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

Authors: Daniel Mueller, Melanie Breitbach, Stefan Cornelius, Sarah Pakulla-Dickel, Margaretha Koenig, Anke Prochnow, Mario Scherer

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The European STR standard set (ESS) of loci as well as the new expanded CODIS core loci set as recommended by the CODIS Core Loci Working Group, has led to a higher standardization and harmonization in STR analysis across borders. Various multiplex PCRs assays have since been developed for the analysis of these 17 ESS or 23 CODIS expansion STR markers that all meet high technical demands. However, forensic analysts are often faced with difficult STR results and the questions thereupon. What is the reason that no peaks are visible in the electropherogram? Did the PCR fail? Was the DNA concentration too low? QIAGEN’s newest Investigator STR kits contain a novel Quality Sensor (QS) that acts as internal performance control and gives useful information for evaluating the amplification efficiency of the PCR. QS indicates if the reaction has worked in general and furthermore allows discriminating between the presence of inhibitors or DNA degradation as a cause for the typical ski slope effect observed in STR profiles of such challenging samples. This information can be used to choose the most appropriate rework strategy.Based on the latest PCR chemistry called FRM 2.0, QIAGEN now provides the next technological generation for STR analysis, the Investigator ESSplex SE QS and Investigator 24plex QS Kits. The new PCR chemistry ensures robust and fast PCR amplification with improved inhibitor resistance and easy handling for a manual or automated setup. The short cycling time of 60 min reduces the duration of the total PCR analysis to make a whole workflow analysis in one day more likely. To facilitate the interpretation of STR results a smart primer design was applied for best possible marker distribution, highest concordance rates and a robust gender typing.

Keywords: PCR, QIAGEN, quality sensor, STR

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Authors: Maxime Merheb, Rachel Matar

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Retrieving ancient DNA sequences which in return permit the entire genome sequencing from fossils have extraordinarily improved in recent years, thanks to sequencing technology and other methodological advances. In any case, the quest to search for ancient DNA is still obstructed by the damage inflicted on DNA which accumulates after the death of a living organism. We can characterize this damage into three main categories: (i) Physical abnormalities such as strand breaks which lead to the presence of short DNA fragments. (ii) Modified bases (mainly cytosine deamination) which cause errors in the sequence due to an incorporation of a false nucleotide during DNA amplification. (iii) DNA modifications referred to as blocking lesions, will halt the PCR extension which in return will also affect the amplification and sequencing process. We can clearly see that the issues arising from breakage and coding errors were significantly decreased in recent years. Fast sequencing of short DNA fragments was empowered by platforms for high-throughput sequencing, most of the coding errors were uncovered to be the consequences of cytosine deamination which can be easily removed from the DNA using enzymatic treatment. The methodology to repair DNA sequences is still in development, it can be basically explained by the process of reintroducing cytosine rather than uracil. This technique is thus restricted to amplified DNA molecules. To eliminate any type of damage (particularly those that block PCR) is a process still pending the complete repair methodologies; DNA detection right after extraction is highly needed. Before using any resources into extensive, unreasonable and uncertain repair techniques, it is vital to distinguish between two possible hypotheses; (i) DNA is none existent to be amplified to begin with therefore completely un-repairable, (ii) the DNA is refractory to PCR and it is worth to be repaired and amplified. Hence, it is extremely important to develop a non-enzymatic technique to detect the most degraded DNA.

Keywords: ancient DNA, DNA barcodong, enzymatic repair, PCR

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Authors: Mohamed Saïd Kahaleras, François Lanzetta, Mohamed Khan, Guillaume Layes, Philippe Nika

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This paper presents an experimental work to characterize the dynamic operation of a metal regenerator crossed by dry compressible air alternating flow. Unsteady dynamic measurements concern the pressure, velocity and temperature of the gas at the ends and inside the channels of the regenerator. The regenerators are tested under isothermal conditions and thermal axial temperature gradient.

Keywords: friction factor, oscillating flow, regenerator, stirling machine

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Authors: M. Irfan Fareed, Muhammad Tahir, Alvina Gul Kazi

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Castor bean (Ricinus communis; family Euphorbiaceae) is cultivated for the production of oil and as an ornamental plant throughout tropical regions. Leaf samples from castor bean plants with leaf curl and vein thickening were collected from areas around Okara (Pakistan) in 2011. PCR amplification using diagnostic primers showed the presence of a begomovirus and subsequently the specific pair (BurNF 5’- CCATGGTTGTGGCAGTTGATTGACAGATAC-3’, BurNR 5’- CCATGGATTCACGCACAGGGGAACCC-3’) was used to amplify and clone the whole genome of the virus. The complete nucleotide sequence was determined to be 2,759 nt (accession No. HE985227). Alignments showed the highest levels of nucleotide sequence identity (98.8%) with Cotton leaf curl Burewala virus (CLCuBuV; accession No. JF416947) No. JF416947). The virus in castor beans lacks on intact C2 gene, as is typical of CLCuBuV in cotton. An amplification product of ca. 1.4 kb was obtained in PCR with primers for betasatellites and the complete nucleotide sequence of a clone was determined to be 1373 nt (HE985228). The sequence showed 96.3% nucleotide sequence identity to the recombinant Cotton leaf curl Multan betasatellite (CLCuMB; JF502389). This is the first report of CLCuBuV and its betasatellite infecting castor bean, showing this plant species as an alternate host of the virus. Already many alternate host have been reported from different alternate host like tobacco, tomato, hibiscus, okra, ageratum, Digera arvensis, habiscus, Papaya and now in Ricinus communis. So, it is suggested that these alternate hosts should be avoided to grow near cotton growing regions.

