Search results for: single nucleotide polymorphism

Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: Apoorva Vinod, Archana Mathur, Snehanshu Saha

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Though there exists a plethora of Activation Functions (AFs) used in single and multiple hidden layer Neural Networks (NN), their behavior always raised curiosity, whether used in combination or singly. The popular AFs –Sigmoid, ReLU, and Tanh–have performed prominently well for shallow and deep architectures. Most of the time, AFs are used singly in multi-layered NN, and, to the best of our knowledge, their performance is never studied and analyzed deeply when used in combination. In this manuscript, we experiment with multi-layered NN architecture (both on shallow and deep architectures; Convolutional NN and VGG16) and investigate how well the network responds to using two different AFs (Sigmoid-Tanh, Tanh-ReLU, ReLU-Sigmoid) used alternately against a traditional, single (Sigmoid-Sigmoid, Tanh-Tanh, ReLUReLU) combination. Our results show that using two different AFs, the network achieves better accuracy, substantially lower loss, and faster convergence on 4 computer vision (CV) and 15 Non-CV (NCV) datasets. When using different AFs, not only was the accuracy greater by 6-7%, but we also accomplished convergence twice as fast. We present a case study to investigate the probability of networks suffering vanishing and exploding gradients when using two different AFs. Additionally, we theoretically showed that a composition of two or more AFs satisfies Universal Approximation Theorem (UAT).

Keywords: activation function, universal approximation function, neural networks, convergence

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Authors: Trupti Chavan, Ramachandra Guda, Kameshwar Rao

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The lack of data is a pain problem in medical image analysis using a convolutional neural network (CNN). This work uses various spatial transformation techniques to address the medical image augmentation issue for knee detection and localization using an enhanced single shot detector (SSD) network. The spatial transforms like a negative, histogram equalization, power law, sharpening, averaging, gaussian blurring, etc. help to generate more samples, serve as pre-processing methods, and highlight the features of interest. The experimentation is done on the OpenKnee dataset which is a collection of knee images from the openly available online sources. The CNN called enhanced single shot detector (SSD) is utilized for the detection and localization of the knee joint from a given X-ray image. It is an enhanced version of the famous SSD network and is modified in such a way that it will reduce the number of prediction boxes at the output side. It consists of a classification network (VGGNET) and an auxiliary detection network. The performance is measured in mean average precision (mAP), and 99.96% mAP is achieved using the proposed enhanced SSD with spatial transformations. It is also seen that the localization boundary is comparatively more refined and closer to the ground truth in spatial augmentation and gives better detection and localization of knee joints.

Keywords: data augmentation, enhanced SSD, knee detection and localization, medical image analysis, openKnee, Spatial transformations

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Authors: Norma Binti Alias, Che Rahim Che The, Norfarizan Mohd Said, Sakinah Abdul Hanan, Akhtar Ali

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This paper discusses on the transportation of magnetic drug targeting through blood within vessels, tissues and cells. There are three integrated mathematical models to be discussed and analyze the concentration of drug and blood flow through magnetic nanoparticles. The cell therapy brought advancement in the field of nanotechnology to fight against the tumors. The systematic therapeutic effect of Single Cells can reduce the growth of cancer tissue. The process of this nanoscale phenomena system is able to measure and to model, by identifying some parameters and applying fundamental principles of mathematical modeling and simulation. The mathematical modeling of single cell growth depends on three types of cell densities such as proliferative, quiescent and necrotic cells. The aim of this paper is to enhance the simulation of three types of models. The first model represents the transport of drugs by coupled partial differential equations (PDEs) with 3D parabolic type in a cylindrical coordinate system. This model is integrated by Non-Newtonian flow equations, leading to blood liquid flow as the medium for transportation system and the magnetic force on the magnetic nanoparticles. The interaction between the magnetic force on drug with magnetic properties produces induced currents and the applied magnetic field yields forces with tend to move slowly the movement of blood and bring the drug to the cancer cells. The devices of nanoscale allow the drug to discharge the blood vessels and even spread out through the tissue and access to the cancer cells. The second model is the transport of drug nanoparticles from the vascular system to a single cell. The treatment of the vascular system encounters some parameter identification such as magnetic nanoparticle targeted delivery, blood flow, momentum transport, density and viscosity for drug and blood medium, intensity of magnetic fields and the radius of the capillary. Based on two discretization techniques, finite difference method (FDM) and finite element method (FEM), the set of integrated models are transformed into a series of grid points to get a large system of equations. The third model is a single cell density model involving the three sets of first order PDEs equations for proliferating, quiescent and necrotic cells change over time and space in Cartesian coordinate which regulates under different rates of nutrients consumptions. The model presents the proliferative and quiescent cell growth depends on some parameter changes and the necrotic cells emerged as the tumor core. Some numerical schemes for solving the system of equations are compared and analyzed. Simulation and computation of the discretized model are supported by Matlab and C programming languages on a single processing unit. Some numerical results and analysis of the algorithms are presented in terms of informative presentation of tables, multiple graph and multidimensional visualization. As a conclusion, the integrated of three types mathematical modeling and the comparison of numerical performance indicates that the superior tool and analysis for solving the complete set of magnetic drug delivery system which give significant effects on the growth of the targeted cancer cell.

