Search results for: Computational Fluid Dynamics

Authors: Jin A Ryu, Hee Sun Kim

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As the number of fire accidents is gradually raising, many studies have been reported on evacuation. Previous studies have mostly focused on evaluating the safety of evacuation and the risk of fire in particular buildings. However, studies on effects of various parameters on evacuation have not been nearly done. Therefore, this paper aims at observing evacuation time under the effect of fire initiated location. In this study, evacuation simulations are performed on a 5-floor building located in Seoul, South Korea using the commercial program, Fire Dynamics Simulator with Evacuation (FDS+EVAC). Only the fourth and fifth floors are modeled with an assumption that fire starts in a room located on the fourth floor. The parameter for evacuation simulations is location of fire initiation to observe the evacuation time and safety. Results show that the location of fire initiation is closer to exit, the more time is taken to evacuate. The case having the nearest location of fire initiation to exit has the lowest ratio of successful occupants to the total occupants. In addition, for safety evaluation, the evacuation time calculated from computer simulation model is compared with the tolerable evacuation time according to code in Japan. As a result, all cases are completed within the tolerable evacuation time. This study allows predicting evacuation time under various conditions of fire and can be used to evaluate evacuation appropriateness and fire safety of building.

Keywords: fire simulation, evacuation simulation, temperature, evacuation safety

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Authors: Maria Ahmadnezhad, Seyedgharani Ghoreishi ‎

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Electrohydraulic servo system have been used in industry in a wide ‎number of applications. Its ‎dynamics are highly nonlinear and also ‎have large extent of model uncertainties and external ‎disturbances. ‎In this thesis, a robust back-stepping control (RBSC) scheme is ‎proposed to overcome ‎the problem of disturbances and system ‎uncertainties effectively and to improve the set-point ‎performance ‎of EHS systems. In order to implement the proposed control ‎scheme, the system ‎uncertainties in EHS systems are considered as ‎total leakage coefficient and effective oil volume. In ‎addition, in ‎order to obtain the virtual controls for stabilizing system, the ‎update rule for the ‎system uncertainty term is induced by the ‎Lyapunov control function (LCF). To verify the ‎performance and ‎robustness of the proposed control system, computer simulation of ‎the ‎proposed control system using Matlab/Simulink Software is ‎executed. From the computer ‎simulation, it was found that the ‎RBSC system produces the desired set-point performance and ‎has ‎robustness to the disturbances and system uncertainties of ‎EHS systems.‎

Keywords: electro hydraulic servo system, back-stepping control, robust back-‎stepping control, Lyapunov redesign‎

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Authors: I. V. Kuzminov

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The research is dedicated to the issue of Bosporus evolution and its key role in the Black Sea forming. Up till nowadays, there is no distinct picture of the historical and geographical events of the last 10 thousand years on the territory from Altai up to the Alps. The present article is an attempt to clarify and, moreover, link the presented version to the historical and climatic events of this period. The paper is a development of the basic idea stated in "Hypothesis on the Black Sea origin". The succession of events in dynamics is offered in this article. In the article, it is shown that fluctuation of the level of the World Ocean is a mirror of the basic events connected with the climate on the Earth on the one hand and hydraulic processes on the other hand. In the present article, it is come out with the assumption that at the formation of passage, there were some cycles of change in a level of the World ocean. The phase of the beginning of climate warming is characterized by an increase in the level of inland water bodies on the way of meltwater runoff and an increase in the World ocean level. The end of the warming phase is characterized by the continuation of a rise in the level of the World ocean and the drying up of inland water bodies deprived of meltwater replenishment.

Keywords: Bosporus, Ryan-Pitman hypothesis, fluctuations of the World Ocean level, the Paratethys Sea, catastrophic breakthrough

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Authors: Fan Gao, Lior Pachter

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The primary tool currently used to pre-process 10X Chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices, and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.

Keywords: single-cell, ATAC-seq, bioinformatics, open chromatin landscape, chromatin interactome

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Authors: H. Bensouilah, H. Boucherit, M. Lahmar

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A theoretical investigation on the effects of both steady-state and dynamic deformations of the foils on the dynamic performance characteristics of a self-acting air foil journal bearing operating under small harmonic vibrations is proposed. To take into account the dynamic deformations of foils, the perturbation method is used for determining the gas-film stiffness and damping coefficients for given values of excitation frequency, compressibility number, and compliance factor of the bump foil. The nonlinear stationary Reynolds’ equation is solved by means of the Galerkins’ finite element formulation while the finite differences method are used to solve the first order complex dynamic equations resulting from the perturbation of the nonlinear transient compressible Reynolds’ equation. The stiffness of a bump is uniformly distributed throughout the bearing surface (generation I bearing). It was found that the dynamic properties of the compliant finite length journal bearing are significantly affected by the compliance of foils especially when the dynamic deformation of foils is considered in addition to the static one by applying the principle of superposition.

