Search results for: consensual domain of interactions

Authors: Ricardo Avila, Gabriel Lopes, Vania Vidal, Jose Macedo

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This article offers a approach to the automatic discovery of semantic concepts and links in the domain of Oil Exploration and Production (E&P). Machine learning methods combined with textual pre-processing techniques were used to detect local patterns in texts and, thus, generate new concepts and new semantic links. Even using more specific vocabularies within the oil domain, our approach has achieved satisfactory results, suggesting that the proposal can be applied in other domains and languages, requiring only minor adjustments.

Keywords: semantic links, data mining, linked data, SKOS

Procedia PDF Downloads 141

Authors: Onyekachi Onwudike, Russell Lock, Iain Phillips

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The variability that exists across governments, her departments and the provisioning of services has been areas of concern in the E-Government domain. There is a need for reuse and integration across government departments which are accompanied by varying degrees of risks and threats. There is also the need for assessment, prevention, preparation, response and recovery when dealing with these risks or threats. The ability of a government to cope with the emerging changes that occur within it is known as resilience. In order to forge ahead with concerted efforts to manage reuse and integration induced risks or threats to governments, the ambiguities contained within resilience must be addressed. Enhancing resilience in the E-Government domain is synonymous with reducing risks governments face with provisioning of services as well as reuse of components across departments. Therefore, it can be said that resilience is responsible for the reduction in government’s vulnerability to changes. In this paper, we present the use of the ontology to measure the resilience of governments. This ontology is made up of a well-defined construct for the taxonomy of resilience. A specific class known as ‘Resilience Requirements’ is added to the ontology. This class embraces the concept of resilience into the E-Government domain ontology. Considering that the E-Government domain is a highly complex one made up of different departments offering different services, the reliability and resilience of the E-Government domain have become more complex and critical to understand. We present questions that can help a government access how prepared they are in the face of risks and what steps can be taken to recover from them. These questions can be asked with the use of queries. The ontology focuses on developing a case study section that is used to explore ways in which government departments can become resilient to the different kinds of risks and threats they may face. A collection of resilience tools and resources have been developed in our ontology to encourage governments to take steps to prepare for emergencies and risks that a government may face with the integration of departments and reuse of components across government departments. To achieve this, the ontology has been extended by rules. We present two tools for understanding resilience in the E-Government domain as a risk analysis target and the output of these tools when applied to resilience in the E-Government domain. We introduce the classification of resilience using the defined taxonomy and modelling of existent relationships based on the defined taxonomy. The ontology is constructed on formal theory and it provides a semantic reference framework for the concept of resilience. Key terms which fall under the purview of resilience with respect to E-Governments are defined. Terms are made explicit and the relationships that exist between risks and resilience are made explicit. The overall aim of the ontology is to use it within standards that would be followed by all governments for government-based resilience measures.

Keywords: E-Government, Ontology, Relationships, Resilience, Risks, Threats

Procedia PDF Downloads 313

Authors: Janneth Gonzalez, Marco Avila, George Barreto

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GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

Procedia PDF Downloads 320

Authors: Frederik Calsius, Mirela Popa, Alexia Briassouli

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In the field of machine learning, it is common practice to use benchmark datasets to prove the working of a method. The domain of action recognition in videos often uses datasets like Kinet-ics, Something-Something, UCF-101 and HMDB-51 to report results. Considering the properties of the datasets, there are no datasets that focus solely on very short clips (2 to 3 seconds), and on highly-similar fine-grained actions within one specific domain. This paper researches how current state-of-the-art action recognition methods perform on a dataset that consists of highly similar, fine-grained actions. To do so, a dataset of skateboarding tricks was created. The performed analysis highlights both benefits and limitations of state-of-the-art methods, while proposing future research directions in the activity recognition domain. The conducted research shows that the best results are obtained by fusing RGB data with OpenPose data for the Temporal Shift Module.

Keywords: activity recognition, fused deep representations, fine-grained dataset, temporal modeling

Procedia PDF Downloads 199

Authors: M. I. Tyletc, O. I. Podgornya, T. G. Shaposhnikova, S. V. Shabelnikov, A. G. Mittenberg, M. A. Daugavet

