Search results for: dynamical localization

Authors: Ananya Ananya, Karthik Rao

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Accurate segmentation of knee cartilage in 3-D magnetic resonance (MR) images for quantitative assessment of volume is crucial for studying and diagnosing osteoarthritis (OA) of the knee, one of the major causes of disability in elderly people. Radiologists generally perform this task in slice-by-slice manner taking 15-20 minutes per 3D image, and lead to high inter and intra observer variability. Hence automatic methods for knee cartilage segmentation are desirable and are an active field of research. This paper presents design and experimental evaluation of 2D convolutional neural networks based fully automated methods for knee cartilage segmentation in 3D MRI. The architectures are validated based on 40 test images and 60 training images from SKI10 dataset. The proposed methods segment 2D slices one by one, which are then combined to give segmentation for whole 3D images. Proposed methods are modified versions of U-net and dilated convolutions, consisting of a single step that segments the given image to 5 labels: background, femoral cartilage, tibia cartilage, femoral bone and tibia bone; cartilages being the primary components of interest. U-net consists of a contracting path and an expanding path, to capture context and localization respectively. Dilated convolutions lead to an exponential expansion of receptive field with only a linear increase in a number of parameters. A combination of modified U-net and dilated convolutions has also been explored. These architectures segment one 3D image in 8 – 10 seconds giving average volumetric Dice Score Coefficients (DSC) of 0.950 - 0.962 for femoral cartilage and 0.951 - 0.966 for tibia cartilage, reference being the manual segmentation.

Keywords: convolutional neural networks, dilated convolutions, 3 dimensional, fully automated, knee cartilage, MRI, segmentation, U-net

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Authors: F. M. Pisano, M. Ciminello

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Aerospace, mechanical, and civil engineering infrastructures can take advantages from damage detection and identification strategies in terms of maintenance cost reduction and operational life improvements, as well for safety scopes. The challenge is to detect so called “barely visible impact damage” (BVID), due to low/medium energy impacts, that can progressively compromise the structure integrity. The occurrence of any local change in material properties, that can degrade the structure performance, is to be monitored using so called Structural Health Monitoring (SHM) systems, in charge of comparing the structure states before and after damage occurs. SHM seeks for any "anomalous" response collected by means of sensor networks and then analyzed using appropriate algorithms. Independently of the specific analysis approach adopted for structural damage detection and localization, textual reports, tables and graphs describing possible outlier coordinates and damage severity are usually provided as artifacts to be elaborated for information extraction about the current health conditions of the structure under investigation. Visual Analytics can support the processing of monitored measurements offering data navigation and exploration tools leveraging the native human capabilities of understanding images faster than texts and tables. Herein, a SHM system enrichment by integration of a Visual Analytics component is investigated. Analytical dashboards have been created by combining worksheets, so that a useful Visual Analytics tool is provided to structural analysts for exploring the structure health conditions examined by a Principal Component Analysis based algorithm.

Keywords: interactive dashboards, optical fibers, structural health monitoring, visual analytics

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Authors: Chi-Ching Lee, Po-Jung Huang, Kuo-Yang Huang, Petrus Tang

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Background: Recent advances in high-throughput research technologies such as new-generation sequencing and multi-dimensional liquid chromatography makes it possible to dissect the complete transcriptome and proteome in a single run for the first time. However, it is almost impossible for many laboratories to handle and analysis these “BIG” data without the support from a bioinformatics team. We aimed to provide a web-based analysis platform for users with only limited knowledge on bio-computing to study the functional genomics and proteomics. Method: We use NCI-60 as an example dataset to demonstrate the power of the web-based analysis platform and data delivering system: C-eXpress takes a simple text file that contain the standard NCBI gene or protein ID and expression levels (rpkm or fold) as input file to generate a distribution map of gene/protein expression levels in a heatmap diagram organized by color gradients. The diagram is hyper-linked to a dynamic html table that allows the users to filter the datasets based on various gene features. A dynamic summary chart is generated automatically after each filtering process. Results: We implemented an integrated database that contain pre-defined annotations such as gene/protein properties (ID, name, length, MW, pI); pathways based on KEGG and GO biological process; subcellular localization based on GO cellular component; functional classification based on GO molecular function, kinase, peptidase and transporter. Multiple ways of sorting of column and rows is also provided for comparative analysis and visualization of multiple samples.

Keywords: cancer, visualization, database, functional annotation

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Authors: Akaash Tawade, Manan Khattar, Lucas Spangher, Costas J. Spanos

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Many grids are increasing the share of renewable energy in their generation mix, which is causing the energy generation to become less controllable. Buildings, which consume nearly 33% of all energy, are a key target for demand response: i.e., mechanisms for demand to meet supply. Understanding the behavior of office workers is a start towards developing demand response for one sector of building technology. The literature notes that dynamic computational modeling can be predictive of individual action, especially given that occupant behavior is traditionally abstracted from demand forecasting. Recent work founded on Social Cognitive Theory (SCT) has provided a promising conceptual basis for modeling behavior, personal states, and environment using control theoretic principles. Here, an adapted linear dynamical system of latent states and exogenous inputs is proposed to simulate energy demand amongst office workers engaged in a social energy shifting game. The energy shifting competition is implemented in an office in Singapore that is connected to a minigrid of buildings with a consistent 'price signal.' This signal is translated into a 'points signal' by a reinforcement learning (RL) algorithm to influence participant energy use. The dynamic model functions at the intersection of the points signals, baseline energy consumption trends, and SCT behavioral inputs to simulate future outcomes. This study endeavors to analyze how the dynamic model trains an RL agent and, subsequently, the degree of accuracy to which load deferability can be simulated. The results offer a generalizable behavioral model for energy competitions that provides the framework for further research on transfer learning for RL, and more broadly— transactive control.

