Search results for: Loop-Mediated Isothermal Amplification (LAMP)

Authors: N. Stoeva, I. Spassova, R. Nickolov, M. Khristova

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Exhaust gases from stationary and mobile combustion sources contain nitrogen oxides that cause a variety of environmentally harmful effects. The most common approach of their elimination is the catalytic reaction in the exhaust using various reduction agents such as NH3, CO and hydrocarbons. Transition metals (Co, Ni, Cu, etc.) are the most widely used as active components for deposition on various supports. However, since the interaction between different catalyst components have been extensively studied in different types of reaction systems, the possible cooperation between active components and the support material and the underlying mechanisms have not been thoroughly investigated. The support structure may affect how these materials maintain an active phase. The objective is to investigate the addition of carbonaceous materials with different nature and texture characteristics on the properties of the resulting silica-carbon support and how it influences of the catalytic properties of the supported copper and cobalt catalysts for reduction of NO with CO. The versatility of the physico-chemical properties of the composites and the supported copper and cobalt catalysts are discussed with an emphasis on the relationship of the properties with the catalytic performance. The catalysts were prepared by sol-gel process and were characterized by XRD, XPS, AAS and BET analysis. The catalytic experiments were carried out in catalytic flow apparatus with isothermal flow reactor in the temperature range 20–300оС. After the catalytic test temperature-programmed desorption (TPD) was carried out. The transient response method was used to study the interaction of the gas phase with the catalyst surface. The role of the interaction between the support and the active phase on the catalyst’s activity in the studied reaction was discussed. We suppose the carbon particles with small sizes to participate in the formation of the active sites for the reduction of NO with CO along with their effect on the kind of deposited metal oxide phase. The existence of micropore texture for some of composites also influences by mass-transfer limitations.

Keywords: catalysts, no reduction, composites, bet analysis

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Authors: G. Ravindranath, S. Savitha

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This paper presents heat transfer analysis of single horizontal bare tube and heat transfer analysis of staggered arrangement of bare tube bundles bare tube bundles in gas-solid (air-solid) fluidized bed and predictions are done by using Artificial Neural Network (ANN) based on experimental data. Fluidized bed provide nearly isothermal environment with high heat transfer rate to submerged objects i.e. due to through mixing and large contact area between the gas and the particle, a fully fluidized bed has little temperature variation and gas leaves at a temperature which is close to that of the bed. Measurement of average heat transfer coefficient was made by local thermal simulation technique in a cold bubbling air-fluidized bed of size 0.305 m. x 0.305 m. Studies were conducted for single horizontal Bare Tube of length 305mm and 28.6mm outer diameter and for bare tube bundles of staggered arrangement using beds of large (average particle diameter greater than 1 mm) particle (raagi and mustard). Within the range of experimental conditions influence of bed particle diameter ( Dp), Fluidizing Velocity (U) were studied, which are significant parameters affecting heat transfer. Artificial Neural Networks (ANNs) have been receiving an increasing attention for simulating engineering systems due to some interesting characteristics such as learning capability, fault tolerance, and non-linearity. Here, feed-forward architecture and trained by back-propagation technique is adopted to predict heat transfer analysis found from experimental results. The ANN is designed to suit the present system which has 3 inputs and 2 out puts. The network predictions are found to be in very good agreement with the experimental observed values of bare heat transfer coefficient (hb) and nusselt number of bare tube (Nub).

Keywords: fluidized bed, large particles, particle diameter, ANN

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Authors: Bouchou Aïssa, Mohamed Akbi

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Contact materials used for electrical breakers are often made with silver alloys. Mechanical and thermo dynamical properties as well as electron emission of such complicated alloys present a lack of reliable and accurate experimental data. This paper deals mainly with electron work function (EWF) measurements about silver-metal oxide (Ag-MeO) electrical contacts (Ag-ZnO (92/8), before and after surface heat treatments at 296 K  813 K, under UHV conditions (residual gas pressure of 1.4 x 10-7 mbar). The electron work function (EWF) of silver zinc oxide materials was measured photoelectrically, using both Fowler’s method of isothermal curves and linearized Fowler plots. In this paper, we present the development of a method for measuring photoelectric work function of contact materials. Also reported in this manuscript are the results of experimental work whose purpose has been the buildup of a reliable photoelectric system and associated monochromatic ultra-violet radiations source, and the photoelectric measurement of the electron work functions (EWF) of contact materials. In order to study the influence of annealing temperature on the EWF, a vacuum furnace was used for heating the metallic samples up to 800 K. The EWF of the silver – zinc oxide materials were investigated to study the influence of annealing temperature on the EWF. In the present study, the photoelectric measurements about Ag-ZnO(92/8) contacts have shown a linear decrease of the EWF with increasing temperature, i.e. the temperature coefficient is constant and negative: for the first annealing # 1, in the temperature range [299 K  823 K]. On the contrary, a linear increase was observed with increasing temperature (i.e. , being constant and positive), for the next annealing # 2, in the temperature range [296 K  813 K]. The EWFs obtained for silver-zinc oxide Ag-ZnO(92/8) show an obvious dependence on the annealing temperature which is strongly associated with the evolution of the arrangement on ZnO nano particles on the Ag-ZnO contact surface as well as surface charge distribution.

