Search results for: massively parallel sequencing (MPS)

Authors: Guna Raj Dhungana, Roshan Nepal, Apshara Parajuli, , Archana Maharjan, Shyam K. Mishra, Pramod Aryal, Rajani Malla

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Introduction: Klebsiella pneumoniae is a well-known opportunistic human pathogen, primarily causing healthcare-associated infections. The global emergence of carbapenemase-producing K. pneumoniaeis a major public health burden, which is often extensively multidrug resistant.Thus, because of the difficulty to treat these ‘superbug’ and menace and some term as ‘apocalypse’ of post antibiotics era, an alternative approach to controlling this pathogen is prudent and one of the approaches is phage mediated control and/or treatment. Objective: In this study, we aimed to isolate novel bacteriophage against carbapenemase-producing K. pneumoniaeand characterize for potential use inphage therapy. Material and Methods: Twenty lytic phages were isolated from river water using double layer agar assay and purified. Biological features, physiochemical characters, burst size, host specificity and activity spectrum of phages were determined. One most potent phage: Phage TU_Kle10O was selected and characterized by electron microscopy. Whole genome sequences of the phage were analyzed for presence/absence of virulent factors, and other lysin genes. Results: Novel phage TU_Kle10O showed multiple host range within own genus and did not induce any BIM up to 5th generation of host’s life cycle. Electron microscopy confirmed that the phage was tailed and belonged to Caudovirales family. Next generation sequencing revealed its genome to be 166.2 Kb. bioinformatical analysis further confirmed that the phage genome ‘did not’ contain any ‘bacterial genes’ within phage genome, which ruled out the concern for transfer of virulent genes. Specific 'lysin’ enzyme was identified phages which could be used as 'antibiotics'. Conclusion: Extensively multidrug resistant bacteria like carbapenemase-producing K. pneumoniaecould be treated efficiently by phages.Absence of ‘virulent’ genes of bacterial origin and presence of lysin proteins within phage genome makes phages an excellent candidate for therapeutics.

Keywords: bacteriophage, Klebsiella pneumoniae, MDR, phage therapy, carbapenemase,

Procedia PDF Downloads 186

Authors: Kevin Molina, Daniel Ortega, Manuel Martinez, Andres Gonzalez-Estrada, William Pinto

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Due to the increasing environmental impact, the wind energy is getting strong. This research studied the relationship between the power produced by a horizontal axis wind turbine (HAWT) and the aerodynamic profiles used for its construction. The analysis is studied using the Computational Fluid Dynamic (CFD), presenting the parallel between the energy generated by a turbine designed with selected profiles and another one optimized. For the study, a selection process was carried out from profile NACA 6 digits recommended by the National Renewable Energy Laboratory (NREL) for the construction of this type of turbines. The selection was taken into account different characteristics of the wind (speed and density) and the profiles (aerodynamic coefficients Cl and Cd to different Reynolds and incidence angles). From the selected profiles, was carried out a sensitivity analysis optimization process between its geometry and the aerodynamic forces that are induced on it. The 3D model of the turbines was realized using the Blade Element Momentum method (BEM) and both profiles. The flow fields on the turbines were simulated, obtaining the forces induced on the blade, the torques produced and an increase of 3% in power due to the optimized profiles. Therefore, the results show that the sensitivity analysis optimization process can assist to increment the wind turbine power.

Keywords: blade element momentum, blade, fluid structure interaction, horizontal axis wind turbine, profile design

Procedia PDF Downloads 253

Authors: Ming-Yang Guo, Cheng-Xian Wu, Wei-Xiang Chen, Chun-Yuan Lin, Yen-Jen Lin, Ann-Shyn Chiang

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With more and more Drosophila Driver and Neuron images, it is an important work to find the similarity relationships among them as the functional inference. There is a general problem that how to find a Drosophila Driver image, which can cover a set of Drosophila Driver/Neuron images. In order to solve this problem, the intersection/union region for a set of images should be computed at first, then a comparison work is used to calculate the similarities between the region and other images. In this paper, three encoding schemes, namely Integer, Boolean, Decimal, are proposed to encode each image as a one-dimensional structure. Then, the intersection/union region from these images can be computed by using the compare operations, Boolean operators and lookup table method. Finally, the comparison work is done as the union region computation, and the similarity score can be calculated by the definition of Tanimoto coefficient. The above methods for the region computation are also implemented in the multi-core CPUs environment with the OpenMP. From the experimental results, in the encoding phase, the performance by the Boolean scheme is the best than that by others; in the region computation phase, the performance by Decimal is the best when the number of images is large. The speedup ratio can achieve 12 based on 16 CPUs. This work was supported by the Ministry of Science and Technology under the grant MOST 106-2221-E-182-070.