Keywords: mathematical modeling, visualization, PDE models, magnetic nanoparticle drug delivery model, drug release model, single cell effects, avascular tumor growth, numerical analysis

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Authors: Taras Agryzkov, Jose L. Oliver, Leandro Tortosa, Jose Vicent

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This paper aims to demonstrate how network models can be used to understand and to deal with some aspects of urban complexity. As it is well known, the Theory of Architecture and Urbanism has been using for decades’ intellectual tools based on the ‘sciences of complexity’ as a strategy to propose theoretical approaches about cities and about architecture. In this sense, it is possible to find a vast literature in which for instance network theory is used as an instrument to understand very diverse questions about cities: from their commercial activity to their heritage condition. The contribution of this research consists in adding one step of complexity to this process: instead of working with one single primal graph as it is usually done, we will show how new network models arise from the consideration of two different primal graphs interacting in two layers. When we model an urban network through a mathematical structure like a graph, the city is usually represented by a set of nodes and edges that reproduce its topology, with the data generated or extracted from the city embedded in it. All this information is normally displayed in a single layer. Here, we propose to separate the information in two layers so that we can evaluate the interaction between them. Besides, both layers may be composed of structures that do not have to coincide: from this bi-layer system, groups of interactions emerge, suggesting reflections and in consequence, possible actions.

Keywords: graphs, mathematics, networks, urban studies

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Authors: J. Niemisto, A. Nissinen, S. Soimakallio

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Aviation causes carbon dioxide (CO2) emissions and other climate forcers which increase the contribution of aviation on climate change. Aviation industry and number of air travellers are constantly increasing. Aviation industry has an ambitious goal to strongly cut net CO2 emissions. Modern fleet, alternative jet fuels technologies and route optimisation are important technological tools in the emission reduction. Faster approaches are needed as well. Emission trade systems, voluntary carbon offset compensation schemes and taxation are already in operation. Global scenarios of aviation industry and its greenhouse gas emissions and other climate forcers are discussed in this review study based on literature and other published data. The focus is on the aviation in Nordic countries, but also European and global situation are considered. Different emission reduction technologies and compensation modes are examined. In addition, the role of aviation in a single passenger’s (a Finnish consumer) annual carbon footprint is analysed and a comparison of available emission calculators and carbon offset systems is performed. Long-haul fights have a significant role in a single consumer´s and company´s carbon footprint, but remarkable change in global emission level would need a huge change in attitudes towards flying.

Keywords: aviation, climate change, emissions, environment

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Authors: Hassan Ali Abood Nassrullah, Jabbar Fadeel Mahdi, Mohammed Salih Mahdi Alkurdi, Ali Al Mousawi, Saad Ibrahim Al-Ghabban, Abdul Amir H. Kadhum, Ahmed Al-Amiery

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Background: Q fever is a zoonotic disease characterized by its clinical polymorphism and can present acutely as fever, pneumonia, hepatitis, and chronically as infective endocarditis, arthritis, osteomyelitis, or hepatitis. Objective: The aim of this study is To estimate the prevalence of cases of Q fever in hospitalized febrile patients in Imam Al Hussain Teaching Medical City in Karbala. Methods: One hundred patients with pyrexia were admitted to the medical ward from 1st August to 31st December 2019. Serological procedures fortified by Enzyme-linked Immunosorbent Assay test. Patients were considered to have acute Q fever when the specific antibodies (IgM and IgG) of phase II of Coxiella burnetii were positive. Results: The mean age of the patients was 35.05±12.93 years; females constituted 60% of them. Eighteen patients (18%) showed positive results for IgM, a lower proportion (13% n=13) had positive IgG levels, and 9% showed equivocal results. Statistical analysis revealed a significant association between positive IgM levels of the female gender and in patients consuming unpasteurized milk. One patient (female aged 60 years) died in the hospital, while all other patients were discharged well. Two female patients were pregnant, and one of them had an abortion. Conclusions: Q fever is more common in febrile patients. The study indicates that this disease should not be overlooked in the differential diagnosis of acute fever. Serological testing should be performed in all patients with acute febrile illness with an unsettling diagnosis.

Keywords: antibodies, frequency, immunoglobulin IgM, Q fever

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Authors: Duane Booysen, Ashraf Kagee

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There is a high prevalence of violent crime and trauma exposure in South African society. Considering the prevalence of continuous violent crimes and traumatization in South Africa, the public mental health sector is required to combat the burgeoning effect of traumatic stress in South Africa. Trauma counselors, especially, provide important mental health services at primary health care to persons affected by traumatic events. Therefore, the evaluation and implementation of evidence-based trauma therapies is essential at a primary health care level in treating traumatic stress. A single-case design was used to evaluate the treatment effect of a Brief Trauma Treatment Programme treating persons who present with symptoms of posttraumatic stress disorder at a primary care trauma centre in Cape Town, South Africa. The sample consisted of six adult participants who presented with symptoms of posttraumatic stress and were assessed at baseline, during treatment, post-intervention and at 3-month follow. All participants received six sessions of trauma therapy. Assessment measures included the posttraumatic stress disorder symptom scale interviews for Diagnostic and Statistical Manual fifth edition (DSM5), the posttraumatic disorder checklist for DSM5, Beck Depression Inventory and Beck Anxiety Inventory. Results demonstrate that participants had noticeable reduced symptoms for traumatic stress, anxiety and depression despite living in contexts of violent crime and trauma. In conclusion, the article critically reflects on the need to evaluate and implement evidence-based treatments for the South African context, and how evidence-based treatments are used in developing socio-economic and cultural diverse contexts with continuous levels of violence and traumatization.