Keywords: Photoemission, Electron work function, Fowler methods, Ag-ZnO contact materials, Vacuum heat treatment

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Authors: Susmiati, Ingrid S. Surono, Jamsari, Nur Indrawati Lipoeto

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There are two contradicting opinions on the relationship between fat mass obesity associated (FTO) rs 9939609 variants and obesity on various ethnics and races. The first opinion agrees that there is an association between the two variables, yet another one disagree. Minangkabau ethnic had a different dietary pattern with other ethnics in Indonesia. They had higher fat and low fiber intakes compared to the other ethnics groups. There is little research in genetic factors that influence eating behavior (food preference or food selection). The objective of this study was to investigate the association between FTO rs 9939609 variants with obesity and eating behavior in adolescent girls of Minangkabau Ethnic. The research design was case control study. A total of 275 adolescent girls aged 12-15 years old (130 obese and 145 normal) were randomly chosen from four districts at West Sumatera (Padang, Padang Pariaman, Padang Panjang and Tanah Datar). Genetic variants of FTO rs 9939609 were analyzed with Tetra-primer Amplification Refractory Mutation System-Polimerase Chain Reaction (AMRS PCR), eating behavior were gathered using eating habits questionnaire, and Body Mass Index (BMI) was calculated according to BMI Z-score (WHO). The result showed that genetic variants of FTO rs 9939609 (TT, TA and AA genotype) had associated with obesity (p = 0,013), whereas subject with An Allele was significantly associated with obesity (odds ratio 1,62 [95% confidential interval, 1,00-2,60]). Subjects with An Allele carrier reported a higher consumption of fried food (p < 0.05) as compared to TT genotypes carriers. There is no association between genetic variants and meal frequency, fruit and fiber intakes p > 0.05. The genetic variants of FTO rs 9939609 are associated with obesity and eating behavior in adolescent of Minangkabau Ethics.

Keywords: FTO rs9939609, obesity, eating behavior, adolescents

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Authors: Erwan Negre, Ewan J. O'Connor, Juha Toivonen

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The need for CO2 monitoring technologies grows simultaneously with the worldwide concerns regarding environmental challenges. To that purpose, we developed a compact coherent all-fiber ranged-resolved Differential Absorption Lidar (RR-DIAL). It has been designed along a tunable 2x1fiber optic switch set to a frequency of 1 Hz between two Distributed FeedBack (DFB) lasers emitting in the continuous-wave mode at 1571.41 nm (absorption line of CO2) and 1571.25 nm (CO2 absorption-free line), with linewidth and tuning range of respectively 1 MHz and 3 nm over operating wavelength. A three stages amplification through Erbium and Erbium-Ytterbium doped fibers coupled to a Radio Frequency (RF) driven Acousto-Optic Modulator (AOM) generates 100 ns pulses at a repetition rate from 10 to 30 kHz with a peak power up to 2.5 kW and a spatial resolution of 15 m, allowing fast and highly resolved CO2 profiles. The same afocal collection system is used for the output of the laser source and the backscattered light which is then directed to a circulator before being mixed with the local oscillator for heterodyne detection. Packaged in an easily transportable box which also includes a server and a Field Programmable Gate Array (FPGA) card for on-line data processing and storing, our setup allows an effective and quick deployment for versatile in-situ analysis, whether it be vertical atmospheric monitoring, large field mapping or sequestration site continuous oversight. Setup operation and results from initial field measurements will be discussed.

Keywords: CO2 profiles, coherent DIAL, in-situ atmospheric sensing, near infrared fiber source

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Authors: Ahmad Ali Shahid, M Shakil Shaukat

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Agriculture is the backbone of economy of Pakistan and Cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat against the developing resistance in the target insects and combating these challenges wholesomely, a novel combination of pyramided/stacked genes was conceptualized and later realized, through the means of biotechnology i.e., transformation of three genes namely, Cry1Ac, Cry2A, and EPSP synthase (glyphosate tolerant) genes in the locally cultivated cotton variety. The progenies of the transformed plants were successfully raised and screened under the tunnel conditions for two generations and the present study focused on the screening of plants which were confirmed for containing all of these three genes and their expressions. Initially, the screening was done through glyphosate spray assay and the plants which were healthy and showed no damage on leaves were selected after 07 days of spray. In the laboratory, the DNA of these plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty were confirmed positive for Cry1Ac gene and ten out of twenty were positive for Cry2A gene and all twenty were positive for presence of EPSP synthase gene. Then, the ten plant samples which were confirmed with presence of all three genes were subjected to expression analysis of these proteins through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the expression levels of the EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes in T3 generation of the triple gene transformed cotton. These plants may be subjected to T4 generation to develop a new stable variety in due course of time.

Keywords: agriculture, cotton, transformation, cry genes, ELISA, PCR

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Authors: Ngonidzashe Mangoma, Caroline Marigold Sebata

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The release of cyanide-rich effluents from gold mines, and other industries, into the environment, is a global concern considering the well-known metabolic effects of cyanide in all forms of life. Such effluents need to be treated to remove cyanide, among other pollutants, before their disposal. This study aimed at investigating the possible use of bacteria in the biological removal of cyanide from cyanide-rich effluents. Firstly, cyanide-degrading bacteria were isolated from gold mine effluents and characterised. The isolates were then tested for their ability to grow in the presence of cyanide and their tolerance to increasing levels of the compound. To evaluate each isolate’s cyanide-degrading activities, isolates were grown in the simulated and actual effluent, and a titrimetric method was used to quantify residual cyanide over a number of days. Cyanide degradation efficiency (DE) was then calculated for each isolate. Identification of positive isolates involved 16S rRNA gene amplification and sequence analysis through BLAST. Six cyanide-utilising bacterial strains were isolated. Two of the isolates were identified as Klebsiella spp. while the other two were shown to be different strains of Clostridium bifermentans. All isolates showed normal growth in the presence of cyanide, with growth being inhibited at 700 mg/L cyanide and beyond. Cyanide degradation efficiency for all isolates in the simulated effluent ranged from 79% to 97%. All isolates were able to remove cyanide from actual gold mine effluent with very high DE values (90 – 94%) being recorded. Isolates obtained in this study were able to efficiently remove cyanide from both simulated and actual effluent. This observation clearly demonstrates the feasibility of the biological removal of cyanide from cyanide-rich gold mine effluents and should, therefore, motivate research towards the possible large-scale application of this technology.