Keywords: Drosophila driver image, Drosophila neuron images, intersection/union computation, parallel processing, OpenMP

Procedia PDF Downloads 233

Authors: Jiang Xu, Daoping Wang, Qun Li, Yinghong Pan

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2,4-Epibrassinolide (EBR), which is a kind of plant hormone Brassinosteroids (BRs), is widely studied and applied in the global scale but the proteomic characteristics of EBR alleviating low temperature stress in rice seedling leaves are still not clear. In this study, seeding rice of Nipponbare were treated with EBR and distilled water, then stressed at 4℃ or 26 ℃, and analyzed by mass spectrometry analysis, verified by parallel reaction monitoring technique (PRM). The results showed that 5778 proteins were identified in total and 4834 proteins were identified with quantitative information. Among them, 401 up-regulated and 220 down-regulated proteins may be related to EBR alleviating low temperature stress in rice seedling leaves. The molecular functions of most of up-regulated proteins are RNA binding and hydrolase activity and are mainly enriched in the pathways of carbon metabolism, folic acid synthesis, and amino acid biosynthesis. The down-regulated proteins are mainly related to catalytic activity and oxidoreductase activity and are mainly enriched in the pathways of limonene and pinene degradation, riboflavin metabolism, porphyrin and chlorophyll metabolism, and other metabolic pathways. PRM validation and literature analysis showed that NADP-malic acidase, peroxidase, 3-phosphoglycerate dehydrogenase, enolase, glyceraldehyde-3- phosphate dehydrogenase and pyruvate kinase are closely related to the effect of EBR on low temperature stress. These results also suggested that BRs could relieve the effect of low temperature stress on rice seed germination in many ways.

Keywords: 2, 4-Epibrassinolid, low temperature stress, proteomic analysis, rice

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Authors: Mohamed Mahmoud Hasan, Hoda M. O. Mokhtar

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With the gigantic increment in portable applications use and the spread of positioning and location-aware technologies that we are seeing today, new procedures and methodologies for location-based strategies are required. Location recommendation is one of the highly demanded location-aware applications uniquely with the wide accessibility of social network applications that are location-aware including Facebook check-ins, Foursquare, and others. In this paper, we aim to present a new methodology for location recommendation. The proposed approach coordinates customary spatial traits alongside other essential components including shortest distance, and user interests. We also present another idea namely, "activity trajectory" that represents trajectory that fulfills the set of activities that the user is intrigued to do. The approach dispatched acquaints the related distance value to select trajectory(ies) with minimum cost value (distance) and spatial-area to prune unneeded directions. The proposed calculation utilizes the idea of movement direction to prescribe most comparable N-trajectory(ies) that matches the client's required action design with least voyaging separation. To upgrade the execution of the proposed approach, parallel handling is applied through the employment of a MapReduce based approach. Experiments taking into account genuine information sets were built up and tested for assessing the proposed approach. The exhibited tests indicate how the proposed approach beets different strategies giving better precision and run time.

Keywords: location based recommendation, map-reduce, recommendation system, trajectory search

Procedia PDF Downloads 219

Authors: Suchitra Sivakumar, Hajime Shingyouchi, Toshinori Okajima, Kyohei Yamaguchi, Jin Kusaka

