Search results for: Molecular biology

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

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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

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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: Jameela Ali Alkrimi, Hamid A. Jalab, Loay E. George, Abdul Rahim Ahmad, Azizah Suliman, Karim Al-Jashamy

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Red blood cells (RBC) are the most common types of blood cells and are the most intensively studied in cell biology. The lack of RBCs is a condition in which the amount of hemoglobin level is lower than normal and is referred to as “anemia”. Abnormalities in RBCs will affect the exchange of oxygen. This paper presents a comparative study for various techniques for classifying the RBCs as normal or abnormal (anemic) using WEKA. WEKA is an open source consists of different machine learning algorithms for data mining applications. The algorithms tested are Radial Basis Function neural network, Support vector machine, and K-Nearest Neighbors algorithm. Two sets of combined features were utilized for classification of blood cells images. The first set, exclusively consist of geometrical features, was used to identify whether the tested blood cell has a spherical shape or non-spherical cells. While the second set, consist mainly of textural features was used to recognize the types of the spherical cells. We have provided an evaluation based on applying these classification methods to our RBCs image dataset which were obtained from Serdang Hospital - Malaysia, and measuring the accuracy of test results. The best achieved classification rates are 97%, 98%, and 79% for Support vector machines, Radial Basis Function neural network, and K-Nearest Neighbors algorithm respectively.

Keywords: K-Nearest Neighbors, Neural Network, Radial Basis Function, Red blood cells, Support vector machine.

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Authors: J. Pazourek, K. Šmejkal, P. Kollár, J. Rajchard, J. Šinko, Z. Balounová, E. Vlková, H. Salmonová

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Pectinatella magnifica (Leidy, 1851) is an invasive freshwater animal that lives in colonies. A colony of Pectinatella magnifica (a gelatinous blob) can be up to several feet in diameter large and under favorable conditions it exhibits an extreme growth rate. Recently European countries around rivers of Elbe, Oder, Danube, Rhine and Vltava have confirmed invasion of Pectinatella magnifica, including freshwater reservoirs in South Bohemia (Czech Republic). Our project (Czech Science Foundation, GAČR P503/12/0337) is focused onto biology and chemistry of Pectinatella magnifica. We monitor the organism occurrence in selected South Bohemia ponds and sandpits during the last years, collecting information about physical properties of surrounding water, and sampling the colonies for various analyses (classification, maps of secondary metabolites, toxicity tests). Because the gelatinous matrix is during the colony lifetime also a host for algae, bacteria and cyanobacteria (co-habitants), in this contribution, we also applied a high performance liquid chromatography (HPLC) method for determination of potentially present cyanobacterial toxins (microcystin-LR, microcystin-RR, nodularin). Results from the last 3-year monitoring show that these toxins are under limit of detection (LOD), so that they do not represent a danger yet. The final goal of our study is to assess toxicity risks related to fresh water resources invaded by Pectinatella magnifica, and to understand the process of invasion, which can enable to control it.

Keywords: Cyanobacteria, freshwater resources, Pectinatella magnifica invasion, toxicity monitoring.

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Authors: Jonmichael A. Weaver, David A. Miller

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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: Pedro Pablo González Pérez, Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo EduardoSánchez Gutiérrez

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Multi-agent system approach has proven to be an effective and appropriate abstraction level to construct whole models of a diversity of biological problems, integrating aspects which can be found both in "micro" and "macro" approaches when modeling this type of phenomena. Taking into account these considerations, this paper presents the important computational characteristics to be gathered into a novel bioinformatics framework built upon a multiagent architecture. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding. The bioinformatics framework is used as a virtual laboratory to explore a minimalist model of protein folding as a test case. In order to show the laboratory concept of the platform as well as its flexibility and adaptability, we studied the folding of two particular sequences, one of 45-mer and another of 64-mer, both described by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice. According to the discussion section of this piece of work, these two sequences were chosen as breaking points towards the platform, in order to determine the tools to be created or improved in such a way to overcome the needs of a particular computation and analysis of a given tough sequence. The backwards philosophy herein is that the continuous studying of sequences provides itself important points to be added into the platform, to any time improve its efficiency, as is demonstrated herein.

Keywords: multi-agent systems, blackboard-based agent architecture, bioinformatics framework, virtual laboratory, protein folding.