Keywords: cyanide effluent, bioremediation, Clostridium bifermentans, Klebsiella spp, environment

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Authors: A. B. M. Rezaul Islam, Ernur Karadogan

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Shape memory alloys (SMAs) are known for their shape memory effect and pseudoelasticity behavior. Their thermomechanical behaviors are modeled by numerous researchers using microscopic thermodynamic and macroscopic phenomenological point of view. Tanaka, Liang-Rogers and Ivshin-Pence models are some of the most popular SMA macroscopic phenomenological constitutive models. They describe SMA behavior in terms of stress, strain and temperature. These models involve material parameters and they have associated uncertainty present in them. At different operating temperatures, the uncertainty propagates to the output when the material is subjected to loading followed by unloading. The propagation of uncertainty while utilizing these models in real-life application can result in performance discrepancies or failure at extreme conditions. To resolve this, we used probabilistic approach to perform the sensitivity and uncertainty analysis of Tanaka, Liang-Rogers, and Ivshin-Pence models. Sobol and extended Fourier Amplitude Sensitivity Testing (eFAST) methods have been used to perform the sensitivity analysis for simulated isothermal loading/unloading at various operating temperatures. As per the results, it is evident that the models vary due to the change in operating temperature and loading condition. The average and stress-dependent sensitivity indices present the most significant parameters at several temperatures. This work highlights the sensitivity and uncertainty analysis results and shows comparison of them at different temperatures and loading conditions for all these models. The analysis presented will aid in designing engineering applications by eliminating the probability of model failure due to the uncertainty in the input parameters. Thus, it is recommended to have a proper understanding of sensitive parameters and the uncertainty propagation at several operating temperatures and loading conditions as per Tanaka, Liang-Rogers, and Ivshin-Pence model.

Keywords: constitutive models, FAST sensitivity analysis, sensitivity analysis, sobol, shape memory alloy, uncertainty analysis

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Authors: Mona T. Kashef, Omneya M. Helmy

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Multidrug resistant (MDR) bacteria have become a significant public health threat. The prevalence rates, of Gram negative MDR bacteria, are in continuous increase. However, few data are available about these resistant strains. Since, third generation cephalosporins are one of the most commonly used antimicrobials, we set out to investigate the prevalence, different mechanisms and clonal relatedness of multidrug resistance among third generation resistant Gram negative clinical isolates. A total of 114 Gram negative clinical isolates, previously characterized as being resistant to at least one of 3rd generation cephalosporins, were included in this study. Each isolate was tested, using Kirby Bauer disk diffusion method, against its assigned categories of antimicrobials. The role of efflux pump in resistance development was tested by the efflux pump inhibitor-based microplate assay using chloropromazine as an inhibitor. Detecting different aminoglycosides, β-lactams and quinolones resistance genes was done using polymerase chain reaction. The genetic diversity of MDR isolates was investigated using Random Amplification of Polymorphic DNA technique. MDR phenotype was detected in 101 isolates (89%). Efflux pump mediated resistance was detected in 49/101 isolates. Aminoglycosides resistance genes; armA and aac(6)-Ib were detected in one and 53 isolates, respectively. The aac(6)-Ib-cr allele, that also confers resistance to floroquinolones, was detected in 28/53 isolates. β-lactam resistance genes; blaTEM, blaSHV, blaCTX-M group 1 and group 9 were detected in 52, 29, 61 and 35 isolates, respectively. Quinolone resistance genes; qnrA, qnrB and qnrS were detectable in 2, 14, 8 isolates respectively, while qepA was not detectable at all. High diversity was observed among tested MDR isolates. MDR is common among 3rd generation cephalosporins resistant Gram negative bacteria, in Egypt. In most cases, resistance was caused by different mechanisms. Therefore, new treatment strategies should be implemented.

Keywords: gram negative, multidrug resistance, RAPD typing, resistance genes

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Authors: Ping Li, Bing Feng, Junpu Zhao, Xudong Xie, Dangpeng Xu, Kuixing Zheng, Qihua Zhu, Xiaofeng Wei

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In laser driven inertial confinement fusion (ICF), the control of the temporal shape of the laser pulse is a key point to ensure an optimal interaction of laser-target. One of the main difficulties in controlling the temporal shape is the foot part control accuracy of high contrast pulse. Based on the analysis of pulse perturbation in the process of amplification and frequency conversion in high power lasers, an approach of beam spatio-temporal multiplexing is proposed to improve the control precision of high contrast pulse. In the approach, the foot and peak part of high contrast pulse are controlled independently, which propagate separately in the near field, and combine together in the far field to form the required pulse shape. For high contrast pulse, the beam area ratio of the two parts is optimized, and then beam fluence and intensity of the foot part are increased, which brings great convenience to the control of pulse. Meanwhile, the near field distribution of the two parts is also carefully designed to make sure their F-numbers are the same, which is another important parameter for laser-target interaction. The integrated calculation results show that for a pulse with a contrast of up to 500, the deviation of foot part can be improved from 20% to 5% by using beam spatio-temporal multiplexing approach with beam area ratio of 1/20, which is almost the same as that of peak part. The research results are expected to bring a breakthrough in power balance of high power laser facility.

Keywords: inertial confinement fusion, laser pulse control, beam spatio-temporal multiplexing, power balance

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Authors: O. H. Gebril, N. A. Meguid

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Background: Iron had been a focus of interest recently as a main exaggerating factor for oxidative stresses in the central nervous system and a link to various neurological disorders is suspected. Many studies with various techniques showed evidence of disturbed iron-related proteins in the cell in human and animal models of neurodegenerative disorders. Also, linkage to significant pathological changes had been evidenced e.g. apoptosis and cell signaling. On the other hand, the role of iron in neurodevelopmental disorders is still unclear. With increasing prevalence of autism worldwide, some changes in iron parameters and its stores were documented in many studies. This study includes Haemochromatosis HFE gene polymorphisms (p.H63D and p.C282Y) and ferroportin gene (SLC40A1) Q248H polymorphism in autism and control children. Materials and Methods: Whole genome DNA was extracted; p.H63D and p.C282Y genotyping was studied using specific sequence amplification followed by restriction enzyme digestion on a sample of autism patients (25 cases) and twenty controls. Results: The p.H63D is seen more than the C282Y among both autism and control samples, with no significant association of p.H63D or p.C282Y polymorphism and autism was revealed. Also, no association with Q248H polymorphism was evidenced. Conclusion: The study results do not prove the role of cellular iron genes polymorphisms as risk factors for neurodevelopmental disorders, and in turn highlights the specificity of cellular iron related pathways in neurodegeneration. These results demand further gene expression studies to elucidate the main pathophysiological pathways that are disturbed in autism and other neurodevelopmental disorders.