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Ascidiacea is the most numerous class of the Tunicata subtype. These chordates' distinctive feature of the anatomical structure is a tunic consisting of cellulose fibrils, protein molecules, and single cells. The mechanisms of the tunic formation are not known in detail; tunic formation could be used as the model system for studying the interaction of cells with the extracellular matrix. Our model species is the ascidian Styela rustica, which is prevalent in benthic communities of the White Sea. As previously shown, the tunic formation involves morula blood cells, which contain the major 48 kDa protein p48. P48 participation in the tunic formation was proved using antibodies against the protein. The nature of the protein and its function remains unknown. The current research aims to determine the amino acid sequence of p48, as well as to clarify its role in the tunic formation. The peptides that make up the p48 amino acid sequence were determined by mass spectrometry. A search for peptides in protein sequence databases identified sequences homologous to p48 in Styela clava, Styela plicata, and Styela canopus. Based on sequence alignment, their level of similarity was determined as 81-87%. The correspondent sequence of ascidian Styela canopus was used for further analysis. The Styela rustica p48 sequence begins with a signal peptide, which could indicate that the protein is secretory. This is consistent with experimentally obtained data: the contents of morula cells secreted in the tunic matrix. The isoelectric point of p48 is 9.77, which is consistent with the experimental results of acid electrophoresis of morula cell proteins. However, the molecular weight of the amino acid sequence of ascidian Styela canopus is 103 kDa, so p48 of Styela rustica is a shorter homolog. The search for conservative functional domains revealed the presence of two Ca-binding EGF-like domains, thrombospondin (TSP1) and tyrosinase domains. The p48 peptides determined by mass spectrometry fall into the region of the sequence corresponding to the last two domains and have amino acid substitutions as compared to Styela canopus homolog. The tyrosinase domain (pfam00264) is known to be part of the phenoloxidase enzyme, which participates in melanization processes and the immune response. The thrombospondin domain (smart00209) interacts with a wide range of proteins, and is involved in several biological processes, including coagulation, cell adhesion, modulation of intercellular and cell-matrix interactions, angiogenesis, wound healing and tissue remodeling. It can be assumed that the tyrosinase domain in p48 plays the role of the phenoloxidase enzyme, and TSP1 provides a link between the extracellular matrix and cell surface receptors, and may also be responsible for the repair of the tunic. The results obtained are consistent with experimental data on p48. The domain organization of protein suggests that p48 is an enzyme involved in the tunic tunning and is an important regulator of the organization of the extracellular matrix.

Keywords: ascidian, p48, thrombospondin, tyrosinase, tunic, tunning

Procedia PDF Downloads 79

Authors: Luis Andrey Fajardo Fajardo

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We are immersed in complex systems. The human brain, the galaxies, the snowflakes are examples of complex systems. An area of interest in Complex systems is the chaos theory. This revolutionary field of science presents different ways of study than determinism and reductionism. Here is where in junction with the Nonlinear DSP, chaos theory offer valuable techniques that establish a link between time series and complex theory in terms of complex networks, so that, the study of signals can be explored from the graph theory. Recently, some people had purposed a method to transform time series in graphs, but no one had developed a suitable implementation in Python with signals extracted from Chaotic Systems or Complex systems. That’s why the implementation in Python of an existing method to transform one dimensional chaotic signals from time domain to graph domain and some measures that may reveal information not extracted in the time domain is proposed.

Keywords: Python, complex systems, graph theory, dynamical systems

Procedia PDF Downloads 479

Authors: Lawrence Williams

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As the mechanism which converts domains to internet protocol (IP) addresses, Domain Name System (DNS) is an essential part of internet usage. It was not designed securely and can be subject to attacks. DNS attacks have become more frequent and sophisticated and the need for detecting and preventing them becomes more important for the modern network. DNS tunnelling attacks are one type of attack that are primarily used for distributed denial-of-service (DDoS) attacks and data exfiltration. Discussion of different techniques to detect and prevent DNS tunneling attacks is done. The methods, models, experiments, and data for each technique are discussed. A proposal about feasibility is made. Future research on these topics is proposed.

Keywords: DNS, tunneling, exfiltration, botnet

Procedia PDF Downloads 39

Authors: Sudipto Sarkar, Anamika Paul

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Pseudoplastic (n<1, n is the power index) fluids have great importance in food, pharmaceutical and chemical process industries which require a lot of attention. Unfortunately, due to its complex flow behavior inadequate research works can be found even in laminar flow regime. A practical problem is solved in the present research work by numerical simulation where we tried to control the vortex shedding from a square cylinder using a horizontal splitter plate placed at the downstream flow region. The position of the plate is at the centerline of the cylinder with varying distance from the cylinder to calculate the critical gap-ratio. If the plate is placed inside this critical gap, the vortex shedding from the cylinder suppressed completely. The Reynolds number considered here is in unsteady laminar vortex shedding regime, Re = 100 (Re = U∞a/ν, where U∞ is the free-stream velocity of the flow, a is the side of the cylinder and ν is the maximum value of kinematic viscosity of the fluid). Flow behavior has been studied for three different gap-ratios (G/a = 2, 2.25 and 2.5, where G is the gap between cylinder and plate) and for a fluid with three different flow behavior indices (n =1, 0.8 and 0.5). The flow domain is constructed using Gambit 2.2.30 and this software is also used to generate the mesh and to impose the boundary conditions. For G/a = 2, the domain size is considered as 37.5a × 16a with 316 × 208 grid points in the streamwise and flow-normal directions respectively after a thorough grid independent study. Fine and equal grid spacing is used close to the geometry to capture the vortices shed from the cylinder and the boundary layer developed over the flat plate. Away from the geometry meshes are unequal in size and stretched out. For other gap-ratios, proportionate domain size and total grid points are used with similar kind of mesh distribution. Velocity inlet (u = U∞), pressure outlet (Neumann condition), symmetry (free-slip boundary condition) at upper and lower domain boundary conditions are used for the simulation. Wall boundary condition (u = v = 0) is considered both on the cylinder and the splitter plate surfaces. Discretized forms of fully conservative 2-D unsteady Navier Stokes equations are then solved by Ansys Fluent 14.5. SIMPLE algorithm written in finite volume method is selected for this purpose which is a default solver inculcate in Fluent. The results obtained for Newtonian fluid flow agree well with previous works supporting Fluent’s usefulness in academic research. A thorough analysis of instantaneous and time-averaged flow fields are depicted both for Newtonian and pseudoplastic fluid flow. It has been observed that as the value of n reduces the stretching of shear layers also reduce and these layers try to roll up before the plate. For flow with high pseudoplasticity (n = 0.5) the nature of vortex shedding changes and the value of critical gap-ratio reduces. These are the remarkable findings for laminar periodic vortex shedding regime in pseudoplastic flow environment.