Keywords: psychological interventions, public mental health, traumatic stress, single-case design

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Authors: Muluneh Ademe, Zeleke Mekonnen

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Objective: to determine the level of bacterial contamination of reused insulin syringes among diabetic patients. Method: A facility based cross-sectional study was conducted among diabetic patients. Data on socio-demographic variables, history of injection syringe reuse, and frequency of reuse of syringes were collected using predesigned questionnaire. Finally, the samples from the syringes were cultured according to standard microbiological techniques. Result: Eighteen diabetic patients at Jimma University Hospital participated. A total of 83.3% of participants reused a single injection syringe for >30 consecutive injections, while 16.7% reused for >30 injections. Our results showed 22.2% of syringes were contaminated with methicillin-resistant Staphylococcus aures. Conclusion: We conclude reuse of syringe is associated with microbial contamination. The findings that 4/18 syringes being contaminated with bacteria is an alarming situation. A mechanism should be designed for patients to get injection syringes with affordable price. If reusing is not avoidable, reducing number of injections per a single syringe and avoiding needle touching with hand or other non-sterile material may be an alternative to reduce the risk of contamination.

Keywords: diabetes mellitus, Ethiopia, subcutaneous insulin injection, syringe reuse

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Authors: My Ali El Khakani

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Single-wall Carbon nanotubes (SWCNTs) possess an unprecedented combination of unique properties that make them highly promising for suitable for a new generation of photovoltaic (PV) devices. Prior to discussing the integration of SWCNTs films into effective PV devices, we will briefly highlight our work on the synthesis of SWCNTs by means of the KrF pulsed laser deposition technique, their purification and transfer onto n-silicon substrates to form p-n junctions. Some of the structural and optoelectronic properties of SWCNTs relevant to PV applications will be emphasized. By varying the SWCNTs film density (µg/cm2), we were able to point out the existence of an optimum value that yields the highest photoconversion efficiency (PCE) of ~10%. Further control of the doping of the p-SWCNTs films, through their exposure to nitric acid vapors, along with the insertion of an optimized hole-extraction-layer in the p-SWCNTs/n-Si hybrid devices permitted to achieve a PCE value as high as 14.2%. Such a high PCE value demonstrates the full potential of these p-SWCNTs/n-Si devices for sunlight photoconversion. On the other hand, by examining both the optical transmission and electrical conductance of the SWCNTs’ films, we established a figure of merit (FOM) that was shown to correlate well with the PCE performance. Such a direct relationship between the FOM and the PCE can be used as a guide for further PCE enhancement of these novel p-SWCNTs/n-Si PV devices.

Keywords: carbon nanotubes (CNTs), CNTs-silicon hybrid devices, photoconversion, photovoltaic devices, pulsed laser deposition

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Authors: Yi Xiong, Tao Kong

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Traditional safety, risk and reliability analysis approaches are problem-oriented, which make it great workload when analyzing complicated and huge system, besides, too much repetitive work would to do if the analyzed system composed by many similar components. It is pressing need an object and function oriented approach to maintain high consistency with problem domain. A new approach is proposed to overcome these shortcomings of traditional approaches, the concepts: class, abstract, inheritance, polymorphism and encapsulation are introduced into FTA and establish the professional class library that the abstractions of physical objects in real word, four areas relevant information also be proposed as the establish help guide. The interaction between classes is completed by the inside or external methods that mapping the attributes to base events through fully search the knowledge base, which forms good encapsulation. The object oriented fault tree analysis system that analyze and evaluate the system safety and reliability according to the original appearance of the problem is set up, where could mapped directly from the class and object to the problem domain of the fault tree analysis. All the system failure situations can be analyzed through this bottom-up fault tree construction approach. Under this approach architecture, FTA approach is developed, which avoids the human influence of the analyst on analysis results. It reveals the inherent safety problems of analyzed system itself and provides a new way of thinking and development for safety analysis. So that object oriented technology in the field of safety applications and development, safety theory is conducive to innovation.

Keywords: FTA, knowledge base, object-oriented technology, reliability analysis

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Authors: Zone-Ching Lin, Hao-Yuan Jheng, Zih-Wun Jhang

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The paper innovatively proposes using the concept of specific down force energy (SDFE) and AFM machine to establish a machining method of cross-shape nanochannel on single-crystal silicon substrate. As for machining a cross-shape nanochannel by AFM machine, the paper develop a method of machining cross-shape nanochannel groove at a fixed down force by using SDFE theory and combining the planned cutting path of cross-shape nanochannel up to 5th machining layer it finally achieves a cross-shape nanochannel at a cutting depth of around 20nm. Since there may be standing burr at the machined cross-shape nanochannel edge, the paper uses a smaller down force to cut the edge of the cross-shape nanochannel in order to lower the height of standing burr and converge the height of standing burr at the edge to below 0.54nm as set by the paper. Finally, the paper conducts experiments of machining cross-shape nanochannel groove on single-crystal silicon by AFM probe, and compares the simulation and experimental results. It is proved that this proposed machining method of cross-shape nanochannel is feasible.