Keywords: iron, neurodevelopmental, oxidative stress, haemohromatosis, ferroportin, genes

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Authors: Bhawna Chandravanshi, Ramesh Bhonde

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In the present study, we focused on the improvisation of islet survival in hypoxia. The Islet-like cell aggregates (ICAs) derived from Wharton's jelly mesenchymal stem cells (WJ-MSC) were cultured with and without WJ-MSC for 48h in hypoxia and normoxia and tested for their direct trophic effect on β cell survival. The WJ MSCs themselves secreted insulin upon glucose challenge and expressed the pancreatic markers at both transcription and translational level (C-peptide, Insulin, Glucagon and Glut 2). Direct contact of MSCs with ICAs facilitate the highest viability under hypoxia as evidenced by fluorescein diacetate/propidium iodide and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The cytokine analysis of the co-cultured ICAs revealed amplification of anti-inflammatory cytokine-like TGFβ and TNFα accompanied by depletion of pro-inflammatory cytokines. The increment in VEGF and PDGFa was also seen showing their ability to vascularize upon transplantation. This was further accompanied by reduction in total reactive oxygen species, nitric oxide, and super oxide ions and down-regulation of Caspase3, Caspase8, p53 and up regulation of Bcl2 confirming prevention of apoptosis in ICAs. There was a significant reduction in the expression of p38 protein in the presence of MSCs making the ICAs responsive to glucose. Taken together our data demonstrate for the first time that the WJ-MSC expressed pancreatic markers and their supplementation protected engineered islets against hypoxia, oxidative stress, and inflammatory cytokines by inhibiting p38 MAPK protein.

Keywords: hypoxia, islet-like cell aggregates, inflammatory cytokines, oxidative stress

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: George Mahalu

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The Chua diode has been configured over time in various ways, using electronic structures like as operational amplifiers (OAs) or devices with gas or semiconductors. When discussing the use of semiconductor devices, tunnel diodes (Esaki diodes) are most often considered, and more recently, transistorized configurations such as lambda diodes. The paper-work proposed here uses in the modeling a lambda diode type configuration consisting of two Junction Field Effect Transistors (JFET). The original scheme is created in the MULTISIM electronic simulation environment and is analyzed in order to identify the conditions for the appearance of evolutionary unpredictability specific to nonlinear dynamic systems with chaos-induced behavior. The chaotic deterministic oscillator is one autonomous type, a fact that places it in the class of Chua’s type oscillators, the only significant and most important difference being the presence of a nonlinear device like the one mentioned structure above. The chaotic behavior is identified both by means of strange attractor-type trajectories and visible during the simulation and by highlighting the hypersensitivity of the system to small variations of one of the input parameters. The results obtained through simulation and the conclusions drawn are useful in the further research of ways to implement such constructive electronic solutions in theoretical and practical applications related to modern small signal amplification structures, to systems for encoding and decoding messages through various modern ways of communication, as well as new structures that can be imagined both in modern neural networks and in those for the physical implementation of some requirements imposed by current research with the aim of obtaining practically usable solutions in quantum computing and quantum computers.

Keywords: chaos, lambda diode, strange attractor, nonlinear system

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Authors: Rabindranath Jana, Plabani Basu, Keka Rana

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Nucleating agents are widely used to modify the properties of various polymers. The rate of crystallization and the size of the crystals have a strong impact on mechanical and optical properties of a polymer. The addition of nucleating agents to the semi-crystalline polymers provides a surface on which the crystal growth can start easily. As a consequence, fast crystal formation will result in many small crystal domains so that the cycle times for injection molding may be reduced. Moreover, the mechanical properties e.g., modulus, tensile strength, heat distortion temperature and hardness may increase. In the present work, multi-walled carbon nanotubes (MWNTs) as nucleating agents for the crystallization of poly (e-caprolactone)diol (PCL). Thus nanocomposites of PCL filled with MWNTs were prepared by solution blending. Differential scanning calorimetry (DSC) tests were carried out to study the effect of CNTs on on-isothermal crystallization of PCL. The polarizing optical microscopy (POM), and wide-angle X-ray diffraction (WAXD) were used to study the morphology and crystal structure of PCL and its nanocomposites. It is found that MWNTs act as effective nucleating agents that significantly shorten the induction period of crystallization and however, decrease the crystallization rate of PCL, exhibiting a remarkable decrease in the Avrami exponent n, surface folding energy σe and crystallization activation energy ΔE. The carbon-based fillers act as templates for hard block chains of PCL to form an ordered structure on the surface of nanoparticles during the induction period, bringing about some increase in equilibrium temperature. The melting process of PCL and its nanocomposites are also studied; the nanocomposites exhibit two melting peaks at higher crystallization temperature which mainly refer to the melting of the crystals with different crystal sizes however, PCL shows only one melting temperature.

