitive on In content is investigated and obtained b = 50.08 for quaternary InxAlyGa1-x-yN alloys. From photoluminescence (PL) measurement, green luminescence (GL) appears at PL spectrum of InxAlyGa1-x-yN, emitted for all x at ~530 nm and it become more pronounced as the In composition (x) increased, which is believed cause by gallium vacancies and related to isolated native defects.

Keywords: HRXRD, nitrides, PL, quaternary, UV-VIS.

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Authors: P. Kowalska, P. Gabka, K. Kamieniarz, M. Kamieniarz, W. Stryla, P. Guzik, T. Krauze

Abstract:

We have developed a computer program consisting of 6 subtests assessing the children hand dexterity applicable in the rehabilitation medicine. We have carried out a normative study on a representative sample of 285 children aged from 7 to 15 (mean age 11.3) and we have proposed clinical standards for three age groups (7-9, 9-11, 12-15 years). We have shown statistical significance of differences among the corresponding mean values of the task time completion. We have also found a strong correlation between the task time completion and the age of the subjects, as well as we have performed the test-retest reliability checks in the sample of 84 children, giving the high values of the Pearson coefficients for the dominant and non-dominant hand in the range 0.740.97 and 0.620.93, respectively. A new MATLAB-based programming tool aiming at analysis of cardiologic RR intervals and blood pressure descriptors, is worked out, too. For each set of data, ten different parameters are extracted: 2 in time domain, 4 in frequency domain and 4 in Poincaré plot analysis. In addition twelve different parameters of baroreflex sensitivity are calculated. All these data sets can be visualized in time domain together with their power spectra and Poincaré plots. If available, the respiratory oscillation curves can be also plotted for comparison. Another application processes biological data obtained from BLAST analysis.

Keywords: Biomedical data base processing, Computer software, Hand dexterity, Heart rate and blood pressure variability.

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Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

Abstract:

We study the biological effects induced by ionizing radiation in view of therapeutic exposure and the idea of space flights beyond Earth's magnetosphere. In particular, we examine the differences between base pair substitution induction by ionizing radiation in model haploid and diploid yeast Saccharomyces cerevisiae cells. Such mutations are difficult to study in higher eukaryotic systems. In our research, we have used a collection of six isogenic trp5-strains and 14 isogenic haploid and diploid cyc1-strains that are specific markers of all possible base-pair substitutions. These strains differ from each other only in single base substitutions within codon-50 of the trp5 gene or codon-22 of the cyc1 gene. Different mutation spectra for two different haploid genetic trp5- and cyc1-assays and different mutation spectra for the same genetic cyc1-system in cells with different ploidy — haploid and diploid — have been obtained. It was linear function for dose-dependence in haploid and exponential in diploid cells. We suggest that the differences between haploid yeast strains reflect the dependence on the sequence context, while the differences between haploid and diploid strains reflect the different molecular mechanisms of mutations.

Keywords: Base pair substitutions, γ-rays, haploid and diploid cells, yeast Saccharomyces cerevisiae.

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Authors: Ratnakar Tripathi, Rajnikant Mishra

Abstract:

The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Innocent Kafodya, Guijun Xian

Abstract:

This paper presents effects of distilled water, seawater and sustained bending strains of 30% and 50% ultimate strain at room temperature, on the durability of unidirectional pultruded carbon fiber reinforced polymer (CFRP) plates. In this study, dynamic mechanical analyzer (DMA) was used to investigate the synergic effects of the immersions and bending strains on the viscoelastic properties of (CFRP) such as storage modulus, tan delta and glass transition temperature. The study reveals that the storage modulus and glass transition temperature increase while tan delta peak decreases in the initial stage of both immersions due to the progression of curing. The storage modulus and Tg subsequently decrease and tan delta increases due to the matrix plasticization. The blister induced damages in the unstrained seawater samples enhance water uptake and cause more serious degradation of Tg and storage modulus than in water immersion. Increasing sustained bending decreases Tg and storage modulus in a long run for both immersions due to resin matrix cracking and debonding. The combined effects of immersions and strains are not clearly reflected due to the statistical effects of DMA sample sizes and competing processes of molecular reorientation and postcuring.

Keywords: Pultruded CFRP plate, bending strain, glass transition temperature, storage modulus, tan delta.

