Search results for: molecular docking and dynamics

Authors: Alexandros Lioulemes, Michail Theofanidis, Varun Kanal, Konstantinos Tsiakas, Maher Abujelala, Chris Collander, William B. Townsend, Angie Boisselle, Fillia Makedon

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This paper presents a home-based robot-rehabilitation instrument, called ”MAGNI Dynamics”, that utilized a vision-based kinematic/dynamic module and an adaptive haptic feedback controller. The system is expected to provide personalized rehabilitation by adjusting its resistive and supportive behavior according to a fuzzy intelligence controller that acts as an inference system, which correlates the user’s performance to different stiffness factors. The vision module uses the Kinect’s skeletal tracking to monitor the user’s effort in an unobtrusive and safe way, by estimating the torque that affects the user’s arm. The system’s torque estimations are justified by capturing electromyographic data from primitive hand motions (Shoulder Abduction and Shoulder Forward Flexion). Moreover, we present and analyze how the Barrett WAM generates a force-field with a haptic controller to support or challenge the users. Experiments show that by shifting the proportional value, that corresponds to different stiffness factors of the haptic path, can potentially help the user to improve his/her motor skills. Finally, potential areas for future research are discussed, that address how a rehabilitation robotic framework may include multisensing data, to improve the user’s recovery process.

Keywords: human-robot interaction, kinect, kinematics, dynamics, haptic control, rehabilitation robotics, artificial intelligence

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Authors: Shaban Aly, Ali Al-Qahtani, Houari B. Khenous

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Synchronization is an important phenomenon commonly observed in nature. A system of periodically forced complex Duffings oscillators was introduced and shown to display chaotic behavior and possess strange attractors. Such complex oscillators appear in many problems of physics and engineering, as, for example, nonlinear optics, deep-water wave theory, plasma physics and bimolecular dynamics. In this paper, we study the remarkable phenomenon of chaotic synchronization on these oscillator systems, using impulsive synchronization techniques. We derive analytical expressions for impulsive control functions and show that the dynamics of error evolution is globally stable, by constructing appropriate Lyapunov functions. This means that, for a relatively large set initial conditions, the differences between the drive and response systems vanish exponentially and synchronization is achieved. Numerical results are obtained to test the validity of the analytical expressions and illustrate the efficiency of these techniques for inducing chaos synchronization in our nonlinear oscillators.

Keywords: complex nonlinear oscillators, impulsive synchronization, chaotic systems, global exponential synchronization

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Authors: Oluyemi O. Awolusi, Abimbola M. Enitan, Sheena Kumari, Faizal Bux

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Nitrification is essential to biological processes designed to remove ammonia and/or total nitrogen. It removes the excess nitrogenous compound in wastewater which could be very toxic to the aquatic fauna or cause a serious imbalance of such aquatic ecosystem. Efficient nitrification is linked to an in-depth knowledge of the structure and dynamics of the nitrifying community structure within the wastewater treatment systems. In this study, molecular technique was employed for characterizing the microbial structure of activated sludge [ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB)] in a municipal wastewater treatment with intention of linking it to the plant efficiency. PCR-based phylogenetic analysis was also carried out for. The average operating and environmental parameters, as well as specific nitrification rate of a plant, was investigated during the study. During the investigation, the average temperature was 23±1.5oC. Other operational parameters such as mixed liquor suspended solids and chemical oxygen demand inversely correlated with ammonia removal. The dissolved oxygen level in the plant was constantly lower than the optimum (between 0.24 and 1.267 mg/l) during this study. The plant was treating wastewater with the influent ammonia concentration of 31.69 and 24.47 mg/l. The influent flow rates (ML/day) was 96.81 during the period. The dominant nitrifiers include: Nitrosomonas spp. Nitrobacter spp. and Nitrospira spp. The AOB had a correlation with nitrification efficiency and temperature. This study shows that the specific ammonia oxidizing rate and the specific nitrate formation rates can serve as a good indicator of the plant overall nitrification performance.

Keywords: Ammonia monooxygenase α-subunit gene, amoA, ammonia-oxidizing bacteria, AOB, nitrite-oxidizing bacteria, NOB, specific nitrification rate

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Authors: Trudon Kabangu Mpinga, Ruth Mutala, Shaloom Mbambu, Yvette Kalubi Kashama, Kabeya Mukeba Yakasham

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A mathematical model is developed to describe the contact dynamics between the landing gear wheels of an aircraft and a wet pavement during landing. The model is based on nonlinear partial differential equations, using the Yakam Matrix to account for the interaction between solid, liquid, and solid phases. This framework incorporates the influence of environmental factors, particularly water or rain on the runway, on braking performance and aircraft stability. Given the absence of exact analytical solutions, our approach enhances the understanding of key physical phenomena, including Coulomb friction forces, hydrodynamic effects, and the deformation of the pavement under the aircraft's load. Additionally, the dynamics of aquaplaning are simulated numerically to estimate the braking performance limits on wet surfaces, thereby contributing to strategies aimed at minimizing risk during landing on wet runways.