Keywords: elasto-aerodynamic lubrication, air foil bearing, steady-state deformation, dynamic deformation, stiffness and damping coefficients, perturbation method, fluid-structure interaction, Galerk infinite element method, finite difference method

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Authors: M. Moody, R. Mahmoodi, A. R. Zolfaghari, A. Aminottojari

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In this study, flow inside the shell side of a shell-and-tube heat exchanger is simulated numerically for laminar and turbulent flows in both steady state and transient mode. Governing equations of fluid flow are discrete using finite volume method and central difference scheme and solved with simple algorithm which is staggered grid by using MATLAB programming language. The heat transfer coefficient is obtained using velocity field from equation Dittus-Bolter. In comparison with, heat exchanger is simulated with ANSYS CFX software and experimental data measured in the THTL test loop. Numerical results obtained from the study show good agreement with experimental data and ANSYS CFX results. In addition, by deliberation the effect of the baffle spacing and the baffle cut on the heat transfer rate for turbulent flow, it is illustrated that the heat transfer rate depends on the baffle spacing and the baffle cut directly. In other word in spied of large turbulence, if these two parameters are not selected properly in the heat exchanger, the heat transfer rate can reduce.

Keywords: shell-and-tube heat exchanger, flow and heat transfer, laminar and turbulence flow, turbulence model, baffle spacing, baffle cut

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Authors: Asma Hanif, A. I. K. Butt, Shabir Ahmad, Rahim Ud Din, Mustafa Inc

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This paper is devoted to a study of the fuzzy fractional mathematical model reviewing the transmission dynamics of the infectious disease Covid-19. The proposed dynamical model consists of susceptible, exposed, symptomatic, asymptomatic, quarantine, hospitalized and recovered compartments. In this study, we deal with the fuzzy fractional model defined in Caputo’s sense. We show the positivity of state variables that all the state variables that represent different compartments of the model are positive. Using Gronwall inequality, we show that the solution of the model is bounded. Using the notion of the next-generation matrix, we find the basic reproduction number of the model. We demonstrate the local and global stability of the equilibrium point by using the concept of Castillo-Chavez and Lyapunov theory with the Lasalle invariant principle, respectively. We present the results that reveal the existence and uniqueness of the solution of the considered model through the fixed point theorem of Schauder and Banach. Using the fuzzy hybrid Laplace method, we acquire the approximate solution of the proposed model. The results are graphically presented via MATLAB-17.

Keywords: Caputo fractional derivative, existence and uniqueness, gronwall inequality, Lyapunov theory

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Authors: Susmita Panda, Arnab Banerjee, Ajinkya Baxy, Bappaditya Manna

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The design of short to medium-span high-speed bridges in critical locations is an essential aspect of vehicle-bridge interaction. Due to dynamic interaction between moving load and bridge, mathematical models or finite element modeling computations become time-consuming. Thus, to reduce the computational effort, a universal approximator using an artificial neural network (ANN) has been used to evaluate the dynamic response of the bridge. The data set generation and training of surrogate models have been conducted over the results obtained from mathematical modeling. Further, the robustness of the surrogate model has been investigated, which showed an error percentage of less than 10% with conventional methods. Additionally, the dependency of the dynamic response of the bridge on various load and bridge parameters has been highlighted through a parametric study.

Keywords: artificial neural network, mode superposition method, moving load analysis, surrogate models

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Authors: Paulo Mendonca, Nzar Faiq Naqeshbandi

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The objective of this study is to propose an interactive design environment that outlines the underlying computational framework to reach self-supporting overhangs. The research demonstrates the digital printability of overhangs taking into consideration factors related to the geometry design, the material used, the applied support, and the printing set-up of slicing and the extruder inclination. Parametric design tools can contribute to the design phase, form-finding, and stability optimization of self-supporting structures while printing in order to hold the components in place until they are sufficiently advanced to support themselves. The challenge is to ensure the stability of the printed parts in the critical inclinations during the whole fabrication process. Facilitating the identification of parameterization will allow to predict and optimize the process. Later, in the light of the previous findings, some guidelines of simulations and physical tests are given to be conducted for estimating the structural and functional performance.