Keywords: Ricinus communis, begomovirus, betasatellite, agriculture

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Authors: Elisa Boatti, Ulisse Stefanelli, Alessandro Reali, Ferdinando Auricchio

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Thanks to their unusual properties, shape memory alloys (SMAs) are good candidates for advanced applications in a wide range of engineering fields, such as automotive, robotics, civil, biomedical, aerospace. In the last decades, the ever-growing interest for such materials has boosted several research studies aimed at modeling their complex nonlinear behavior in an effective and robust way. Since the constitutive response of SMAs is strongly thermomechanically coupled, the investigation of the non-isothermal evolution of the material must be taken into consideration. The present study considers an existing three-dimensional phenomenological model for SMAs, able to reproduce the main SMA properties while maintaining a simple user-friendly structure, and proposes a variational reformulation of the full non-isothermal version of the model. While the considered model has been thoroughly assessed in an isothermal setting, the proposed formulation allows to take into account the full nonisothermal problem. In particular, the reformulation is inspired to the GENERIC (General Equations for Non-Equilibrium Reversible-Irreversible Coupling) formalism, and is based on a generalized gradient flow of the total entropy, related to thermal and mechanical variables. Such phrasing of the model is new and allows for a discussion of the model from both a theoretical and a numerical point of view. Moreover, it directly implies the dissipativity of the flow. A semi-implicit time-discrete scheme is also presented for the fully coupled thermomechanical system, and is proven unconditionally stable and convergent. The correspondent algorithm is then implemented, under a space-homogeneous temperature field assumption, and tested under different conditions. The core of the algorithm is composed of a mechanical subproblem and a thermal subproblem. The iterative scheme is solved by a generalized Newton method. Numerous uniaxial and biaxial tests are reported to assess the performance of the model and algorithm, including variable imposed strain, strain rate, heat exchange properties, and external temperature. In particular, the heat exchange with the environment is the only source of rate-dependency in the model. The reported curves clearly display the interdependence between phase transformation strain and material temperature. The full thermomechanical coupling allows to reproduce the exothermic and endothermic effects during respectively forward and backward phase transformation. The numerical tests have thus demonstrated that the model can appropriately reproduce the coupled SMA behavior in different loading conditions and rates. Moreover, the algorithm has proved effective and robust. Further developments are being considered, such as the extension of the formulation to the finite-strain setting and the study of the boundary value problem.

Keywords: generalized gradient flow, GENERIC formalism, shape memory alloys, thermomechanical coupling

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Authors: Mohamed ElMasry, Ahmad Ragheb, Tareq AbdelAziz, Mohamed Ghazy

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Choosing the suitable infrastructure system is becoming more challenging with the increase in demand for heavier structures contemporarily. This is the case where piled raft foundations have been widely used around the world to support heavy structures without extensive settlement. In the latter system, piles are rigidly connected to the raft, and most of the load goes to the soil layer on which the piles are bearing. In spite of that, when soil profiles contain thicker soft clay layers near the surface, or at relatively shallow depths, it is unfavorable to use the rigid piled raft foundation system. Consequently, the disconnected piled raft system was introduced as an alternative approach for the rigidly connected system. In this system, piles are disconnected from the raft using a cushion of soil, mostly of a granular interlayer. The cushion is used to redistribute the stresses among the piles and the subsoil. Piles are also used to stiffen the subsoil, and by this way reduce the settlement without being rigidly connected to the raft. However, the seismic loading effect on such disconnected foundation systems remains a problem, since the soil profiles may include thick clay layers which raise risks of amplification of the dynamic earthquake loads. In this paper, the effects of seismic behavior on the connected and disconnected piled raft systems are studied through a numerical model using Midas GTS NX Software. The study concerns the soil-structure interaction and the expected behavior of the systems. Advantages and disadvantages of each foundation approach are studied, and a comparison between the results are presented to show the effects of using disconnected piled raft systems in highly seismic zones. This was done by showing the excitation amplification in each of the foundation systems.

Keywords: soil-structure interaction, disconnected piled-raft, risks, seismic zones

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

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Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

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Authors: Lopez J., Mehrvar M., Quinones E., Suarez A., RomeroC.