Keywords: aircraft, modeling, simulation, yakam matrix, contact, wet runway

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Authors: Olukunle C. Olawole, Dilip K. De, Moses Emetere, Omoje Maxwell

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Graphene can stand very high temperature up to 4500 K in vacuum and has potential for application in thermionic energy converter. In this paper, we discuss the application of energy dynamics principles and the modified Richardson-Dushman Equation, to estimate the efficiency of solar power conversion to electrical power by a solar thermionic energy converter (STEC) containing emitter made of graphene. We present detailed simulation of power output for different solar insolation, diameter of parabolic concentrator, area of the graphene emitter (same as that of the collector), temperature of the collector, physical dimensions of the emitter-collector etc. After discussing possible methods of reduction or elimination of space charge problem using magnetic field and gate, we finally discuss relative advantages of using emitters made of graphene, carbon nanotube and metals respectively in a STEC.

Keywords: graphene, high temperature, modified Richardson-Dushman equation, solar thermionic energy converter

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Authors: S. M. Azad, H. Ghodsi Pour, F. Roshannafasa

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In recent years ‘technology management and policymaking’ is one of the most important problems in management science. In this field, different generations of innovation and technology management are presented which the earliest one is Innovation System (IS) approach. In a general classification, innovation systems are divided in to 4 approaches: Technical, sectoral, regional, and national. There are many researches in relation to each of these approaches in different academic fields. Every approach has some benefits. If two or more approaches hybrid, their benefits would be combined. In addition, according to the sectoral structure of the governance model in Iran, in many sectors such as information technology, the combination of three other approaches with sectoral approach is essential. Hence, in this paper, combining two IS approaches (technical and sectoral) and using system dynamics, a generic model is presented for a sample of software industry. As a complimentary point, this article is introducing a new hybrid approach called Techno-Sectoral Innovation System. This TSIS model is accomplished by Changing concepts of the ‘functions’ which came from Technological IS literature and using them into sectoral system as measurable indicators.

Keywords: innovation system, technology, techno-sectoral system, functional indicators, system dynamics

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Authors: Nariman Shahhosseini, Sadegh Chinikar

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Introduction: Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe disease with fatality rates of 30%. The virus is transmitted to humans through the bite of an infected tick, direct contact with the products of infected livestock and nosocomially. The disease occurs sporadically throughout many of African, Asian, and European countries. Different species of ticks serve either as vector or reservoir for CCHFV. Materials and Methods: A molecular survey was conducted on hard ticks (Ixodidae) in Golestan province, north of Iran during 2014-2015. Samples were sent to National Reference Laboratory of Arboviruses (Pasteur Institute of Iran) and viral RNA was detected by RT-PCR. Results: Result revealed the presence of CCHFV in 5.3% of the selected ticks. The infected ticks belonged to Hy. dromedarii, Hy. anatolicum, Hy. marginatum, and Rh. sanguineus. Conclusions: These data demonstrates that Hyalomma ticks are the main vectors of CCHFV in Golestan province. Thus, preventive strategies such as using acaricides and repellents in order to avoid contact with Hyalomma ticks are proposed. Also, personal protective equipment (PPE) must be utilized at abattoirs.

Keywords: tick, CCHFV, surveillance, vector diversity

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Authors: Merouane Salhi, Toufik Zebbiche

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When the stagnation pressure of perfect gas increases, the specific heat and their ratio do not remain constant anymore and start to vary with this pressure. The gas doesn’t remain perfect. Its state equation change and it becomes for a real gas. In this case, the effects of molecular size and intermolecular attraction forces intervene to correct the state equation. The aim of this work is to show and discuss the effect of stagnation pressure on supersonic thermodynamical, physical and geometrical flow parameters, to find a general case for real gas. With the assumptions that Berthelot’s state equation accounts for the molecular size and intermolecular force effects, expressions are developed for analyzing supersonic flow for thermally and calorically imperfect gas lower than the dissociation molecules threshold. The designs parameters for supersonic nozzle like thrust coefficient depend directly on stagnation parameters of the combustion chamber. The application is for air. A computation of error is made in this case to give a limit of perfect gas model compared to real gas model.