Keywords: additive manufacturing, overhangs, self-support overhangs, printability, parametric tools

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Authors: Barzin Rajabloo, Martin Desilets

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First, an electrochemical model for the reduction of CO₂ into CH₃OH is developed in which mass and charge transfer, reactions at the surface of the electrodes and fluid flow of the electrolyte are considered. This mathematical model is developed in COMSOL Multiphysics® where both secondary and tertiary current distribution interfaces are coupled to consider concentrations and potentials inside different parts of the cell. Constant reaction rates are assumed as the fitted parameters to minimize the error between experimental data and modeling results. The model is validated through a comparison with experimental data in terms of faradaic efficiency for production of CH₃OH, the current density in different applied cathode potentials as well as current density in different electrolyte flow rates. The comparison between model outputs and experimental measurements shows a good agreement. The model indicates the higher hydrogen evolution in comparison with CH₃OH production as well as mass transfer limitation caused by CO₂ concentration, which are consistent with findings in the literature. After validating the model, in the second part of the study, some design parameters of the cell, such as cathode geometry and catholyte/anolyte channel widths, are modified to reach better performance and higher faradaic efficiency of methanol production.

Keywords: carbon dioxide, electrochemical reduction, methanol, modeling

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Authors: Boudemagh Naime

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Automatic radar detection requires some methods of adapting to variations in the background clutter in order to control their false alarm rate. The problem becomes more complicated in non-Gaussian environment. In fact, the conventional approach in real time applications requires a complex statistical modeling and much computational operations. To overcome these constraints, we propose another approach based on artificial neural network (ANN-CMLD-CFAR) using a Back Propagation (BP) training algorithm. The considered environment follows a log-normal distribution in the presence of multiple Rayleigh-targets. To evaluate the performances of the considered detector, several situations, such as scale parameter and the number of interferes targets, have been investigated. The simulation results show that the ANN-CMLD-CFAR processor outperforms the conventional statistical one.

Keywords: radat detection, ANN-CMLD-CFAR, log-normal clutter, statistical modelling

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Authors: Nur Rokhman

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A mathematical function gives relationship between the variables composing the function. Interpolation can be viewed as a process of finding mathematical function which goes through some specified points. There are many interpolation methods, namely: Lagrange method, Newton method, Spline method etc. For some specific condition, such as, big amount of interpolation points, the interpolation function can not be written explicitly. This such function consist of computational steps. The solution of equations involving the interpolation function is a problem of solution of non linear equation. Newton method will not work on the interpolation function, for the derivative of the interpolation function cannot be written explicitly. This paper shows the use of Secton method to determine the numerical solution of the function involving the interpolation function. The experiment shows the fact that Secton method works better than Newton method in finding the root of Lagrange interpolation function.

Keywords: Secton method, interpolation, non linear function, numerical solution

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Authors: Shirley Lamptey, Lingling Li, Junhong Xie

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Agriculture in the semi-arid is often challenged by overuse of N, inadequate soil water, and heavy carbon emissions thereby threatening sustainability. Field experiments were conducted to investigate the effect of nitrogen fertilization levels (0-N₀, 100-N₁₀₀, 200-N₂₀₀, and 300 kg ha⁻¹-N₃₀₀) on soil water dynamics, soil respiration (Rs), net ecosystem production (NEP), and biomass yield. Zero nitrogen soils decreased Rs by 23% and 16% compared to N₃₀₀ and N₂₀₀ soils, respectively. However, biomass yield was greatest under N₃₀₀ compared with N₀, which therefore translated into increased net primary production (NPP) by 89% and NEP by 101% compared to N₀. To a lesser extent, N₂₀₀ increased net primary production by 69% and net ecosystem production by 79% compared to N₀. Grain yields were greatest under N₃₀₀ compared with N₁₀₀ and N₀, which therefore translated into increased carbon emission efficiency (CEE) by 53%, 39% and 3% under N₃₀₀ compared to N₀, N₁₀₀, and N₂₀₀ treatments respectively. Under the conditions of this study, crop yield and CEE may be optimized at nitrogen application rates in the range of 200-300 kg ha⁻¹. Based on these results, there appears potential for 200 kg N ha⁻¹ to be used to improve yield and increase CEE in the context of the rainfall-limiting environment.