Keywords: atomic force microscopy (AFM), cross-shape nanochannel, silicon substrate, specific down force energy (SDFE)

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Authors: A. E. El-Henawey, A. A. El-Kouny, M. M. Abd –El-Halim

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Moving target indication (MTI) which is an anti-clutter technique that limits the display of clutter echoes. It uses the radar received information primarily to display moving targets only. The purpose of MTI is to discriminate moving targets from a background of clutter or slowly-moving chaff particles as shown in this paper. Processing system in these radars is so massive and complex; since it is supposed to perform a great amount of processing in very short time, in most radar applications the response of a single canceler is not acceptable since it does not have a wide notch in the stop-band. A double-delay canceler is an MTI delay-line canceler employing the two-delay-line configuration to improve the performance by widening the clutter-rejection notches, as compared with single-delay cancelers. This canceler is also called a double canceler, dual-delay canceler, or three-pulse canceler. In this paper, a double delay line canceler is chosen for study due to its simplicity in both concept and implementation. Discussing the implementation of a simple digital moving target indicator (DMTI) using FPGA which has distinct advantages compared to other application specific integrated circuit (ASIC) for the purposes of this work. The FPGA provides flexibility and stability which are important factors in the radar application.

Keywords: FPGA, MTI, double delay line canceler, Doppler Shift

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Authors: Antonio Pratelli, Lorenzo Brocchini, Reginald Roy Souleyrette

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A rotary is a traffic circle intersection where vehicles entering from branches give priority to circulating flow. Vehicles entering the intersection from converging roads move around the central island and weave out of the circle into their desired exiting branch. This creates merging and diverging conflicts among any entry and its successive exit, i.e., a section. Therefore, rotary capacity models are usually based on the weaving of the different movements in any section of the circle, and the maximum rate of flow value is then related to each weaving section of the rotary. Nevertheless, the single-section capacity value does not lead to the typical performance characteristics of the intersection, such as the entry average delay which is directly linked to its level of service. From another point of view, modern roundabout capacity models are based on the limitation of the flow entering from the single entrance due to the amount of flow circulating in front of the entrance itself. Modern roundabouts capacity models generally lead also to a performance evaluation. This paper aims to incorporate a modern roundabout capacity model into an old rotary capacity method to obtain from the latter the single input capacity and ultimately achieve the related performance indicators. Put simply; the main objective is to calculate the average delay of each single roundabout entrance to apply the most common Highway Capacity Manual, or HCM, criteria. The paper is organized as follows: firstly, the rotary and roundabout capacity models are sketched, and it has made a brief introduction to the model combination technique with some practical instances. The successive section is deserved to summarize the TRRL old rotary capacity model and the most recent HCM-7th modern roundabout capacity model. Then, the two models are combined through an iteration-based algorithm, especially set-up and linked to the concept of roundabout total capacity, i.e., the value reached due to a traffic flow pattern leading to the simultaneous congestion of all roundabout entrances. The solution is the average delay for each entrance of the rotary, by which is estimated its respective level of service. In view of further experimental applications, at this research stage, a collection of existing rotary intersections operating with the priority-to-circle rule has already started, both in the US and in Italy. The rotaries have been selected by direct inspection of aerial photos through a map viewer, namely Google Earth. Each instance has been recorded by location, general urban or rural, and its main geometrical patterns. Finally, conclusion remarks are drawn, and a discussion on some further research developments has opened.

Keywords: mixed methods, old rotary and modern roundabout capacity models, total capacity algorithm, level of service estimation

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Authors: Tanveer Hussain, Misbah Hussain, Masroor Ellahi Babar, Muhammad Traiq Pervez, Fiaz Hussain, Sana Zahoor, Rashid Saif

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Interleukin 2 (IL-2) is a cytokine which is produced by activated T cells, play important role in immune response against antigen. It act in both autocrine and paracrine manner. It can stimulate B cells and various other phagocytic cells like monocytes, lymphokine-activated killer cells and natural killer cells. Acting in autocrine fashion, IL-2 protein plays a crucial role in proliferation of T cells. IL-2 triggers the release of pro and anti- inflammatory cytokines by activating several pathways. In present study, exon 1 of IL-2 gene of four local Pakistani breeds (Dera Din Panah, Beetal, Nachi and Kamori) from two provinces was amplified by using reported Ovine IL-2 primers, yielding PCR product of 501 bp. The sequencing of all samples was done to identify the polymorphisms in amplified region of IL-2 gene. Analysis of sequencing data resulted in identification of one novel nucleotide substitution (T→A) in amplified non-coding region of IL-2 gene. Comparison of IL-2 gene sequence of all four breeds with other goat breeds showed high similarity in sequence. While phylogenetic analysis of our local breeds with other mammals showed that IL-2 is a variable gene which has undergone many substitutions. This high substitution rate can be due to the decreased or increased changed selective pressure. These rapid changes can also lead to the change in function of immune system. This pioneering study of Pakistani goat breeds urge for further studies on immune system of each targeted breed for fully understanding the functional role of IL-2 in goat immunity.