Keywords: energy demand forecasting, social cognitive behavioral modeling, social game, transfer learning

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Authors: Abdelkrim Belhaoua, Jean-Pierre Radoux, Mariana Kuras, Vincent Récamier, Martial Piotto, Karim Elbayed, François Proust, Izzie Namer

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This paper proposes an augmented reality system dedicated to neurosurgery in order to assist the surgeon during an operation. This work is part of the ExtempoRMN project (Funded by Bpifrance) which aims at analyzing during a surgical operation the metabolic content of tumoral brain biopsy specimens by HRMAS NMR. Patients affected with a brain tumor (gliomas) frequently need to undergo an operation in order to remove the tumoral mass. During the operation, the neurosurgeon removes biopsy specimens using image-guided surgery. The biopsy specimens removed are then sent for HRMAS NMR analysis in order to obtain a better diagnosis and prognosis. Image-guided refers to the use of MRI images and a computer to precisely locate and target a lesion (abnormal tissue) within the brain. This is performed using preoperative MRI images and the BrainLab neuro-navigation system. With the patient MRI images loaded on the Brainlab Cranial neuro-navigation system in the operating theater, surgeons can better identify their approach before making an incision. The Brainlab neuro-navigation tool tracks in real time the position of the instruments and displays their position on the patient MRI data. The results of the biopsy analysis by 1H HRMAS NMR are then sent back to the operating theater and superimposed on the 3D localization system directly on the MRI images. The method we have developed to communicate between the HRMAS NMR analysis software and Brainlab makes use of a combination of C++, VTK and the Insight Toolkit using OpenIGTLink protocol.

Keywords: neuro-navigation, augmented reality, biopsy, BrainLab, HR-MAS NMR

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Authors: Naoki Yamamoto, Hidenobu Ozaki, Taiichiro Ookawa, Youming Liu, Kazunori Okada, Aiping Zheng

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Rice sheath blight is one of the destructive fungal diseases in rice. We have thought that rice sheath blight resistance is a polygenic trait. Host-pathogen interactions and secondary metabolites such as lignin and phytoalexins are likely to be involved in defense against R. solani. However, to our knowledge, it is still unknown how sheath blight resistance can be enhanced in rice breeding. To seek for an alternative genetic factor that contribute to sheath blight resistance, we mined relevant allelic variations from rice core collections created in Japan. Based on disease lesion length on detached leaf sheath, we selected 30 varieties of the top tail-end and the bottom tail-end, respectively, from the core collections to perform genome-wide association mapping. Re-sequencing reads for these varieties were used for calling single nucleotide polymorphisms among the 60 varieties to create a SNP panel, which contained 1,137,131 homozygous variant sites after filitering. Association mapping highlighted a locus on the long arm of chromosome 11, which is co-localized with three sheath blight QTLs, qShB11-2-TX, qShB11, and qSBR-11-2. Based on the localization of the trait-associated alleles, we identified an ankyryn repeat-containing protein gene (ANK-M) as an uncharacterized candidate factor for rice sheath blight resistance. Allelic distributions for ANK-M in the whole rice population supported the reliability of trait-allele associations. Gene expression characteristics were checked to evaluiate the functionality of ANK-M. Since an ANK-M homolog (OsPIANK1) in rice seems a basal defense regulator against rice blast and bacterial leaf blight, ANK-M may also play a role in the rice immune system.

Keywords: allele mining, GWAS, QTL, rice sheath blight

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Authors: Wiqar Hussain Shah

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The Structural, magnetic and transport behavior of La1-xCaxMnO3+ (x=0.48, 0.50, 0.52 and 0.55 and =0.015) compositions close to charge ordering, was studied through XRD, resistivity, DC magnetization and AC susceptibility measurements. With time and thermal cycling (T<300 K) there is an irreversible transformation of the low-temperature phase from a partially ferromagnetic and metallic to one that is less ferromagnetic and highly resistive. For instance, an increase of resistivity can be observed by thermal cycling, where no effect is obtained for lower Ca concentration. The time changes in the magnetization are logarithmic in general and activation energies are consistent with those expected for electron transfer between Mn ions. The data suggest that oxygen non-stoichiometry results in mechanical strains in this two-phase system, leading to the development of irreversible metastable states, which relax towards the more stable charge-ordered and antiferromagnetic microdomains at the nano-meter size. This behavior is interpreted in terms of strains induced charge localization at the interface between FM/AFM domains in the antiferromagnetic matrix. Charge, orbital ordering and phase separation play a prominent role in the appearance of such properties, since they can be modified in a spectacular manner by external factor, making the different physical properties metastable. Here we describe two factors that deeply modify those properties, viz. the doping concentration and the thermal cycling. The metastable state is recovered by the high temperature annealing. We also measure the magnetic relaxation in the metastable state and also the revival of the metastable state (in a relaxed sample) due to high temperature (800 ) thermal treatment.

Keywords: Rare-earth maganites, nano-structural materials, doping effects on electrical, magnetic properties, competing interactions

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Authors: Farzaneh Shayeganfar, Ali Ramazani

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Exciton (strong electronic interaction of electron-hole) and hot carriers created by surface plasmon polaritons has been demonstrated in nanoscale optoelectronic devices, enhancing the photoresponse of the system. Herein, we employ a quantum framework to consider coupled exciton- hot carriers effects on photovoltaiv energy distribution, scattering process, polarizability and light emission of 2D-semicnductor. We use density functional theory (DFT) to design computationally a semi-functionalized 2D honeycomb silicon boride (SiB) monolayer with H atoms, suitable for photovoltaics. The dynamical stability, electronic and optical properties of SiB and semi-hydrogenated SiB structures were investigated utilizing the Tran-Blaha modified Becke-Johnson (TB-mBJ) potential. The calculated phonon dispersion shows that while an unhydrogenated SiB monolayer is dynamically unstable, surface semi-hydrogenation improves the stability of the structure and leads to a transition from metallic to semiconducting conductivity with a direct band gap of about 1.57 eV, appropriate for photovoltaic applications. The optical conductivity of this H-SiB structure, determined using the random phase approximation (RPA), shows that light adsorption should begin at the boundary of the visible range of light. Additionally, due to hydrogenation, the reflectivity spectrum declines sharply with respect to the unhydrogenated reflectivity spectrum in the IR and visible ranges of light. The energy band gap remains direct, increasing from 0.9 to 1.8 eV, upon increasing the strain from -6% (compressive) to +6% (tensile). Additionally, compressive and tensile strains lead, respectively, to red and blue shifts of optical the conductivity threshold around the visible range of light. Overall, this study suggests that H-SiB monolayers are suitable as two-dimensional solar cell materials.