Keywords: carbon emission, carbon emission efficiency, C sequestration, N rates, semi-arid

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Authors: Yetunde I. Bulu, Moses B. Adewole, Julius O. Faluyi

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This study investigates the effect of aggressive application of herbicide on weed succession in an urban environment in Ile-Ife, Osun State. An inspection of the communities was carried out to identify sites maintained by herbicides (test plots) and those without herbicide history (control plots). Four different experimental plots located at Olasode, Eleweran, Ife City and Parakin within Ile-Ife town were monitored during the study. Comprehensive enumeration and identification of plant populations to species level was carried out on each of the plots and at every visit to determine the direction of succession. Index of similarities was used to determine the relationship in plant species composition between plots treated with herbicide and the untreated plots. The trend of increasing plant species was observed in all the study plots. Low Similarity Index between the treated plots and the control vegetation was observed at all visitations. Low similarity was also observed between the above-ground vegetation and the seed bank in all the plots. The study concluded that the weed population observed from the experimental plots showed an increase in species richness and diversity when the plots were left to recover compared to the control plots.

Keywords: herbicide, index of similarity, population, soil seed bank, succession

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Authors: Abhishek Kumar, Nilam

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As we know that, time delay exists almost in every biological phenomenon. Therefore, in the present study, we propose a susceptible–infected–recovered (SIR) epidemic model along with time delay, modulated incidence rate of infection, and Holling Type II nonlinear treatment rate. The present model aims to provide a strategy to control the spread of epidemics. In the mathematical study of the model, it has been shown that the model has two equilibriums which are named as disease-free equilibrium (DFE) and endemic equilibrium (EE). Further, stability analysis of the model is discussed. To prove the stability of the model at DFE, we derived basic reproduction number, denoted by (R₀). With the help of basic reproduction number (R₀), we showed that the model is locally asymptotically stable at DFE when the basic reproduction number (R₀) less than unity and unstable when the basic reproduction number (R₀) is greater than unity. Furthermore, stability analysis of the model at endemic equilibrium has also been discussed. Finally, numerical simulations have been done using MATLAB 2012b to exemplify the theoretical results.

Keywords: time delayed SIR epidemic model, modulated incidence rate, Holling type II nonlinear treatment rate, stability

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Authors: Duc Dong Do, Ngoc Ha Tran, Thanh Hai Dang, Cao Cuong Dang, Xuan Huan Hoang

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Global aligning two protein-protein interaction networks is an essentially important task in bioinformatics/computational biology field of study. It is a challenging and widely studied research topic in recent years. Accurately aligned networks allow us to identify functional modules of proteins and/ororthologous proteins from which unknown functions of a protein can be inferred. We here introduce a novel efficient heuristic global network alignment algorithm called FASTAn, including two phases: the first to construct an initial alignment and the second to improve such alignment by exerting a local optimization repeated procedure. The experimental results demonstrated that FASTAn outperformed the state-of-the-art global network alignment algorithm namely SPINAL in terms of both commonly used objective scores and the run-time.

Keywords: FASTAn, Heuristic algorithm, biological network alignment, protein-protein interaction networks

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Authors: Hae-Yeoun Lee

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Quantification of cardiac function is performed by calculating blood volume and ejection fraction in routine clinical practice. However, these works have been performed by manual contouring,which requires computational costs and varies on the observer. In this paper, an automatic left ventricle segmentation algorithm on cardiac magnetic resonance images (MRI) is presented. Using knowledge on cardiac MRI, a K-mean clustering technique is applied to segment blood region on a coil-sensitivity corrected image. Then, a graph searching technique is used to correct segmentation errors from coil distortion and noises. Finally, blood volume and ejection fraction are calculated. Using cardiac MRI from 15 subjects, the presented algorithm is tested and compared with manual contouring by experts to show outstanding performance.

Keywords: cardiac MRI, graph searching, left ventricle segmentation, K-means clustering

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Authors: Muhammad Noor Ul Ane, Dong-Soon Kim, Myron P. Zalucki

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Models can be useful to help understand population dynamics of insects under diverse environmental conditions and in developing strategies to manage pest species better. Adult longevity and fecundity of Helicoverpa armigera (Hübner) were evaluated against a wide range of constant temperatures (15, 20, 25, 30, 35 and 37.5ᵒC). The modified Sharpe and DeMichele model described adult aging rate and was used to estimate adult physiological age. Maximum fecundity of H. armigera was 973 egg/female at 25ᵒC decreasing to 72 eggs/female at 37.5ᵒC. The relationship between adult fecundity and temperature was well described by an extreme value function. Age-specific cumulative oviposition rate and age-specific survival rate were well described by a two-parameter Weibull function and sigmoid function, respectively. An oviposition model was developed using three temperature-dependent components: total fecundity, age-specific oviposition rate, and age-specific survival rate. The oviposition model was validated against independent field data and described the field occurrence pattern of egg population of H. armigera very well. Our model should be a useful component for population modeling of H. armigera and can be independently used for the timing of sprays in management programs of this key pest species.