Keywords: interleukin 2, mutational analysis, phylogeny, goat breeds, Pakistan

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Authors: Y. Roumila, D. Meziani, R. Bagtache, K. Abdmeziem, M. Trari

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Heterogeneous photocatalysis over semiconductors has proved its effectiveness in the treatment of wastewaters since it works under soft conditions. It has emerged as a promising technique, giving rise to less toxic effluents and offering the opportunity of using sunlight as a sustainable and renewable source of energy. Many compounds have been used as photocatalysts. Though synthesized ones are intensively used, they remain expensive, and their synthesis involves special conditions. We thus thought of implementing a natural material, a phosphate ore, due to its low cost and great availability. Our work is devoted to the removal of hazardous organic pollutants, which cause several environmental problems and health risks. Among them, dye pollutants occupy a large place. This work relates to the study of the photodegradation of methyl violet (MV) and rhodamine B (RhB), in single and binary systems, under UV light and sunlight irradiation. Methyl violet is a triarylmethane dye, while RhB is a heteropolyaromatic dye belonging to the Xanthene family. In the first part of this work, the natural compound was characterized using several physicochemical and photo-electrochemical (PEC) techniques: X-Ray diffraction, chemical, and thermal analyses scanning electron microscopy, UV-Vis diffuse reflectance measurements, and FTIR spectroscopy. The electrochemical and photoelectrochemical studies were performed with a Voltalab PGZ 301 potentiostat/galvanostat at room temperature. The structure of the phosphate material was well characterized. The photo-electrochemical (PEC) properties are crucial for drawing the energy band diagram, in order to suggest the formation of radicals and the reactions involved in the dyes photo-oxidation mechanism. The PEC characterization of the natural phosphate was investigated in neutral solution (Na₂SO₄, 0.5 M). The study revealed the semiconducting behavior of the phosphate rock. Indeed, the thermal evolution of the electrical conductivity was well fitted by an exponential type law, and the electrical conductivity increases with raising the temperature. The Mott–Schottky plot and current-potential J(V) curves recorded in the dark and under illumination clearly indicate n-type behavior. From the results of photocatalysis, in single solutions, the changes in MV and RhB absorbance in the function of time show that practically all of the MV was removed after 240 mn irradiation. For RhB, the complete degradation was achieved after 330 mn. This is due to its complex and resistant structure. In binary systems, it is only after 120 mn that RhB begins to be slowly removed, while about 60% of MV is already degraded. Once nearly all of the content of MV in the solution has disappeared (after about 250 mn), the remaining RhB is degraded rapidly. This behaviour is different from that observed in single solutions where both dyes are degraded since the first minutes of irradiation.

Keywords: environment, organic pollutant, phosphate ore, photodegradation

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Authors: Faisal Nouroz, Mukaramin Mukaramin

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Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Marek Dlapa

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The algebraic approach is applied to the control of the HiMAT (Highly Maneuverable Aircraft Technology). The objective is to find a robust controller which guarantees robust stability and decoupled control of longitudinal model of a scaled remotely controlled vehicle version of the advanced fighter HiMAT. Control design is performed by decoupling the nominal MIMO (multi-input multi-output) system into two identical SISO (single-input single-output) plants which are approximated by a 4th order transfer function. The algebraic approach is then used for pole placement design, and the nominal closed-loop poles are tuned so that the peak of the µ-function is minimal. As an optimization tool, evolutionary algorithm Differential Migration is used in order to overcome the multimodality of the cost function yielding simple controller with decoupling for nominal plant which is compared with the D-K iteration through simulations of standard longitudinal manoeuvres documenting decoupled control obtained from algebraic approach for nominal plant as well as worst case perturbation.

Keywords: algebraic approach, evolutionary computation, genetic algorithms, HiMAT, robust control, structured singular value

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Authors: Ayad Al-Mahturi, Herman Wahid

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This paper presents an optimal state feedback controller based on Linear Quadratic Regulator (LQR) for a two-rotor aero-dynamical system (TRAS). TRAS is a highly nonlinear multi-input multi-output (MIMO) system with two degrees of freedom and cross coupling. There are two parameters that define the behavior of LQR controller: state weighting matrix and control weighting matrix. The two parameters influence the performance of LQR. Particle Swarm Optimization (PSO) is proposed to optimally tune weighting matrices of LQR. The major concern of using LQR controller is to stabilize the TRAS by making the beam move quickly and accurately for tracking a trajectory or to reach a desired altitude. The simulation results were carried out in MATLAB/Simulink. The system is decoupled into two single-input single-output (SISO) systems. Comparing the performance of the optimized proportional, integral and derivative (PID) controller provided by INTECO, results depict that LQR controller gives a better performance in terms of both transient and steady state responses when PSO is performed.

Keywords: LQR controller, optimal control, particle swarm optimization (PSO), two rotor aero-dynamical system (TRAS)

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Authors: Warda Nasir, M. N. S. Qureshi

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Whistler waves are right handed circularly polarized waves and are frequently observed in space plasmas. The Low frequency branch of the Whistler waves having frequencies nearly around 100 Hz, known as Lion roars, are frequently observed in magnetosheath. Another feature of the magnetosheath is the observations of flat top electron distributions with single as well as two electron populations. In the past, lion roars were studied by employing kinetic model using classical bi-Maxwellian distribution function, however, could not be justified both on quantitatively as well as qualitatively grounds. We studied Whistler waves by employing kinetic model using non-Maxwellian distribution function such as the generalized (r,q) distribution function which is the generalized form of kappa and Maxwellian distribution functions by employing kinetic theory with single or two electron populations. We compare our results with the Cluster observations and found good quantitative and qualitative agreement between them. At times when lion roars are observed (not observed) in the data and bi-Maxwellian could not provide the sufficient growth (damping) rates, we showed that when generalized (r,q) distribution function is employed, the resulted growth (damping) rates exactly match the observations.