Keywords: poly(e-caprolactone)diol, multiwalled carbon nanotubes, composite materials, nonisothermal crystallization, crystal structure, nucleation

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Authors: Md. Asif Ullah, M. A. R. Sarkar

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This paper illustrates 2-D and 3-D simulations of sub-channels of a Pressurized Water Reactor (PWR) having hexagonal array of fuel rods. At a steady state, the temperature of outer surface of the cladding of fuel rod is kept about 1200°C. The temperature of this isothermal surface is taken as boundary condition for simulation. Water with temperature of 290°C is given as a coolant inlet to the primary water circuit which is pressurized upto 157 bar. Turbulent flow of pressurized water is used for heat removal. In 2-D model, temperature, velocity, pressure and Nusselt number distributions are simulated in a vertical sectional plane through the sub-channels of a hexagonal fuel rod assembly. Temperature, Nusselt number and Y-component of convective heat flux along a line in this plane near the end of fuel rods are plotted for different Reynold’s number. A comparison between X-component and Y-component of convective heat flux in this vertical plane is analyzed. Hexagonal fuel rod assembly has three types of sub-channels according to geometrical shape whose boundary conditions are different too. In 3-D model, temperature, velocity, pressure, Nusselt number, total heat flux magnitude distributions for all the three sub-channels are studied for a suitable Reynold’s number. A horizontal sectional plane is taken from each of the three sub-channels to study temperature, velocity, pressure, Nusselt number and convective heat flux distribution in it. Greater values of temperature, Nusselt number and Y-component of convective heat flux are found for greater Reynold’s number. X-component of convective heat flux is found to be non-zero near the bottom of fuel rod and zero near the end of fuel rod. This indicates that the convective heat transfer occurs totally along the direction of flow near the outlet. As, length to radius ratio of sub-channels is very high, simulation for a short length of the sub-channels are done for graphical interface advantage. For the simulations, Turbulent Flow (K-Є ) module and Heat Transfer in Fluids (ht) module of COMSOL MULTIPHYSICS 5.0 are used.

Keywords: sub-channels, Reynold’s number, Nusselt number, convective heat transfer

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Authors: Olumayowa M. Olowe, Michael D. Asemoloye Odunayo J. Olawuyi, Hilda Vasanthakaalam

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Poor management of maize ear rot caused by fungal infection in Nigeria affected the quantity and quality of maize. This study, therefore, aims at characterizing and controlling Fusarium strains using arbuscular mycorrhizal fungi. Maize ear showing rot symptoms were obtained from some selected farms located at Ilesa East and West using random sampling technique. Isolation of Fusarium pathogen from infected maize grain was done using direct pour plate method on potato dextrose agar (PDA) and was characterized based on morphological and molecular ITS-amplification methods. The reaction of PVASYN8F2, T2LCOMP1STR SYN-W-1, and T2LCOMP4 maize varieties, to the Fusarium ear rot pathogens and biocontrol efficacy of the mycorrhizal fungi were assessed on growth, yield, agronomic parameters and symptoms observed. The strains; olowILH1 and olowILH2 identified as Fusarium napiforme were the most dominant and virulent pathogens associated with the maize. They showed genetic similarity with documented ear rot pathogens on NCBI with accession numbers Fusarium proliferatum KT224027, KT224023, and Fusarium sp AY237110. They both exhibited varying inhibitory effects on the three maize varieties compare to control (uninfected plant) which had better growth characteristics. It was also observed that strain olowILH1 was more virulent than olowILH2. T2LCOMP4 was generally more susceptible to both fungal strains compared to the other two maize (T2LCOMP1STR SYN-W-1 and T2LCOMP4 ). In all, strain olowILH1 was more virulent than olowILH2, and Glomus clarum had higher inhibitory pathogenic effect against Fusarium strains compared to G. deserticola.

Keywords: arbuscular mycorrhizal fungi, disease management, Fusarium strains, identification

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Authors: M. D. Asemoloye, S. G. Jonathan, A. Rafiq, O. J. Olawuyi, D. O. Adejoye

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Calmodulin is one of the intracellular calcium proteins that regulates large spectrum of enzymes and cellular functions including metabolism of cyclic nucleotides and glycogen. The potentials of calmodulin gene in fungi necessitates their genetic response and their strong cassette of enzyme secretions for pesticide degradation. Therefore, this study was carried out to investigate the ‘Transcriptomic’ response of calmodulin encoding genes in Talaromyces fungi in response to 2, 2-dichlorovinyl dimethyl phosphate (DDVP or Dichlorvos) an organophosphate pesticide and γ-Hexachlorocyclohexane (Lindane) an organochlorine pesticide. Fungi strains isolated from rhizosphere from grasses rhizosphere in pesticide polluted sites were subjected to percentage incidence test. Two most frequent fungi were further characterized using ITS gene amplification (ITS1 and ITS4 combinations), they were thereafter subjected to In-vitro DDVP and lindane tolerance tests at different concentrations. They were also screened for presence and expression of calmodulin gene (caM) using RT-PCR technique. The two Talaromyces strains had the highest incidence of 50-72% in pesticide polluted site, they were both identified as Talaromyces astroroseus asemoG and Talaromyces purpurogenum asemoN submitted in NCBI gene-bank with accession numbers KY488464 and KY488468 respectively. T. astroroseus KY488464 tolerated DDVP (1.23±0.023 cm) and lindane (1.11±0.018 cm) at 25 % concentration while T. purpurogenum KY488468 tolerated DDVP (1.33±0.061 cm) and lindane (1.54±0.077 cm) at this concentration. Calmodulin gene was detected in both strains, but RT-PCR expression of caM gene revealed at 900-1000 bp showed an under-expression of caM in T. astrorosues KY488464 but overexpressed in T. purpurogenum KY488464. Thus, the calmodulin gene response of these fungal strains to both pesticides could be considered in monitoring the potentials of fungal strains to pesticide tolerance and bioremediation of pesticide in polluted soil.

Keywords: Calmodulin gene, pesticide, RT-PCR, talaromyces, tolerance

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Authors: Magarò Floriana, Zinno Raffaele

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Since 2009, with the coming into force of the January 14, 2008 Ministerial Decree "New technical standards for construction", and the explanatory ministerial circular N°.617 of February 2, 2009, the question of seismic hazard and the design of seismic-resistant structures in Italy has acquired increasing importance. One of the most discussed aspects in recent Italian and international scientific literature concerns the dynamic interaction between land and structure, and the effects which dynamic coupling may have on individual buildings. In effect, from systems dynamics, it is well known that resonance can have catastrophic effects on a stimulated system, leading to a response that is not compatible with the previsions in the design phase. The method used in this study to estimate the frequency of oscillation of the structure is as follows: the analysis of HVSR (Horizontal to Vertical Spectral Ratio) relations. This allows for evaluation of very simple oscillation frequencies for land and structures. The tool used for data acquisition is an experimental digital tromograph. This is an engineered development of the experimental Languamply RE 4500 tromograph, equipped with an engineered amplification circuit and improved electronically using extremely small electronic components (size of each individual amplifier 16 x 26 mm). This tromograph is a modular system, completely "free" and "open", designed to interface Windows, Linux, OSX and Android with the outside world. It an amplifier designed to carry out microtremor measurements, yet which will also be useful for seismological and seismic measurements in general. The development of single amplifiers of small dimension allows for a very clean signal since being able to position it a few centimetres from the geophone eliminates cable “antenna” phenomena, which is a necessary characteristic in seeking to have signals which are clean at the very low voltages to be measured.