Keywords: cotton bollworm, life table, temperature-dependent adult development, temperature-dependent fecundity

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Authors: Arif İsmailov, Naila Hasanova, Gunay Orujalieva

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Homocysteine (HCY) is an indicator of prognostic value in monitoring regenerative processes in osteoporosis and osteoporotic fractures. The osteoporosis is known to be a serious health and economic problem, especially for women in the postmenopausal period. The study was carried out on patients 45-83 years old divided into 3 groups: group I – 14 patients with osteoporosis , group II – 15 patients with non-osteoporotic fractures, group III – 25 patients with osteoporotic fractures. The control group consisted of practically healthy 14 people. A blood sample was taken at 3 stages to monitor the dynamics of HCY level: on the 1st day before treatment, on the 10th day of treatment and 1 month after it. Blood levels of Hcy were determined at a wavelength of 450 nm by the ELİSA(Cloud Clone Corp.Elisa kits,USA). The statistical evaluation was performed by using SPSS 26.0 program (IBM SPSS Inc., USA).The results showed that on the 1st day before the treatment HCY concentration was statistically increased 2.7 times(PU = 0.108) in group I, 5.6 times (PU <0.001) in group II and 6.5 times (PU <0.001) in group III compared to the control group. Thus, the average value of HCY in group I was 1.76 ± 0.56 μg/ml; in group II – 3.57 ± 0.62 μg/ml; in group III – 4.2 ± 0.50 μg/ml. HCY level increases more sharply after fractures,especially in osteoporotic patients. In treatment period Vitamin D plays an important role in synthesis of the Cystathionine β‐synthase enzyme, which regulates HCY metabolism. Increased Hcy levels could lead to an increase in the risk of fracture through the interference in collagen cross-linking.

Keywords: homocysteine, osteoporosis, osteoporotic fractures, Vitamin D

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Authors: Pawel Twardowski, Tadeusz Chwalczuk, Szymon Wojciechowski

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Inconel 718 is a material characterized by the unique mechanical properties, high temperature strength, high thermal conductivity and the corrosion resistance. However, these features affect the low machinability of this material, which is usually manifested by the intense tool wear and low surface finish. Therefore, this paper is focused on the evaluation of surface roughness during hybrid machining of Inconel 718. The primary aim of the study was to determine the relations between the vibrations generated during hybrid turning and the formed surface roughness. Moreover, the comparison of tested machining techniques in terms of vibrations, tool wear and surface roughness has been made. The conducted tests included the face turning of Inconel 718 with laser assistance in the range of variable cutting speeds. The surface roughness was inspected with the application of stylus profile meter and accelerations of vibrations were measured with the use of three-component piezoelectric accelerometer. The carried out research shows that application of laser assisted machining can contribute to the reduction of surface roughness and cutting vibrations, in comparison to conventional turning. Moreover, the obtained results enable the selection of effective cutting speed allowing the improvement of surface finish and cutting dynamics.

Keywords: hybrid machining, nickel alloys, surface roughness, turning, vibrations

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Authors: Sachin Saxena, Manju Srivastava

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The present study describes a stable, highly sensitive and selective analytical sensor. Fe-BTC was synthesized at room temperature using the noble Iron-trimesate system. The high surface area of as synthesized Fe-BTC proved MOFs as ideal modifiers for glassy carbon electrode. The characterization techniques such as TGA, XRD, FT-IR, BET (BET surface area= 1125 m2/gm) analysis explained the electrocatalytic behaviour of Fe-BTC towards these two drugs. The material formed is cost effective and exhibit higher catalytic behaviour towards analyte systems. The synergism between synthesized Fe-BTC and electroanalytical techniques helped in developing a highly sensitive analytical method for studying the redox fate of ARP and RZ, respectively. Cyclic voltammetry of ferricyanide system proved Fe-BTC/GCE with an increase in 132% enhancement in peak current value as compared to that of GCE. The response characteristics of cyclic voltammetry (CV) and square wave voltammetry (SWV) revealed that the ARP and RZ could be effectively accumulated at Fe-BTC/GCE. On the basis of the electrochemical measurements, electrode dynamics parameters have been evaluated. Present study opens up new field of applications of MOFs modified GCE for drug sensing.