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The progressing need for powertrain electrification calls for more accurate and reliable simulation models. A battery pack serves as the most vital component for energy storage in an electrified powertrain. Hybrid electric vehicles (HEV) do not behave the same way as they age, and there are several environmental factors that account for the degradation of the battery on a system level. Therefore, in this work, a battery model was proposed to study the state of charge (SOC) variation and the internal dynamic changes that contribute to aging and performance degradation in HEV batteries. An equivalent circuit battery model (ECM) is built using MATLAB Simulink to investigate the output characteristics of the lithium-ion battery. The ECM comprises of circuit elements like a voltage source, a series resistor and a parallel RC network connected in series. A parameter estimation study is conducted on the ECM to study the dependencies of the circuit elements with the state of charge (SOC) and the terminal voltage of the battery. The battery model is extended to simulate the temperature dependence of the individual battery cell and the battery pack with the environment. The temperature dependence model accounts for the heat loss due to internal resistance build up in the battery pack during charging, discharging, and due to atmospheric temperature. The model was validated for a lithium-ion battery pack with an independent drive cycle showing a voltage accuracy of 4% and SOC accuracy of about 2%.

Keywords: battery model, hybrid electric vehicle, lithium-ion battery, thermal model

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Authors: Liaqat Ali, Hubert E. Blum, Türkân Sakinc

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Enterococcus faecium is an emerging multidrug-resistant nosocomial pathogen increased dramatically worldwide and causing bacteremia, endocarditis, urinary tract and surgical site infections in immunocomprised patients. The capsular polysaccharides that contribute to pathogenesis through evasion of the host innate immune system are also involved in hindering leukocyte killing of enterococci. The gene cluster (enterococcal polysaccharide antigen) of E. faecalis encoding homologues of many genes involved in polysaccharide biosynthesis. We identified two putative loci with 22 kb and 19 kb which contained 11 genes encoding for glycosyltransferases (GTFs); this was confirmed by using genome comparison of already sequenced strains that has no homology to known capsule genes and the epa-locus. The polysaccharide-conjugate vaccines have rapidly emerged as a suitable strategy to combat different pathogenic bacteria, therefore, we investigated a polysaccharide biosynthesis CapD protein in E. faecium contains 336 amino acids and had putative function for N-linked glycosylation. The deletion/knock-out capD mutant was constructed and complemented by homologues recombination method and confirmed by using PCR and sequencing. For further characterization and functional analysis, in-vitro cell culture and in-vivo a mouse infection models were used. Our ΔcapD mutant shows a strong hydrophobicity and all strains exhibited biofilm production. Subsequently, the opsonic activity was tested in an opsonophagocytic assay which shows increased in mutant compared complemented and wild type strains but more than two fold decreased in colonization and adherence was seen on surface of uroepithelial cells. However, a significant higher bacterial colonialization was observed in capD mutant during animal bacteremia infection. Unlike other polysaccharides biosynthesis proteins, CapD does not seems to be a major virulence factor in enterococci but further experiments and attention is needed to clarify its function, exact mechanism and involvement in pathogenesis of enteroccocal nosocomial infections eventually to develop a vaccine/ or targeted therapy.

Keywords: E. faecium, pathogenesis, polysaccharides, biofilm formation

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Authors: Karol Rodriguez-Peña, Martha L. Macias-Rubalcava, Leticia Rocha-Zavaleta, Sergio Sanchez

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A bioassay-guided study for anti-cancer compounds from endophytes of the Mexican medicinal plant Amphipteryygium adstringens resulted in the isolation of a streptomycete capable of producing a group of compounds with high cytotoxic activity. Microorganisms from surface sterilized samples of various sections of the plant were isolated and all the actinomycetes found were evaluated for their potential to produce compounds with cytotoxic activity against cancer cell lines MCF7 (breast cancer) and HeLa (cervical cancer) as well as the non-tumoural cell line HaCaT (keratinocyte). The most active microorganism was picked for further evaluation. The identification of the microorganism was carried out by 16S rDNA gene sequencing, finding the closest proximity to Streptomyces scabrisporus, but with the additional characteristic that the strain isolated in this study was capable of producing colorful compounds never described for this species. Crude extracts of dichloromethane and ethyl acetate showed IC50 values of 0.29 and 0.96 μg/mL for MCF7, 0.51 and 1.98 μg/mL for HeLa and 0.96 and 2.7 μg/mL for HaCaT. Scaling the fermentation to 10 L in a bioreactor generated 1 g of total crude extract, which was fractionated by silica gel open column to yield 14 fractions. Nine of the fractions showed cytotoxic activity. Fraction 4 was chosen for subsequent purification because of its high activity against cancerous cell lines, lower activity against keratinocytes. HPLC-UV-MS/ESI was used for the evaluation of this fraction, finding at least 10 different compounds with high values of m/z (≈588). Purification of the compounds was carried out by preparative thin-layer chromatography. The prevalent compound was Steffimycin B, a molecule known for its antibiotic and cytotoxic activities and also for its low solubility in aqueous solutions. Along with steffimycin B, another five compounds belonging to the steffimycin family were isolated and at this moment their structures are being elucidated, some of which display better solubility in water: an attractive property for the pharmaceutical industry. As a conclusion to this study, the isolation of endophytes resulted in the discovery of a strain capable of producing compounds with high cytotoxic activity that need to be studied for their possible utilization.