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The Silver Nanoparticles (AgNP) are used as deliver of heat on surface of Membrane Distillation in order to fight against Thermal Polarization and improving the Desalination Process. In this study AgNPwere deposited by dip coating process over PVDF, FG hydrophilic, and PTFE hydrophobic commercial membranes as substrate. Membranes were characterized by SEM, EDS, contact angle, Pore size distributionand using a UV lamp and a thermal camera were measured the performance of heat deliver. The presence of AgNP 50 – 150 nm and the increase in absorption of energy over membrane were verified.

Keywords: silver nanoparticles, membrane distillation, plasmon effect, heat deliver

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Authors: Jian-Jun Shu

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A cold, thin film of liquid impinging on an isothermal hot, horizontal surface has been investigated. An approximate solution for the velocity and temperature distributions in the flow along the horizontal surface is developed, which exploits the hydrodynamic similarity solution for thin film flow. The approximate solution may provide a valuable basis for assessing flow and heat transfer in more complex settings.

Keywords: flux, free impinging jet, solid-surface, uniform wall temperature

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Authors: Shrawan Baghel, Helen Cathcart, Biall J. O'Reilly

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Amorphous drug formulations have great potential to enhance solubility and thus bioavailability of BCS class II drugs. However, the higher free energy and molecular mobility of the amorphous form lowers the activation energy barrier for crystallization and thermodynamically drives it towards the crystalline state which makes them unstable. Accurate determination of the crystallization tendency/kinetics is the key to the successful design and development of such systems. In this study, dipyridamole (DPM) and cinnarizine (CNZ) has been selected as model compounds. Thermodynamic fragility (m_T) is measured from the heat capacity change at the glass transition temperature (Tg) whereas dynamic fragility (m_D) is evaluated using methods based on extrapolation of configurational entropy to zero 〖(m〗_(D_CE )), and heating rate dependence of Tg 〖(m〗_(D_Tg)). The mean relaxation time of amorphous drugs was calculated from Vogel-Tammann-Fulcher (VTF) equation. Furthermore, the correlation between fragility and glass forming ability (GFA) of model drugs has been established and the relevance of these parameters to crystallization of amorphous drugs is also assessed. Moreover, the crystallization kinetics of model drugs under isothermal conditions has been studied using Johnson-Mehl-Avrami (JMA) approach to determine the Avrami constant ‘n’ which provides an insight into the mechanism of crystallization. To further probe into the crystallization mechanism, the non-isothermal crystallization kinetics of model systems was also analysed by statistically fitting the crystallization data to 15 different kinetic models and the relevance of model-free kinetic approach has been established. In addition, the crystallization mechanism for DPM and CNZ at each extent of transformation has been predicted. The calculated fragility, glass forming ability (GFA) and crystallization kinetics is found to be in good correlation with the stability prediction of amorphous solid dispersions. Thus, this research work involves a multidisciplinary approach to establish fragility, GFA and crystallization kinetics as stability predictors for amorphous drug formulations.

Keywords: amorphous, fragility, glass forming ability, molecular mobility, mean relaxation time, crystallization kinetics, stability

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Authors: A. Elgendi, H. Farag, M. E. Ossman, M. Abd-Elfatah

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This paper explores the using of waste cooking oil (WCO) as an attractive option to reduce the raw material cost for the biodiesel production. This can be achieved through two steps; esterification using g-C3N4photocatalyst and then alkali transesterification. Several parameters have been studied to determine the yield of the biodiesel produced such as: Reaction time (2-6 hrs), catalyst concentration (0.3-1.5 wt.%), number of UV lamps (1or 3 lamps) and methanol: oil ratio (6:1-12:1). From the obtained results, the highest percentage yield was obtained using methanol: Oil molar ratio of 12:1, catalyst dosage 0.3%, time of 4 hrs and using 1 lamp. From the results it was clear that the produced biodiesel from waste cooking oil can be used as fuel.

Keywords: biodiesel, heterogeneous catalyst, photocatalytic esterification, waste cooking oil

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Authors: Hongquan Zhang

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Inspired by endogenous protein motors, researchers have constructed various synthetic DNA motors based on the specificity and predictability of Watson-Crick base pairing. However, the application of DNA motors to signal amplification and biosensing is limited because of low mobility and difficulty in real-time monitoring of the walking process. The objective of our work was to construct a new type of DNA motor termed target-triggered DNA motors that can walk for hundreds of steps in response to a single target binding event. To improve the mobility and processivity of DNA motors, we used gold nanoparticles (AuNPs) as scaffolds to build high-density, three-dimensional tracks. Hundreds of track strands are conjugated to a single AuNP. To enable DNA motors to respond to specific protein and nucleic acid targets, we adapted the binding-induced DNA assembly into the design of the target-triggered DNA motors. In response to the binding of specific target molecules, DNA motors are activated to autonomously walk along AuNP, which is powered by a nicking endonuclease or DNAzyme-catalyzed cleavage of track strands. Each moving step restores the fluorescence of a dye molecule, enabling monitoring of the operation of DNA motors in real time. The motors can translate a single binding event into the generation of hundreds of oligonucleotides from a single nanoparticle. The motors have been applied to amplify the detection of proteins and nucleic acids in test tubes and live cells. The motors were able to detect low pM concentrations of specific protein and nucleic acid targets in homogeneous solutions without the need for separation. Target-triggered DNA motors are significant for broadening applications of DNA motors to molecular sensing, cell imagining, molecular interaction monitoring, and controlled delivery and release of therapeutics.