Keywords: surface plasmon, hot carrier, strain engineering, valley polariton

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Authors: Jinyoung Park, Eun Joo Song

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Introduction: Deubiquitinating enzymes (DUBs) are proteases that cleave ubiquitin or ubiquitin-like modifications on substrates. Deubiquitination could regulate cellular physiology, such as signal transduction, DNA damage and repair, and cell cycle progression. Although more than 100 DUBs are encoded in the human and the importance of DUBs has been realized, the functions of most DUBs are unknown. This study aims to identify the molecular mechanism by which deubiquitinating enzyme USP35 regulates cell cycle progression for the first time. Methods: USP35 RNAi was mainly used to identify the function of USP35 in cell cycle progression. To find substrates of USP35, we analyzed protein-protein interaction using LC-MS. Several biological methods, such as ubiquitination assay, cell synchronization, immunofluorescence, and immunoprecipitation assay were used to investigate the exact mechanism by which USP35 affects successful completion of mitosis. Results: USP35 knockdown caused not only reduction of mitotic cell number but also induction of mitotic cells with abnormal spindle formation. Actually, cell proliferation was decreased by USP35 knockdown. Interestingly, we found that loss of USP35 decreased the stability and expression of Aurora B, a member of chromosomal passenger complex (CPC), and the phosphorylation of its substrate. Indeed, USP35 interacted with Aurora B and deubiquitinated it. In addition, USP35 knockdown induced abnormal localization of Aurora B in mitotic cells. Finally, CDH1-mediated ubiquitination of Aurora B level was rescued by USP35 overexpression, but not inactive form of USP35, USP35 C450A. Discussion: Our findings suggest that USP35 regulates Aurora B-mediated mitotic spindle assembly and G2-M transition by blocking CDH1-induced degradation of Aurora B.

Keywords: USP35, HSP90, Aurora B, cell cycle progression

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Authors: G. Judakova, M. Bause

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The ability to model and simulate numerically natural gas flow in pipelines has become of high importance for the design of pipeline systems. The understanding of the formation of hydrate particles and their dynamical behavior is of particular interest, since these processes govern the operation properties of the systems and are responsible for system failures by clogging of the pipelines under certain conditions. Mathematically, natural gas flow can be described by multiphase flow models. Using the two-fluid modeling approach, the gas phase is modeled by the compressible Euler equations and the particle phase is modeled by the pressureless Euler equations. The numerical simulation of compressible multiphase flows is an important research topic. It is well known that for nonlinear fluxes, even for smooth initial data, discontinuities in the solution are likely to occur in finite time. They are called shock waves or contact discontinuities. For hyperbolic and singularly perturbed parabolic equations the standard application of the Galerkin finite element method (FEM) leads to spurious oscillations (e.g. Gibb's phenomenon). In our approach, we use stabilized FEM, the streamline upwind Petrov-Galerkin (SUPG) method, where artificial diffusion acting only in the direction of the streamlines and using a special treatment of the boundary conditions in inviscid convective terms, is added. Numerical experiments show that the numerical solution obtained and stabilized by SUPG captures discontinuities or steep gradients of the exact solution in layers. However, within this layer the approximate solution may still exhibit overshoots or undershoots. To suitably reduce these artifacts we add a discontinuity capturing or shock capturing term. The performance properties of our numerical scheme are illustrated for two-phase flow problem.

Keywords: two-phase flow, gas-particle mixture, inviscid two-fluid model, euler equation, finite element method, streamline upwind petrov-galerkin, shock capturing

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Authors: Bipin Popat Sonawane

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After 1988 Electron muon Collaboration (EMC) announcement of measurement of spin dependent structure function, it has been found that it has become a need to understand spin structure of a hadron. In the study of three-dimensional spin structure of a proton, we need to understand the foundation of quantum field theory in terms of electro-weak and strong theories using rigorous mathematical theories and models. In the process of understanding the inner dynamical stricture of proton we need understand the mathematical formalism in perturbative quantum chromodynamics (pQCD). In QCD processes like proton-proton collision at high energy we calculate cross section using conventional collinear factorization schemes. In this calculations, parton distribution functions (PDFs) and fragmentation function are used which provide the information about probability density of finding quarks and gluons ( partons) inside the proton and probability density of finding final hadronic state from initial partons. In transverse momentum dependent (TMD) PDFs and FFs, collectively called as TMDs, take an account for intrinsic transverse motion of partons. The TMD factorization in the calculation of cross sections provide a scheme of hadronic and partonic states in the given QCD process. In this study we review Transverse Momentum Dependent (TMD) factorization scheme using Collins-Soper-Sterman (CSS) Formalism. CSS formalism considers the transverse momentum dependence of the partons, in this formalism the cross section is written as a Fourier transform over a transverse position variable which has physical interpretation as impact parameter. Along with this we compare this formalism with improved CSS formalism. In this work we study the TMD evolution schemes and their comparison with other schemes. This would provide description in the process of measurement of transverse single spin asymmetry (TSSA) in hadro-production and electro-production of J/psi meson at RHIC, LHC, ILC energy scales. This would surely help us to understand J/psi production mechanism which is an appropriate test of QCD.