Keywords: amphipterygium adstringens, cytotoxicity, streptomyces scabrisporus, steffimycin

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Authors: Muhammad Tanveer Altaf, Mehmet Bedir, Waqas Liaqat, Gönül Cömertpay, Volkan Çatalkaya, Celaluddin Barutçular, Nergiz Çoban, Ibrahim Cerit, Muhammad Azhar Nadeem, Tolga Karaköy, Faheem Shehzad Baloch

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Food production needs to be almost double by 2050 in order to feed around 9 billion people around the Globe. Plant production mostly relies on fertilizers, which also have one of the main roles in environmental pollution. In addition to this, climatic conditions are unpredictable, and the earth is expected to face severe drought conditions in the future. Therefore, water and fertilizers, especially nitrogen are considered as main constraints for future food security. To face these challenges, developing integrative approaches for germplasm characterization and selecting the resilient genotypes performing under limiting conditions is very crucial for effective breeding to meet the food requirement under climatic change scenarios. This study is part of the European Research Area Network (ERANET) project for the characterization of the diversity panel of 172 sorghum accessions and six hybrids as control cultivars under limiting (+N/-H2O, -N/+H2O) and non-limiting conditions (+N+H2O). This study was planned to characterize the sorghum diversity in relation to resource Use Efficiency (RUE), with special attention on harnessing the interaction between genotype and environment (GxE) from a physiological and agronomic perspective. Experiments were conducted at Adana, a Mediterranean climate, with augmented design, and data on various agronomic and physiological parameters were recorded. Plentiful diversity was observed in the sorghum diversity panel and significant variations were seen among the limiting water and nitrogen conditions in comparison with the control experiment. Potential genotypes with the best performance are identified under limiting conditions. Whole genome resequencing was performed for whole germplasm under investigation for diversity analysis. GWAS analysis will be performed using genotypic and phenotypic data and linked markers will be identified. The results of this study will show the adaptation and improvement of sorghum under climate change conditions for future food security.

Keywords: germplasm, sorghum, drought, nitrogen, resources use efficiency, sequencing

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Authors: Ricardo de Oliveira Orsi, Aline Astolfi, Daniel Diego Mendes, Isabella Cristina de Castro Lippi, Jaine da Luz Scheffer, Yan Souza Lima, Juliana Lunardi, Giovanna do Padro Ribeiro, Samir Moura Kadri

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NECTAR Brazilian group (Center of Education, Science, and Technology in Rational Beekeeping) conducted studies on the pesticides honey bees effects using the transcriptome sequencing (RNA-Seq) analyzes for gene expression studies. In this way, we analyzed the effects of Pyraclostrobin and Fipronil on the honey bees with 21 old-days (forager) in laboratory conditions. For this, frames containing sealed brood were removed from the beehives and maintenance on the stove (32°C and 75% humidity) until the bees were born. So, newly emerged workers were marked on the pronotum with a non-toxic pen and reintroduced into their original hives. After 21 days, 120 marked bees were collected with an entomological forces and immediately stored in Petri dishes, perforated to ensure ventilation, and kept fasted for 3 hours. These honeybees were exposed to food contaminated or not with the sublethal dose of Pyraclostrobin (850 ppb/bee) or Fipronil (2.5 ppb/bee). After four hours of exposure, 15 bees from each treatment were referred to transcriptome analysis. Total RNA analysis was extracted from the brain pools (03 brains per pool) using the TRIzol® reagent protocol according to the manufacturer's instructions. cDNA libraries were constructed, and the FASTQC program was used to check adapter content and assess the quality of raw reads. Differential expression analysis was performed with the DESeq2 package. Genes that had an adjusted value of less than 0.05 were considered to be significantly up-regulated. Regarding the Pyraclostrobin, alterations were observed in the pattern of 17 gene related to of antioxidant system, cellular respiration, glucose metabolism, and regulation of juvenile hormone and the hormone insulin. Glyphosate altered the 10 gene related to the digestive system, exoskeleton composition, vitamin E transport, and antioxidant system. The results indicate that the necessity of studies using the sublethal doses to evaluate the pesticides uses and risks on crops and its effects on the honey bees.