Keywords: CFD, pseudoplastic fluid flow, wake-boundary layer interactions, critical gap-ratio

Procedia PDF Downloads 77

Authors: Wen-Shyong Tzou, Chih-Ching Huang, Chin-Hwa Hu, Ying-Tsang Lo, Tun-Wen Pai, Chia-Yin Chiang, Chung-Hao Li, Hong-Jyuan Jian

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Plasmin plays an important role in the human circulatory system owing to its catalytic ability of fibrinolysis. The immediate injection of plasmin in patients of strokes has intrigued many scientists to design vectors that can transport plasmin to the desired location in human body. Here we predict the structure of human plasmin and investigate the interaction of plasmin with the gold-nanoparticle. Because the crystal structure of plasminogen has been solved, we deleted N-terminal domain (Pan-apple domain) of plasminogen and generate a mimic of the active form of this enzyme (plasmin). We conducted a simulated annealing process on plasmin and discovered a very large conformation occurs. Kringle domains 1, 4 and 5 had been observed to leave its original location relative to the main body of the enzyme and the original doughnut shape of this enzyme has been transformed to a V-shaped by opening its two arms. This observation of conformational change is consistent with the experimental results of neutron scattering and centrifugation. We subsequently docked the plasmin on the simulated gold surface to predict their interaction. The V-shaped plasmin could utilize its Kringle domain and catalytic domain to contact the gold surface. Our findings not only reveal the flexibility of plasmin structure but also provide a guide for the design of a plasmin-gold nanoparticle.

Keywords: docking, gold nanoparticle, molecular simulation, plasmin

Procedia PDF Downloads 450

Authors: S. Hosseini, M. Ahmadi Najafabadi, M. Akhlaghi

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The health of the journal bearings is very important in preventing unforeseen breakdowns in rotary machines, and poor lubrication is one of the most important factors for producing the bearing failures. Hydrodynamic lubrication (HL), mixed lubrication (ML), and boundary lubrication (BL) are three regimes of a journal bearing lubrication. This paper uses acoustic emission (AE) measurement technique to correlate features of the AE signals to the three lubrication regimes. The transitions from HL to ML based on operating factors such as rotating speed, load, inlet oil pressure by time domain and time-frequency domain signal analysis techniques are detected, and then metal-to-metal contacts between sliding surfaces of the journal and bearing are identified. It is found that there is a significant difference between theoretical and experimental operating values that are obtained for defining the lubrication regions.

Keywords: acoustic emission technique, pressure fed journal bearing, time and frequency signal analysis, metal-to-metal contact

Procedia PDF Downloads 126

Authors: Veepaul Kaur Mann Balwinder Singh

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The COVID-19 had an intense impact on several countries across the world. National governments have imposed widespread restrictions to prevent the growth of this pandemic. The new health competitive scenario induced by the COVID-19 crisis raised many issues on how business activities should be reorganized due to the difficulties of physical interactions with distributors, suppliers and customers. The pandemic has particularly affected the whole selling process because of the relevant issues that emerged in managing physical sale channels and interactions with one another, both in the Business-to-Consumer and in the Business-to-Business markets. Recent research about the appropriate actions and strategies that could help firms overcome the crisis has highlighted the key role of digital expertise that may ensure connections and, thus, help business activities run smoothly. This could be true, especially with the occurrence of strong limitations on physical interactions during the COVID-19 pandemic. The catastrophe changes life publically and economically. People are living alone for following the social distancing norms. In that set-up, Digital Marketing is playing an important role in civilization. Anyone can buy any item, pay bills, transfer money and compare items through Digital Marketing without physical interactions. After COVID-19, people will be more aware of health safety and trust. So, through Digital Marketing, organizations can approach customers and provide good service environments. In such a situation, the online network becomes the most important encouraging for online customers to get in contact with the firm and carry out online selling and purchasing activities around the world.