Keywords: QCD, PDF, TMD, CSS

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Authors: Rania Hanafi Said, Rasha Mohamed Taha

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Background: By using nanoparticles as drug delivery, it may be possible to avoid the drawbacks of systemic antibiotic dosing, including bacterial antibiotic resistance. The goal of this study was to see how well tetracycline loaded on nanochitosan worked to treat gingival inflammation in albino rats caused by Porphyromonas gingivalis. The study analyzed immunohistochemically the localization of the pro-inflammatory cytokine Interleukin-1beta (IL-1β). Material and methods: In this study, fifty mature male albino rats weighing 150 to 180 grams each were used. They were randomly divided into five groups. We checked for weight changes in rats. Ten male albino rats were included in Group I, which served as a negative control group. Ten rats were included in Group II, where they were exposed once to Porphyromonas. Group III contained ten rats, which were treated the same as Group II plus daily injections of diluted tetracycline powder at the infection sites. Ten rats in Group IV received the same procedure as those in Group II before receiving daily injections of nanochitosan at the injection sites. Finally, Group V, which had ten rats. Following the same protocol as Group II, they received localized injections of tetracycline loaded on nanochitosan once daily. Rats' gingivae were extracted and prepared after they were anesthetized. The biopsies were examined histologically and immunohistochemically by light microscopy. Results: Groups I and V had a nearly normal histological appearance of gingival tissue. In Groups II, III, and IV, degeneration was seen because the epithelial cells were bigger, collagen fibers were pulling away from the lamina propria connective tissue, and the basement membranes had come to an end. There was no discernible difference between groups V and I when they were examined immunohistochemically. Conclusion: The use of nano chitosan as a tetracycline carrier is a novel technique to overcome the drug's rising level of resistance.

Keywords: Immunohistochemistry, Nanochitosan, porphyromonas gingivitis, Tetracycline

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Authors: C. F. Alegretti, F. R. Cunha, R. G. Gontijo

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This work investigates the effects of an applied magnetic field on the geometry-driven boundary layer detachment flow of a ferrofluid over a sudden expansion. Both constitutive equation and global magnetization equation for a ferrofluid are considered. Therefore, the proposed formulation consists in a coupled magnetic-hydrodynamic problem. Computational simulations are carried out in order to explore, not only the viability to control flow instabilities, but also to evaluate the consistency of theoretical aspects. The unidirectional sudden expansion in a ferrofluid flow is investigated numerically under the perspective of Ferrohydrodynamics in a two-dimensional domain using a Finite Differences Method. The boundary layer detachment induced by the sudden expansion results in a recirculating zone, which has been extensively studied in non-magnetic hydrodynamic problems for a wide range of Reynolds numbers. Similar investigations can be found in literature regarding the sudden expansion under the magnetohydrodynamics framework, but none considering a colloidal suspension of magnetic particles out of the superparamagnetic regime. The vorticity-stream function formulation is implemented and results in a clear coupling between the flow vorticity and its magnetization field. Our simulations indicate a systematic decay on the length of the recirculation zone as increasing physical parameters of the flow, such as the intensity of the applied field and the volume fraction of particles. The results all are discussed from a physical point of view in terms of the dynamical non-dimensional parameters. We argue that the decrease/reduction in the recirculation region of the flow is a direct consequence of the magnetic torque balancing the action of the torque produced by viscous and inertial forces of the flow. For the limit of small Reynolds and magnetic Reynolds parameters, the diffusion of vorticity balances the diffusion of the magnetic torque on the flow. These mechanics control the growth of the recirculation region.

Keywords: boundary layer detachment, ferrofluid, ferrohydrodynamics, magnetization, sudden expansion

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Authors: Domenico Chizzoniti, Monica Moscatelli, Letizia Cattani, Piero Favino, Luca Preis

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A settlement strategy is to anticipate and respond the needs of existing and future communities through the provision of primary health care facilities in marginalized areas. Access to a health care network is important to improving healthcare coverage, often lacking, in developing countries. The study explores that a good sanitary system strategy of rural contexts brings advantages to an existing settlement: improving transport, communication, water and social facilities. The objective of this paper is to define a possible methodology to implement primary health care facilities in disadvantaged areas of emerging countries. In this research, we analyze the case study of Lauro de Freitas, a municipality in the Brazilian state of Bahia, part of the Metropolitan Region of Salvador, with an area of 57,662 km² and 194.641 inhabitants. The health localization system in Lauro de Freitas is an integrated process that involves not only geographical aspects, but also a set of factors: population density, epidemiological data, allocation of services, road networks, and more. Data were collected also using semi-structured interviews and questionnaires to the local population. Synthesized data suggest that moving away from the coast where there is the greatest concentration of population and services, a network of primary health care facilities is able to improve the living conditions of small-dispersed communities. Based on the health service needs of populations, we have developed a methodological approach that is particularly useful in rural and remote contexts in emerging countries.

Keywords: healthcare, settlement strategy, urban health, rural

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Authors: Gao Youtao, Zhao Tanran, Jin Bingyu, Xu Bo

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Global navigation satellite system(GNSS) can deliver navigation information for spacecraft orbiting on low-Earth orbits and medium Earth orbits. However, the GNSS cannot navigate the spacecraft on high-Earth orbit or deep space probes effectively. With the deep space exploration becoming a hot spot of aerospace, the demand for a deep space satellite navigation system is becoming increasingly prominent. Many researchers discussed the feasibility and performance of a satellite navigation system on periodic orbits around the Earth-Moon libration points which can be called Lagrangian point satellite navigation system. Autonomous orbit determination (AOD) is an important performance for the Lagrangian point satellite navigation system. With this ability, the Lagrangian point satellite navigation system can reduce the dependency on ground stations. AOD also can greatly reduce total system cost and assure mission continuity. As the elliptical restricted three-body problem can describe the Earth-Moon system more accurately than the circular restricted three-body problem, we study the autonomous orbit determination of Lagrangian navigation constellation using only crosslink range based on elliptical restricted three body problem. Extended Kalman filter is used in the autonomous orbit determination. In order to compare the autonomous orbit determination results based on elliptical restricted three-body problem to the results of autonomous orbit determination based on circular restricted three-body problem, we give the autonomous orbit determination position errors of a navigation constellation include four satellites based on the circular restricted three-body problem. The simulation result shows that the Lagrangian navigation constellation can achieve long-term precise autonomous orbit determination using only crosslink range. In addition, the type of the libration point orbit will influence the autonomous orbit determination accuracy.

