Search results for: gene transfer

Authors: Pooja Sharma

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In the present paper the effects of radiation is studied on unsteady flow of viscous incompressible electrically conducting fluid past a vertical porous plate embedded in the porous medium in the presence of constant heat flux. A uniform Transverse Magnetic field is considered and induced magnetic field is supposed as negligible. The non-linear governing equations are solved numerically. Numerical results of the velocity and temperature fields are shown through graphs. The results illustrates that the appropriator combination of regulated values of thermo-physical parameters is expedient for controlling the flow system.

Keywords: heat transfer, radiation, MHD flow, porous medium

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Authors: Rakesh Kumar Mishra, Tarun Kumar Dan

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Lead-Lag based Internal Model Control method is proposed based on Internal Model Control (IMC) strategy. In this paper, we have designed the Lead-Lag based Internal Model Control for binary distillation column for SISO process (considering only bottom product). The transfer function has been taken from Wood and Berry model. We have find the composition control and disturbance rejection using Lead-Lag based IMC and comparing with the response of simple Internal Model Controller.

Keywords: SISO, lead-lag, internal model control, wood and berry, distillation column

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Authors: Sheng-Hui Lan, Shan-Ying Wu, Shu-Ching Lin, Wei-Chen Wang, Hsiao-Sheng Liu

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Autophagy is an essential mechanism to maintain cellular homeostasis through its degradation function, and the autophagy deficiency is related various diseases including tumorigenesis in several cancers. MicroRNAs (miRNAs) are small none coding RNAs, which regulate gene expression through degradation of mRNA or inhibition of translation. However, the relationship between autophagy deficiency and dysregulated miRNAs is still unclear. We revealed a mechanism that autophagy up-regulates miR-449a expression at the transcriptional level through activation of forkhead transcription factor family member FoxO1 and then suppresses tumorigenesis in CRC. Our data showed that the autophagic activity and miR-449a expression were lower in colorectal cancer (CRC) and has a positive correlation. We further reveal that autophagy degrades p300 expression and then suppresses acetylation of FoxO1. Under autophagic induction conditions, FoxO1 is transported from the cytoplasm to the nucleus and binds to the miR-449a promoter and then promotes miR-449a expression. In addition, either miR-449a overexpression or amiodarone-induced autophagy inhibits cell cycle progression, proliferation, colony formation migration, invasion, and tumor formation of SW480 cells. Our findings indicate that autophagy inducers may have the potential to be used for prevention and treatment of CRC through upregulation of miR-449a expression.

Keywords: autophagy, MiR-449a, FoxO1, colorectal cancer

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Authors: Olivia Rybak-Karkosz

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The purpose of this paper is to present the result of scientific research using forensic handwriting analysis. It was conducted to verify the stability and lability of handwriting of engravers and check if gravers transfer their traits from handwriting to plates and other surfaces they rework. This research methodology consisted of completing representative samples of signatures of gravers written on a piece of paper using a ballpen and signatures engraved on other surfaces. The forensic handwriting analysis was conducted using the graphic-comparative method (graphic method), and all traits were analysed. The paper contains a concluding statement of the similarities and differences between the samples.

Keywords: artist’s signatures, engraving, forensic handwriting analysis, graphic-comparative method

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Authors: Ilknur Tuncer, Nihayet Bizsel

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The scarcity of research in bacterial diversity and antimicrobial resistance in coastal environments as in Turkish coasts leads to difficulties in developing efficient monitoring and management programs. In the present study, biogeochemical analysis of sediments and antimicrobial susceptibility analysis of bacteria in Izmir Bay, eastern Aegean Sea under high anthropogenic pressure were aimed in summer period when anthropogenic input was maximum and at intertidal zone where the first terrigenious contact occurred for aquatic environment. Geochemical content of the intertidal zone of Izmir Bay was firstly illustrated such that total and organic carbon, nitrogen and phosphorus contents were high and the grain size distribution varied as sand and gravel. Bacterial diversity and antibiotic resistance were also firstly given for Izmir Bay. Antimicrobially assayed isolates underlined the multiple resistance in the inner, middle and outer bays with overall 19% high MAR (multiple antibiotic resistance) index. Phylogenetic analysis of 16S rRNA gene sequences indicated that 67 % of isolates belonged to the genus Bacillus and the rest included the families Alteromonadaceae, Bacillaceae, Exiguobacteriaceae, Halomonadaceae, Planococcaceae, and Staphylococcaceae.