Keywords: supersonic flow, real gas model, Berthelot’s state equation, Simpson’s method, condensation function, stagnation pressure

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: John Onolame Unuofin, Uchechukuw U. Nwodo, Anthony I. Okoh

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Laccase is constantly gaining status as important biocatalyst in biotechnology. The illimitable potential of its industrial applications and the corresponding aggressive need for phenomenal volumes of extracellularly secreted laccases have called for its interminable production from sources which are able to meet this demand within a relatively short period of time, preferably bacteria. In response to this call, this study was designed to source for laccase-producing bacteria from different environmental matrices. Three sampling environments were chosen such as wastewater treatment plants, University of Fort Hare vicinity and the Hogback woodland, all within the Eastern Cape, South Africa. Samples such as effluents, sediments, leaf litters, degrading wood and rock scrapings were selectively enriched with some model aromatic compounds and were further screened qualitatively and quantitatively on five phenolic substrates ABTS (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid), Guaiacol, 1-Naphthol, Potassium Ferric Cyanide and Syringaldazine). Basis for selection was their ability to elicit a colour change on at least three of the above mentioned agar based assay substrates. The choice isolates were further identified based on 16S rRNA molecular identification techniques. 33 isolates were screened out of the 40 representative distinct colonies during the qualitative plate screens, while quantitative screens selected out 11 bacterial isolates. They were, based on molecular identification, desginated as members of the genera Pseudomonas, Stenotrophomonas and Citrobacter of the gammaproteobacteria and Bordetalla and Achromobacter of the betaproteobacteria respectively. We therefore conclude based on our outcomes that we may have isolated efficient laccase-producing bacteria, which might be of beneficial significance in catalysis and biotechnology.

Keywords: beta proteobacteria, catalysis, gammaproteobacteria, laccase

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Authors: Tomoaki Hashimoto

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Recent technological advance has prompted significant interest in developing the control theory of quantum systems. Following the increasing interest in the control of quantum dynamics, this paper examines the control problem of Schrödinger equation because quantum dynamics is basically governed by Schrödinger equation. From the practical point of view, stochastic disturbances cannot be avoided in the implementation of control method for quantum systems. Thus, we consider here the robust stabilization problem of Schrödinger equation against stochastic disturbances. In this paper, we adopt model predictive control method in which control performance over a finite future is optimized with a performance index that has a moving initial and terminal time. The objective of this study is to derive the stability criterion for model predictive control of Schrödinger equation under stochastic disturbances.

Keywords: optimal control, stochastic systems, quantum systems, stabilization

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Authors: Wael M. Elawady, Mohamed F. Asar, Amany M. Sarhan

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This paper adopts a continuous sliding mode control scheme for trajectory tracking control of robot manipulators with structured and unstructured uncertain dynamics and external disturbances. In this algorithm, the equivalent control in the conventional sliding mode control is replaced by a PID control action. Moreover, the discontinuous switching control signal is replaced by a continuous proportional-integral (PI) control term such that the implementation of the proposed control algorithm does not require the prior knowledge of the bounds of unknown uncertainties and external disturbances and completely eliminates the chattering phenomenon of the conventional sliding mode control approach. The closed-loop system with the adopted control algorithm has been proved to be globally stable by using Lyapunov stability theory. Numerical simulations using the dynamical model of robot manipulators with modeling uncertainties demonstrate the superiority and effectiveness of the proposed approach in high speed trajectory tracking problems.

Keywords: PID, robot, sliding mode control, uncertainties

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Authors: Yuxi Zhu, Zhenqian Chen

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It is of great interest to investigate the thermal properties of non-precious metal catalysts for Proton exchange membrane fuel cell (PEMFC) based on the thermal management requirements. Due to the low symmetry of materials, to accurately obtain the thermal conductivity of materials, it is necessary to obtain the second and third order force constants by combining density functional theory and machine learning interatomic potential. To be specific, the interatomic force constants are obtained by moment tensor potential (MTP), which is trained by the computational trajectory of Ab initio molecular dynamics (AIMD) at 50, 300, 600, and 900 K for 1 ps each, with a time step of 1 fs in the AIMD computation. And then the thermal conductivity can be obtained by solving the Boltzmann transport equation. In this paper, the thermal transport properties of single metal atom catalysts are studied for the first time to our best knowledge by machine-learning interatomic potential (MLIP). Results show that the single metal atom catalysts exhibit anisotropic thermal conductivities and partially exhibit good thermal conductivity. The average lattice thermal conductivities of G-FeN₄, G-CoN₄ and G-NiN₄ at 300 K are 88.61 W/mK, 205.32 W/mK and 210.57 W/mK, respectively. While other single metal atom catalysts show low thermal conductivity due to their low phonon lifetime. The results also show that low-frequency phonons (0-10 THz) dominate thermal transport properties. The results provide theoretical insights into the application of single metal atom catalysts in thermal management.