Keywords: extended Kalman filter, autonomous orbit determination, quasi-periodic orbit, navigation constellation

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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Authors: Abu Afree Andalib, Rafiur Rahman, Md Mezbah Uddin

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The main objective of this work is to anatomize on the various parameters of AGM 88 missile anatomized using FSI module in Ansys. Computational fluid dynamics is used for the study of fluid flow pattern and fluidic phenomenon such as drag, pressure force, energy dissipation and shockwave distribution in water. Using finite element analysis module of Ansys, structural parameters such as stress and stress density, localization point, deflection, force propagation is determined. Separate analysis on structural parameters is done on Abacus. State of the art coupling module is used for FSI analysis. Fine mesh is considered in every case for better result during simulation according to computational machine power. The result of the above-mentioned parameters is analyzed and compared for two phases using graphical representation. The result of Ansys and Abaqus are also showed. Computational Fluid Dynamics and Finite Element analyses and subsequently the Fluid-Structure Interaction (FSI) technique is being considered. Finite volume method and finite element method are being considered for modelling fluid flow and structural parameters analysis. Feasible boundary conditions are also utilized in the research. Significant change in the interaction and interference pattern while the impact was found. Theoretically as well as according to simulation angled condition was found with higher impact.

Keywords: FSI (Fluid Surface Interaction), impact, missile, high viscous fluid, CFD (Computational Fluid Dynamics), FEM (Finite Element Analysis), FVM (Finite Volume Method), fluid flow, fluid pattern, structural analysis, AGM-88, Ansys, Abaqus, meshing, k-omega, turbulence model

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Authors: Kushal Gowda Jayaram, Joseph Huret, Jonathan Quibel, Walter-John Chitty, Gilbert Henaff

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Thermal aging is one of the concerns for the long-term operation of nuclear power plants. Indeed, components in the primary circuit undergo thermal aging while exposed to the chemically active environment of Pressurized Water Reactors (PWRs) over time. Among the materials used in the reactor components, Alloy 690 can be found in some critical components for nuclear safety. Despite its importance, research on the effect of thermal aging on the microstructural changes and low cycle fatigue (LCF) behavior of Alloy 690 remains limited. This study aims to assess the impact of thermal aging on the fatigue life of Alloy 690. The as-received sample underwent aging at 420°C for 4000 hours, representing the equivalent aging of 60 years in reactor working conditions. First, the characterization of the area and density of intergranular and intragranular precipitates was performed to understand the microstructural changes in the aged specimen. Then, low cycle fatigue tests were conducted on the as received and aged samples at varying strain amplitudes. To investigate the influence of thermal aging on the fatigue behavior of Alloy 690, fracture surfaces were analyzed to estimate fatigue crack growth rates based on striation spacing measurements. Additionally, the axially cut fractured samples have undergone analysis using Electron Backscatter Diffraction (EBSD) to understand the effect of aging on strain localization near the crack path. Results indicate that while the characterization of the area and density of intergranular precipitates in the aged specimen (for 2000 hours, approximately 30 years) showed no significant changes, there was a slight increase in the area and density of intragranular precipitates under the same conditions.

Keywords: alloy 690, thermal aging, low cycle fatigue, precipitates

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Authors: Ali Al-Ghalib, Fouad Mohammad

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The identification of damage in reinforced concrete structures subjected to incremental cracking performance exploiting vibration data is recognized as a challenging topic in the published and heavily cited literature. Therefore, this paper attempts to shine light on the extent of dynamic methods when applied to reinforced concrete beams simulated with various scenarios of defects. For this purpose, three different reinforced concrete beams are tested through the course of the study. The three beams are loaded statically to failure in incremental successive load cycles and later rehabilitated. After each static load stage, the beams are tested under free-free support condition using experimental modal analysis. The beams were all of the same length and cross-sectional area (2.0x0.14x0.09)m, but they were different in concrete compressive strength and the type of damage presented. The experimental modal parameters as damage identification parameters were showed computationally expensive, time consuming and require substantial inputs and considerable expertise. Nonetheless, they were proved plausible for the condition monitoring of the current case study as well as structural changes in the course of progressive loads. It was accentuated that a satisfactory localization and quantification for structural changes (Level 2 and Level 3 of damage identification problem) can only be achieved reasonably through considering frequencies and mode shapes of a system in a proper analytical model. A convenient post analysis process for various datasets of vibration measurements for the three beams is conducted in order to extract, check and correlate the basic modal parameters; namely, natural frequency, modal damping and mode shapes. The results of the extracted modal parameters and their combination are utilized and discussed in this research as quantification parameters.

Keywords: experimental modal analysis, damage identification, structural health monitoring, reinforced concrete beam

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Authors: Nijole Savickiene, Antonella Di Sotto, Gabriela Mazzanti, Rasa Starselskyte, Silvia Di Giacomo, Annabella Vitalone