Keywords: bacterial phylogeny, multiple antibiotic resistance, 16S rRNA genes, Izmir Bay, Aegean Sea

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Authors: Naso Isaiah Thanavisuth, Patompong Satapornpong

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Introduction: Covid-19 has been a global pandemic for some time now, causing severe symptoms to patients that received the virus. However, there has been no report on this gene in the Thai population. Objective: Our aim in this study is to explore and compare the frequency of HLA-C allele that is associated with severe COVID-19 symptoms in Thais and other populations. Method: 200 general Thai population were enrolled in this study. The genotyping of HLA -C alleles were determined by the polymerase chain reaction with sequence-specific oligonucleotide probes (PCR-SSOP) and Luminex®IS 100 system (Luminex Corporation, Austin, Texas, USA). Results: We found that the frequency of alleles HLA-C* 01:02 (16.00%), HLA-C* 08:01(10.50%), HLA-C* 03:04 (10.25%),HLA-C* 07:02 (10.00%), HLA-C* 03:02 (9.25%), HLA-C* 07:01 (6.75%), HLA-C* 04:01 (5.00%), HLA-C* 06:02 (4.00%), HLA-C* 04:03 (4.00%), and HLA-C* 07:04 (3.75%) were more common in the Thai population. HLA-C* 01:02 (16.00%) allele was the highest frequency in the North, Center, and North East groups in Thailand, but there was the South region that was not significantly different when compared with the other groups of the region. Additionally, HLA-C∗14:02 allele was similarly distributed in Thais (3.00%), African Americans (1.98%), Caucasians (2.08%), Hispanics (1.71%), North American Natives (1.34%) and Asians (5.01%) by p-value = 0.6506, 0.6506, 0.6506, 0.6135 and 0.7182, respectively. Conclusion: Genetic variation database is important to identify HLA can be a risk factor for severe COVID-19 in many populations. In this study, we will support the research of the HLA markers for screening severe COVID-19 in many populations.

Keywords: HLA-C * 14:02, COVID-19, allele frequency, Thailand

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Authors: Ali Oztuna, Meral Sarper, Deniz Torun, Fatma Bayrakdar, Selcuk Kilic, Mehmet Baysallar

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Bacillus anthracis is one of the biological agents most likely to be used in case of bioterrorist attack as well as being the cause of anthrax. The bacterium's major virulence factors are the anthrax toxins and an antiphagocytic polyglutamic capsule. TEM8 (ANTXR1) and CMG2 (ANTXR2) are ubiquitously expressed type I transmembrane proteins, and ANTXR2 is the major receptor for anthrax toxins. MicroRNAs are 21-24 bp small noncoding RNAs that regulate gene expression by base pairing with the 3' UTR (untranslated regions) of their target mRNAs resulting in mRNA degradation and/or translational repression. MicroRNAs contribute to regulation of most biological processes and influence numerous pathological states like infectious disease. In this study, post-exposure (toxins) protective effect of the hsa-miR-124-3p against Bacillus anthracis was examined. In this context, i) THP-1 and U937 cells were differentiated to MΦ macrophage, ii) miRNA transfection efficiencies were evaluated by flow cytometry and qPCR, iii) protection against Bacillus anthracis toxins were investigated by XTT, cAMP ELISA and MEK2 cleavage assays. Acknowledgements: This work was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) under Grant SBAG-218S467.