Keywords: proton exchange membrane fuel cell, single metal atom catalysts, density functional theory, thermal conductivity, machine-learning interatomic potential

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Authors: Turky Al-Qahtani, Roustem Miftahof

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Introduction: Under common assumptions of excitabi-lity, morphological (cellular) homogeneity, and spatial structural anomalies added as required, it has been shown that biological systems are able to display travelling wave dynamics. Being not self-sustainable, existence depends on the electrophysiological state of transmembrane ion channels and it requires an extrinsic/intrinsic periodic source. However, organs in the body are highly multicellular, heterogeneous, and their functionality is the outcome of electro-mechanical conjugation, rather than excitability only. Thus, peristalsis in the gut relies on spatiotemporal myoelectrical pattern formations between the mechanical, represented by smooth muscle cells (SM), and the control, comprised of a chain of primary sensory and motor neurones, components. Synaptically linked through the afferent and efferent pathways, they form a functional unit (FU) of the gut. Aims: These are: i) to study numerically the complex dynamics, and ii) to investigate the possibility of self-sustained myoelectrical activity in the FU. Methods: The FU recreates the following sequence of physiological events: deformation of mechanoreceptors of located in SM; generation and propagation of electrical waves of depolarisation - spikes - along the axon to the soma of the primary neurone; discharge of the primary neurone and spike propagation towards the motor neurone; burst of the motor neurone and transduction of spikes to SM, subsequently producing forces of contraction. These are governed by a system of nonlinear partial and ordinary differential equations being a modified version of the Hodgkin-Huxley model and SM fibre mechanics. In numerical experiments; the source of excitation is mechanical stretches of SM at a fixed amplitude and variable frequencies. Results: Low frequency (0.5 < v < 2 Hz) stimuli cause the propagation of spikes in the neuronal chain and, finally, the generation of active forces by SM. However, induced contractions are not sufficient to initiate travelling wave dynamics in the control system. At frequencies, 2 < v < 4 Hz, multiple low amplitude and short-lasting contractions are observed in SM after the termination of stretching. For frequencies (0.5 < v < 4 Hz), primary and sensory neurones demonstrate strong connectivity and coherent electrical activity. Significant qualitative and quantitative changes in dynamics of myoelectical patterns with a transition to a self-organised mode are recorded with the high degree of stretches at v = 4.5 Hz. Increased rates of deformation lead to the production of high amplitude signals at the mechanoreceptors with subsequent self-sustained excitation within the neuronal chain. Remarkably, the connection between neurones weakens resulting in incoherent firing. Further increase in a frequency of stimulation (v > 4.5 Hz) has a detrimental effect on the system. The mechanical and control systems become disconnected and exhibit uncoordinated electromechanical activity. Conclusion: To our knowledge, the existence of periodic activity in a multicellular, functionally heterogeneous biological system with mechano-electrical dynamics, such as the FU, has been demonstrated for the first time. These findings support the notion of possible peristalsis in the gut even in the absence of intrinsic sources - pacemaker cells. Results could be implicated in the pathogenesis of intestinal dysrythmia, a medical condition associated with motor dysfunction.

Keywords: complex dynamics, functional unit, the gut, dysrythmia

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Authors: Dalal Alghawas, Jetty Lee, Kaisa Poutanen, Hani El-Nezami

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Oat β-glucan a water soluble non starch linear polysaccharide has been approved as a cholesterol lowering agent by various food safety administrations and is commonly used to reduce the risk of heart disease. The molecular weight of oat β-glucan can vary depending on the extraction and fractionation methods. It is not clear whether the molecular weight has a significant impact at reducing the acceleration of atherosclerosis. The aim of this study was to investigate three different oat β-glucan fractionations on the development of atherosclerosis in vivo. With special focus on plaque stability and the intestinal barrier function. To test this, ApoE-/- female mice were fed a high fat diet supplemented with oat bran, high molecular weight (HMW) oat β-glucan fractionate and low molecular weight (LMW) oat β-glucan fractionate for 16 weeks. Atherosclerosis risk markers were measured in the plasma, heart and aortic tree. Plaque size was measured in the aortic root and aortic tree. ICAM-1, VCAM-1, E-Selectin, P-Selectin, protein levels were assessed from the aortic tree to determine plaque stability at 16 weeks. The expression of p22phox at the aortic root was evaluated to study the NADPH oxidase complex involved in nitric oxide bioavailability and vascular elasticity. The tight junction proteins E-cadherin and beta-catenin from western blot analyses were analysed as an intestinal barrier function test. Plasma LPS, intestinal D-lactate levels and hepatic FMO gene expression were carried out to confirm whether the compromised intestinal barrier lead to endotoxemia. The oat bran and HMW oat β-glucan diet groups were more effective than the LMW β-glucan diet group at reducing the plaque size and showed marked improvements in plaque stability. The intestinal barrier was compromised for all the experimental groups however the endotoxemia levels were higher in the LMW β-glucan diet group. The oat bran and HMW oat β-glucan diet groups were more effective at attenuating the development of atherosclerosis. Reasons for this could be due to the LMW oat β-glucan diet group’s low viscosity in the gut and the inability to block the reabsorption of cholesterol. Furthermore the low viscosity may allow more bacterial endotoxin translocation through the impaired intestinal barrier. In future food technologists should carefully consider how to incorporate LMW oat β-glucan as a health promoting food.