Keywords: microtremor, HVSR, tromograph, structural engineering

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Authors: Pardeep, Yugandhar Bitla, A. K. Patra, G. A. Basheed

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The topological protected nanosized particle-like swirling spin textures, “skyrmion,” has been observed in various ferromagnets with chiral crystal structures like MnSi, FeGe, Cu₂OSeO₃ alloys, however the magnetic ordering in these systems takes place at very low temperatures. For skyrmion-based spintronics devices, the skyrmion phase is required to stabilize in a wide temperature – field (T - H) region. The equilibrium skyrmion phase (SkX) in Co₇Zn₇Mn₆ alloy exists in a narrow T – H region just below transition temperature (TC ~ 215 K) and can be quenched by field cooling as a metastable skyrmion phase (MSkX) below SkX region. To realize robust MSkX at 110 K, field sweep ac susceptibility χ(H) measurements were performed after the zero field cooling (ZFC) and field cooling (FC) process. In ZFC process, the sample was cooled from 320 K to 110 K in zero applied magnetic field and then field sweep measurement was performed (up to 2 T) in positive direction (black curve). The real part of ac susceptibility (χ′(H)) at 110 K in positive field direction after ZFC confirms helical to conical phase transition at low field HC₁ (= 42 mT) and conical to ferromagnetic (FM) transition at higher field HC₂ (= 300 mT). After ZFC, FC measurements were performed i.e., sample was initially cooled in zero fields from 320 to 206 K and then a sample was field cooled in the presence of 15 mT field down to the temperature 110 K. After FC process, isothermal χ(H) was measured in positive (+H, red curve) and negative (-H, blue curve) field direction with increasing and decreasing field upto 2 T. Hysteresis behavior in χ′(H), measured after ZFC and FC process, indicates the stabilization of MSkX at 110 K which is in close agreement with literature. Also, the asymmetry between field-increasing curves measured after FC process in both sides confirm the stabilization of MSkX. In the returning process from the high field polarized FM state, helical state below HC₁ is destroyed and only the conical state is observed. Thus, the robust MSkX state is stabilized below its SkX phase over a much wider T - H region by FC in polycrystalline Co₇Zn₇Mn₆ alloy.

Keywords: skyrmions, magnetic susceptibility, metastable phases, topological phases

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Authors: Maimona A. E. Elimam, Suhair Rehan, Miskelyemen A. Elmekki, Mogahid M. Elhassan

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Staphylococcus aureus (Staph. aureus), a major cause of potentially life-threatening infections acquired in healthcare and community settings, has developed resistance to most classes of antimicrobial agents as determined by the dramatic increase. The present study aimed to determine the prevalence of MRSA, and VRSA in patients with different clinical manifestations in Khartoum state. The study population (n, 426) were males and females with different age categories, suffering either from wound infections (105), ear infections (121), or UTI (101), in addition to nasal carriers of medical staff (100). Cultures, Gram staining, and other biochemical tests were performed for conventional identification. Modified Kirby-Bauer disk diffusion method was applied and DNA was extracted from MRSA and VRSA isolates and PCR was then performed for amplification of arc, mecA, VanA, and VanB genes. The results confirmed the existence of Staph. aureus in 49/426 (11.5%) cases among which MRSA were isolated from 34/49 (69.4%) when modified Kirby-Bauer disk diffusion method was applied. Ten out of these 34 MRSA were confirmed as VRSA by cultures on BHI agar containing 6μg/ml vancomycin according to NCCLS criteria. PCR revealed that out of the 34 MRSA isolates, 26 were mecA positive (76.5%) while 8 (23.5%) were arcC positive. No vanA or VanB genes were detected. Molecular method confirmed the results for MRSA through the presence of either arcC or mecA genes while it failed to approve the occurrence of VRSA since neither VanA or VanB genes were detected. Thus, VRSA may be attributed to other factors.

Keywords: antibiotic resistance, Staphylococcus aureus, VRSA, MRSA, Khartoum, Sudan

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Authors: Marius Sebastian Secula, Mihaela Darie, Gabriela Carja

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Ibuprofen is a non-steroidal anti-inflammatory drug (NSAIDs) and is among the most frequently detected pharmaceuticals in environmental samples and among the most widespread drug in the world. Its concentration in the environment is reported to be between 10 and 160 ng L-1. In order to improve the abatement efficiency of this compound for water source prevention and reclamation, the development of innovative technologies is mandatory. AOPs (advanced oxidation processes) are known as highly efficient towards the oxidation of organic pollutants. Among the promising combined treatments, photo-Fenton processes using layered double hydroxides (LDHs) attracted significant consideration especially due to their composition flexibility, high surface area and tailored redox features. This work presents the self-supported Fe, Mn or Ti on ZnFeAl LDHs obtained by co-precipitation followed by reconstruction method as novel efficient photo-catalysts for Fenton-like catalysis. Fe, Mn or Ti/ZnFeAl LDHs nano-hybrids were tested for the degradation of a model pharmaceutical agent, the anti-inflammatory agent ibuprofen, by photocatalysis and photo-Fenton catalysis, respectively, by means of a lab-scale system consisting of a batch reactor equipped with an UV lamp (17 W). The present study presents comparatively the degradation of Ibuprofen in aqueous solution UV light irradiation using four different types of LDHs. The newly prepared Ti/ZnFeAl 4:1 catalyst results in the best degradation performance. After 60 minutes of light irradiation, the Ibuprofen removal efficiency reaches 95%. The slowest degradation of Ibuprofen solution occurs in case of Fe/ZnFeAl 4:1 LDH, (67% removal efficiency after 60 minutes of process). Evolution of Ibuprofen degradation during the photo Fenton process is also studied using Ti/ZnFeAl 2:1 and 4:1 LDHs in the presence and absence of H2O2. It is found that after 60 min the use of Ti/ZnFeAl 4:1 LDH in presence of 100 mg/L H2O2 leads to the fastest degradation of Ibuprofen molecule. After 120 min, both catalysts Ti/ZnFeAl 4:1 and 2:1 result in the same value of removal efficiency (98%). In the absence of H2O2, Ibuprofen degradation reaches only 73% removal efficiency after 120 min of degradation process. Acknowledgements: This work was supported by a grant of the Romanian National Authority for Scientific Research and Innovation, CNCS - UEFISCDI, project number PN-II-RU-TE-2014-4-0405.