Keywords: ANTXR2, hsa-miR-124-3p, MΦ macrophage, THP-1, U937

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Authors: Boukhatem Mohamed Belkaid, Lahdi Mourad

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In this paper, we propose a new encryption system for security issues medical images. The hybrid encryption scheme is based on AES and RSA algorithms to validate the three security services are authentication, integrity, and confidentiality. Privacy is ensured by AES, authenticity is ensured by the RSA algorithm. Integrity is assured by the basic function of the correlation between adjacent pixels. Our system generates a unique password every new session of encryption, that will be used to encrypt each frame of the medical image basis to strengthen and ensure his safety. Several metrics have been used for various tests of our analysis. For the integrity test, we noticed the efficiencies of our system and how the imprint cryptographic changes at reception if a change affects the image in the transmission channel.

Keywords: AES, RSA, integrity, confidentiality, authentication, medical images, encryption, decryption, key, correlation

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Authors: Mojtaba Hakimi-Moghaddam

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Positive realness as the most important property of driving point impedance of passive electrical networks appears in the control systems stability theory in 1960’s. There are three important subsets of positive real (PR) systems are introduced by researchers, that is, loos-less positive real (LLPR) systems, weakly strictly positive real (WSPR) systems and strictly positive real (SPR) systems. In this paper, definitions, properties, lemmas, and theorems related to family of positive real systems are summarized. Properties in both frequency domain and state space representation of system are explained. Also, several illustrative examples are presented.

Keywords: real rational matrix transfer functions, positive realness property, strictly positive realness property, Hermitian form asymptotic property, pole-zero properties

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Authors: Leila Graini

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In this paper, we demonstrate basic all-optical functions for 2R regeneration (Re-amplification and Re-shaping) based on self-similar spectral broadening in low normal dispersion and highly nonlinear fiber (ND-HNLF) to regenerate the signal through optical filtering including the transfer function characteristics, and output extinction ratio. Our approach of all-optical 2R regeneration is based on those of Mamyshev. The numerical study reveals the self-similar spectral broadening very effective for 2R all-optical regeneration; the proposed design presents high stability compared to a conventional regenerator using SPM broadening with reduction of the intensity fluctuations and improvement of the extinction ratio.

Keywords: all-optical function, 2R optical regeneration, self-similar broadening, Mamyshev regenerator

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Authors: Seyed M. Zahrai, Saeid Lotfi

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If an infill panel does not have enough ductility against the loading, it breaks and gets damaged before depreciation and load transfer. As steel infill panel has appropriate ductility before fracture, it can be used as an alternative to typical infill panels under blast loading. Concerning enough ductility of out-of-plane behavior the infill panel, the impact force enters the horizontal diaphragm and is distributed among the lateral elements which can be made from steel infill panels. This article investigates the behavior of steel infill panels with different thickness and stiffeners using finite element analysis with geometric and material nonlinearities for optimization of the steel plate thickness and stiffeners arrangement to obtain more efficient design for its out-of-plane behavior.

Keywords: blast loading, ductility, maximum displacement, steel infill panel

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Authors: Xiran Wang, Johanna Trinkl, Thomas Hoffmann, Wilfried Schwab

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Malonyltransferases (MATs) are enzymes that play a key role in the biosynthesis of secondary metabolites in plants, such as flavonoids and anthocyanins. As a kind of flavonoid-rich fruit, strawberries are an ideal model to study MATs. From Goodberry metabolome data, in the hybrid generation of 2 strawberries various, Fragaria × ananassa cv. 'Senga Sengana' and 'Candonga', we found the malonylated flavonoid concentration is significantly higher in 'Senga Sengana' compared with 'Candonga'. Therefore, we aimed to identify and characterize the malonyltransferases responsible for the different malonylated flavonoid concentrations in two different strawberry cultivars. In this study, we have found 6 MATs via genome mapping, metabolome analysis, gene cloning, and enzyme assay from strawberries, which catalyzed the malonylation of flavonoid substrates: quercetin-3-glucoside, kaempferol-3-glucoside, pelargonidin-3-glucoside, and cyanidin-3-glucoside. All four compounds reacted with FaMATs to varying degrees. These MATs have important implication into strawberries’ flavonoid biosynthesis, and also provide insights into insights into flavonoid biosynthesis, potential applications in agriculture, plant science, and pharmacy, and information on the regulation of secondary metabolism in plants.