Keywords: Atherosclerosis, beta glucan, endotoxemia, intestinal barrier function

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Authors: Anne T. Herr, Clemens Lorei

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Employees of organizations with security tasks, such as emergency services, public order services, or police forces, work every day to ensure people's safety. Violence against police is, therefore, a relevant topic both socially and politically. An increase in violence is often discussed without there being any verifiable and generally valid data. So far, scientific research has mainly focused on offender characteristics and crime statistics. These surveys are mostly subjective, retrospective, and neglect the dynamics and interactions in concrete violent situations. Therefore, more recent research methods attempt to capture the issue of violence against emergency forces more comprehensively. However, the operationalization of the constructs and the methodological approach pose particular challenges. This contribution provides an overview of new perspectives on the understanding of violent assaults and identifies current research gaps. In addition, a new research project of the Hessian University of Police and Administration in Germany is presented. In the 'AMBOSafe' study, different theoretical backgrounds for understanding violence against police and emergency services personnel will be combined in order to capture as many different perspectives of violent assaults as possible in a multimodal research approach. In a retrospective as well as in a longitudinal survey, the conditions of escalation dynamics in the assaults are recorded and supplemented by the current and valid prevalence of physical and verbal assaults in a period of four months. In addition, qualitative interviews with those affected will be used to record more detailed descriptions of and the feelings during the assaults, as well as possible causes and connections between the different groups of people. In addition to the reports of the police forces, the motives of the attackers will be collected and supplemented by analyzing the criminal case files. This knowledge can contribute to a more comprehensive understanding of violent assaults against police forces in order to be able to derive scientifically based preventive measures.

Keywords: assaults, crime statistics, escalation dynamics, police

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Authors: Brian J. Biroscak

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In the United States (US), “sex trafficking” is defined at the federal level in the Trafficking Victims Protection Act of 2000 as encompassing a number of processes such as recruitment, transportation, and provision of a person for the purpose of a commercial sex act. It involves the use of force, fraud, or coercion, or in which the person induced to perform such act has not attained 18 years of age. Accumulating evidence suggests that sex trafficking is exacerbated by social and environmental stressors (e.g., pandemics). Given that “provision” is a key part of the definition, “provisioning systems” may offer a useful lens through which to study sex trafficking dynamics. Provisioning systems are the social systems connecting individuals, small groups, entities, and embedded communities as they seek to satisfy their needs and wants for goods, services, experiences and ideas through value-based exchange in communities. This project presents a conceptual framework for understanding sex trafficking dynamics in the context of the COVID pandemic. The framework is developed as a system dynamics simulation model based on published evidence, social and behavioral science theory, and key informant interviews with stakeholders from the Protection, Prevention, Prosecution, and Partnership sectors in one US state. This “4 P Paradigm” has been described as fundamental to the US government’s anti-trafficking strategy. The present research question is: “How do sex trafficking systems (e.g., supply, demand and price) interact with other provisioning systems (e.g., networks of organizations that help sexually exploited persons) to influence trafficking over time vis-à-vis the COVID pandemic?” Semi-structured interviews with stakeholders (n = 19) were analyzed based on grounded theory and combined for computer simulation. The first step (Problem Definition) was completed by open coding video-recorded interviews, supplemented by a literature review. The model depicts provision of sex trafficking services for victims and survivors as declining in March 2020, coincidental with COVID, but eventually rebounding. The second modeling step (Dynamic Hypothesis Formulation) was completed by open- and axial coding of interview segments, as well as consulting peer-reviewed literature. Part of the hypothesized explanation for changes over time is that the sex trafficking system behaves somewhat like a commodities market, with each of the other subsystems exhibiting delayed responses but collectively keeping trafficking levels below what they would be otherwise. Next steps (Model Building & Testing) led to a ‘proof of concept’ model that can be used to conduct simulation experiments and test various action ideas, by taking model users outside the entire system and seeing it whole. If sex trafficking dynamics unfold as hypothesized, e.g., oscillated post-COVID, then one potential leverage point is to address the lack of information feedback loops between the actual occurrence and consequences of sex trafficking and those who seek to prevent its occurrence, prosecute the traffickers, protect the victims and survivors, and partner with the other anti-trafficking advocates. Implications for researchers, administrators, and other stakeholders are discussed.