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Authors: L. K. Davis

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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: Luciana C. Ramos, Leandro J. Sousa, Antônio Ferreira da Silva, Valéria Gomes Oliveira Falcão, Suzana T. Cunha Lima

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The commercial production of biodiesel using microalgae demands a high-energy input for harvesting biomass, making production economically unfeasible. Methods currently used involve mechanical, chemical, and biological procedures. In this work, a flocculation system is presented as a cost and energy effective process to increase biomass production of Phaeodactylum tricornutum. This diatom is the only species of the genus that present fast growth and lipid accumulation ability that are of great interest for biofuel production. The algae, selected from the Bank of Microalgae, Institute of Biology, Federal University of Bahia (Brazil), have been bred in tubular reactor with photoperiod of 12 h (clear/dark), providing luminance of about 35 μmol photons m^-2s^-1, and temperature of 22 °C. The medium used for growing cells was the Conway medium, with addition of silica. The seaweed growth curve was accompanied by cell count in Neubauer camera and by optical density in spectrophotometer, at 680 nm. The precipitation occurred at the end of the stationary phase of growth, 21 days after inoculation, using two methods: centrifugation at 5000 rpm for 5 min, and electro-flocculation at 19 EPD and 95 W. After precipitation, cells were frozen at -20 °C and, subsequently, lyophilized. Biomass obtained by electro-flocculation was approximately four times greater than the one achieved by centrifugation. The benefits of this method are that no addition of chemical flocculants is necessary and similar cultivation conditions can be used for the biodiesel production and pharmacological purposes. The results may contribute to improve biodiesel production costs using marine microalgae.

Keywords: Biomass, diatom, flocculation, microalgae.

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Authors: Eda Gök

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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: 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

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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: Eggertson, E.C. Kapulla, R, Fokken, J, Prasser, H.M.

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The turbulent mixing of coolant streams of different temperature and density can cause severe temperature fluctuations in piping systems in nuclear reactors. In certain periodic contraction cycles these conditions lead to thermal fatigue. The resulting aging effect prompts investigation in how the mixing of flows over a sharp temperature/density interface evolves. To study the fundamental turbulent mixing phenomena in the presence of density gradients, isokinetic (shear-free) mixing experiments are performed in a square channel with Reynolds numbers ranging from 2-500 to 60-000. Sucrose is used to create the density difference. A Wire Mesh Sensor (WMS) is used to determine the concentration map of the flow in the cross section. The mean interface width as a function of velocity, density difference and distance from the mixing point are analyzed based on traditional methods chosen for the purposes of atmospheric/oceanic stratification analyses. A definition of the mixing layer thickness more appropriate to thermal fatigue and based on mixedness is devised. This definition shows that the thermal fatigue risk assessed using simple mixing layer growth can be misleading and why an approach that separates the effects of large scale (turbulent) and small scale (molecular) mixing is necessary.

Keywords: Concentration measurements, Mixedness, Stablystratified turbulent isokinetic mixing layer, Wire mesh sensor

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

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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

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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

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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

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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: A.Gandomkar, K. Fouladi

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Water is the key of national development. Wherever a spring has been dried out or a river has changed its course, the area-s people have migrated and have been scattered and the area-s civilization has lost its brilliance. Today, air pollution, global warming and ozone layer damage are as the problems of countries, but certainly in the next decade the shortage and pollution of waters will be important issues of the world. The polluted waters are more dangerous in when they are used in agriculture. Because they infect plants and these plants are used in human and livestock consumption in food chain. With the increasing population growth and after that, the increase need to facilities and raw materials, human beings has started to do haste actions and wanted or unwanted destroyed his life basin. They try to overuse and capture his environment extremely, instead of having futurism approach in sustainable use of nature. This process includes Zayanderood recession, and caused its pollution after the transition from industrial and urban areas. Zayandehrood River in Isfahan is a vital artery of a living ecosystem. Now is the location of disposal waste water of many cities, villages and existing industries. The central area of the province is an important industrial place, and its environmental situation has reached a critical stage. Not only a large number of pollution-generating industries are active in the city limits, but outside of the city and adjacent districts Zayandehrood River, heavy industries like steel, Mobarakeh Steel and other tens great units pollute wild life. This article tries to study contaminant sources of Zayanderood and their severity, and determine and discuss the share of each of these resources by major industrial centers located in areas. At the end, we represent suitable strategy.

Keywords: Environmental, industrial pollution, Zayandehrood Basin

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Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

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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: Innocent Kafodya, Guijun Xian

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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. W. Lau, C. O. Ng

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This is a study on numerical simulation of the convection-diffusion transport of a chemical species in steady flow through a small-diameter tube, which is lined with a very thin layer made up of retentive and absorptive materials. The species may be subject to a first-order kinetic reversible phase exchange with the wall material and irreversible absorption into the tube wall. Owing to the velocity shear across the tube section, the chemical species may spread out axially along the tube at a rate much larger than that given by the molecular diffusion; this process is known as dispersion. While the long-time dispersion behavior, well described by the Taylor model, has been extensively studied in the literature, the early development of the dispersion process is by contrast much less investigated. By early development, that means a span of time, after the release of the chemical into the flow, that is shorter than or comparable to the diffusion time scale across the tube section. To understand the early development of the dispersion, the governing equations along with the reactive boundary conditions are solved numerically using the Flux Corrected Transport Algorithm (FCTA). The computation has enabled us to investigate the combined effects on the early development of the dispersion coefficient due to the reversible and irreversible wall reactions. One of the results is shown that the dispersion coefficient may approach its steady-state limit in a short time under the following conditions: (i) a high value of Damkohler number (say Da ≥ 10); (ii) a small but non-zero value of absorption rate (say Γ* ≤ 0.5).