Keywords: kinetic model, whistler waves, non-maxwellian distribution function, space plasmas

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Authors: Gaddafi Sani Shehu, Tankut Yalcınoz, Abdullahi Bala Kunya

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Multilevel inverters such as flying capacitor, diode-clamped, and cascaded H-bridge inverters are very popular particularly in medium and high power applications. This paper focuses on a cascaded H-bridge module using a single direct current (DC) source in order to generate an 11-level output voltage. The noble approach reduces the number of switches and gate drivers, in comparison with a conventional method. The anticipated topology produces more accurate result with an isolation transformer at high switching frequency. Different modulation techniques can be used for the multilevel inverter, but this work features modulation techniques known as selective harmonic elimination (SHE).This modulation approach reduces the number of carriers with reduction in Switching Losses, Total Harmonic Distortion (THD), and thereby increasing Power Quality (PQ). Based on the simulation result obtained, it appears SHE has the ability to eliminate selected harmonics by chopping off the fundamental output component. The performance evaluation of the proposed cascaded multilevel inverter is performed using PSIM simulation package and THD of 0.94% is obtained.

Keywords: cascaded H-bridge multilevel inverter, power quality, selective harmonic elimination

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Authors: Li Yang, Yang Song, Martin Y. M. Chiang

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Objective: To experimentally substantiate the micromechanical compatibility between cell and scaffold, in the regenerative medicine approach for restoring bone volume, is essential for phenotypic transitions Methods: Through nanotechnology and electrospinning process, nanofibrous scaffolds were fabricated to host dental follicle stem cells (DFSCs). Blends (50:50) of polycaprolactone (PCL) and silk fibroin (SF), mixed with various content of cellulose nanocrystals (CNC, up to 5% in weight), were electrospun to prepare nanofibrous scaffolds with heterogeneous microstructure in terms of fiber size. Colloidal probe atomic force microscopy (AFM) and conventional uniaxial tensile tests measured the scaffold stiffness at the micro-and macro-scale, respectively. The cell elastic modulus and cell-scaffold adhesive interaction (i.e., a chemical function) were examined through single-cell force spectroscopy using AFM. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to determine if the mechanotransduction signal (i.e., Yap1, Wwr2, Rac1, MAPK8, Ptk2 and Wnt5a) is upregulated by the scaffold stiffness at the micro-scale (cellular scale). Results: The presence of CNC produces fibrous scaffolds with a bimodal distribution of fiber diameter. This structural heterogeneity, which is CNC-composition dependent, remarkably modulates the mechanical functionality of scaffolds at microscale and macroscale simultaneously, but not the chemical functionality (i.e., only a single material property is varied). In in vitro tests, the osteogenic differentiation and gene expression associated with mechano-sensitive cell markers correlate to the degree of micromechanical compatibility between DFSCs and the scaffold. Conclusion: Cells require compliant scaffolds to encourage energetically favorable interactions for mechanotransduction, which are converted into changes in cellular biochemistry to direct the phenotypic evolution. The micromechanical compatibility is indeed important to the efficacy of regenerative medicine.

Keywords: phenotype transition, scaffold stiffness, electrospinning, cellulose nanocrystals, single-cell force spectroscopy

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Authors: Madhujit Deb, G. R. K. Sastry, R. S. Panua, Rahul Banerjee, P. K. Bose

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The present work attempts to investigate the combustion, performance and emission characteristics of an existing single-cylinder four-stroke compression-ignition engine operated in dual-fuel mode with hydrogen as an alternative fuel. Environmental concerns and limited amount of petroleum fuels have caused interests in the development of alternative fuels like hydrogen for internal combustion (IC) engines. In this experimental investigation, a diesel engine is made to run using hydrogen in dual fuel mode with diesel, where hydrogen is introduced into the intake manifold using an LPG-CNG injector and pilot diesel is injected using diesel injectors. A Timed Manifold Injection (TMI) system has been developed to vary the injection strategies. The optimized timing for the injection of hydrogen was 100 CA after top dead center (ATDC). From the study it was observed that with increasing hydrogen rate, enhancement in brake thermal efficiency (BTHE) of the engine has been observed with reduction in brake specific energy consumption (BSEC). Furthermore, Soot contents decrease with an increase in indicated specific NOx emissions with the enhancement of hydrogen flow rate.

Keywords: diesel engine, hydrogen, BTHE, BSEC, soot, NOx

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

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The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, sport performance, Slovakia

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Authors: Jeong Hwan Joo, Keun Pil Kim

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During meiosis, meiotic recombination is initiated by Spo11-mediated DSB formation and exonuclease-mediated DSB resection occurs to expose single stranded DNA formation. RPA is further required to inhibit secondary structure formation of ssDNA that can be formed Watson-Crick pairing. Rad51-Dmc1, RecA homologs in eukaryote and their accessory factors involve in searching homolog templates to mediate strand exchange. In this study, we investigate the recombinational roles of replication protein A (RPA), which is heterotrimeric protein that is composed of RPA1, RPA2, and RPA3. Here, we investigated meiotic recombination using DNA physical analysis at the HIS4LEU2 hot spot. In rfa1-119 (K45E, N316S) cells, crossover (CO) and non-crossover (NCO) products reduced than WT. rfa1-119 delayed in single end invasion-to-double holiday junction (SEI-to-dHJ) transition and exhibits a defect in second-end capture that is also modulated by Rad52. In the further experiment, we observed that in rfa1-119 mutant, RPA could not be released in timely manner. Furthermore, rfa1-119 exhibits failure in the second end capture, implying reduction of COs and NCOs. In this talk, we will discuss more detail how RPA involves in chromatin axis association via formation of axis-bridge and why RPA is required for Rad52-mediated second-end capture progression.