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Authors: Sarkar M. A. Kawsar, Sarkar M. A. Mamun, Md S. Rahman, Hidetaro Yasumitsu, Yasuhiro Ozeki

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Lectins have a good scope in current clinical microbiology research. In the present study evaluated the antimicrobial activities of a D-galactose binding lectin (PnL) was purified from the annelid, Perinereis nuntia (polychaeta) by affinity chromatography. The molecular mass of the lectin was determined to be 32 kDa as a single polypeptide by SDS-PAGE under both reducing and non-reducing conditions. The hemagglutinating activity of the PnL showed against trypsinized and glutaraldehyde-fixed human erythrocytes was specifically inhibited by D-Gal, GalNAc, Galβ1-4Glc and Galα1-6Glc. PnL was evaluated for in vitro antibacterial screening studies against 11 gram-positive and gram-negative microorganisms. From the screening results, it was revealed that PnL exhibited significant antibacterial activity against gram-positive bacteria. Bacillus megaterium showed the highest growth inhibition by the lectin (250 μg/disc). However, PnL did not inhibit the growth of gram-negative bacteria such as Vibrio cholerae and Pseudomonas sp. PnL was also examined for in vitro antifungal activity against six fungal phytopathogens. PnL (100 μg/mL) inhibited the mycelial growth of Alternaria alternata (24.4%). These results indicate that future findings of lectin applications obtained from annelids may be of importance to life sciences.

Keywords: Perinereis nuntia, Lectin, Inhibition zone, Mycelial growth.

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Authors: Wen-Shyong Tzou, Chih-Ching Huang, Chin-Hwa Hu, Ying-Tsang Lo, Tun-Wen Pai, Chia-Yin Chiang, Chung-Hao Li, Hong-Jyuan Jian

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Plasmin plays an important role in the human circulatory system owing to its catalytic ability of fibrinolysis. The immediate injection of plasmin in patients of strokes has intrigued many scientists to design vectors that can transport plasmin to the desired location in human body. Here we predict the structure of human plasmin and investigate the interaction of plasmin with the gold-nanoparticle. Because the crystal structure of plasminogen has been solved, we deleted N-terminal domain (Pan-apple domain) of plasminogen and generate a mimic of the active form of this enzyme (plasmin). We conducted a simulated annealing process on plasmin and discovered a very large conformation occurs. Kringle domains 1, 4 and 5 had been observed to leave its original location relative to the main body of the enzyme and the original doughnut shape of this enzyme has been transformed to a V-shaped by opening its two arms. This observation of conformational change is consistent with the experimental results of neutron scattering and centrifugation. We subsequently docked the plasmin on the simulated gold surface to predict their interaction. The V-shaped plasmin could utilize its Kringle domain and catalytic domain to contact the gold surface. Our findings not only reveal the flexibility of plasmin structure but also provide a guide for the design of a plasmin-gold nanoparticle.

Keywords: Docking, gold nanoparticle, molecular simulation, plasmin.

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Authors: Joseph E. Estevez, Mahdi Ghazizadeh, James G. Ryan, Ajit D. Kelkar

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Radiation shielding is an obstacle in long duration space exploration. Boron Nitride Nanotubes (BNNTs) have attracted attention as an additive to radiation shielding material due to B¹⁰’s large neutron capture cross section. The B¹⁰ has an effective neutron capture cross section suitable for low energy neutrons ranging from 10^-5 to 10⁴ eV and hydrogen is effective at slowing down high energy neutrons. Hydrogenated BNNTs are potentially an ideal nanofiller for radiation shielding composites. We use Molecular Dynamics (MD) Simulation via Material Studios Accelrys 6.0 to model the Young’s Modulus of Hydrogenated BNNTs. An extrapolation technique was employed to determine the Young’s Modulus due to the deformation of the nanostructure at its theoretical density. A linear regression was used to extrapolate the data to the theoretical density of 2.62g/cm³. Simulation data shows that the hydrogenated BNNTs will experience a 11% decrease in the Young’s Modulus for (6,6) BNNTs and 8.5% decrease for (8,8) BNNTs compared to non-hydrogenated BNNT’s. Hydrogenated BNNTs are a viable option as a nanofiller for radiation shielding nanocomposite materials for long range and long duration space exploration.

Keywords: Boron Nitride Nanotube, Radiation Shielding, Young Modulus, Atomistic Modeling.