Keywords: Dispersion coefficient, early development of dispersion, FCTA, wall reactions.

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

Abstract:

The present study has been taken to explore the screening of in vitro antimicrobial activities of D-galactose-binding sponge lectin (HOL-30). HOL-30 was purified from the marine demosponge Halichondria okadai by affinity chromatography. The molecular mass of the lectin was determined to be 30 kDa with a single polypeptide by SDS-PAGE under non-reducing and reducing conditions. HOL-30 agglutinated trypsinized and glutaraldehydefixed rabbit and human erythrocytes with preference for type O erythrocytes. The lectin was subjected to evaluation for inhibition of microbial growth by the disc diffusion method against eleven human pathogenic gram-positive and gram-negative bacteria. The lectin exhibited strong antibacterial activity against gram-positive bacteria, such as Bacillus megaterium and Bacillus subtilis. However, it did not affect against gram-negative bacteria such as Salmonella typhi and Escherichia coli. The largest zone of inhibition was recorded of Bacillus megaterium (12 in diameter) and Bacillus subtilis (10 mm in diameter) at a concentration of the lectin (250 μg/disc). On the other hand, the antifungal activity of the lectin was investigated against six phytopathogenic fungi based on food poisoning technique. The lectin has shown maximum inhibition (22.83%) of mycelial growth of Botrydiplodia theobromae at a concentration of 100 μg/mL media. These findings indicate that the lectin may be of importance to clinical microbiology and have therapeutic applications.

Keywords: Antibacterial, Halichondria okadai, Inhibition zone, Lectin.

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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: 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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Authors: Gabi N. Nehme

Abstract:

Below-knee amputees commonly experience asymmetrical gait patterns. It is generally believed that ischemia is related to the formation of pressure sores due to uneven distribution of forces. Micro-vascular responses can reveal local malnutrition. Changes in local skin blood supply under various external loading conditions have been studied for a number of years. Radionuclide clearance, photo-plethysmography, trans-cutaneous oxygen tension along with other studies showed that the blood supply would be influenced by the epidermal forces, and the rate and the amount of blood supply would decrease with increased epidermal loads being shear forces or normal forces. Several cases of socket designs were investigated using Finite Element Model (FEM) and Design of Experiment (DOE) to increase flexibility and minimize the pressure at the limb/socket interface using ultra high molecular weight polyethylene (UHMWPE) and polyamide 6 (PA6) or Duraform. The pressure reliefs at designated areas where reducing thickness is involved are seen to be critical in determination of amputees’ comfort and are very important to clinical applications. Implementing a hole between the Patellar Tendon (PT) and Distal Tibia (DT) would decrease stiffness and increase prosthesis range of motion where flexibility is needed. In addition, displacement and prosthetic energy storage increased without compromising mechanical efficiency and prosthetic design integrity.

Keywords: Patellar tendon, distal tibia, prosthetic socket, relief areas, hole implementation.

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Authors: Fereshteh Shacheraghi, Mohammad Reza Shakibaie, Hanieh Noveiri

Abstract:

Fourty one strains of ESBL producing P.aeruginosa which were previously isolated from burn patients in Kerman University general hospital, Iran were subjected to PCR, RFLP and sequencing in order to determine the type of extended spectrum β- lactamases (ESBL), the restriction digestion pattern and possibility of mutation among detected genes. DNA extraction was carried out by phenol chloroform method. PCR for detection of bla genes was performed using specific primer for each gene. Restriction Fragment Length Polymorphism (RFLP) for ESBL genes was carried out using EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The PCR products were subjected to direct sequencing of both the strands for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1, blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the (n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29) 70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates respectively. The RFLP analysis showed that each ESBL gene has identical pattern of digestion among the isolated strains. Sequencing of the ESBL genes confirmed the genuinety of PCR products and revealed no mutation in the restriction sites of the above genes. From results of the present investigation it can be concluded that blaVEB-1 and blaCTX-M were the most and the least frequently isolated ESBL genes among the P.aeruginosa strains isolated from burn patients. The RFLP and sequencing analysis revealed that same clone of the bla genes were indeed existed among the antibiotic resistant strains.

Keywords: ESBL genes, PCR, RFLP, Sequencing, P.aeruginosa

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