Keywords: homolog interaction, meiotic recombination, replication protein A, RPA1

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Authors: Mohammed Kamil, M. M. Rahman, Rosli A. Bakar

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Modeling of hydrogen fueled engine (H₂ICE) injection system is a very important tool that can be used for explaining or predicting the effect of advanced injection strategies on combustion and emissions. In this paper, a common rail injection system (CRIS) is proposed for 4-strokes 4-cylinders hydrogen fueled engine with port injection feeding system (PIH₂ICE). For this system, a numerical one-dimensional gas dynamic model is developed considering single injection event for each injector per a cycle. One-dimensional flow equations in conservation form are used to simulate wave propagation phenomenon throughout the CR (accumulator). Using this model, the effect of common rail on the injection system characteristics is clarified. These characteristics include: rail pressure, sound velocity, rail mass flow rate, injected mass flow rate and pressure drop across injectors. The interaction effects of operational conditions (engine speed and rail pressure) and geometrical features (injector hole diameter) are illustrated; and the required compromised solutions are highlighted. The CRIS is shown to be a promising enhancement for PIH₂ICE.

Keywords: common rail, hydrogen engine, port injection, wave propagation

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Authors: Sue S. Feldman

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As clinical and nursing informatics mature, an area that has gotten a lot of attention is the value capstone projects. Capstones are meant to address authentic and complex domain-specific problems. While capstone projects have not always been essential in graduate clinical and nursing informatics education, employers are wanting to see evidence of the prospective employee's knowledge and skills as an indication of employability. Capstones can be organized in many ways: a single course over a single semester, multiple courses over multiple semesters, as a targeted demonstration of skills, as a synthesis of prior knowledge and skills, mentored by one single person or mentored by various people, submitted as an assignment or presented in front of a panel. Because of the potential for capstones to enhance the educational experience, and as a mechanism for application of knowledge and demonstration of skills, a rigorous capstone can accelerate a graduate's potential in the workforce. In 2016, the capstone at the University of Alabama at Birmingham (UAB) could feel the external forces of a maturing Clinical and Nursing Informatics discipline. While the program had a capstone course for many years, it was lacking the depth of knowledge and demonstration of skills being asked for by those hiring in a maturing Informatics field. Since the program is online, all capstones were always in the online environment. While this modality did not change, other contributors to instruction modality changed. Pre-2016, the instruction modality was self-guided. Students checked in with a single instructor, and that instructor monitored progress across all capstones toward a PowerPoint and written paper deliverable. At the time, the enrollment was few, and the maturity had not yet pushed hard enough. By 2017, doubling enrollment and the increased demand of a more rigorously trained workforce led to restructuring the capstone so that graduates would have and retain the skills learned in the capstone process. There were three major changes: the capstone was broken up into a 3-course sequence (meaning it lasted about 10 months instead of 14 weeks), there were many chunks of deliverables, and each faculty had a cadre of about 5 students to advise through the capstone process. Literature suggests that the chunking, breaking up complex projects (i.e., the capstone in one summer) into smaller, more manageable chunks (i.e., chunks of the capstone across 3 semesters), can increase and sustain learning while allowing for increased rigor. By doing this, the teaching responsibility was shared across faculty with each semester course being taught by a different faculty member. This change facilitated delving much deeper in instruction and produced a significantly more rigorous final deliverable. Having students advised across the faculty seemed like the right thing to do. It not only shared the load, but also shared the success of students. Furthermore, it meant that students could be placed with an academic advisor who had expertise in their capstone area, further increasing the rigor of the entire capstone process and project and increasing student knowledge and skills.

Keywords: capstones, clinical informatics, health informatics, informatics

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Authors: Hussein Yousif Aziz

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This paper discussed the design and analysis of bridge foundation subjected to load of train with three codes, namely AASHTO code, British Standard BS Code 8004 (1986), and Chinese code (TB10002.5-2005).The study focused on the design and analysis of bridge’s foundation manually with the three codes and found which code is better for design and controls the problem of high settlement due to the applied loads. The results showed the Chinese codes are costly that the number of reinforcement bars in the pile cap and piles is more than those with AASHTO code and BS code with the same dimensions. Settlement of the bridge was calculated depending on the data collected from the project site. The vertical ultimate bearing capacity of single pile for three codes is also discussed. Other analyses by using the two-dimensional Plaxis program and other programs like SAP2000 14, PROKON many parameters are calculated. The maximum values of the vertical displacement are close to the calculated ones. The results indicate that the AASHTO code is economics and safer in the bearing capacity of single pile. The purpose of this project is to study out the pier on the basis of the design of the pile foundation. There is a 32m simply supported beam of box section on top of the structure. The pier of bridge is round-type. The main component of the design is to calculate pile foundation and the settlement. According to the related data, we choose 1.0m in diameter bored pile of 48m. The pile is laid out in the rectangular pile cap. The dimension of the cap is 12m 9 m. Because of the interaction factors of pile groups, the load-bearing capacity of simple pile must be checked, the punching resistance of pile cap, the shearing strength of pile cap, and the part in bending of pile cap, all of them are very important to the structure stability. Also, checking soft sub-bearing capacity is necessary under the pile foundation. This project provides a deeper analysis and comparison about pile foundation design schemes. Firstly, here are brief instructions of the construction situation about the Bridge. With the actual construction geological features and the upper load on the Bridge, this paper analyzes the bearing capacity and settlement of single pile. In the paper the Equivalent Pier Method is used to calculate and analyze settlements of the piles.