Keywords: malonyltransferase, strawberry, flavonoid biosynthesis, enzyme assay

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Authors: Sanghoon Park, Ki-Jin Kim, Kwang-Ho Ahn

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This paper discusses the undesirable charge transfer by the parasitic capacitances of the input transistors in a voltage sense amplifier. Due to its intrinsic rail-to-rail voltage transition, the input sides are inevitably disturbed. It can possible disturb the stabilities of the reference voltage levels. Moreover, it becomes serious in multi-channel systems by altering them for other channels, and so degrades the linearity of the systems. In order to alleviate the internal node voltage transition, the internal node stabilization technique is proposed by utilizing an additional biasing circuit. It achieves 47% and 43% improvements for node stabilization and input referred disturbance, respectively.

Keywords: voltage sense amplifier, voltage transition, node stabilization, biasing circuits

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Authors: Geoffrey A. Wright

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In an attempt to address shortcomings revealed in international assessments and lamented in legislation, many schools are reducing or eliminating elective courses, applying the rationale that replacing "non-essential" subjects with core subjects, such as mathematics and language arts, will better position students in the global market. However, there is evidence that systematically pairing a core subject with another complementary subject may lead to greater overall learning in both subjects. In this paper, we outline the methods and preliminary findings from a study we conducted analyzing the influence learning programming has on student mathematical comprehension and ability. The purpose of this research is to demonstrate in what ways two subjects might complement each other, and to better understand the principles and conditions that encourage what we call lateral transfer, the synergistic effect that occurs when a learner studies two complementary subjects.

Keywords: programming, engineering, technology, complementary subjects

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Authors: S. Ghammamy, M. Mirzaabdollahiha

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Quantum mechanical calculations of energies, geometries, and vibrational wavenumbers of fluorous 1,3-dion compounds are carried out using density functional theory (DFT/B3LYP) method with LANL2DZ basis sets. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecules. The thermodynamic functions of fluorous 1,3-dion compounds have been performed at B3LYP/LANL2DZ basis sets. The theoretical spectrograms for F NMR spectra of fluorous 1,3-dion compounds have also been constructed. The F NMR nuclear shieldings of fluoride ligands in fluorous 1,3-dion compounds have been studied quantum chemical.

Keywords: density function theory, natural bond orbital, HOMO, LOMO, fluorous

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Authors: Weiwei Shan, Wenjing Ding, Juan Ning, Chao He, Zijuan Wang

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Gravity circulation loop for the cryopumps of the space simulator is introduced, and two phase mathematic model of flow heat transfer is analyzed as well. Based on this model, the liquid nitrogen (LN₂) gravity circulation loop including its equipment and layout is designed and has served as LN₂ feeding system for cryopumps in one large space simulator. With the help of control software and human machine interface, this system can be operated flexibly, simply, and automatically under four conditions. When running this system, the results show that the cryopumps can be cooled down and maintained under the required temperature, 120 K.

Keywords: cryopumps, gravity circulation loop, liquid nitrogen, two-phase

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Authors: Guoyu Wang, Meilian Zhang, Chunhui LI, Bing Ren