Keywords: COVID-19, business, digital marketing, online customer

Procedia PDF Downloads 17

Authors: Adriano Trono, Federico Pinto, Diego Turello, Marcelo A. Ceballos

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Numerical modeling of dynamic soil-structure interaction problems requires an adequate representation of the unbounded characteristics of the ground, material non-linearity of soils, and geometrical non-linearities such as large displacements due to rocking of the structure. In order to account for these effects simultaneously, it is often required that the equations of motion are solved in the time domain. However, boundary conditions in conventional finite element codes generally present shortcomings in fully absorbing the energy of outgoing waves. In this sense, the Perfectly Matched Layers (PML) technique allows a satisfactory absorption of inclined body waves, as well as surface waves. However, the PML domain is inherently unstable, meaning that it its instability does not depend upon the discretization considered. One way to stabilize the PML domain is to use multiaxial stretching functions. This development is questionable because some Jacobian terms of the coordinate transformation are not accounted for. For this reason, the resulting absorbing layer element is often referred to as "uncorrected M-PML” in the literature. In this work, the strong formulation of the "corrected M-PML” absorbing layer is proposed using multiaxial stretching functions that incorporate all terms of the coordinate transformation. The results of the stable model are compared with reference solutions obtained from extended domain models.

Keywords: mixed finite elements, multiaxial stretching functions, perfectly matched layer, soil-structure interaction

Procedia PDF Downloads 35

Authors: Kedibone Masenya, Memory Tekere, Jasper Rees

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Sorghum is an important cereal crop in the world. In particular, it has attracted breeders due to capacity to serve as food, feed, fiber and bioenergy crop. Like any other plant, sorghum hosts a variety of microbes, which can either, have a neutral, negative and positive influence on the plant. In the current study, regions (V3/V4) of 16 S rRNA were targeted to extensively assess bacterial multitrophic interactions in the phyllosphere of sorghum. The results demonstrated that the presence of a pathogen has a significant effect on the endophytic bacterial community. Understanding these interactions is key to develop new strategies for plant protection.

Keywords: bacteria, multitrophic, sorghum, target sequencing

Procedia PDF Downloads 254

Authors: Kuo-Cheng Liu

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In the latest research efforts, the structures of the image in the spatial domain have been successfully analyzed and proved to deduce the visual masking for accurately estimating the visibility thresholds of the image. If the structural properties of the video sequence in the temporal domain are taken into account to estimate the temporal masking, the improvement and enhancement of the as-sessing spatio-temporal visibility thresholds are reasonably expected. In this paper, the temporal characteristics of human perception to the change in block structures on the time axis are analyzed. The temporal characteristics of human perception are represented in terms of the significant variation in block structures for the analysis of human visual system (HVS). Herein, the block structure in each frame is computed by combined the pattern masking and the contrast masking simultaneously. The contrast masking always overestimates the visibility thresholds of edge regions and underestimates that of texture regions, while the pattern masking is weak on a uniform background and is strong on the complex background with spatial patterns. Under considering the significant variation of block structures between successive frames, we extend the block structures of images in the spatial domain to that of video sequences in the temporal domain to analyze the relation between the inter-frame variation of structures and the temporal masking. Meanwhile, the subjective viewing test and the fair rating process are designed to evaluate the consistency of the temporal characteristics with the HVS under a specified viewing condition.

Keywords: temporal characteristic, block structure, pattern masking, contrast masking

Procedia PDF Downloads 380

Authors: Mehraveh Taghizadeh

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Iran is home to a diverse range of ethnic groups such as Baloch, Kurds, Persians, Lors, Arabs, and Turks. The Persian ethnicity is the largest group, while Baloch people are considered a minority residing on the southeastern border of the country with different language and religion. As a consequence, Political discussions have often prioritized national identity and national security over Baloch ethnic identity. However, to improve intercultural understanding and reduce cultural schemas, it's crucial to decrease ethnocentrism and increase intercultural communication. In the meantime, Kerman, a multicultural province that borders Sistan and Baluchistan, has become a destination for Baloch immigrants. By recognizing the current status of intercultural competence, we can develop effective policies for expanding intercultural communication and creating a more inclusive and peaceful society. As a result, this research aims to study the domain of intercultural sensitivity between Persians and Baloch in Kerman. Therefore, the question is how do Persians and Baloch ethnicities perceive each other? This study represents the first exploration of communication dynamics between Persians and Baloch individuals. Utilizing a qualitative approach, this study employs thematic analysis in conjunction with Bennett's intercultural sensitivities model. The model comprises two components: ethnocentrism, which spans from denial and defense to minimization, and ethno-relativism, which ranges from acceptance and adaptation to integration. To attain this objective, 30 individuals from Persian and Baloch ethnicities were interviewed using a semi-structured format. it analysis suggests that the Baluch and Persians exhibit a range of intercultural sensitivities characterized by defensive and minimizing attitudes in the ethnocentrism domain, and accepting attitudes in the ethno-relativism domain. The concept of minimization involves recognizing the shared humanity and positive schemas of both groups. Furthermore, in the adaptation domain, Persians' efforts to assimilate into Baloch culture at an acceptance level are primarily focused on the civilizational dimension, including using traditional Balochi clothing designs on their clothes. The Persians hold intercultural schemas about the Baloch people, including notions of religious fanaticism, tribalism, poverty, smuggling, and a nomadic way of life. Conversely, the Baloch people have intercultural schemas about Persians including religious fanaticism, disdain towards the Baloch, and ethnocentrism. Both groups tend to tie ethnicity to religion and judge each other accordingly. Also, the origin of these schemas is in the representation of the media and the encounter without interaction between the two ethnic groups. These findings indicate that they have not received adaptation and integration levels in ethno-relativism. Furthermore, the results indicate that developing personal communication in multicultural environments reduces intercultural sensitivity, and increases positive interactions and civilizational dialogues. People can understand each other better and perform better in their daily lives.