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Plant lectins are non-enzymic and non-immune origin proteins that specifically recognize and bind to various sugar structures and possess the activity to agglutinate cells and/or precipitate polysaccharides and glycoconjugates. The emerging evidences showed that plant lectins contribute not only to tumour cell recognition but also to cell adhesion and localization, to signal transduction, to mitogenic cytotoxicity and apoptosis. Among chitin-binding lectins, the Urtica dioica agglutinin (UDA), which is a complex of different isoforms, has been poorly studied for its biological activity. In this context and according to the increasing interest for lectins as novel antitumor drugs, present paper aimed at evaluating the potential antimutagenic activity of a lectin-like glycoprotein-enriched fraction from aerial part of Urtica dioica L. Aim: to evaluate the potential chemopreventive properties of a protein - lectin fraction from the aerial part of Urtica dioica. Materials and methods: Protein – lectin fraction has been tested for the antimutagenic activity in bacteria (50–800 mg/plate; Ames test by the preincubation method) and for the cytotoxicity on human hepatoma HepG2 cells (0.06–2 mg/mL; 24 and 48 h incubation). Results: Protein – lectin fraction from stinging nettle was not cytotoxic on HepG2 cells up to 2 mg/mL; conversely, it exhibited a strong antimutagenic activity against the mutagen 2-aminoanthracene (2AA) in all strains tested (maximum inhibition of 56.78 and 61% in TA98, TA100, and WP2uvrA strains, respectively, at 800 mg/plate). Discussion and conclusions: Protein – lectin fraction from Urtica dioica L. possesses antimutagenic and radical scavenging properties. Being 2AA a pro-carcinogenic agent, we hypothesize that the antimutagenicity of it can be due to the inhibition of CYP450-isoenzymes, involved in the mutagen bioactivation.

Keywords: lectins, antimutagenicity, chemoprevention, Urtica dioica

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Authors: Amrashaa Singh

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In the digital age and the large cyberspace, Data Protection and Privacy have become major issues in this technological era. There was a time when social media and online shopping websites were treated as a blessing for the people. But now the tables have turned, and the people have started to look at them with suspicion. They are getting aware of the privacy implications, and they do not feel as safe as they used to initially. When Edward Snowden informed the world about the snooping United States Security Agencies had been doing, that is when the picture became clear for the people. After the Cambridge Analytica case where the data of Facebook users were stored without their consent, the doubts arose in the minds of people about how safe they actually are. In India, the case of spyware Pegasus also raised a lot of concerns. It was used to snoop on a lot of human right activists and lawyers and the company which invented the spyware claims that it only sells it to the government. The paper will be dealing with the privacy concerns in the Indian perspective with an analytical methodology. The Supreme Court here had recently declared a right to privacy a Fundamental Right under Article 21 of the Constitution of India. Further, the Government is also working on the Data Protection Bill. The point to note is that India is still a developing country, and with the bill, the government aims at data localization. But there are doubts in the minds of many people that the Government would actually be snooping on the data of the individuals. It looks more like an attempt to curb dissenters ‘lawfully’. The focus of the paper would be on these issues in India in light of the European Union (EU) General Data Protection Regulation (GDPR). The Indian Data Protection Bill is also said to be loosely based on EU GDPR. But how helpful would these laws actually be is another concern since the economic and social conditions in both countries are very different? The paper aims at discussing these concerns, how good or bad is the intention of the government behind the bill, and how the nations can act together and draft common regulations so that there is some uniformity in the laws and their application.

Keywords: Article 21, data protection, dissent, fundamental right, India, privacy

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Authors: Kira Toxopeus, Kamran Siddiqui

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Channel flows are common in a wide range of engineering applications. In some types of channel flows, particularly the ones involving chemical or biological processes, the control of the flow temperature is crucial to maintain the optimal conditions for the chemical reaction or to control the growth of biological species. This often becomes an issue when the flow experiences temperature fluctuations due to external conditions. While active heating and cooling could regulate the channel temperature, it may not be feasible logistically or economically and is also regarded as a non-sustainable option. Thermal energy storage utilizing phase change material (PCM) could provide the required thermal regulation sustainably by storing the excess heat from the channel and releasing it back as required, thus regulating the channel temperature within a range in the proximity of the PCM melting temperature. However, in designing such systems, the configuration of the PCM storage within the channel is critical as it could influence the channel flow dynamics, which would, in turn, affect the heat exchange between the channel fluid and the PCM. The present research is focused on the investigation of the flow dynamical behavior in the channel during heat transfer from the channel flow to the PCM thermal energy storage. Offset vertical columns in a narrow channel were used that contained the PCM. Two different column shapes, square and circular, were considered. Water was used as the channel fluid that entered the channel at a temperature higher than that of the PCM melting temperature. Hence, as the water was passing through the channel, the heat was being transferred from the water to the PCM, causing the PCM to store the heat through a phase transition from solid to liquid. Particle image velocimetry (PIV) was used to measure the two-dimensional velocity field of the channel flow as it flows between the PCM columns. Thermocouples were also attached to the PCM columns to measure the PCM temperature at three different heights. Three different water flow rates (0.5, 0.75 and 1.2 liters/min) were considered. At each flow rate, experiments were conducted at three different inlet water temperatures (28ᵒC, 33ᵒC and 38ᵒC). The results show that the flow rate and the inlet temperature influenced the flow behavior inside the channel.

Keywords: channel flow, phase change material, thermal energy storage, thermal regulation

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Authors: Jeremy Attard, Jordan François, Serge Lazzarini, Thierry Masson

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Gauge theories are the natural background for describing geometrically fundamental interactions using principal and associated fiber bundles as dynamical entities. The central notion of these theories is their local gauge symmetry implemented by the local action of a Lie group H. There exist several methods used to reduce the symmetry of a gauge theory, like gauge fixing, bundle reduction theorem or spontaneous symmetry breaking mechanism (SSBM). This paper is a presentation of another method of gauge symmetry reduction, distinct from those three. Given a symmetry group H acting on a fiber bundle and its naturally associated fields (Ehresmann (or Cartan) connection, curvature, matter fields, etc.) there sometimes exists a way to erase (in whole or in part) the H-action by just reconfiguring these fields, i.e. by making a mere change of field variables in order to get new (‘composite‘) fields on which H (in whole or in part) does not act anymore. Two examples: the re-interpretation of the BEHGHK (Higgs) mechanism, on the one hand, and the top-down construction of Tractor and Penrose's Twistor spaces and connections in the framework of conformal Cartan geometry, one the other, will be discussed. They have, of course, nothing to do with each other but the dressing field method can be applied on both to get a new insight. In the first example, it turns out, indeed, that generation of masses in the Standard Model can be separated from the symmetry breaking, the latter being a mere change of field variables, i.e. a dressing. This offers an interpretation in opposition with the one usually found in textbooks. In the second case, the dressing field method applied to the conformal Cartan geometry offer a way of understanding the deep geometric nature of the so-called Tractors and Twistors. The dressing field method, distinct from a gauge transformation (even if it can have apparently the same form), is a systematic way of finding and erasing artificial symmetries of a theory, by a mere change of field variables which redistributes the degrees of freedom of the theories.