Keywords: pandemics, provisioning systems, sex trafficking, system dynamics modeling

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Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi

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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.

Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene

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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: Ahmed Al-Saadi, Ali Hassanpour, Tariq Mahmud

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The main objective of this study is to investigate ways to reduce the aerodynamic drag coefficient and to increase the stability of the full-size Sport Utility Vehicle using three-dimensional Computational Fluid Dynamics (CFD) simulation. The baseline model in the simulation was the Land Rover Discovery 4. Many aerodynamic devices and external design modifications were used in this study. These reduction aerodynamic techniques were tested individually or in combination to get the best design. All new models have the same capacity and comfort of the baseline model. Uniform freestream velocity of the air at inlet ranging from 28 m/s to 40 m/s was used. ANSYS Fluent software (version 16.0) was used to simulate all models. The drag coefficient obtained from the ANSYS Fluent for the baseline model was validated with experimental data. It is found that the use of modern aerodynamic add-on devices and modifications has a significant effect in reducing the aerodynamic drag coefficient.

Keywords: aerodynamics, RANS, sport utility vehicle, turbulent flow

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Authors: Ciro Moreno-Ramirez, Maria Tomas-Rodriguez, Simos A. Evangelou

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A motorcycle's front end links the front wheel to the motorcycle's chassis and has two main functions: the front wheel suspension and the vehicle steering. Up to this date, several suspension systems have been developed in order to achieve the best possible front end behavior, being the telescopic fork the most common one and already subjected to several years of study in terms of its kinematics, dynamics, stability and control. A motorcycle telescopic fork suspension model consists of a couple of outer tubes which contain the suspension components (coil springs and dampers) internally and two inner tubes which slide into the outer ones allowing the suspension travel. The outer tubes are attached to the frame through two triple trees which connect the front end to the main frame through the steering bearings and allow the front wheel to turn about the steering axis. This system keeps the front wheel's displacement in a straight line parallel to the steering axis. However, there exist alternative suspension designs that allow different trajectories of the front wheel with the suspension travel. In this contribution, the authors investigate an alternative front suspension system (Hossack suspension) and its influence on the motorcycle nonlinear dynamics to identify and reduce stability risks that a new suspension systems may introduce in the motorcycle dynamics. Based on an existing high-fidelity motorcycle mathematical model, the front end geometry is modified to accommodate a Hossack suspension system. It is characterized by a double wishbone design that varies the front end geometry on certain maneuverings and, consequently, the machine's behavior/response. It consists of a double wishbone structure directly attached to the chassis. In here, the kinematics of this system and its impact on the motorcycle performance/stability are analyzed and compared to the well known telescopic fork suspension system. The framework of this research is the mathematical modelling and numerical simulation. Full stability analyses are performed in order to understand how the motorcycle dynamics may be affected by the newly introduced front end design. This study is carried out by a combination of nonlinear dynamical simulation and root-loci methods. A modal analysis is performed in order to get a deeper understanding of the different modes of oscillation and how the Hossack suspension system affects them. The results show that different kinematic designs of a double wishbone suspension systems do not modify the general motorcycle's stability. The normal modes properties remain unaffected by the new geometrical configurations. However, these normal modes differ from one suspension system to the other. It is seen that the normal modes behaviour depends on various important dynamic parameters, such as the front frame flexibility, the steering damping coefficient and the centre of mass location.

Keywords: nonlinear mechanical systems, motorcycle dynamics, suspension systems, stability

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Authors: Sakura Ganegama Bogodage, Andrew Yee Tat Leung

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This paper describes experimental, Computational Fluid Dynamics (CFD) and theoretical analysis of a cyclone performance, operated 1.0 g/m3 solid loading rate, at two different inlet velocities (5 m/s and 10 m/s). Comparing experimental results with theoretical and CFD simulation results, it is pronounced that the influence of solid in processing flow is significant than expected. Experimental studies based on gas- solid flows of cyclone separators are complicated as they required advanced sensitive measuring techniques, especially flow characteristics. Thus, CFD modelling and theoretical analysis are economical in analyzing cyclone separator performance but detailed clarifications of the application of these in cyclone separator performance evaluation is not yet discussed. The present study shows the limitations of influencing parameters of CFD and theoretical considerations, comparing experimental results and flow characteristics from CFD modelling.