Keywords: biosensing, DNA motors, gold nanoparticles, signal amplification

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Authors: Aminah Salim, Idrees Ahmed Nasir, Abdul Qayyum Rao, Muhammad Ali, Muhammad Sohail Anjum, Ayesha Hameed, Bushra Tabassum, Anwar Khan, Arfan Ali, Mariyam Zameer, Tayyab Husnain

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Risk assessment of transgenic herbicide tolerant sugarcane having CEMB codon optimized cp4EPSPS gene was done in present study. Fifteen days old chicks taken from K&Ns Company were randomly assorted into four groups with eight chicks in each group namely control chicken group fed with commercial diet, non-transgenic group fed with non-experimental sugarcane and transgenic group fed with transgenic sugarcane with minimum and maximum level. Body weights, biochemical analysis for Urea, alkaline phosphatase, alanine transferase, aspartate transferase, creatinine and bilirubin determination and histological examination of chicks fed with four types of feed was taken at fifteen days interval and no significant difference was observed in body weight biochemical and histological studies of all four groups. Protein isolated from the serum sample was analyzed through dipstick and SDS-PAGE, showing the absence of transgene protein in the serum sample of control and experimental groups. Moreover the amplification of cp4EPSPS gene with gene specific primers of DNA isolated from chicks blood and also from commercial diet was done to determine the presence and mobility of any nucleotide fragment of the transgene in/from feed and no amplification was obtained in feed as well as in blood extracted DNA of any group. Also no mRNA expression of cp4EPSPS gene was obtained in any tissue of four groups of chicks. From the results it is clear that there is no deleterious or harmful effect of the CEMB codon optimized transgenic cp4EPSPS sugarcane on the chicks health.

Keywords: chicks, cp4EPSPS, glyphosate, sugarcane

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Authors: David Nieto Simavilla, Wilco M. H. Verbeeten

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The viscoelastic behavior of polymeric flows under isothermal conditions has been extensively researched. However, most of the processing of polymeric materials occurs under non-isothermal conditions and understanding the linkage between the thermo-physical properties and the process state variables remains a challenge. Furthermore, the cost and energy required to manufacture, recycle and dispose polymers is strongly affected by the thermo-physical properties and their dependence on state variables such as temperature and stress. Experiments show that thermal conductivity in flowing polymers is anisotropic (i.e. direction dependent). This phenomenon has been previously omitted in the study and simulation of industrially relevant flows. Our work combines experimental evidence of a universal relationship between thermal conductivity and stress tensors (i.e. the stress-thermal rule) with differential constitutive equations for the viscoelastic behavior of polymers to provide predictions for the anisotropy in thermal conductivity in uniaxial, planar, equibiaxial and shear flow in commercial polymers. A particular focus is placed on the eXtended Pom-Pom model which is able to capture the non-linear behavior in both shear and elongation flows. The predictions provided by this approach are amenable to implementation in finite elements packages, since viscoelastic and thermal behavior can be described by a single equation. Our results include predictions for flow-induced anisotropy in thermal conductivity for low and high density polyethylene as well as confirmation of our method through comparison with a number of thermoplastic systems for which measurements of anisotropy in thermal conductivity are available. Remarkably, this approach allows for universal predictions of anisotropy in thermal conductivity that can be used in simulations of complex flows in which only the most fundamental rheological behavior of the material has been previously characterized (i.e. there is no need for additional adjusting parameters other than those in the constitutive model). Accounting for polymers anisotropy in thermal conductivity in industrially relevant flows benefits the optimization of manufacturing processes as well as the mechanical and thermal performance of finalized plastic products during use.