Keywords: layered double hydroxide, advanced oxidation process, micropollutant, heterogeneous Fenton

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Authors: Isadora Bugarin, Taygoara F. de Oliveira

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Binary fluids and emulsions, in general, are present in a vast range of industrial, medical, and scientific applications, showing complex behaviors responsible for defining the flow dynamics and the system operation. However, the literature describing those highlighted fluids in non-isothermal models is currently still limited. The present work brings a detailed investigation on droplet migration due to natural convection in square enclosure, aiming to clarify the effects of drop viscosity on the flow dynamics by showing how distinct viscosity ratios (droplet/ambient fluid) influence the drop motion and the final movement pattern kept on stationary regimes. The analysis was taken by observing distinct combinations of Rayleigh number, drop initial position, and viscosity ratios. The Navier-Stokes and Energy equations were solved considering the Boussinesq approximation in a laminar flow using the finite differences method combined with the Level Set method for binary flow solution. Previous results collected by the authors showed that the Rayleigh number and the drop initial position affect drastically the motion pattern of the droplet. For Ra ≥ 10⁴, two very marked behaviors were observed accordingly with the initial position: the drop can travel either a helical path towards the center or a cyclic circular path resulting in a closed cycle on the stationary regime. The variation of viscosity ratio showed a significant alteration of pattern, exposing a large influence on the droplet path, capable of modifying the flow’s behavior. Analyses on viscosity effects on the flow’s unsteady Nusselt number were also performed. Among the relevant contributions proposed in this work is the potential use of the flow initial conditions as a mechanism to control the droplet migration inside the enclosure.

Keywords: binary fluids, droplet motion, level set method, natural convection, viscosity

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Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

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The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

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Authors: Lola T. Alimkhodjaeva, Lola T. Zakirova, Soniya S. Ziyavidenova

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Background: Breast cancer occupies the first place among the cancer in women in the world. It is urgent today to study the role of molecular markers which are capable of predicting the dynamics and outcome of the disease. The aim of this study is to define the prognostic value of the content of estrogen receptor (ER), progesterone receptor (PgR), and amplification of HER-2 / neu oncoprotein by studying 3 and 5-year overall and relapse-free survival in 470 patients with primary operable and 280 patients with locally–advanced breast cancer. Materials and methods: Study results of 3 and 5-year overall and relapse-free survival, depending on the content of RE, PgR in primary operable patients showed that ER positive (+) and PgR (+) survival was 100 (96.2%) and 97.3 (94.6%), for ER negative (-) and PgR (-) - 69.2 (60.3%) and 65.4 (57.7%), for ER positive (+) and negative PgR (-) 87.4 (80.1%) and 81.5 (79.3%), for ER negative (-) and positive PgR (+) - 97.4 (93.4%) and 90.4 (88.5%), respectively. Survival results depended also on the level of HER-2 / neu expression. In patients with HER-2 / neu negative the survival rates were as follows: 98.6 (94.7%) and 96.2 (92.3%). In group of patients with the level of HER-2 / neu (2+) expression these figures were: 45.3 (44.3%) and 45.1 (40.2%), and in group of patients with the level of HER-2 / neu (3+) expression - 41.2 (33.1%) and 34.3 (29.4%). The combination of ER negative (-), PgR (-), HER-2 / neu (-) they were 27.2 (25.4%) and 19.5 (15.3%), respectively. In patients with locally-advanced breast cancer the results of 3 and 5-year OS and RFS for ER (+) and PgR (+) were 76.3 (69.3%) and 62.2 (61.4%), for ER (-) and RP (-) 29.1 (23.7%) and 18.3 (12.6%), for ER (+) and PgR (-) 61.2 (47.2%) and 39.4 (25.6%), for ER (-) and PgR (+) 54.3 (43.1%) and 41.3 (18.3%), respectively. The level of HER-2 / neu expression also affected the survival results. Therefore, in HER-2/ neu negative patients the survival rate was 74.1 (67.6%) and 65.1 (57.3%), with the level of expression (2+) 20.4 (14.2%) and 8.6 (6.4%), with the level of expression (3+) 6.2 (3.1%) and 1.2 (1.5%), respectively. The combination for ER, PgR, HER-2 / neu negative was 22.1 (14.3%) and 8.4 (1.2%). Conclusion: Thus, the presence of steroid hormone receptors in breast tumor tissues at primary operable and locally- advanced process as the lack of HER-2/neu oncoprotein correlates with the highest rates of 3- and 5-year overall and relapse-free survival. The absence of steroid hormone receptors as well as of HER-2/neu overexpression in malignant breast tissues significantly degrades the 3- and 5-year overall and relapse-free survival. Tumors with ER, PgR and HER-2/neu negative have the most unfavorable prognostics.