Keywords: MOFs, anti-psychotic, electrochemical sensor, anti-migraine drugs

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Authors: Lya Porto, Giulia Giacchè, Mario Aquino Alves

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The paper aims to describe the linkage between government and civil society proposing a study on agro-ecological agriculture policy and urban action in São Paulo city underling the main achievements obtained. The negotiation processes between social movements and the government (inputs) and its results on political regulation and public action for Urban Agriculture (UA) in São Paulo city (outputs) have been investigated. The method adopted is qualitative, with techniques of semi-structured interviews, participant observation, and documental analysis. The authors conducted 30 semi-structured interviews with organic farmers, activists, governmental and non-governmental managers. Participant observation was conducted in public gardens, urban farms, public audiences, democratic councils, and social movements meetings. Finally, public plans and laws were also analyzed. São Paulo city with around 12 million inhabitants spread out in a 1522 km2 is the economic capital of Brazil, marked by spatial and socioeconomic segregation, currently aggravated by environmental crisis, characterized by water scarcity, pollution, and climate changes. In recent years, Urban Agriculture (UA) social movements gained strength and struggle for a different city with more green areas, organic food production, and public occupation. As the dynamics of UA occurs by the action of multiple actresses and institutions that struggle to build multiple senses on UA, the analysis will be based on literature about solidarity economy, governance, public action and networks. Those theories will mark out the analysis that will emphasize the approach of inter-subjectivity built between subjects, as well as the hybrid dynamics of multiple actors and spaces in the construction of policies for UA. Concerning UA we identified four main typologies based on land ownership, main function (economic or activist), form of organization of the space, and type of production (organic or not). The City Hall registers 500 productive unities of agriculture, with around 1500 producers, but researcher estimated a larger number of unities. Concerning the social movements we identified three categories that differ in goals and types of organization, but all of them work by networks of activists and/or organizations. The first category does not consider themselves as a movement, but a network. They occupy public spaces to grow organic food and to propose another type of social relations in the city. This action is similar to what became known as the green guerrillas. The second is configured as a movement that is structured to raise awareness about agro-ecological activities. The third one is a network of social movements, farmers, organizations and politicians that work focused on pressure and negotiation with executive and legislative government to approve regulations and policies on organic and agro-ecological Urban Agriculture. We conclude by highlighting how the interaction among institutions and civil society produced important achievements for recognition and implementation of UA within the city. Some results of this process are awareness for local production, legal and institutional recognition of the rural zone around the city into the planning tool, the investment on organic school public procurements, the establishment of participatory management of public squares, the inclusion of UA on Municipal Strategic Plan and Master Plan.

Keywords: public action, policies, agroecology, urban and peri-urban agriculture, Sao Paulo

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Authors: S. A. Che Osmi, W. M. F. Wan Ishak, H. Kim, M. A. Azman, M. A. Ramli

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River is one of important water sources for many activities including industrial and domestic usage such as daily usage, transportation, power supply and recreational activities. However, increasing activities in a river has grown the sources of pollutant enters the water bodies, and degraded the water quality of the river. It becomes a challenge to develop an effective river management to ensure the water sources of the river are well managed and regulated. In Malaysia, several approaches for river management have been implemented such as Integrated River Basin Management (IRBM) program for coordinating the management of resources in a natural environment based on river basin to ensure their sustainability lead by Department of Drainage and Irrigation (DID), Malaysia. Nowadays, Total Maximum Daily Load (TMDL) is one of the best approaches for river management in Malaysia. TMDL implementation is regulated and implemented in the United States. A study on the development of TMDL in Malacca River has been carried out by doing water quality monitoring, the development of water quality model by using Environmental Fluid Dynamic Codes (EFDC), and TMDL implementation plan. The implementation of TMDL will help the stakeholders and regulators to control and improve the water quality of the river. It is one of the good approaches for river management in Malaysia.

Keywords: EFDC, river management, TMDL, water quality modelling

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Authors: Sirilak Kongkaew, Pathumwadee Yodmanee, Nopporn Kaiyawet, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Toshikatsu Kaburaki, Hiroshi Noguchi, Fujio Takeuch, Nawee Kungwan, Supot Hannongbua