Keywords: intercultural communication, intercultural sensitivity, interethnic communication, Iran, Baloch, Persians

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Authors: Nick Farid, Roghoyeh Salmeh

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The planning and operation of the power grid is becoming much more complex because of the introduction of renewable energy resources, the digitalization of the electricity industry, as well as the coupling of efficiency and greener energy trends. These changes, along with new trends, make interactions between grid users and the other stakeholders more complex. This paper focuses on the main “physical” and “logical” interactions between grid users and the grid stakeholders, both from power system equipment and information management standpoints, and proposes a new interoperability model for Smart Grids.

Keywords: user interface, interoperability layers, grid architecture framework, smart grid

Procedia PDF Downloads 62

Authors: Leila Motamed-Jahromi, Mohsen Hatami, Alireza Keshavarz

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This research aims at obtaining the equations of pulse propagation in nonlinear plasmonic waveguides created with As₂S₃ chalcogenide materials. Via utilizing Helmholtz equation and first-order perturbation theory, two components of electric field are determined within frequency domain. Afterwards, the equations are formulated in time domain. The obtained equations include two coupled differential equations that considers nonlinear dispersion.

Keywords: nonlinear optics, plasmonic waveguide, chalcogenide, propagation equation

Procedia PDF Downloads 373

Authors: Sanjay M. Tailor, Urmila H. Patel

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Phthalyl Sulfacetamide belongs to well-known member of antimicrobial sulfonamide family. It is a potent antitumor drug. Structural characteristics of 4-amino-N-(2quinoxalinyl) benzene-sulfonamides (Phthalyl Sulfacetamide), C14H12N4O2S has been studied by method of X-ray crystallography. The compound crystallizes in monoclinic space group P21/n with unit cell parameters a= 7.9841 Ǻ, b= 12.8208 Ǻ, c= 16.6607 Ǻ, α= 90˚, β= 93.23˚, γ= 90˚and Z=4. The X-ray based three-dimensional structure analysis has been carried out by direct methods and refined to an R-value of 0.0419. The crystal structure is stabilized by intermolecular N-H…N, N-H…O and π-π interactions. The Hirshfeld surfaces and consequently the fingerprint analysis have been performed to study the nature of interactions and their quantitative contributions towards the crystal packing. An analysis of Hirshfeld surfaces and fingerprint plots facilitates a comparison of intermolecular interactions, which are the key elements in building different supramolecular architectures. Docking is used for virtual screening for the prediction of the strongest binders based on various scoring functions. Docking studies are carried out on Phthalyl Sulfacetamide for better activity, which is important for the development of a new class of inhibitors.

Keywords: phthalyl sulfacetamide, crystal structure, hirshfeld surface analysis, docking

Procedia PDF Downloads 310

Authors: Mohammed Islam, Jungyong Wang, Dong Cheol Seo

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The Smoothed Particle Hydrodynamics (SPH) method is a novel, meshless, and Lagrangian technique based numerical method that has shown promises to accurately predict the hydrodynamics of water and structure interactions in violent flow conditions. The main goal of this study is to build confidence on the versatility of the Smoothed Particle Hydrodynamics (SPH) based tool, to use it as a complementary tool to the physical model testing capabilities and support research need for the performance evaluation of ships and offshore platforms exposed to an extreme and harsh environment. In the current endeavor, an open-sourced SPH-based tool was used and validated for modeling and predictions of the hydrodynamic interactions of a 6-DOF ship and bergy bits. The study involved the modeling of a modern generic drillship and simplified bergy bits in floating and towing scenarios and in regular and irregular wave conditions. The predictions were validated using the model-scale measurements on a moored ship towed at multiple oblique angles approaching a floating bergy bit in waves. Overall, this study results in a thorough comparison between the model scale measurements and the prediction outcomes from the SPH tool for performance and accuracy. The SPH predicted ship motions and forces were primarily within ±5% of the measurements. The velocity and pressure distribution and wave characteristics over the free surface depicts realistic interactions of the wave, ship, and the bergy bit. This work identifies and presents several challenges in preparing the input file, particularly while defining the mass properties of complex geometry, the computational requirements, and the post-processing of the outcomes.

Keywords: SPH, ship and bergy bit, hydrodynamic interactions, model validation, physical model testing

Procedia PDF Downloads 109

Authors: Sergio Curilef, Boris Atenas

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Systems with long-range interactions are very common in nature. They are observed from the atomic scale to the astronomical scale and exhibit anomalies, such as inequivalence of ensembles, negative heat capacity, ergodicity breaking, nonequilibrium phase transitions, quasistationary states, and anomalous diffusion. These anomalies are exacerbated when special initial conditions are imposed; in particular, we use the so-called water bag initial conditions that stand for a uniform distribution. Several theoretical and practical implications are discussed here. A potential energy inspired by dipole-dipole interactions is proposed to build the dipole-type Hamiltonian mean-field model. As expected, the dynamics is novel and general to the behavior of systems with long-range interactions, which is obtained through molecular dynamics technique. Two plateaus sequentially emerge before arriving at equilibrium, which are corresponding to two different quasistationary states. The first plateau is a type of quasistationary state the lifetime of which depends on a power law of N and the second plateau seems to be a true quasistationary state as reported in the literature. The general behavior of the model according to its dynamics and thermodynamics is described. Using numerical simulation we characterize the mean kinetic energy, caloric curve, and the diffusion law through the mean square of displacement. The present challenge is to characterize the distributions in phase space. Certainly, the equilibrium state is well characterized by the Gaussian distribution, but quasistationary states in general depart from any Gaussian function.