Keywords: anisotropy, differential constitutive models, flow simulations in polymers, thermal conductivity

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Authors: Anjali Sadanand, R. V. Nagarajan

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Architecture morphs with advances in technology and the roof, wall, and floor as basic elements of a building, follow in redefining themselves over time. Their contribution is bound by time and held by design principles that deal with function, sturdiness, and beauty. Architecture engages with people to give joy through its form, material, design structure, and spatial qualities. This paper attempts to re-interpret John Ruskin’s “Seven lamps of Architecture” in the context of the architecture of the modern and present period. The paper focuses on the “wall” as an element of study in this context. Four of Ruskin’s seven lamps will be discussed, namely beauty, truth, life, and memory, through examples of architecture ranging from modernism to contemporary architecture of today. The study will focus on the relevance of Ruskin’s principles to the “wall” in specific, in buildings of different materials and over a range of typologies from all parts of the world. Two examples will be analyzed for each lamp. It will be shown that in each case, there is relevance to the significance of Ruskin’s lamps in modern and contemporary architecture. Nature to which Ruskin alludes to for his lamp of “beauty” is found in the different expressions of interpretation used by Corbusier in his Villa Stein façade based on proportion found in nature and in the direct expression of Toyo Ito in his translation of an understanding of the structure of trees into his façade design of the showroom for a Japanese bag boutique. “Truth” is shown in Mies van der Rohe’s Crown Hall building with its clarity of material and structure and Studio Mumbai’s Palmyra House, which celebrates the use of natural materials and local craftsmanship. “Life” is reviewed with a sustainable house in Kerala by Ashrams Ravi and Alvar Aalto’s summer house, which illustrate walls as repositories of intellectual thought and craft. “Memory” is discussed with Charles Correa’s Jawahar Kala Kendra and Venturi’s Vana Venturi house and discloses facades as text in the context of its materiality and iconography. Beauty is reviewed in Villa Stein and Toyo Ito’s Branded Retail building in Tokyo. The paper thus concludes that Ruskin’s Lamps can be interpreted in today’s context and add richness to meaning to the understanding of architecture.

Keywords: beauty, design, facade, modernism

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Authors: Amar F. Siddique

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The Guwahati city is one of the fastest growing cities of the north-eastern region of India, situated on the South Bank of the Brahmaputra River falls in the highest seismic zone level V. The city has witnessed many high magnitude earthquakes in the past decades. The Assam earthquake occurred on August 15, 1950, of moment magnitude 8.7 epicentered near Rima, Tibet was one of the major earthquakes which caused a serious structural damage and widespread soil liquefaction in and around the region. Hence the study of ground motion characteristics of Guwahati city is very essential. In this present work 1D equivalent linear ground response analysis (GRA) has been adopted using Deep soil software. The analysis has been done for two typical sites namely, Panbazar and Azara comprising total four boreholes location in Guwahati city of India. GRA of the sites is carried out by using an input motion recorded at Nongpoh station (recorded PGA 0.048g) and Nongstoin station (recorded PGA 0.047g) of 1997 Indo-Burma earthquake. In comparison to motion recorded at Nongpoh, different amplifications of bedrock peak ground acceleration (PGA) are obtained for all the boreholes by the motion recorded at Nongstoin station; although, the Fourier amplitude ratios (FAR) and fundamental frequencies remain almost same. The difference in recorded duration and frequency content of the two motions mainly influence the amplification of motions thus getting different surface PGA and amplification factor keeping a constant bedrock PGA. From the results of response spectra, it is found that at the period of less than 0.2 sec the ground motion recorded at Nongpoh station will give a high spectral acceleration (SA) on the structures than at Nongstoin station. Again for a period greater than 0.2 sec the ground motion recorded at Nongstoin station will give a high SA on the structures than at Nongpoh station.

Keywords: fourier amplitude ratio, ground response analysis, peak ground acceleration, spectral acceleration

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Authors: Boitumelo Setlhare, Mduduzi P. Mokoena, Ademola O. Olaniran

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Agricultural and industrial activities have led to increasing production of xenobiotics such as 2,4-dichlorophenol (2,4-DCP), a derivative of 2,4-dichlorophenoxyacetic acid (2,4-D), which is a widely used herbicide. Bioremediation offers an efficient, cost-effective and environmentally friendly method for degradation of the compound through the activities of the various microbial enzymes involved in the catabolic pathway. The aim of this study was to isolate and characterize bacterial isolate indigenous to contaminated sites in Durban, South Africa for 2,4-DCP degradation. One bacterium capable of utilizing 2,4-DCP as sole carbon source was isolated using culture enrichment technique and identified as Pseudomonas chlororaphis strain UFB2 via PCR amplification and analysis of 16S rRNA gene sequence. This isolate was able to degrade up to 75.11% of 2,4-DCP in batch cultures within 10 days, with the degradation rate constant of 0.14 mg/l/d. Phylogenetic analysis revealed the relatedness of this bacterial isolate to other Pseudomonas sp. previously characterized for chlorophenol degradation. PCR amplification of the catabolic genes involved in 2,4-DCP degradation revealed the presence of the correct amplicons for phenol hydroxylase (600 bp), catechol 1,2-dioxygenase (214 bp), muconate isomerase (851 bp), cis-dienelactone hydrolase (577 bp), and trans-dienelactone hydrolase (491 bp) genes. Enzyme assays revealed activity as high as 21840 mU/mg, 15630 mU/mg, 2340 mU/mg and 1490 mU/mg obtained for phenol hydroxylase, catechol 1,2-dioxygenase, cis-dienelactone hydroxylase and trans-dienelactone hydroxylase, respectively. The absence of catechol 2,3-dioxygenase gene and the corresponding enzyme in this isolate suggests that the organism followed ortho-pathway for 2,4-DCP degradation. Furthermore, the absence of malaycetate reductase genes showed that the bacterium may not be able to completely mineralize 2,4-DCP. Further studies are required to optimize 2,4-DCP degradation by this isolate as well as to elucidate the mechanism of 2,4-DCP degradation.