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Behçet’s disease (BD) is a genetic autoimmune expressed by multisystemic inflammatory disorder mostly occurred at the skin, joints, gastrointestinal tract, and genitalia, including ocular, oral, genital, and central nervous systems. Most BD patients in Japan and Korea were strongly indicated by the genetic factor namely HLA-B*51 (especially, HLA-B*51:01) marker in HMC class I, while HLA-A*26:01 allele has been detected from the BD patients in Greek, Japan, and Taiwan. To understand the selective binding of the MICA-TM peptide towards the HLAs associated with BD, the molecular dynamics simulations were applied on the four HLA alleles (B*51:01, B*35:01, A*26:01, and A*11:01) in complex with such peptide. As a result, the key residues in the binding groove of HLA protein which play an important role in the MICA-TM peptide binding and stabilization were revealed. The Van der Waals force was found to be the main protein-protein interaction. Based on the binding free energy prediction by MM/PBSA method, the MICA-TM peptide interacted stronger to the HLA alleles associated to BD in the identical class by 7-12 kcal/mol. The obtained results from the present study could help to differentiate the HLA alleles and explain a source of Behçet’s disease.

Keywords: Behçet’s disease, MD simulations, HMC class I, autoimmune

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Authors: Ch. Surawut, D. Sukawat

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In order to utilize results from global climate models, dynamical and statistical downscaling techniques have been developed. For dynamical downscaling, usually a limited area numerical model is used, with associated high computational cost. This research proposes dynamic equation for specific space-time regional climate downscaling from the Educational Global Climate Model (EdGCM) for Southeast Asia. The equation is for surface air temperature. These equations provide downscaling values of surface air temperature at any specific location and time without running a regional climate model. In the proposed equations, surface air temperature is approximated from ground temperature, sensible heat flux and 2m wind speed. Results from the application of the equation show that the errors from the proposed equations are less than the errors for direct interpolation from EdGCM.

Keywords: dynamic equation, downscaling, inverse distance, weight interpolation

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Authors: Tai Nguyen, Minh Bui, Huong Ninh, Tu Nguyen, Hai Tran

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GraphCut algorithm has been widely utilized to solve various types of computer vision problems. Its expensive computational cost encouraged many researchers to improve the speed of the algorithm. Recent works proposed schemes that work on parallel computing platforms such as CUDA. However, the problem of low convergence speed prevents the usage of GraphCut for real time applications. In this paper, we propose global suppression heuristic to boost the conver-gence process of the algorithm. A parallel implementation of GraphCut algorithm on CUDA designed for the image stitching problem is introduced. Our method achieves up to 3× time boost on the graph of size 80 × 480 compared to the best sequential GraphCut algorithm while achieving satisfactory stitched images, suitable for panorama applications. Our source code will be soon available for further research.

Keywords: CUDA, graph cut, image stitching, texture synthesis, maxflow/mincut algorithm

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Authors: Almudena Espin Perez, Tyler Risom, Carl Pelz, Isabel English, Robert M. Angelo, Rosalie Sears, Andrew J. Gentles

Abstract:

Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly malignancies. The role of the tumor microenvironment (TME) is gaining significant attention in cancer research. Despite ongoing efforts, the nature of the interactions between tumors, immune cells, and stromal cells remains poorly understood. The cell-intrinsic properties that govern cell lineage plasticity in PDAC and extrinsic influences of immune populations require technically challenging approaches due to the inherently heterogeneous nature of PDAC. Understanding the cell lineage plasticity of PDAC will improve the development of novel strategies that could be translated to the clinic. Members of the team have demonstrated that the acquisition of ductal to neuroendocrine lineage plasticity in PDAC confers therapeutic resistance and is a biomarker of poor outcomes in patients. Our approach combines computational methods for deconvolving bulk transcriptomic cancer data using CIBERSORTx and high-throughput single-cell imaging using Multiplexed Ion Beam Imaging (MIBI) to study lineage plasticity in PDAC and its relationship to the infiltrating immune system. The CIBERSORTx algorithm uses signature matrices from immune cells and stroma from sorted and single-cell data in order to 1) infer the fractions of different immune cell types and stromal cells in bulked gene expression data and 2) impute a representative transcriptome profile for each cell type. We studied a unique set of 300 genomically well-characterized primary PDAC samples with rich clinical annotation. We deconvolved the PDAC transcriptome profiles using CIBERSORTx, leveraging publicly available single-cell RNA-seq data from normal pancreatic tissue and PDAC to estimate cell type proportions in PDAC, and digitally reconstruct cell-specific transcriptional profiles from our study dataset. We built signature matrices and optimized by simulations and comparison to ground truth data. We identified cell-type-specific transcriptional programs that contribute to cancer cell lineage plasticity, especially in the ductal compartment. We also studied cell differentiation hierarchies using CytoTRACE and predict cell lineage trajectories for acinar and ductal cells that we believe are pinpointing relevant information on PDAC progression. Collaborators (Angelo lab, Stanford University) has led the development of the Multiplexed Ion Beam Imaging (MIBI) platform for spatial proteomics. We will use in the very near future MIBI from tissue microarray of 40 PDAC samples to understand the spatial relationship between cancer cell lineage plasticity and stromal cells focused on infiltrating immune cells, using the relevant markers of PDAC plasticity identified from the RNA-seq analysis.