Keywords: dipole-type interactions, dynamics and thermodynamics, mean field model, quasistationary states

Procedia PDF Downloads 182

Authors: Sara Arafeh, Kovriguine Evguine

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Cytochromes P450 are enzymes that require a supply of electrons to catalyze the synthesis of steroid hormones, fatty acids, and prostaglandin hormone. Cytochrome P450 Oxidoreductase (CYPOR), a membrane bound enzyme, provides these electrons in its open conformation. CYPOR has two cytosolic domains (FAD domain and FMN domain) and an N-terminal in the membrane. In its open conformation, electrons flow from NADPH, FAD, and finally to FMN where cytochrome P450 picks up these electrons. In the closed conformation, cytochrome P450 does not bind to the FMN domain to take the electrons. It was found that when the cytosolic domains are isolated, CYPOR could not bind to cytochrome P450. This suggested that the membrane environment is important for CYPOR function. This project takes the initiative to better understand the dynamics of CYPOR in its full length. Here, we determine the distance between specific sites in the FAD and FMN binding domains in CYPOR by Forster Resonance Energy Transfer (FRET) and Ultrafast TA spectroscopy with and without NADPH. The approach to determine these distances will rely on labeling these sites with red and infrared fluorophores. Mimic membrane attachment is done by inserting CYPOR in lipid nanodiscs. By determining the distances between the donor-acceptor sites in these domains, we can observe the open/closed conformations upon reducing CYPOR in the presence and absence of cytochrome P450. Such study is important to better understand CYPOR mechanism of action in various endosomal membranes including hepatic CYPOR which is vital in plasma cholesterol homeostasis. By investigating the conformational cycles of CYPOR, we can synthesize drugs that would be more efficient in affecting the steroid hormonal levels and metabolism of toxins catalyzed by Cytochrome P450.

Keywords: conformational cycle of CYPOR, cytochrome P450, cytochrome P450 oxidoreductase, FAD domain, FMN domain, FRET, Ultrafast TA Spectroscopy

Procedia PDF Downloads 245

Authors: M. Kowalik, J. Masternak, K. Kazimierczuk, O. V. Khavryuchenko, B. Kupcewicz, B. Barszcz

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Recently, the growing interest of chemists in metal-organic coordination polymers (MOCPs) is primarily derived from their intriguing structures and potential applications in catalysis, gas storage, molecular sensing, ion exchanges, nonlinear optics, luminescence, etc. Currently, we are devoting considerable effort to finding the proper method of synthesizing new coordination polymers containing S- or N-heteroaromatic carboxylates as linkers and characterizing the obtained Pb(II) compounds according to their structural diversity, luminescence, and thermal properties. The choice of Pb(II) as the central ion of MOCPs was motivated by several reasons mentioned in the literature: i) a large ionic radius allowing for a wide range of coordination numbers, ii) the stereoactivity of the 6s2 lone electron pair leading to a hemidirected or holodirected geometry, iii) a flexible coordination environment, and iv) the possibility to form secondary bonds and unusual non-covalent interactions, such as classic hydrogen bonds and π···π stacking interactions, as well as nonconventional hydrogen bonds and rarely reported tetrel bonds, Pb(lone pair)···π interactions, C–H···Pb agostic-type interactions or hydrogen bonds, and chelate ring stacking interactions. Moreover, the construction of coordination polymers requires the selection of proper ligands acting as linkers, because we are looking for materials exhibiting different network topologies and fluorescence properties, which point to potential applications. The reaction of Pb(NO₃)₂ with 1H-pyrrole-2-carboxylic acid (2prCOOH) leads to the formation of a new four-nuclear Pb(II) polymer, [Pb4(2prCOO)₈(H₂O)]ₙ, which has been characterized by CHN, FT-IR, TG, PL and single-crystal X-ray diffraction methods. In view of the primary Pb–O bonds, Pb1 and Pb2 show hemidirected pentagonal pyramidal geometries, while Pb2 and Pb4 display hemidirected octahedral geometries. The topology of the strongest Pb–O bonds was determined as the (4·8²) fes topology. Taking the secondary Pb–O bonds into account, the coordination number of Pb centres increased, Pb1 exhibited a hemidirected monocapped pentagonal pyramidal geometry, Pb2 and Pb4 exhibited a holodirected tricapped trigonal prismatic geometry, and Pb3 exhibited a holodirected bicapped trigonal prismatic geometry. Moreover, the Pb(II) lone pair stereoactivity was confirmed by DFT calculations. The 2D structure was expanded into 3D by the existence of non-covalent O/C–H···π and Pb···π interactions, which was confirmed by the Hirshfeld surface analysis. The above mentioned interactions improve the rigidity of the structure and facilitate the charge and energy transfer between metal centres, making the polymer a promising luminescent compound.