Keywords: breast cancer, estrogen receptor, oncoprotein, progesterone receptor

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Authors: Kevin A. Droguett, Edwin G. Pérez, Denis Fuentealba, Margarita E. Aliaga, Angélica M. Fierro

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Supramolecular chemistry is a field of growing interest. Moreover, studying the formation of host-guest complexes between macrocycles and dyes is highly attractive due to their potential applications. Examples of the above are drug delivery, catalytic process, and sensing, among others. There are different dyes of interest in the literature; one example is the quinolinone derivatives. Those molecules have good optical properties and chemical and thermal stability, making them suitable for developing fluorescent probes. Secondly, several macrocycles can be seen in the literature. One example is the cucurbiturils. This water-soluble macromolecule family has a hydrophobic cavity and two identical carbonyl portals. Additionally, the thermodynamic analysis of those supramolecular systems could help understand the affinity between the host and guest, their interaction, and the main stabilization energy of the complex. In this work, two 7-(diethylamino) quinoline-2 (1H)-one derivative (QD1-2) and their interaction with cucurbit[7]uril (CB[7]) were studied from an experimental and in-silico point of view. For the experimental section, the complexes showed a 1:1 stoichiometry by HRMS-ESI and isothermal titration calorimetry (ITC). The inclusion of the derivatives on the macrocycle lends to an upward shift in the fluorescence intensity, and the pKa value of QD1-2 exhibits almost no variation after the formation of the complex. The thermodynamics of the inclusion complexes was investigated using ITC; the results demonstrate a non-classical hydrophobic effect with a minimum contribution from the entropy term and a constant binding on the order of 106 for both ligands. Additionally, dynamic molecular studies were carried out during 300 ns in an explicit solvent at NTP conditions. Our finding shows that the complex remains stable during the simulation (RMSD ~1 Å), and hydrogen bonds contribute to the stabilization of the systems. Finally, thermodynamic parameters from MMPBSA calculations were obtained to generate new computational insights to compare with experimental results.

Keywords: host-guest complexes, molecular dynamics, quinolin-2(1H)-one derivatives dyes, thermodynamics

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Authors: Michael Dare Asemoloye, Segun Gbolagade Jonathan, Rafiq Ahmad, Odunayo Joseph Olawuyi, D. O. Adejoye

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Fungi have potentials for degrading hydrocarbons through the secretion of different enzymes. Crude oil tolerance and degradation by Trichoderma harzianum was investigated in this study with its ability to produce peroxidase enzymes (LiP and MnP). Many fungal strains were isolated from rhizosphere of grasses growing on a crude oil spilled site, and the most frequent strain based on percentage incidence was further characterized using morphological and molecular characteristics. Molecular characterization was done through the amplification of Ribosomal-RNA regions of 18s (1609-1627) and 28s (287-266) using ITS1 and ITS4 combinations and it was identified using NCBI BLAST tool. The selected fungus was also subjected to an in-vitro tolerance test at crude oil concentrations of 5, 10, 15, 20 and 25% while 0% served as control. In addition, lignin peroxidase genes (lig1-6) and manganese peroxidase gene (mnp) were detected and expressed in this strain using RT-PCR technique, its peroxidase producing activities was also studied in aliquots (U/ml). This strain had highest incidence of 80%, it was registered in NCBI as Trichoderma harzianum asemoJ KY488466. The strain KY488466 responded to crude oil concentrations as it increase, the dose inhibition response percentage (DIRP) increased from 41.67 to 95.41 at 5 to 25 % crude oil concentrations. All the peroxidase genes are present in KY488466, and expressed with amplified 900-1000 bp through RT-PCR technique. In this strain, lig2, lig4 and mnp genes were over-expressed, lig 6 was moderately expressed, while none of the genes was under-expressed. The strain also produced 90±0.87 U/ml lignin peroxidase and 120±1.23 U/mil manganese peroxidase enzymes in aliquots. These results imply that KY488466 can tolerate and survive high crude oil concentration and could be exploited for bioremediation of oil-spilled soils, the produced peroxidase enzymes could also be exploited for other biotechnological experiments.

Keywords: crude oil, enzymes, expression, peroxidase genes, tolerance, Trichoderma harzianum

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Authors: Sara A. Al-Jaberi, Salma Ben-Salem, Meriam Messedi, Fatma Ayadi, Lihadh Al-Gazali, Bassam R. Ali

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Background: The chemokine receptor components play crucial roles in the immune system and some of them serve as co-receptors for the HIV virus. Several studies have documented those variants in chemokine receptors are correlated with susceptibility and resistance to infection with HIV virus. For example, mutations in the chemokine receptor 5 gene (CCR5) resulting in loss-of-function (such as the homozygous CCR5Δ32) confer high degree of resistance to HIV infection. Heterozygotes for these variants exhibit slow progression to AIDS. The prevalence of CCR5 polymorphisms varies among ethnic and geographical groups. For example, the CCR5 Δ32 variant is present in 10–15% of north Europeans but is rarely encountered among Africans. This study aims to identify the prevalence of some CCR5 variants in two geographically distant Arab populations (namely Emiratis and Tunisians). Methodology: The prevalence of CCR5 gene variants including CCR5Δ32, FS299, C101X, A29S and C178R has been determined using PCR and direct DNA sequencing. A total of 403 unrelated healthy individuals (253 Emiratis and 150 Tunisians) were genotyped for the CCR5Δ32 variant using PCR amplification and gel electrophoresis. In addition, 200 Emiratis have been screened for other SNPs using Sanger DNA sequencing. Results: Among Emiratis, the allele frequency of the CCR5Δ32 variant has been found to be 0.002. In addition, two variants L55Q and A159 were found at a frequency of 0.002.Moreover, the prevalence of the CCR5Δ32 variant in Tunisians was estimated to be 0.013 which is relatively higher than its frequency in Emiratis but lower than Europeans. Conclusion: We conclude that the allele frequency of the most critical CCR5 polymorphism (Δ32) is extremely low among Emiratis compared to other Arabs and North Europeans. In addition, very low allele frequencies of other CCR5 polymorphisms have been detected among Emiratis.

Keywords: chemokine receptors, CCR5Δ32, CCR5 polymorphisms, Emiratis, Arab populations

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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