Keywords: deconvolution, imaging, microenvironment, PDAC

Procedia PDF Downloads 108

Authors: Sanele Lionel Khanyile, Emmanuel Nahayo

Abstract:

Geomagnetic jerks are jumps observed in the second derivative of the main magnetic field that occurs on annual to decadal timescales. Understanding these jerks is crucial as they provide valuable insights into the complex dynamics of the Earth’s outer liquid core. In this study, we investigate the occurrence of geomagnetic jerks in geomagnetic observatory data collected at southern African magnetic observatories, Hermanus (HER), Tsumeb (TSU), Hartebeesthoek (HBK) and Keetmanshoop (KMH) between 2017 and 2023. The observatory data was processed and analyzed by retaining quiet night-time data recorded during quiet geomagnetic activities with the help of Kp, Dst, and ring current RC indices. Results confirm the occurrence of the 2019-2020 geomagnetic jerk in the region and identify the recent 2021 jerk detected with V-shaped secular variation changes in X and Z components at all four observatories. The highest estimated 2021 jerk secular acceleration amplitudes in X and Z components were found at HBK, 12.7 nT/year² and 19. 1 nT/year², respectively. Notably, the global CHAOS-7 model aptly identifies this 2021 jerk in the Z component at all magnetic observatories in the region.

Keywords: geomagnetic jerks, secular variation, magnetic observatory data, South Atlantic Anomaly

Procedia PDF Downloads 46

Authors: Sung Duk Kim, Kwan U. Kim, Jin Sim, Ryong Jin Jang

Abstract:

The phenomenon of seasonal variations in the Earth’s rotation velocity was discovered in the 1930s when a crystal clock was developed and analyzed in a quantitative way for the first time between 1955 and 1968 when observation data of the seasonal variations was analyzed by an atomic clock. According to the previous investigation, atmospheric circulation is supposed to be a factor affecting the seasonal variations in the Earth’s rotation velocity in many cases, but the problem has not been solved yet. In order to solve the problem, it is necessary to apply dynamics to consider the Earth’s spatial motion, rotation, and change of shape of the Earth (movement of materials in and out of the Earth and change of the Earth’s figure) at the same time and in interrelation to the accuracy of post-Newtonian approximation regarding the Earth body as a system of mass points because the stability of the Earth’s rotation angular velocity is in the range of 10⁻⁸~10⁻⁹. For it, the equation was derived, which can consider the 3 kinds of motion above mentioned at the same time by taking the effect of the resultant external force on the Earth’s rotation into account in a relativistic way to the accuracy of post-Newtonian approximation. Therefore, the equation has been solved to obtain the theoretical values of periodic change in the Earth’s rotation velocity, and they have been compared with the astronomical observation data so to reveal the cause for the periodic change in the Earth’s rotation velocity.

Keywords: Earth rotation, moment function, periodic change, seasonal variation, relativistic change

Procedia PDF Downloads 38

Authors: Niya Chen, Jennifer Chan

Abstract:

In the financial market, risk management helps to minimize potential loss and maximize profit. There are two ways to assess risks; the first way is to calculate the risk directly based on the volatility. The most common risk measurements are Value at Risk (VaR), sharp ratio, and beta. Alternatively, we could look at the quantile of the return to assess the risk. Popular return models such as GARCH and stochastic volatility (SV) focus on modeling the mean of the return distribution via capturing the volatility dynamics; however, the quantile/expectile method will give us an idea of the distribution with the extreme return value. It will allow us to forecast VaR using return which is direct information. The advantage of using these non-parametric methods is that it is not bounded by the distribution assumptions from the parametric method. But the difference between them is that expectile uses a second-order loss function while quantile regression uses a first-order loss function. We consider several quantile functions, different volatility measures, and estimates from some volatility models. To estimate the expectile of the model, we use Realized Conditional Autoregressive Expectile (CARE) model with the bayesian method to achieve this. We would like to see if our proposed models outperform existing models in cryptocurrency, and we will test it by using Bitcoin mainly as well as Ethereum.

Keywords: expectile, CARE Model, CARR Model, quantile, cryptocurrency, Value at Risk

Procedia PDF Downloads 96