Keywords: BEHGHK (Higgs) mechanism, conformal gravity, gauge theory, spontaneous symmetry breaking, symmetry reduction, twistors and tractors

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Authors: Neda Nabid

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Friction-based supplemental devices have been extensively used for seismic protection and strengthening of structures, however, the conventional use of these dampers may not necessarily lead to an efficient structural performance. Conventionally designed friction dampers follow a uniform height-wise distribution pattern of slip load values for more practical simplicity. This can lead to localizing structural damage in certain story levels, while the other stories accommodate a negligible amount of relative displacement demand. A practical performance-based optimization methodology is developed to tackle with structural damage localization of RC frame buildings with friction energy dissipation devices under severe earthquakes. The proposed methodology is based on the concept of uniform damage distribution theory. According to this theory, the slip load values of the friction dampers redistribute and shift from stories with lower relative displacement demand to the stories with higher inter-story drifts to narrow down the discrepancy between the structural damage levels in different stories. In this study, the efficacy of the proposed design methodology is evaluated through the seismic performance of five different low to high-rise RC frames equipped with friction wall dampers under six real spectrum-compatible design earthquakes. The results indicate that compared to the conventional design, using the suggested methodology to design friction wall systems can lead to, by average, up to 40% reduction of maximum inter-story drift; and incredibly more uniform height-wise distribution of relative displacement demands under the design earthquakes.

Keywords: friction damper, nonlinear dynamic analysis, RC structures, seismic performance, structural damage

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Authors: Asim Alsharif, Christophe Pinna, Hassan Ghadbeigi

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The development of next-generation advanced high strength steels (AHSS) used in the automotive industry requires a better understanding of local deformation and damage development at the scale of their microstructures. This work is focused on dual-phase DP1000 steels and involves micro-mechanical tensile testing inside a scanning electron microscope (SEM) combined with digital image correlation (DIC) to quantify the heterogeneity of deformation in both ferrite and martensite and its evolution up to fracture. Natural features of the microstructure are used for the correlation carried out using Davis LaVision software. Strain localization is observed in both phases with tensile strain values up to 130% and 110% recorded in ferrite and martensite respectively just before final fracture. Damage initiation sites have been observed during deformation in martensite but could not be correlated to local strain values. A finite element (FE) model of the microstructure has then been developed using Abaqus to map stress distributions over representative areas of the microstructure by forcing the model to deform as in the experiment using DIC-measured displacement maps as boundary conditions. A MATLAB code has been developed to automatically mesh the microstructure from SEM images and to map displacement vectors from DIC onto the FE mesh. Results show a correlation of damage initiation at the interface between ferrite and martensite with local principal stress values of about 1700MPa in the martensite phase. Damage in ferrite is now being investigated, and results are expected to bring new insight into damage development in DP steels.

Keywords: advanced high strength steels, digital image correlation, finite element modelling, micro-mechanical testing

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Authors: Bushra Zafar, Usman Qamar

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Large data sample size and dimensions render the effectiveness of conventional data mining methodologies. A data mining technique are important tools for collection of knowledgeable information from variety of databases and provides supervised learning in the form of classification to design models to describe vital data classes while structure of the classifier is based on class attribute. Classification efficiency and accuracy are often influenced to great extent by noisy and undesirable features in real application data sets. The inherent natures of data set greatly masks its quality analysis and leave us with quite few practical approaches to use. To our knowledge first time, we present a new approach for investigation of structure and quality of datasets by providing a targeted analysis of localization of noisy and irrelevant features of data sets. Machine learning is based primarily on feature selection as pre-processing step which offers us to select few features from number of features as a subset by reducing the space according to certain evaluation criterion. The primary objective of this study is to trim down the scope of the given data sample by searching a small set of important features which may results into good classification performance. For this purpose, a heuristic for wrapper-based feature selection using genetic algorithm and for discriminative feature selection an external classifier are used. Selection of feature based on its number of occurrence in the chosen chromosomes. Sample dataset has been used to demonstrate proposed idea effectively. A proposed method has improved average accuracy of different datasets is about 95%. Experimental results illustrate that proposed algorithm increases the accuracy of prediction of different diseases.

Keywords: data mining, generic algorithm, KNN algorithms, wrapper based feature selection

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Authors: P. Selyshchev

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Construction materials for nuclear facilities are operated under extreme thermal and radiation conditions. First of all, they are nuclear fuel, fuel assemblies, and reactor vessel. It places high demands on the control of their state, stability of their state, and their operating conditions. An irradiated material is a typical example of an open non-equilibrium system with nonlinear feedbacks between its elements. Fluxes of energy, matter and entropy maintain states which are far away from thermal equilibrium. The links that arise under irradiation are inherently nonlinear. They form the mechanisms of feed-backs that can lead to instability. Due to this instability the temperature of the sample, heat transfer, and the defect density can exceed the steady-state value in several times. This can lead to change of typical operation and an accident. Therefore, it is necessary to take into account the thermal instability to avoid the emergency situation. The point is that non-thermal energy can be accumulated in materials because irradiation produces defects (first of all these are vacancies and interstitial atoms), which are metastable. The stored energy is about energy of defect formation. Thus, an annealing of the defects is accompanied by releasing of non-thermal stored energy into thermal one. Temperature of the material grows. Increase of temperature results in acceleration of defect annealing. Density of the defects drops and temperature grows more and more quickly. The positive feed-back is formed and self-reinforcing annealing of radiation defects develops. To describe these phenomena a theoretical approach to thermal instability is developed via formalism of complex systems. We consider system of nonlinear differential equations for different components of microstructure and temperature. The qualitative analysis of this non-linear dynamical system is carried out. Conditions for development of instability have been obtained. Points of bifurcation have been found. Convenient way to represent obtained results is a set of phase portraits. It has been shown that different regimes of material state under irradiation can develop. Thus degradation of irradiated material can be limited by means of choice appropriate kind of evolution of materials under irradiation.