Keywords: biodegradation, catechol 1, 2-dioxygenase, 2, 4-dichlorophenol, phenol hydroxylase, Pseudomonas chlororaphis

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Authors: Shringika Soni, Utkarsh Jain, Nidhi Chauhan

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Aptamers are recently discovered ~80-100 bp long artificial oligonucleotides that not only demonstrated their applications in therapeutics; it is tremendously used in diagnostic and sensing application to detect different biomarkers and drugs. Synthesizing aptamers for proteins or genomic template is comparatively feasible in laboratory, but drugs or other chemical target based aptamers require major specification and proper optimization and validation. One has to optimize all selection, amplification, and characterization steps of the end product, which is extremely time-consuming. Therefore, we performed asymmetric PCR (polymerase chain reaction) for random oligonucleotides pool synthesis, and further use them in Systematic evolution of ligands by exponential enrichment (SELEX) for anti-psychotic drugs based aptamers synthesis. Anti-psychotic drugs are major tranquilizers to control psychosis for proper cognitive functions. Though their low medical use, their misuse may lead to severe medical condition as addiction and can promote crime in social and economical impact. In this work, we have approached the in-vitro SELEX method for ssDNA synthesis for anti-psychotic drugs (in this case ‘target’) based aptamer synthesis. The study was performed in three stages, where first stage included synthesis of random oligonucleotides pool via asymmetric PCR where end product was analyzed with electrophoresis and purified for further stages. The purified oligonucleotide pool was incubated in SELEX buffer, and further partition was performed in the next stage to obtain target specific aptamers. The isolated oligonucleotides are characterized and quantified after each round of partition, and significant results were obtained. After the repetitive partition and amplification steps of target-specific oligonucleotides, final stage included sequencing of end product. We can confirm the specific sequence for anti-psychoactive drugs, which will be further used in diagnostic application in clinical and forensic set-up.

Keywords: anti-psychotic drugs, aptamer, biosensor, ssDNA, SELEX

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Authors: E. S. Manuylovich, V. A. Astapenko, P. A. Golovinsky

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The dispersion relation binding the constant of propagation and frequency is calculated for silver cone. The evolution of the electric field of ultrashort pulse during its propagation in conical structure is considered. Increasing of electric field during pulse propagation to the top of the cone is observed. Reduction of the pulse duration at a certain distance is observed. The dependence of minimum pulse duration on initial chirp and cone angle is investigated.

Keywords: ultrashort pulses, surface plasmon polariton, dispersion, silver cone

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Authors: Sonia Ben Hamza, Sabra Habli, Nejla Mahjoub Said, Hervé Bournot, Georges Le Palec

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In this work, we determine the turbulent dynamic structure of pollutant dispersion in two-phase free surface flow. The numerical simulation was performed using ANSYS Fluent. The flow study is three-dimensional, unsteady and isothermal. The study area has been endowed with a rectangular obstacle to analyze its influence on the hydrodynamic variables and progression of the pollutant. The numerical results show that the hydrodynamic model provides prediction of the dispersion of a pollutant in an open channel flow and reproduces the recirculation and trapping the pollutant downstream near the obstacle.

Keywords: CFD, free surface, polluant dispersion, turbulent flows

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Authors: J. A. Gbadeyan, R. A. Kareem

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In this paper, we investigated the effects of unsteady internal heat generation of a two-step exothermic reactive hydromagnetic fluid flow under different chemical kinetics namely: Sensitized, Arrhenius and Bimolecular kinetics through an isothermal wall temperature channel. The resultant modeled nonlinear partial differential equations were simplified and solved using a combined Laplace-Differential Transform Method (LDTM). The solutions obtained were discussed and presented graphically to show the salient features of the fluid flow and heat transfer characteristics.