Keywords: coordination polymers, fluorescence properties, lead(II), lone electron pair stereoactivity, non-covalent interactions

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Authors: Yingqi Cui, Changran Huang, Raymond Lee

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In this paper, we proposed an AI Tutor using ontology and natural language process techniques to generate a computer science domain knowledge graph and answer users’ questions based on the knowledge graph. We define eight types of relation to extract relationships between entities according to the computer science domain text. The AI tutor is separated into two agents: learning agent and Question-Answer (QA) agent and developed on JADE (a multi-agent system) platform. The learning agent is responsible for reading text to extract information and generate a corresponding knowledge graph by defined patterns. The QA agent can understand the users’ questions and answer humans’ questions based on the knowledge graph generated by the learning agent.

Keywords: artificial intelligence, natural Language processing, knowledge graph, intelligent agents, QA system

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Authors: Charbel Aoun, Loic Lagadec

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A Sensor Network (SN) is considered as an operation of two phases: (1) the observation/measuring, which means the accumulation of the gathered data at each sensor node; (2) transferring the collected data to some processing center (e.g., Fusion Servers) within the SN. Therefore, an underwater sensor network can be defined as a sensor network deployed underwater that monitors underwater activity. The deployed sensors, such as Hydrophones, are responsible for registering underwater activity and transferring it to more advanced components. The process of data exchange between the aforementioned components perfectly defines the Marine Observatory (MO) concept which provides information on ocean state, phenomena and processes. The first step towards the implementation of this concept is defining the environmental constraints and the required tools and components (Marine Cables, Smart Sensors, Data Fusion Server, etc). The logical and physical components that are used in these observatories perform some critical functions such as the localization of underwater moving objects. These functions can be orchestrated with other services (e.g. military or civilian reaction). In this paper, we present an extension to our MO meta-model that is used to generate a design tool (ArchiMO). We propose new constraints to be taken into consideration at design time. We illustrate our proposal with an example from the MO domain. Additionally, we generate the corresponding simulation code using our self-developed domain-specific model compiler. On the one hand, this illustrates our approach in relying on Enterprise Architecture (EA) framework that respects: multiple views, perspectives of stakeholders, and domain specificity. On the other hand, it helps reducing both complexity and time spent in design activity, while preventing from design modeling errors during porting this activity in the MO domain. As conclusion, this work aims to demonstrate that we can improve the design activity of complex system based on the use of MDE technologies and a domain-specific modeling language with the associated tooling. The major improvement is to provide an early validation step via models and simulation approach to consolidate the system design.

Keywords: smart sensors, data fusion, distributed fusion architecture, sensor networks, domain specific modeling language, enterprise architecture, underwater moving object, localization, marine observatory, NS-3, IMS

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Authors: Farideh Halakou, Emel Sen, Attila Gursoy, Ozlem Keskin

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Protein–Protein Interactions (PPIs) mediate major biological processes in living cells. The study of PPIs as networks and analyze the network properties contribute to the identification of genes and proteins associated with diseases. In this study, we have created the sub-networks of brain and lung metastasis from primary tumor in breast cancer. To do so, we used seed genes known to cause metastasis, and produced their interactions through a network-topology based prioritization method named GUILDify. In order to have the experimental support for the sub-networks, we further curated them using STRING database. We proceeded by modeling structures for the interactions lacking complex forms in Protein Data Bank (PDB). The functional enrichment analysis shows that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing are more involved in brain metastasis. The structural analyses of the sub-networks vividly demonstrated their difference in terms of using specific interfaces in lung and brain metastasis. Furthermore, the topological analysis identified genes such as RPL5, MMP2, CCR5 and DPP4, which are already known to be associated with lung or brain metastasis. Additionally, we found 6 and 9 putative genes that are specific for lung and brain metastasis, respectively. Our analysis suggests that variations in genes and pathways contributing to these different breast metastasis types may arise due to change in tissue microenvironment. To show the benefits of using structural PPI networks instead of traditional node and edge presentation, we inspect two case studies showing the mutual exclusiveness of interactions and effects of mutations on protein conformation which lead to different signaling.

Keywords: breast cancer, metastasis, PPI networks, protein conformational changes