Keywords: beekeeping, honey bees, pesticides, transcriptome

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Authors: Sebahat Seker

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Since there is a parallel connection between drinking water quality and public health, studies on drinking and domestic water are of vital importance. Ardahan Province is one of the provinces located in the Northeast Anatolian Region, where animal husbandry and agriculture are carried out economically. City mains water uses underground spring water as a source and is chlorinated and given to the city center by gravity. However, mains water cannot be used outside the central district of the city, and the majority of the people meet their drinking and utility water needs from the wells they have opened individually. The water element, which is vital for all living things, is the most important substance that sustains life for humans. Under normal conditions, a healthy person consumes approximately 1.8-2 liters of water. The quality and use of potable water is one of the most important issues in terms of health. The quality parameters of drinking and utility water have been revealed by the scientific world. Scientific studies on drinking water quality in the world and its impact on public health are among the most popular topics. Although our country is surrounded by water on three sides, potable water resources are very few. In the Eastern Anatolia Region, it is difficult for the public to access drinking and utility water due to the difficult conditions both climatically and geographically. In this study, samples taken from drinking and utility water at certain intervals from the stations determined, and water quality parameters will be determined. The fact that such a study has not been carried out in the region before and the knowledge of the local people about water quality is very important in terms of its original and widespread effect.

Keywords: water quality, modelling, evaluation, northeastern anatolia

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Authors: Luz Hurtado, Rodrigo Rojas, Jaime Romero, Christopher Concha

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The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture which is a Chilean native species of high gastronomic demand and market value. The microbiota was analyzed in terms of diversity and structure using massive Illumina sequencing. The analysis of alpha diversity was performed in samples of G. chilensis larvae of 6, 18 and 32 dph (days post-hatching) and it was observed that there were significant differences (P = 0.05) between the days of culture for the Chao1 index, being the larvae of 18 dph the one with the highest index followed by the larvae of 6 dph, The lowest value for this index was presented in larvae of 32 dph. There were no significant differences in larvae between the days of culture for the Shannon (P=0.0857) and Simpson (P=0.0714) indices. In general, the larvae of G. chilensis have high rates of diversity. When analyzing the beta diversity, a differentiation between the bacterial communities is observed depending on the day of the culture of the larvae. Considering the PCoA elaborated from the unweighted UniFrac statistic, the explained variance was 46.2% (PC1 29.2% and PC2 17.0%) and in the case of the PCoA elaborated with the weighted UniFrac statistic; the explained variance was 65.5% (PC1 41.8% and PC2 23.7%) these differences were significant based on the Permanova statistical analysis (P= 0.002 and 0.037 respectively). When analyzing the taxonomic composition of the microbiota of the larvae in the different days of culture it was observed that at the phyla level the most abundant in the larvae of 6 dph were Proteobacteria (57%) Verrucomicrobia (24%) and Firmicutes (14%), for the larvae of 18 dph the predominant phyla were Proteobacteria (90%), Dependientiae (5%), Actinobacteria (2%) and Plactomyces (2%), for the larvae of 32 dph the phyla that presented the highest relative abundance were Proteobacteria (57%), Firmicutes (29%), Verrucomicrobia (5%) and Actinobacteria (5%), when comparing the larvae between the days it was observed that the phylum Proteobacteria was the most abundant in the samples of larvae of 6, 18 and 32 dph being the larvae of 18 dph those that present the highest relative abundance, the larvae of 6 dph were those that presented the highest relative abundance for the phylum Verrucomicrobia and in the larvae of 32 dph was observed greater abundance of the phylum Firmicutes compared to the other days of larval culture. At the level of genera, those with the highest relative abundance in larvae of 6 dph were Rubritalea (30%), Psychrobacter (28%), staphylococcus (17%) and Ralstonia (10%), for the larvae of 18 dph the genera with the highest abundance were Psychrobacter (47%), Litoreibacter (13%), Nautella (9%) and Cohesibacter (8%), for the larvae of 32 dph the most abundant genera were Alloiococcus (25%), Dialister (14%), Neptunomonas (13%) and Piscirickettsia (11%). When observing the taxonomic composition of the larvae between the days of larval culture, it is observed that there are differences between them.