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In recent decades, a variety of floating structures have played a crucial role in ocean and marine engineering, such as ships, offshore platforms, floating breakwaters, fish farms, floating airports, etc. It is common for floating structures to suffer from loadings under waves, and the responses of the structures mounted in marine environments have a significant relation to the wave impacts. The interaction between surface waves and floating structures is one of the important issues in ship or marine structure design to increase performance and efficiency. With the progress of computational fluid dynamics, a number of numerical models based on the NS equations in the time domain have been developed to explore the above problem, such as the finite difference method or the finite volume method. Those traditional numerical simulation techniques for moving bodies are grid-based, which may encounter some difficulties when treating a large free surface deformation and a moving boundary. In these models, the moving structures in a Lagrangian formulation need to be appropriately described in grids, and the special treatment of the moving boundary is inevitable. Nevertheless, in the mesh-based models, the movement of the grid near the structure or the communication between the moving Lagrangian structure and Eulerian meshes will increase the algorithm complexity. Fortunately, these challenges can be avoided by the meshless particle methods. In the present study, a moving particle semi-implicit model is explored for the numerical simulation of fluid–structure interaction with surface flows, especially for coupling of fluid and moving rigid body. The equivalent momentum transfer method is proposed and derived for the coupling of fluid and rigid moving body. The structure is discretized into a group of solid particles, which are assumed as fluid particles involved in solving the NS equation altogether with the surrounding fluid particles. The momentum conservation is ensured by the transfer from those fluid particles to the corresponding solid particles. Then, the position of the solid particles is updated to keep the initial shape of the structure. Using the proposed method, the motions of a free-floating body in regular waves are numerically studied. The wave surface evaluation and the dynamic response of the floating body are presented. There is good agreement when the numerical results, such as the sway, heave, and roll of the floating body, are compared with the experimental and other numerical data. It is demonstrated that the presented MPS model is effective for the numerical simulation of fluid-structure interaction.

Keywords: floating body, fluid structure interaction, MPS, particle method, waves

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Authors: Asma'u Mahe, Abdullahi A. Imam, Adamu J. Alhassan, Nasiru Abdullahi, Sadiya A. Bichi, Nura Lawal, Kamaluddeen Babagana

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Malaria is a disease with global health significance. It is caused by parasites and transmitted by Anopheles mosquitoes. Increase in insecticide resistance threatens the disease vector control. The strength of selection pressure acting on a mosquito population in relation to insecticide resistance can be assess by determining the genetic diversity of a fragment spanning exon- 20 of IIS6 of the voltage gated sodium channel (VGSC). Larval samples reared to adulthood were identified and kdr (knock down resistance) profile was determined. The DNA sequences were used to assess the patterns of genetic differentiation by determining the levels of genetic variability between the Anopheles mosquitoes. Genetic differentiation of the Anopheles mosquitoes based on a portion of the voltage gated sodium channel gene was obtained. Polymorphisms were detected; sequence variation and analysis were presented as a phylogenetic tree. Phylogenetic tree of VGSC haplotypes was constructed for samples of the Anopheles mosquitoes using the maximum likelihood method in MEGA 6.0 software. DNA sequences were edited using BioEdit sequence editor. The edited sequences were aligned with reference sequence (Kisumu strain). Analyses were performed as contained in dnaSP 5.10. Results of genetic parameters of polymorphism and haplotype reconstruction were presented in count. Twenty sequences were used for the analysis. Regions selected were 1- 576, invariable (monomorphic) sites were 460 while variable (polymorphic) sites were 5 giving the number of total mutations observed in this study. Mutations obtained from the study were at codon 105: TTC- Phenylalanine replaces TCC- Serine, codon 513: TAG- Termination replaces TTG- Leucine, codon 153, 300 and 553 mutations were non-synonymous. From the constructed phylogenetic tree, some groups were shown to be closer with Exon20Gambiae Kisumu (Reference strain) having some genetic distance, while 5-Exon20Gambiae-F I13.ab1, 18-Exon20Gambiae-F C17.ab1, and 2-Exon20Gambiae-F C13.ab1 clustered together genetically differentiated away from others. Mutations observed in this study can be attributed to the high insecticide resistance profile recorded in the study areas. Haplotype networks of pattern of genetic variability and polymorphism for the fragment of the VGSC sequences of sampled Anopheles mosquitoes revealed low haplotypes for the present study. Haplotypes are set of closely linked DNA variation on X-chromosome. Haplotypes were scaled accordingly to reflect their respective frequencies. Low haplotype number, four VGSC-1014F haplotypes were observed in this study. A positive association was previously established between low haplotype number of VGSC diversity and pyrethroid resistance through kdr mechanism. Significant values at (P < 0.05) of Tajima D and Fu and Li D’ were observed for some of the results indicating possible signature of positive selection on the fragment of VGSC in the study. This is the first report of VGSC-1014F in the study site. Based on the results, the mutation was present in low frequencies. However, the roles played by the observed mutations need further investigation. Mutations, environmental factors among others can affect genetic diversity. The study area has recorded increase in insecticide resistance that can affect vector control in the area. This finding might affect the efforts made against malaria. Sequences were deposited in GenBank for Accession Number.