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Authors: M. J. Pourvaghar, M. E. Bahram

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Obesity and overweight is one of the most common metabolic disorders in industrialized countries and in developing countries. One consequence of pathological obesity is cardiovascular disease and metabolic syndrome. Chemerin is an adipocyne that plays a role in the regulation of the adipocyte function and the metabolism of glucose in the liver and musculoskeletal system. Most likely, chemerin is involved in obesity-related disorders such as type 2 diabetes and cardiovascular disease. Aerobic exercises reduce the level of chemerin and cause macrophage penetration into fat cells and inflammatory factors. Several efforts have been made to clarify the cellular and molecular mechanisms of hypertrophy and muscular atrophy. Myostatin, a new member of the TGF-β family, is a transforming growth factor β that its expression negatively regulates the growth of the skeletal muscle; and the increase of this hormone has been observed in conditions of muscular atrophy. While in response to muscle overload, its levels decrease after the atrophy period, TGF-β is the most important cytokine in the development of skeletal muscle. Myostatin plays an important role in muscle control, and animal and human studies show a negative role of myostatin in the growth of skeletal muscle. Separation of myostatin from Golgi begins on the ninth day of the onset period and continues until birth at all times of muscle growth. Higher levels of myostatin are found in obese people. Resistance training for 10 weeks could reduce levels of plasma myostatin.

Keywords: Chemerin, myostatin, obesity, physical activity.

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Authors: Sayyed R Mousavi

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The Far From Most Strings Problem (FFMSP) is to obtain a string which is far from as many as possible of a given set of strings. All the input and the output strings are of the same length, and two strings are said to be far if their hamming distance is greater than or equal to a given positive integer. FFMSP belongs to the class of sequences consensus problems which have applications in molecular biology. The problem is NP-hard; it does not admit a constant-ratio approximation either, unless P = NP. Therefore, in addition to exact and approximate algorithms, (meta)heuristic algorithms have been proposed for the problem in recent years. On the other hand, in the recent years, hybrid algorithms have been proposed and successfully used for many hard problems in a variety of domains. In this paper, a new metaheuristic algorithm, called Constructive Beam and Local Search (CBLS), is investigated for the problem, which is a hybridization of constructive beam search and local search algorithms. More specifically, the proposed algorithm consists of two phases, the first phase is to obtain several candidate solutions via the constructive beam search and the second phase is to apply local search to the candidate solutions obtained by the first phase. The best solution found is returned as the final solution to the problem. The proposed algorithm is also similar to memetic algorithms in the sense that both use local search to further improve individual solutions. The CBLS algorithm is compared with the most recent published algorithm for the problem, GRASP, with significantly positive results; the improvement is by order of magnitudes in most cases.

Keywords: Bioinformatics, Far From Most Strings Problem, Hybrid metaheuristics, Matheuristics, Sequences consensus problems.

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Authors: M. A. Gad, A. Z. Al-Herrawy

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Microsporidia comprises various pathogenic species can infect humans by means of water. Moreover, chlorine disinfection of drinking-water has limitations against this protozoan pathogen. A total of 48 water samples were collected from two drinking water treatment plants having two different filtration systems (slow sand filter and rapid sand filter) during one year period. Samples were collected from inlet and outlet of each plant. Samples were separately filtrated through nitrocellulose membrane (142 mm, 0.45 µm), then eluted and centrifuged. The obtained pellet from each sample was subjected to DNA extraction, then, amplification using genus-specific primer for microsporidia. Each microsporidia-PCR positive sample was performed by two species specific primers for Enterocytozoon bieneusi and Encephalitozoon intestinalis. The results of the present study showed that the percentage of removal for microsporidia through different treatment processes reached its highest rate in the station using slow sand filters (100%), while the removal by rapid sand filter system was 81.8%. Statistically, the two different drinking water treatment plants (slow and rapid) had significant effect for removal of microsporidia. Molecular identification of microsporidia-PCR positive samples using two different primers for Enterocytozoon bieneusi and Encephalitozoon intestinalis showed the presence of the two pervious species in the inlet water of the two stations, while Encephalitozoon intestinalis was detected in the outlet water only. In conclusion, the appearance of virulent microsporidia in treated drinking water may cause potential health threat.

Keywords: Removal, efficacy, microsporidia, drinking water treatment plants, PCR.