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: Guillaume P. Fernandez

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Individual language use is a matter of choice in particular interactions. The paper proposes a conceptual and theoretical framework with methodological consideration to develop how language produced in dyadic relations is to be considered and situated in the larger social configuration the interaction is embedded within. An integrated and comprehensive view is taken: social interactions are expected to be ruled by a normative context, defined by the chain of interdependences that structures the personal network. In this approach, the determinants of discursive practices are not only constrained by the moment of production and isolated from broader influences. Instead, the position the individual and the dyad have in the personal network influences the discursive practices in a twofold manner: on the one hand, the network limits the access to linguistic resources available within it, and, on the other hand, the structure of the network influences the agency of the individual, by the social control inherent to particular network characteristics. Concretely, we investigate how and to what extent consistent ego is from one interaction to another in his or her use of adverbs. To do so, social network analysis (SNA) methods are mobilized. Participants (N=130) are college students recruited in the french speaking part of Switzerland. The personal network of significant ones of each individual is created using name generators and edge interpreters, with a focus on social support and conflict. For the linguistic parts, respondents were asked to record themselves with five of their close relations. From the recordings, we computed an average similarity score based on the adverb used across interactions. In terms of analyses, two are envisaged: First, OLS regressions including network-level measures, such as density and reciprocity, and individual-level measures, such as centralities, are performed to understand the tenets of linguistic similarity from one interaction to another. The second analysis considers each social tie as nested within ego networks. Multilevel models are performed to investigate how the different types of ties may influence the likelihood to use adverbs, by controlling structural properties of the personal network. Primary results suggest that the more cohesive the network, the less likely is the individual to change his or her manner of speaking, and social support increases the use of adverbs in interactions. While promising results emerge, further research should consider a longitudinal approach to able the claim of causality.

Keywords: personal network, adverbs, interactions, social influence

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Authors: Murad Ghanim

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The citrus greening disease, also known as Huanglongbing, caused by the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas) has resulted in tremendous losses and the death of millions of citrus trees worldwide. CLas is transmitted by the Asian citrus psyllid (ACP) Diaphorina citri. The closely-related bacterium Candidatus Liberibacter solanacearum (CLso), which is associated with vegetative disorders in carrots and the zebra chips disease in potatoes, is transmitted by other psyllid species including Bactericera trigonica in carrots and B. ckockerelli in potatoes. Chemical sprays are currently the prevailing method for managing these diseases for limiting psyllid populations; however, they are limited in their effectiveness. A promising approach to prevent the transmission of these pathogens is to interfere with the vector-pathogen interactions, but our understanding of these processes is very limited. CLas induces changes in the nuclear architecture in the midgut of ACP and activates programmed cell death (apoptosis) in this organ. Strikingly, CLso displayed an opposite effect in the gut of B. trigonica, showing limited apoptosis, but widespread necrosis. Electron and fluorescent microscopy further showed that CLas induced the formation of Endoplasmic reticulum (ER) inclusion- and replication-like bodies, in which it increases and multiplies. ER involvement in bacterial replication is hypothesized to be the first stage of an immune response leading to the apoptotic and necrotic responses. ER exploitation and the subsequent events that lead to these cellular and stress responses might activate a cascade of molecular responses ending up with apoptosis and necrosis. Understanding the molecular interactions that underlay the necrotic/apoptotic responses to the bacteria will increase our knowledge of ACP-CLas, and BT-CLso interactions, and will set the foundation for developing novel, and efficient strategies to disturb these interactions and inhibit the transmission.

Keywords: Liberibacter, psyllid, transmission, apoptosis, necrosis

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Authors: Maher Gzam, Noureddine Elmejdoub, Younes Jedoui

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Physical parameters involved in the depositional process on stromatolites, which grow in salt marsh domain, are elucidated in this study. Stromatolites start to grow where surface altimetry of the intertidal flat is high enough to reduce water cover (above mean high tide) and to guarantee a lamellar stream flow. Stromatolite aggrades as a thick laminated layer (stromatolite package) allowing pioneer vascular plants (Salicornia Arabica) to colonize this elevated area (6 cm a.m.s.l). In turn halophytic plant, regularly flooded on spring tide, reduce hydrodynamics velocities causing deposition of sediment, as a result, intertidal zone shift on the flat surface with an expanded marsh domain. This positive feedback invokes self organization between stromatolite growth, vegetation proliferation and deposition of sediment and may be applicable to ancient progradational sequence.

Keywords: stromatolites, marsh, deposition of sediment, aggradation, progradation, gulf of Gabes, Tunisia

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Authors: Angela U. Makolo, Temitayo A. Olagunju

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The knowledge of signaling pathways is central to understanding the biological mechanisms of organisms since it has been identified that in eukaryotic organisms, the number of signaling pathways determines the number of ways the organism will react to external stimuli. Signaling pathways are studied using protein interaction networks constructed from protein-protein interaction data obtained using high throughput experimental procedures. However, these high throughput methods are known to produce very high rates of false positive and negative interactions. In order to construct a useful protein interaction network from this noisy data, computational methods are applied to validate the protein-protein interactions. In this study, a computational technique to identify signaling pathways from a protein interaction network constructed using validated protein-protein interaction data was designed. A weighted interaction graph of the Saccharomyces cerevisiae (Baker’s Yeast) organism using the proteins as the nodes and interactions between them as edges was constructed. The weights were obtained using Bayesian probabilistic network to estimate the posterior probability of interaction between two proteins given the gene expression measurement as biological evidence. Only interactions above a threshold were accepted for the network model. A pathway was formalized as a simple path in the interaction network from a starting protein and an ending protein of interest. We were able to identify some pathway segments, one of which is a segment of the pathway that signals the start of the process of meiosis in S. cerevisiae.

Keywords: Bayesian networks, protein interaction networks, Saccharomyces cerevisiae, signalling pathways

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