Keywords: unsteady, reactive, hydromagnetic, couette ow, exothermi creactio

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Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia(CIN)and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, p53, miR-146a, rs2910164, polymorphism

Procedia PDF Downloads 468

Authors: Khalil Ullah Khan

Abstract:

Linguistic abilities in students with hearing impairment yet remain a concern for educationists. The emerging technological support and provisions in the recent era vow to have addressed the situation and claim significant contributions in terms of linguistic repertoire. Being a descriptive and quantitative paradigm of study, the purpose of this research set forth was to assess the linguistic competencies of students with hearing impairment in the English language. The goals were further broken down to identify the level of reading abilities in the subject population. The population involved students with HI studying at a higher secondary level in Lahore. A simple random sampling technique was used to choose a sample of fifty students. A purposive curriculum-based assessment was designed in line with the accelerated learning program by the Punjab Government to assess Linguistic competence among the sample. Further to it, an Informal Reading Inventory (IRI) corresponding to reading levels was also developed by researchers duly validated and piloted before the final use. Descriptive and inferential statistics were utilized to reach the findings. Spearman’s correlation was used to find out the relationship between the degree of hearing loss, grade level, gender and type of amplification device. An Independent sample t-test was used to compare means among groups. Major findings of the study revealed that students with hearing impairment exhibit significant deviation from the mean scores when compared in terms of grades, severity and amplification device. The study divulged that respective students with HI have yet failed to qualify for an independent level of reading according to their grades, as the majority fall at the frustration level of word recognition and passage comprehension. The poorer performance can be attributed to lower linguistic competence, as it is shown in the frustration levels of reading, writing and comprehension. The correlation analysis did reflect an improved performance grade. Wise. However, scores could only correspond to frustration level, and independent levels were never achieved. Reported achievements at the instructional level of the subject population may further to linguistic skills if practiced purposively.

Keywords: linguistic competence, hearing impairment, reading levels, educationist

Procedia PDF Downloads 41

Authors: Hossein Rassi, Marjan Moradi fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human Papillomavirus (HPV) infection is the leading risk factor for Cervical Intraepithelial Neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33, and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99 bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, miR-146a rs2910164 polymorphism, p53 polymorphism, intraepithelial, neoplasia, HPV

Procedia PDF Downloads 398

Authors: K. Digheche, K. Saadi, Z. Boumerzoug

Abstract:

Welding is one of the most important technological processes used in many branches of industry such as industrial engineering, shipbuilding, pipeline fabrication among others. Generally, welding is the preferred joining method and most common steels are weldable. This investigation is a contribution to scientific work of welding of low carbon steel. This work presents the results of the isothermal heat treatment effect at 200, 400 and 600 °C on microstructural evolution in weld region of X70 pipeline steel. The welding process has been realized in three passes by industrial arc welding. We have found that the heat treatments cause grain growth reaction.

Keywords: heat treatments, low carbon steel, microstructures, welding

Procedia PDF Downloads 460

Authors: Shreyas Srinivas Rangan, Jurgis Porins

Abstract:

The internet traffic has increased exponentially due to the high demand for data rates by the users, and the constantly increasing metro networks and access networks are focused on improving the maximum transmit distance of the long-reach optical networks. One of the common methods to improve the maximum transmit distance of the long-reach optical networks at the component level is to use broadband optical amplifiers. The Erbium Doped Fiber Amplifier (EDFA) provides high amplification with low noise figure but due to the characteristics of EDFA, its operation is limited to C-band and L-band. In contrast, the Raman amplifier exhibits a wide amplification spectrum, and negative noise figure values can be achieved. To obtain such results, high powered pumping sources are required. Operating Raman amplifiers with such high-powered optical sources may cause fire hazards and it may damage the optical system. In this paper, we implement a hybrid optical amplifier configuration. EDFA and Raman amplifiers are used in this hybrid setup to combine the advantages of both EDFA and Raman amplifiers to improve the reach of the system. Using this setup, we analyze the maximum transmit distance of the network by obtaining a correlation diagram between the length of the single-mode fiber (SMF) and the Bit Error Rate (BER). This hybrid amplifier configuration is implemented in a Wavelength Division Multiplexing (WDM) system with a BER of 10⁻⁹ by using NRZ modulation format, and the gain uniformity noise ratio (signal-to-noise ratio (SNR)), the efficiency of the pumping source, and the optical signal gain efficiency of the amplifier are studied experimentally in a mathematical modelling environment. Numerical simulations were implemented in RSoft OptSim simulation software based on the nonlinear Schrödinger equation using the Split-Step method, the Fourier transform, and the Monte Carlo method for estimating BER.

Keywords: Raman amplifier, erbium doped fibre amplifier, bit error rate, hybrid optical amplifiers

Procedia PDF Downloads 70

Authors: Dahi Ghareab Abdelsalam Ibrahim

Abstract:

Scanning interferometry is commonly used for measuring the three-dimensional profiling of surfaces. Here, we used a scanning stage calibrated with standard gauge blocks to measure a standard step height of 200μm. The stage measures precisely the envelope of interference at the platen and at the surface of the step height. From the difference between the two envelopes, we measured the step height of the sample. Experimental measurements show that the measured value matches well with the nominal value of the step height. A light beam of 532nm from a Tungsten Lamp is collimated and incident on the interferometer. By scanning, two envelopes were produced. The envelope at the platen surface and the envelope at the object surface were determined precisely by a written program code, and then the difference between them was measured from the calibrated scanning stage. The difference was estimated to be in the range of 198 ± 2 μm.