Keywords: cyclone performance, inlet velocity, pressure drop, solid loading rate

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Authors: Tomas Menard

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The design of control-law for engineering systems has been investigated for many decades. While many results are concerned with continuous systems with continuous output, nowadays, many controlled systems have to transmit their output measurements through network, hence making it discrete-time. But it is well known that the sampling of a system whose control-law is based on the continuous output may render the system unstable, especially when this sampling period is long compared to the system dynamics. The control design then has to be adapted in order to cope with this issue. In this paper, we consider systems which can be modeled as double integrator with uncertainty on the input since many mechanical systems can be put under such form. We present a control scheme based on an observer using only discrete time measurement and which provides continuous time estimation of the state, combined with a continuous control law, which stabilized a system with second-order dynamics even in the presence of uncertainty. It is further shown that arbitrarily long sampling periods can be dealt with properly setting the control scheme parameters.

Keywords: dynamical system, control law design, sampled output, observer design

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Authors: Vineeta Kaushik, Manisha Goel

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Chaperones are proteins that help other proteins fold correctly, and are found in all domains of life i.e., prokaryotes, eukaryotes and archaea. Various comparative genomic studies have suggested that the archaeal protein folding machinery appears to be highly similar to that found in eukaryotes. In case of protein folding; slow rotation of peptide prolyl-imide bond is often the rate limiting step. Formation of the prolyl-imide bond during the folding of a protein requires the assistance of other proteins, termed as peptide prolyl cis-trans isomerases (PPIases). Cyclophilins constitute the class of peptide prolyl isomerases with a wide range of biological function like protein folding, signaling and chaperoning. Most of the cyclophilins exhibit PPIase enzymatic activity and play active role in substrate protein folding which classifies them as a category of molecular chaperones. Till date, there is not very much data available in the literature on archaeal cyclophilins. We aim to compare the structural and biochemical features of the cyclophilin protein from within the three domains to elucidate the features affecting their stability and enzyme activity. In the present study, we carry out in-silico analysis of the cyclophilin proteins to predict their conserved residues, sites under positive selection and compare these proteins to their bacterial and eukaryotic counterparts to predict functional divergence. We also aim to clone and express these proteins in heterologous system and study their biophysical characteristics in detail using techniques like CD and fluorescence spectroscopy. Overall we aim to understand the features contributing to the folding, stability and dynamics of the archaeal cyclophilin proteins.

Keywords: biophysical characterization, x-ray crystallography, chaperone-like activity, cyclophilin, PPIase activity

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Malik I. Al-Amayreh, Mohammad I. Kilani, Ahmed S. Al-Salaymeh

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This works presents a Computational Fluid Dynamics (CFD) simulation of a butterfly valve used to control the flow of combustible gas mixture in an industrial process setting. The work uses CFD simulation to analyze the flow characteristics in the vicinity of the valve, including the velocity distributions, streamlines and path lines. Frequency spectrum of the pressure pulsations downstream the valves, and the vortex shedding allow predicting the torque fluctuations acting on the valve shaft and the possibility of generating mechanical vibration and resonance. These fluctuations are due to aerodynamic torque resulting from fluid turbulence and vortex shedding in the valve vicinity. The valve analyzed is located in a pipeline between two opposing 90o elbows, which exposes the valve and the surrounding structure to the turbulence generated upstream and downstream the elbows at either end of the pipe. CFD simulations show that the best location for the valve from a vibration point of view is in the middle of the pipe joining the elbows.

Keywords: butterfly valve vibration analysis, computational fluid dynamics, fluid flow circuit design, fluctuation

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Authors: Elizabeth M. Seabrook, Nikki S. Rickard

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Examining time-dependent measures of emotion such as variability, instability, and inertia, provide critical and complementary insights into mental health status. Observing changes in the pattern of emotional expression over time could act as a tool to identify meaningful shifts between psychological well- and ill-being. From a practical standpoint, however, examining emotion dynamics day-to-day is likely to be burdensome and invasive. Utilizing social media data as a facet of lived experience can provide real-world, temporally specific access to emotional expression. Emotional language on social media may provide accurate and sensitive insights into individual and community mental health and well-being, particularly with focus placed on the within-person dynamics of online emotion expression. The objective of the current study was to examine the dynamics of emotional expression on the social network platform Facebook for active users and their relationship with psychological well- and ill-being. It was expected that greater positive and negative emotion variability, instability, and inertia would be associated with poorer psychological well-being and greater depression symptoms. Data were collected using a smartphone app, MoodPrism, which delivered demographic questionnaires, psychological inventories assessing depression symptoms and psychological well-being, and collected the Status Updates of consenting participants. MoodPrism also delivered an experience sampling methodology where participants completed items assessing positive affect, negative affect, and arousal, daily for a 30-day period. The number of positive and negative words in posts was extracted and automatically collated by MoodPrism. The relative proportion of positive and negative words from the total words written in posts was then calculated. Preliminary analyses have been conducted with the data of 9 participants. While these analyses are underpowered due to sample size, they have revealed trends that greater variability in the emotion valence expressed in posts is positively associated with greater depression symptoms (r(9) = .56, p = .12), as is greater instability in emotion valence (r(9) = .58, p = .099). Full data analysis utilizing time-series techniques to explore the Facebook data set will be presented at the conference. Identifying the features of emotion dynamics (variability, instability, inertia) that are relevant to mental health in social media emotional expression is a fundamental step in creating automated screening tools for mental health that are temporally sensitive, unobtrusive, and accurate. The current findings show how monitoring basic social network characteristics over time can provide greater depth in predicting risk and changes in depression and positive well-being.