Keywords: anopheles mosquitoes, insecticide resistance, kdr, malaria, voltage gated sodium channel

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Authors: G. Petruzzelli, F. Pedron, M. Grifoni, A. Pera, I. Rosellini, B. Pezzarossa

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The addition of lime as Ca(OH)2 to sewage sludge to destroy pathogens (Escherichia coli), was evaluated also in relation to heavy metal bioavailability. The obtained results show that the use of calcium hydroxide at the dose of 3% effectively destroyed pathogens ensuring the stability at high pH values over long period and the duration of the sewage sludge stabilization. In general, lime addition decreased the total extractability of heavy metals indicating a reduced bioavailability of these elements. This is particularly important for a safe utilization in agricultural soils to reduce the possible transfer of heavy metals to the food chain.

Keywords: biological sludge, Ca(OH)2, copper, pathogens, sanitation, zinc

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Authors: Artem Sedov, Aigerim Uyzbayeva, Valeriya Tyo

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The presented article is showing results of dynamic modeling with Mathlab software of optimal automatic room climate control system for two experimental houses in Astana, one of which has circle plan and the other one has square plan. These results are showing that building geometry doesn't influence on climate system PID-controls configuring. This confirms theoretical implication that optimal automatic climate control system parameters configuring should depend on building's internal space volume, envelope heat transfer, number of people inside, supply ventilation air flow and outdoor temperature.

Keywords: climate control system, climate physics, dome-like building, mathematical modeling

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Authors: Maryam Vaezjalali, Koroush Rahimian, Maryam Asli, Tahmineh Kandelouei, Foad Davoodbeglou, Amir H. Kashi

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Objectives: The present study was conducted to assess the HBV molecular profiles including genotypes, subgenotypes, subtypes & mutations in hepatitis B genes. Materials/Patients and Methods: This study was conducted on 229 intravenous drug users who referred to three Drop- in-Centers and a hospital in Tehran. HBV DNA was extracted from HBsAg positive serum samples and amplified by Nested PCR. HBV genotype, subgenotypes, subtype and genes mutation were determined by direct sequencing. Phylogenetic tree was constructed using neighbor- joining (NJ) method. Statistical analyses were carried out by SPSS 20. Results: HBV DNA was found in 3 HBsAg positive cases. Phylogenetic tree of derived HBV DNAs showed the existence of genotype D (subgenotype D1, subtype ayw2). Also immune escape mutations were determined in S gene. Conclusion: There were a few variations and genotypes and subtypes among infected intravenous drug users. This study showed the predominance of genotype D among intravenous drug users. Our study concurs with other reports from Iran, that all showing currently only genotype D is the only detectable genotype in Iran.

Keywords: drug users, genotype, HBV, phylogenetic tree

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Authors: Raj Nandkeolyar, Precious Sibanda

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The flow of a viscous, incompressible, and electrically conducting fluid under the influence of aligned magnetic field acting along the direction of fluid flow over an exponentially stretching sheet is investigated numerically. The nonlinear partial differential equations governing the flow model is transformed to a set of nonlinear ordinary differential equations using suitable similarity transformation and the solution is obtained using a local linearization method followed by the Chebyshev spectral collocation method. The effects of various parameters affecting the flow and heat transfer as well as the induced magnetic field are discussed using suitable graphs and tables.

Keywords: aligned magnetic field, exponentially stretching sheet, induced magnetic field, magnetohydrodynamic flow

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Authors: J. Mohammadpour, G. E. Lau, S. Cheng, A. Lee

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Numerical study was conducted using two synthetic jet actuators attached underneath a micro-channel. By fixing the oscillating frequency and diaphragm amplitude, the effects on the heat transfer within the micro-channel were investigated with two synthetic jets being in-phase and 180° out-of-phase at different orifice spacing. There was a significant benefit identified with two jets being 180° out-of-phase with each other at the orifice spacing of 2 mm. By having this configuration, there was a distinct pattern of vortex forming which disrupts the main channel flow as well as promoting thermal mixing at high velocity within the channel. Therefore, this configuration achieved higher cooling performance compared to the other cases studied in terms of the reduction in the maximum temperature and cooling uniformity in the silicon wafer.