Keywords: pile foundation, settlement, bearing capacity, civil engineering

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Authors: Devendra Gupta, Vikash Arya, Prabhat K. Singh

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Background: Ultrasound guidance could be beneficial in placing central venous catheters by improving the success rate, reducing the number of needle passes, and decreasing complications. Central venous cannulation set has a single puncture needle of a fixed length of 6.4 cm. However, the average distance of midpoint of IJV to the skin is around 1 cm to 2 cm. The long length needle has tendency to go in depth more than required and this is very common during learning period of any individual. Therefore, we devised a long needle with a guard which can be adjusted according to the required length. Methods: After approval from the institute ethics committee and patient’s written informed consent, a prospective, randomized, single-blinded controlled study was conducted. Adult patient aged of both sexes with ASA grade 1-2 undergoing surgery requiring internal jugular venous (IJV) access was included. After intubation, the head was rotated to the contralateral side at 30 degree head rotation on the position of the right IJV. The transducer probe a 6.5 to 13-MHz linear transducer (Sonosite, USA) had been placed at the apex of triangle with minimal pressure to avoid IJV compression. The distance from skin to midpoint of the right IJV and skin to anterior wall of Common Carotid Artery (CCA) had been done using B-mode duplex sonography with a 6.5 to 13-MHz linear transducer. Depending upon the results of randomization 420 patients had been divided into two groups of equal numbers (n=210). Group 1. USG guided right sided IJV cannulation was done with conventional (6.4 cm) needle; and Group 2. USG guided right sided IJV cannulation was done with conventional (6.4 cm) needle with guard fixed to a required length (length between skin and midpoint of IJV) by an experienced anesthesiologist. Independent observer has noted the number of attempts and occurrence of complications (CCA puncture, pneumothorax or adjacent tissue damage). Results: Demographic data were similar in both the group. The groups were comparable when considered for relationship of IJV to CCA. There was no significant difference between groups as regard to distance of midpoint of IJV to the skin (p<0.05). IJV cannulation was successfully done in single attempts in 180 (85.7%), in two attempts in 27 (12.9%) and three attempts in 3 (1.4%) in group I, whereas in single attempt in 207 (98.6%) and second attempts in 3 (1.4%) in group II (p <0.000). Incidence of carotid artery puncture was significantly more in group I (7.1%) compared to group II (0%) (p<0.000). Incidence of adjacent tissue puncture was significantly more in group I (8.6%) compared to group II (0%) (p<0.000). Conclusion: Therefore IJV catheterization using guard over the needle at predefined length with the help of real-time ultrasound results in better success rates and lower immediate complications.

Keywords: ultrasound guided, internal jugular vein cannulation, measured guided needle, common carotid artery puncture

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Authors: Bahar Tunctan, Sefika Pinar Kucukkavruk, Meryem Temiz-Resitoglu, Demet Sinem Guden, Ayse Nihal Sari, Seyhan Sahan-Firat, Mahesh P. Paudyal, John R. Falck, Kafait U. Malik

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We hypothesized that 20-hydroxyeicosatetraenoic acid (20-HETE) mimetics such as N-(20-hydroxyeicosa-5[Z],14[Z]-dienoyl)glycine (5,14-HEDGE) may be beneficial for preventing mortality due to inflammation induced by lipopolysaccharide (LPS). This study aims to assess the effect of 5,14-HEDGE on the LPS-induced changes in nucleotide binding domain and leucine-rich repeat protein 3 (NLRP3)/apoptosis-associated speck-like protein containing a caspase activation and recruitment domain (ASC)/pro-caspase-1 inflammasome. Rats were injected with saline (4 ml/kg) or LPS (10 mg/kg) at time 0. Blood pressure and heart rate were measured using a tail-cuff device. 5,14-HEDGE (30 mg/kg) was administered to rats 1 h after injection of saline or LPS. The rats were sacrificed 4 h after saline or LPS injection and kidney, heart, thoracic aorta, and superior mesenteric artery were isolated for measurement of caspase-1/11 p20, NLRP3, ASC, and β-actin proteins as well as interleukin-1β (IL-1β) levels. Blood pressure decreased by 33 mmHg and heart rate increased by 63 bpm in the LPS-treated rats. In the LPS-treated rats, tissue protein expression of caspase-1/11 p20, NLRP3, and ASC in addition to IL-1β levels were increased. 5,14-HEDGE prevented the LPS-induced changes. Our findings suggest that inhibition of renal, cardiac, and vascular formation/activity of NLRP3/ASC/pro-caspase-1 inflammasome involved in the protective effect of 5,14-HEDGE on LPS-induced septic shock in rats. This work was financially supported by the Mersin University (2015-AP3-1343) and USPHS NIH (PO1 HL034300).

Keywords: 5, 14-HEDGE, lipopolysaccharide, NLRP3, inflammasome, septic shock

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