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Authors: Naira Sahakyan, Margarit Petrosyan, Armen Trchounian

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One of the tasks in contemporary biotechnology, pharmacology and other fields of human activities is to obtain biologically active substances from plants. They are very essential in the treatment of many diseases due to their actually high therapeutic value without visible side effects. However, sometimes the possibility of obtaining the metabolites is limited due to the reduction of wild-growing plants. That is why the plant cell cultures are of great interest as alternative sources of biologically active substances. Besides, during the monitored cultivation, it is possible to obtain substances that are not synthesized by plants in nature. Isolated culture of Ajuga genevensis with high growth activity and ability of regeneration was obtained using MS nutrient medium. The agar-diffusion method showed that aqueous extracts of callus culture revealed high antimicrobial activity towards various gram-positive (Bacillus subtilis A1WT; B. mesentericus WDCM 1873; Staphylococcus aureus WDCM 5233; Staph. citreus WT) and gram-negative (Escherichia coli WKPM M-17; Salmonella typhimurium TA 100) microorganisms. The broth dilution method revealed that the minimal and half maximal inhibitory concentration values against E. coli corresponded to the 70 μg/mL and 140 μg/mL concentration of the extract respectively. According to the photochemiluminescent analysis, callus tissue extracts of leaf and root origin showed higher antioxidant activity than the same quantity of A. genevensis intact plant extract. A. genevensis intact plant and callus culture extracts showed no cytotoxic effect on K-562 suspension cell line of human chronic myeloid leukemia. The GC-MS analysis showed deep differences between the qualitative and quantitative composition of callus culture and intact plant extracts. Hexacosane (11.17%); n-hexadecanoic acid (9.33%); and 2-methoxy-4-vinylphenol (4.28%) were the main components of intact plant extracts. 10-Methylnonadecane (57.0%); methoxyacetic acid, 2-tetradecyl ester (17.75%) and 1-Bromopentadecane (14.55%) were the main components of A. genevensis callus culture extracts. Obtained data indicate that callus culture of A. genevensis can be used as an alternative source of biologically active substances.

Keywords: Ajuga genevensis, antibacterial activity, antioxidant activity, callus cultures.

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Authors: J. Subbalakshmi, G. Dhruvasamhith, S. M. Hussain

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Polyaniline (PANI) is one of the most extensively studied material among the conducting polymers due to its simple synthesis by chemical and electrochemical routes. PANIs have advantages of chemical stability and high conductivity making their commercial applications quite attractive. However, to our knowledge, very little work has been reported on the tensile strength properties of templated PANIs processed with polyvinyl alcohol and also, detailed study has not been carried out. We have investigated the effect of small molecule and polymers as templates on PANI. Stable aqueous colloidal suspensions of trisodium citrate (TSC), poly(ethylenedioxythiophene)-polystyrene sulfonate (PEDOT-PSS), and polyethylene glycol (PEG) templated PANIs were prepared through chemical synthesis, processed with polyvinyl alcohol (PVA) and were fabricated into films by solution casting. Absorption and infra-red spectra were studied to gain insight into the possible molecular interactions. Surface morphology was studied through scanning electron microscope and optical microscope. Interestingly, tensile testing studies revealed least strain for pure PVA when compared to the blends of templated PANI. Furthermore, among the blends, TSC templated PANI possessed maximum elasticity. The ultimate tensile strength for PVA processed, PEG-templated PANI was found to be five times more than other blends considered in this study. We establish structure–property correlation with morphology, spectral characterization and tensile testing studies.

Keywords: Processed films, polyvinyl alcohol, spectroscopy, surface morphology, templated polyanilines, tensile test.

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Authors: N. Baspinar, A. Basoglu, O. Ozdemir, C. Ozel, F. Terzi, O. Yaman

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Current research is targeting new molecular mechanisms that underlie non-alcoholic fatty liver disease (NAFLD) and associated metabolic disorders like non-alcoholic steatohepatitis (NASH). Forty New Zealand White rabbits have been used and fed a high protein (HP) and energy diet based on grains and containing 11.76 MJ/kg. Boron added to 3 experimental groups’ drinking waters (30 mg boron/L) as boron compounds. Biochemical analysis including boron levels, and nuclear magnetic resonance (NMR) based metabolomics evaluation, and mRNA expression of peroxisome proliferator-activated receptor (PPAR) family was performed. LDLcholesterol concentrations alone were decreased in all the experimental groups. Boron levels in serum and feces were increased. Content of acetate was in about 2x higher for anhydrous borax group, at least 3x higher for boric acid group. PPARα mRNA expression was significantly decreased in boric acid group. Anhydrous borax attenuated mRNA levels of PPARγ, which was further suppressed by boric acid. Boron supplementation decreased the degenerative alterations in hepatocytes. Except borax group other boron groups did not have a pronounced change in tubular epithels of kidney. In conclusion, high protein and energy diet leads hepatocytes’ degenerative changes which can be prevented by boron supplementation. Boric acid seems to be more effective in this situation.

Keywords: High protein and energy diet, boron, metabolomic, transcriptomic.

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