Keywords: synthetic jets, microchannel, electronic cooling, computational fluid dynamics

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Authors: Patsarawadee Paojinda, Waranya Imprasittichai, Sudaratana R. Krungkrai, Nirianne Marie Q. Palacpac, Toshihiro Horii, Jerapan Krungkrai

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Fusion of the last two enzymes in the pyrimidine biosynthetic pathway in the inversed order by having COOH-terminal orotate phosphoribosyltransferase (OPRT) and NH2-terminal orotidine 5'-monophosphate decarboxylase (OMPDC), as OMPDC-OPRT, are described in many organisms. Here, we produced gene fusions of Plasmodium falciparum OMPDC-OPRT and expressed the bifunctional protein in Escherichia coli. The enzyme was purified to homogeneity using affinity and anion-exchange chromatography, exhibited enzymatic activities and functioned as a dimer. The activities, although unstable, can be stabilized by its substrate and product during purification and long-term storage. Furthermore, the enzyme expressed a perfect catalytic efficiency (kcat/Km). The kcat was selectively enhanced up to 3 orders of magnitude, while the Km was not much affected and remained at low µM levels when compared to the monofunctional enzymes. The fusion of the two enzymes, creating a “super-enzyme” with perfect catalytic power and more flexibility, reflects cryptic relationship of enzymatic reactivaties and metabolic functions on molecular evolution.

Keywords: bifunctional enzyme, orotate phosphoribosyltransferase, orotidine 5'-monophosphate decarboxylase, plasmodium falciparum

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Authors: Eugene Stepanov, Arkadi Ponossov

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Ordinary differential equations with switching nonlinearities constitute a very useful tool in many applications. The solutions of such equations can usually be calculated analytically if they cross the discontinuities transversally. Otherwise, one has trajectories that slides along the discontinuity, and the calculations become less straightforward in this case. For instance, one of the problems one faces is non-uniqueness of the sliding modes. In the presentation, it is proposed to apply the theory of hybrid dynamical systems to calculate the solutions that are ‘hidden’ in the discontinuities. Roughly, one equips the underlying switched system with an explicitly designed discrete dynamical system (‘automaton’), which governs the dynamics of the switched system. This construction ‘splits’ the dynamics, which, as it is shown in the presentation, gives uniqueness of the resulting hybrid trajectories and at the same time provides explicit formulae for them. Projecting the hybrid trajectories back onto the original continuous system explains non-uniqueness of its trajectories. The automaton is designed with the help of the attractors of the specially constructed adjoint dynamical system. Several examples are provided in the presentation, which supports the efficiency of the suggested scheme. The method can be of interest in control theory, gene regulatory networks, neural field models and other fields, where switched dynamics is a part of the analysis.

Keywords: hybrid dynamical systems, singular perturbation analysis, sliding modes, switched dynamics

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Authors: Ping-Ben Liu, Chien-Chou Tseng

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The objective of this study is to investigate the relationship between the lift coefficient and dynamic behaviors of cavitating flow around a two-dimensional Clark Y hydrofoil at 8° angle of attack, cavitation number of 0.8, and Reynolds number of 7.10⁵. The flow field is investigated numerically by using a vapor transfer equation and a modified turbulence model which applies the filter and local density correction. The results including time-averaged lift/drag coefficient and shedding frequency agree well with experimental observations, which confirmed the reliability of this simulation. According to the variation of lift coefficient, the cycle which consists of growth and shedding of cavitation can be divided into three stages, and the lift coefficient at each stage behaves similarly due to the formation and shedding of the cavity around the trailing edge.