Keywords: irradiation, material, non-equilibrium state, nonlinear feed-back, thermal instability

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Authors: M. F. Slim, A. Alhussein, F. Sanchette, M. François

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Thin films are widely used in various applications to enhance the surface properties and characteristics of materials. They are used in many domains such as: biomedical, automotive, aeronautics, military, electronics and energy. Depending on the elaboration technique, the elastic behavior of thin films may be different from this of bulk materials. This dependence on the elaboration techniques and their parameters makes the control of the elasticity constants of coated components necessary. Our work is focused on the characterization of the elasticity constants of isotropic thin films by means of Impulse Excitation Techniques. The tests rely on the measurement of the sample resonance frequency before and after deposition. In this work, a finite element model was performed with ABAQUS software. This model was then compared with the analytical approaches used to determine the Young’s and shear moduli. The best model to determine the film Young’s modulus was identified and a relation allowing the determination of the shear modulus of thin films of any thickness was developed. In order to confirm the model experimentally, Tungsten films were deposited on glass substrates by DC magnetron sputtering of a 99.99% purity tungsten target. The choice of tungsten was done because it is well known that its elastic behavior at crystal scale is ideally isotropic. The macroscopic elasticity constants, Young’s and shear moduli and Poisson’s ratio of the deposited film were determined by means of Impulse Excitation Technique. The Young’s modulus obtained from IET was compared with measurements by the nano-indentation technique. We did not observe any significant difference and the value is in accordance with the one reported in the literature. This work presents a new methodology on the determination of the elasticity constants of thin films using Impulse Excitation Technique. A formulation allowing the determination of the shear modulus of a coating, whatever the thickness, was developed and used to determine the macroscopic elasticity constants of tungsten films. The developed model was validated numerically and experimentally.

Keywords: characterization, coating, dynamical resonant method, Poisson's ratio, PVD, shear modulus, Young's modulus

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Authors: Svitlana Antonenko, Gennady Telegeev

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Introductive statement: The development of chronic myeloid leukemia (CML) is caused by Bcr-Abl oncoprotein. Modern treatments with tyrosine kinase inhibitors are greatly complicated by the mutational variability of the Bcr-Abl oncoprotein, which causes drug resistance. Therefore, there is an urgent need to develop new approaches to the treatment of the disease, which will allow modeling the level of Bcr-Abl oncoprotein in the cell. Promising in this direction is the identification of proteases that can selectively promote cellular proteolysis of oncoproteins. The aim of the study was to study the effect of the interaction of Bcr-Abl with deubiquitinase USP1 on the level of oncoprotein in CML cells. Methodology: K562 cells were selected for the experiment. Сells were incubated with ML323 inhibitor for 24 hours. Precipitation of endogenous proteins from K562 cell lysate was performed using anti-Bcr-Abl antibodies. Cell lysates and precipitation results were studied by Western blot. Subcellular localization of proteins was studied by immunofluorescence analysis followed by confocal microscopy. The results were analyzed quantitatively and statistically. Major findings: The Bcr-Abl/USP1 protein complex was detected in CML cells, and it was found that inhibition of USP1 deubiquitinating activity by the compound ML323 leads to disruption of this protein complex and a decrease in the level of Bcr-Abl oncoprotein in cells. The interaction of Bcr-Abl with USP1 may result in deubiquitination of the oncoprotein, which disrupts its proteasomal degradation and leads to the accumulation of CML in cells. Conclusion: We believe that the interaction of oncoprotein with USP1 may be one of the prerequisites that contribute to malignant cell transformation due to the deubiquitination of oncoprotein, which leads to its accumulation and disease progression. A correlation was found between the deubiquitinating activity of USP1 and the level of oncoprotein in CML cells. Thus, we identify deubiquitinase USP1 as a promising therapeutic target for the development of a new strategy for the treatment of CML by modulating the level of Bcr-Abl in the cell.

Keywords: chronic myeloid leukemia, Bcr-Abl, USP1, deubiquitination Bcr-Abl, K562 cell

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Authors: Adeleye Johnson Adelagunayeja

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The concept of making cities, communities, and neighborhoods smart, intelligent, and responsive is relatively new to Africa and its urban renewal agencies. Efforts must be made by relevant agencies to begin a holistic review of the implementation of infrastructural facilities and urban renewal methodologies that will revolve around the appreciation and application of artificial intelligence. The propagation of the ideals and benefits of the smart city concept are key factors that can encourage governments of African nations, the African Union, and other regional organizations in Africa to embrace the ideology. The ability of this smart city concept to curb insecurities – armed robbery, assassination, terrorism, and civil disorder – is one major reason, amongst others, why African governments must speedily embrace this contemporary developmental concept whose time has come! The seamlessness to access information and virtually cross-pollinate ideas with people living in already established smart cities, when combined with the great efficiency that the emergence of smart cities brings with it, are other reasons why Africa must come up with action plans that can enable the existing cities to metamorphose into smart cities. Innovations will be required to enable Africa to develop a smart city concept that will be compatible with the basic patterns of livelihood because the essence of the smart city evolution is to make life better for people to co-exist, to be productive and to enjoy standard infrastructural facilities. This research paper enumerates the multifaceted adaptive factors that have the potentials of making the adoption of smartcity concept in Africa seamless. It also proffers solutions to potential bottlenecks capable of undermining the execution of the smart city concept in Africa.

Keywords: smartcity compactibility innovation Africa government evolution, Africa as global village member, evolution in Africa, ways to make Africa adopt smartcity, localizing smartcity concept in Africa, bottleneck to smartcity developmet in Africa

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