Keywords: microbiota, diversity, G. Chilensis, larvae

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: Dilsad Akal

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Aim: Companies communicate with each other and with their costumers via call centers. Call centers are defined as stressful because of their uncertain working hours, inadequate relief time, performance based system and heavy workload. In literature, this sector is defined as risky as mining sector by means of health and safety. The aim of this research is to enlight the relatively dark area. Subject and Methods: The collection of data for this study completed during April-May 2015 for the two selected call centers in different parts of Turkey. The applied question mostly investigated the health conditions of call center workers. Electromagnetic field measurements were completed at the same time with applying the question poll. The ratio of employee accessibility noted as 73% for the first call center and 87% for the second. Results: The results of electromagnetic field measurements were as between 371 V/m-32 V/m for the first location and between 370 V/m-61 V/m for the second. The general complaints of the employees for both workplaces can be counted as; inadequate relief time, inadequate air conditioning, disturbance, poor thermal conditions, inadequate or extreme lighting. Furthermore, musculoskeletal discomfort, stress, ear and eye discomfort are main health problems of employees. Conclusion: The measured values and the responses to the question poll were found parallel with the other similar research results in literature. At the end of this survey, a risk map of workplace was prepared in terms of safety and health at work in general and some suggestions for resolution were provided.

Keywords: call center, health and safety, electromagnetic field, risk map

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Authors: Yun Chol Kang, Myong Nam Kong, Nam Chol Yu, Jin Sim Kim, Un Yong Paek, Song Ho Kim

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This study focuses on the calculating approach of the thermal conductivity of 8 mol% yttria-stabilized zirconia (8YSZ) in different relative humidity corresponding to low water contents. When water content in 8YSZ is low, water droplets can accumulate in the neck regions. We assume that spherical water droplets are randomly located in the neck regions formed by grains and surrounded by the pores. Based on this, a new hypothetical pore constituted by air and water is proposed using the microstructural modeling. We consider 8YSZ is a two-phase material constituted by the solid region and the hypothetical pore region where the water droplets are penetrated in the pores, randomly. The results showed that the thermal conductivity of the hypothetical pore is calculated using the parallel resistance for low water contents, and the effective thermal conductivity of 8YSZ material constituted by solid and hypothetical pore in different relative humidities using EMPT. When the numbers of water layers on the surface of 8YSZ are less than 1.5, the proposed approach gives a good interpretation of the experimental results. When the theoretical value of the number of water layers on 8YSZ surface is 1, the water content is not enough to cover the internal solid surface completely. The proposed approach gives a better interpretation of the experimental results in different relative humidities that numbers of water layers on the surface of 8YSZ are less than 1.5.

Keywords: 8YSZ, microstructure, thermal conductivity, relative humidity

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Authors: Maha Z. Rizk, Sami A. Fattah, Heba M. Darwish, Sanaa A. Ali, Mai O. Kadry