Keywords: emotion, experience sampling methods, mental health, social media

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Authors: Michal Biały, Konrad Pietrykowski, Rafal Sochaczewski

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The kinematics and dynamics analysis of crank-piston system of aircraft engine. The object of the study was the high power aircraft engine ASz 62-IR. This engine is produced by a Polish company WSK "PZL-KALISZ" S.A.". All analyzes were performed numerically using CAD and CAE environment. Three-dimensional model of the crank-piston system was developed based on real engine located in the Laboratory of Centre of Innovation and Advanced Technologies of Lublin University of Technology. During the development of the model, the technique of reverse engineering - 3D scanning was used. ASz 62-IR engine is characterized by a radial type of crank-piston system. In this system the cylinders are arranged radially around the circle. This crank-piston system consists of a main connecting rod and eight additional connecting rods. In addition, three-dimensional model consists of a piston pins, pistons and piston rings. As a result of the specific engine design, characteristics of the piston individual movement are slightly different from each other. But the model assumes that they are the same during the analysis. Three-dimensional model of the engine was implemented into the MSC Adams software. The environment of MSC Adams allows for multibody simulation of the dynamic phenomena. This determines the state parameters of the moving elements, among which the load or force distribution on each kinematic node can be distinguished. Materials and characteristic materials parameters were adopted on the basis of commonly used materials for engine parts. The mass values of individual elements were adopted on the basis of real engine parts. The piston gas forces were replaced by calculation of pressure variations recorded during engine tests on the engine test bench. The research the changes of forces acting in the individual kinematic pairs of crank-piston system. The model allows to determine the load on the crankshaft main bearings. This gives the possibility for the main supports forces analysis The model allows for testing and simulation of kinematics and dynamics of a radial aircraft engine. This is the first stage of the work, which aims to numerical simulation of vibration of multi-cylinder aircraft engine. This work has been financed by the Polish National Centre for Research and Development, INNOLOT, under Grant Agreement No. INNOLOT/I/1/NCBR/2013.

Keywords: aircraft engine, CAD, CAE, dynamics, kinematics, MSC Adams, numerical simulation

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Authors: Ertuğ Yıldırım, Dile Kara, Salih Zeki Yıldız

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Metal containing polymers (MCPs) are macro molecules usually containing metal-ligand coordination units and are a multidisciplinary research field mainly based at the interface between coordination chemistry and polymer science. The progress of this area has also been reinforced by the growth of several other closely related disciplines including macro molecular engineering, crystal engineering, organic synthesis, supra molecular chemistry and colloidal and material science. Schiff base ligands are very effective in constructing supra molecular architectures such as coordination polymers, double helical and triple helical complexes. In addition, Schiff base derivatives incorporating a fluorescent moiety are appealing tools for optical sensing of metal ions. MCPs are well-known systems in which the combinations of local parameters are possible by means of fluoro metric techniques. Generally, without incorporation of the fluorescent groups with polymers is unspecific, and it is not useful to analyze their fluorescent properties. Therefore, it is necessary to prepare a new type epoxy polymers with fluorescent groups in terms of metal sensing prop and the other photo chemical applications. In the present study metal containing polymers were prepared via poly functional monomeric Schiff base metal chelate complexes in the presence of dis functional monomers such as diglycidyl ether Bisphenol A (DGEBA). The synthesized complexes and polymers were characterized by FTIR, UV-VIS and mass spectroscopies. The preparations of epoxy polymers have been carried out at 185 °C. The prepared composites having sharp and narrow excitation/emission properties are expected to be applicable in various systems such as heat-resistant polymers and photo voltaic devices. The prepared composite is also ideal for various applications, easily prepared, safe, and maintain good fluorescence properties.

Keywords: Schiff base ligands, crystal engineering, fluorescence properties, Metal Containing Polymers (MCPs)

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Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

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Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

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