Keywords: Computational Fluid Dynamics, cavitation, turbulence, lift coefficient

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Authors: Hugo Badia

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This research answers which is the most suitable transit network structure to serve specific demand requirements in an increasing urban dispersion process. Two main approaches of network design are found in the literature. On the one hand, a traditional answer, widespread in our cities, that develops a high number of lines to connect most of origin-destination pairs by direct trips; an approach based on the idea that users averse to transfers. On the other hand, some authors advocate an alternative design characterized by simple networks where transfer is essential to complete most of trips. To answer which of them is the best option, we use a two-step methodology. First, by means of an analytical model, three basic network structures are compared: a radial scheme, starting point for the other two structures, a direct trip-based network, and a transfer-based one, which represent the two alternative transit network designs. The model optimizes the network configuration with regard to the total cost for each structure. For a scenario of dispersion, the best alternative is the structure with the minimum cost. This dispersion degree is defined in a simple way considering that only a central area attracts all trips. If this area is small, we have a high concentrated mobility pattern; if this area is too large, the city is highly decentralized. In this first step, we can determine the area of applicability for each structure in function to that urban dispersion degree. The analytical results show that a radial structure is suitable when the demand is so centralized, however, when this demand starts to scatter, new transit lines should be implemented to avoid transfers. If the urban dispersion advances, the introduction of more lines is no longer a good alternative, in this case, the best solution is a change of structure, from direct trips to a network based on transfers. The area of applicability of each network strategy is not constant, it depends on the characteristics of demand, city and transport technology. In the second step, we translate analytical results to a real case study by the relationship between the parameters of dispersion of the model and direct measures of dispersion in a real city. Two dimensions of the urban sprawl process are considered: concentration, defined by Gini coefficient, and centralization by area based centralization index. Once it is estimated the real dispersion degree, we are able to identify in which area of applicability the city is located. In summary, from a strategic point of view, we can obtain with this methodology which is the best network design approach for a city, comparing the theoretical results with the real dispersion degree.

Keywords: analytical network design model, network structure, public transport, urban dispersion

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Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

Abstract:

The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

Procedia PDF Downloads 196

Authors: Y. Ruchi, A. Prerna, S. Deepshikha

Abstract:

Amyotrophic lateral sclerosis (ALS), also known as “Lou Gehrig’s disease”. It is a neurodegenerative disease associated with degeneration of motor neurons in the cerebral cortex, brain stem, and spinal cord characterized by distal muscle weakness, atrophy, normal sensation, pyramidal signs and progressive muscular paralysis reflecting. ALS2 is a juvenile autosomal recessive disorder, slowly progressive, that maps to chromosome 2q33 and is associated with mutations in the alsin gene, a putative GTPase regulator. In this paper we have done homology modeling of alsin2 protein using multiple templates (3KCI_A, 4LIM_A, 402W_A, 4D9S_A, and 4DNV_A) designed using the Prime program in Schrödinger software. Further modeled structure is used to identify effective binding sites on the basis of structural and physical properties using sitemap program in Schrödinger software, structural and function analysis is done by using Prosite and ExPASy server that gives insight into conserved domains and motifs that can be used for protein classification. This paper summarizes the structural, functional and binding site property of alsin2 protein. These binding sites can be potential drug target sites and can be used for docking studies.

Keywords: ALS, binding site, homology modeling, neuronal degeneration

Procedia PDF Downloads 391

Authors: A. Kazemi Jouybari, A. Mirabdolah Lavasani

Abstract:

This paper seeks to the solution of condensation around of a flat plate, circular and elliptical tube in way of numerical and analytical methods. Also, it calculates the entropy production rates. The first, problem was solved by using mesh dynamic and rational assumptions, next it was compared with the numerical solution that the result had acceptable errors. An additional supporting relation was applied based on a characteristic of condensation phenomenon for condensing elements. As it has been shown here, due to higher rates of heat transfer for elliptical tubes, they have more entropy production rates, in comparison to circular ones. Findings showed that two methods were efficient. Furthermore, analytical methods can be used to optimize the problem and reduce the entropy production rate.

Keywords: condensation, numerical solution, analytical solution, entropy rate

Procedia PDF Downloads 219