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The increasing use of nanomaterials in consumer and industrial products has aroused global concern regarding their fate in biological systems resulting in demand for parallel risk assessment. The objective of this study is investigating either the effect of individual or combined doses of idebenone, carnosine and vitamin E on amelioration of some biochemical indices of nano sized titanium dioxide (TiO2 NPS) induced metabolic disorders in mice liver. TiO2-NPS was administered in an oral dose of 150 mg/kg for consecutive 14 days followed by oral daily doses of the aforementioned antioxidants for 1 month. TiO2-NPS induced a significant elevation in serum level of ALT and AST, hepatic inflammatory markers (tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6)) and increased the percent of DNA damage which was assessed by COMET assay in addition to the apoptotic marker Caspase-3. Moreover, mRNA gene expression observed by RT-PCR showed a significant overexpression in nuclear factor relation-2 (Nrf2), nuclear factor kappa beta (NF-Kβ) and the apoptotic factor (bax), and a significant down-regulation in the antiapoptotic factor (bcl2) level. In conclusion, idebenone, carnosine and vitamin E ameliorated the deviated parameters with a variable degree with the most pronounced role in alleviating the hazardous effect of TiO2 NPS toxicity following the combination regimen.

Keywords: idebenone, carnosine, vitamin E, TiO2 NPS, caspase-3, NrF2, NF-KB

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Authors: Noura El-Ahmady El-Naggar

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L-asparaginase is an important enzyme as therapeutic agents used in combination therapy with other drugs in the treatment of acute lymphoblastic leukemia in children. L-asparaginase producing actinomycete strain, NEAE-K, was isolated from soil sample and identified on the basis of morphological, cultural, physiological and biochemical properties, together with 16S rDNA sequence as new subsp. Streptomyces rochei subsp. chromatogenes NEAE-K and sequencing product (1532 bp) was deposited in the GenBank database under accession number KJ200343. The study was conducted to screen parameters affecting the production of L-asparaginase by Streptomyces rochei subsp. chromatogenes NEAE-K on solid state fermentation using Plackett–Burman experimental design. Sixteen different independent variables including incubation time, moisture content, inoculum size, temperature, pH, soybean meal+ wheat bran, dextrose, fructose, L-asparagine, yeast extract, KNO3, K2HPO4, MgSO4.7H2O, NaCl, FeSO4. 7H2O, CaCl2, and three dummy variables were screened in Plackett–Burman experimental design of 20 trials. The most significant independent variables affecting enzyme production (dextrose, L-asparagine and K2HPO4) were further optimized by the central composite design. As a result, a medium of the following formula is the optimum for producing an extracellular L-asparaginase by Streptomyces rochei subsp. chromatogenes NEAE-K from solid state fermentation: g/L (soybean meal+ wheat bran 15, dextrose 3, fructose 4, L-asparagine 8, yeast extract 2, KNO3 1, K2HPO4 2, MgSO4.7H2O 0.5, NaCl 0.1, FeSO4. 7H2O 0.02, CaCl2 0.01), incubation time 7 days, moisture content 50%, inoculum size 3 mL, temperature 30°C, pH 8.5.

Keywords: streptomyces rochei subsp. chromatogenes neae-k, 16s rrna, identification, solid state fermentation, l-asparaginase production, plackett-burman design, central composite design

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Authors: C. B. Le, V. N. Pham

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In modern data analysis, multi-source data appears more and more in real applications. Multi-source data clustering has emerged as a important issue in the data mining and machine learning community. Different data sources provide information about different data. Therefore, multi-source data linking is essential to improve clustering performance. However, in practice multi-source data is often heterogeneous, uncertain, and large. This issue is considered a major challenge from multi-source data. Ensemble is a versatile machine learning model in which learning techniques can work in parallel, with big data. Clustering ensemble has been shown to outperform any standard clustering algorithm in terms of accuracy and robustness. However, most of the traditional clustering ensemble approaches are based on single-objective function and single-source data. This paper proposes a new clustering ensemble method for multi-source data analysis. The fuzzy optimized multi-objective clustering ensemble method is called FOMOCE. Firstly, a clustering ensemble mathematical model based on the structure of multi-objective clustering function, multi-source data, and dark knowledge is introduced. Then, rules for extracting dark knowledge from the input data, clustering algorithms, and base clusterings are designed and applied. Finally, a clustering ensemble algorithm is proposed for multi-source data analysis. The experiments were performed on the standard sample data set. The experimental results demonstrate the superior performance of the FOMOCE method compared to the existing clustering ensemble methods and multi-source clustering methods.