Keywords: optical metrology, digital holography, interferometry, phase unwrapping

Procedia PDF Downloads 73

Authors: Hossein Rassi, Marjan Moradi Fard, Masoud Houshmand

Abstract:

Background: Cervical cancer is multistep disease that is thought to result from an interaction between genetic background and environmental factors. Human papillomavirus (HPV) infection is the leading risk factor for cervical intraepithelial neoplasia (CIN) and cervical cancer. In other hand, some of p53 and miRNA polymorphism may plays an important role in carcinogenesis. This study attempts to clarify the relation of p53 genotypes and miR-146a rs2910164 polymorphism in cervical lesions. Method: Forty two archival samples with cervical lesion retired from Khatam hospital and 40 sample from healthy persons used as control group. A simple and rapid method was used to detect the simultaneous amplification of the HPV consensus L1 region and HPV-16,-18, -11, -31, 33 and -35 along with the b-globin gene as an internal control. We use Multiplex PCR for detection of P53 and miR-146a rs2910164 genotypes in our lab. Finally, data analysis was performed using the 7 version of the Epi Info(TM) 2012 software and test chi-square(x2) for trend. Results: Cervix lesions were collected from 42 patients with Squamous metaplasia, cervical intraepithelial neoplasia, and cervical carcinoma. Successful DNA extraction was assessed by PCR amplification of b-actin gene (99bp). According to the results, p53 GG genotype and miR-146a rs2910164 CC genotype was significantly associated with increased risk of cervical lesions in the study population. In this study, we detected 13 HPV 18 from 42 cervical cancer. Conclusion: The connection between several SNP polymorphism and human virus papilloma in rare researches were seen. The reason of these differences in researches' findings can result in different kinds of races and geographic situations and also differences in life grooves in every region. The present study provided preliminary evidence that a p53 GG genotype and miR-146a rs2910164 CC genotype may effect cervical cancer risk in the study population, interacting synergistically with HPV 18 genotype. Our results demonstrate that the testing of p53 codon 72 polymorphism genotypes and miR-146a rs2910164 polymorphism genotypes in combination with HPV18 can serve as major risk factors in the early identification of cervical cancers. Furthermore, the results indicate the possibility of primary prevention of cervical cancer by vaccination against HPV18 in Iran.

Keywords: cervical cancer, HPV18, p53 codon 72 polymorphism, miR-146a rs2910164 polymorphism

Procedia PDF Downloads 457

Authors: Raj Banerjee, Aniruddha Sengupta

Abstract:

An earthquake event, associated with a typical fault rupture, initiates at the source, propagates through a rock or soil medium and finally daylights at a surface which might be a populous city. The detrimental effects of an earthquake are often quantified in terms of the responses of superstructures resting on the soil. Hence, there is a need for the estimation of amplification of the bedrock motions due to the influence of local site conditions. In the present study, field borehole log data of Mangalwadi and Walkeswar sites in Mumbai city are considered. The data consists of variation of SPT N-value with the depth of soil. A correlation between shear wave velocity (Vₛ) and SPT N value for various soil profiles of Mumbai city has been developed using various existing correlations which is used further for site response analysis. MATLAB program is developed for studying the ground response analysis by performing two dimensional linear and equivalent linear analysis for some of the typical Mumbai soil sites using pure shear (Multi Point Constraint) boundary condition. The model is validated in linear elastic and equivalent linear domain using the popular commercial program, DEEPSOIL. Three actual earthquake motions are selected based on their frequency contents and durations and scaled to a PGA of 0.16g for the present ground response analyses. The results are presented in terms of peak acceleration time history with depth, peak shear strain time history with depth, Fourier amplitude versus frequency, response spectrum at the surface etc. The peak ground acceleration amplification factors are found to be about 2.374, 3.239 and 2.4245 for Mangalwadi site and 3.42, 3.39, 3.83 for Walkeswar site using 1979 Imperial Valley Earthquake, 1989 Loma Gilroy Earthquake and 1987 Whitter Narrows Earthquake, respectively. In the absence of any site-specific response spectrum for the chosen sites in Mumbai, the generated spectrum at the surface may be utilized for the design of any superstructure at these locations.

Keywords: deepsoil, ground response analysis, multi point constraint, response spectrum

Procedia PDF Downloads 180

Authors: Zh. M. Blednova, P. O. Rusinov

Abstract:

Results of research on the formation of the surface layers of a material with shape memory effect (SME) based on TiNi diffusion metallization in molten Pb-Bi under isothermal conditions in an argon atmosphere are presented. It is shown that this method allows obtaining of uniform surface layers in nanostructured state of internal surfaces on the articles of complex shapes with stress concentrators. Structure, chemical and phase composition of the surface layers provide a manifestation of TiNi shape memory. The average grain size of TiNi coatings ranges between 60 ÷ 160 nm.

Keywords: diffusion metallization, nikelid titanium surface layers, shape memory effect, nanostructures

Procedia PDF Downloads 324