Keywords: clustering ensemble, multi-source, multi-objective, fuzzy clustering

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Authors: Lasha Mskhaladze, Guram Burchuladze, Khvicha Datunashvili

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Technological changes have an impact not only on economic but also on social elements of society which in turn has created new challenges for states’ political systems and their regimes. As a result of unprecedented growth of information technologies and communications digital democracy and electronic governance have emerged. Nowadays effective state functioning cannot be imagined without electronic governance. In Georgia, special attention is paid to the development of such new systems and establishment of electronic governance. Therefore, in parallel to intensive development of information technologies an important priority for public sector in Georgia is the development of electronic governance. In spite of the fact that today Georgia with its economic indicators satisfies the standards of western informational society, and major part of its gross domestic product comes from the service sector (59.6%), it still remains a backward country on the world map in terms of information technologies and electronic governance. E-transparency in Georgia should be based on such parameters as government accountability when the government provides citizens information about their activities; e-participation which involves government’s consideration of external expert assessments; cooperation between officials and citizens in order to solve national problems. In order to improve electronic systems the government should actively do the following: Fully develop electronic programs concerning HR and exchange of data between public organizations; develop all possible electronic services; improve existing electronic programs; make electronic services available on different mobile platforms (iPhone, Android, etc.).

Keywords: electronic transparency, electronic services, information technology, information society, electronic systems

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Authors: Berredjem Hajira, Benlaifa Meriem, Becheker Imene, Bardi Rafika, Djebar Med Reda

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Recent acquired or reactivation T.gondii infection is a serious complication in HIV patients. Classical serological diagnosis relies on the detection of anti-Toxoplasma immunoglobulin ; however, serology may be unreliable in HIV immunodeficient patients who fail to produce significant titers of specific antibodies. PCR assays allow a rapid diagnosis of Toxoplasma infection. In this study, we compared the value of the PCR for diagnosing active toxoplasmosis in cerebrospinal fluid and blood samples from HIV patients. Anti-Toxoplasma antibodies IgG and IgM titers were determined by ELISA. In parallel, nested PCR targeting B1 gene and conventional PCR-ELISA targeting P30 gene were used to detect T. gondii DNA in 25 blood samples and 12 cerebrospinal fluid samples from patients in whom toxoplasmic encephalitis was confirmed by clinical investigations. A total of 15 negative controls were used. Serology did not contribute to confirm toxoplasmic infection, as IgG and IgM titers decreased early. Only 8 out 25 blood samples and 5 out 12 cerebrospinal fluid samples PCRs yielded a positive result. 5 patients with confirmed toxoplasmosis had positive PCR results in either blood or cerebrospinal fluid samples. However, conventional nested B1 PCR gave best results than the P30 gene one for the detection of T.gondii DNA in both samples. All samples from control patients were negative. This study demonstrates the unusefulness of the serological tests and the high sensitivity and specificity of PCR in the diagnosis of toxoplasmic encephalitis in HIV patients.

Keywords: cerebrospinal fluid, HIV, Toxoplasmosis, PCR

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Authors: Isaac Laryea

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Underwater remote-operated vehicles (ROVs) are highly useful in aquatic research and underwater operations. Unfortunately, unsteady and unpredictable conditions underwater make it difficult for underwater vehicles to maintain a steady attitude during motion. Existing underwater vehicles make use of multiple thrusters positioned at specific positions on their frame to maintain a certain pose. This study proposes an alternate way of maintaining a steady attitude during horizontal motion at low speeds by making use of a thrust vector-controlled propulsion system. The study began by carrying out some preliminary calculations to get an idea of a suitable shape and form factor. Flow simulations were carried out to ensure that enough thrust could be generated to move the system. Using the Lagrangian approach, a mathematical system was developed for the ROV, and this model was used to design a control system. A PID controller was selected for the control system. However, after tuning, it was realized that a PD controller satisfied the design specifications. The designed control system produced an overshoot of 6.72%, with a settling time of 0.192s. To achieve the effect of thrust vectoring, an inverse kinematics synthesis was carried out to determine what angle the actuators need to move to. After building the system, intermittent angular displacements of 10°, 15°, and 20° were given during bench testing, and the response of the control system as well as the servo motor angle was plotted. The final design was able to move in water but was not able to handle large angular displacements as a result of the small angle approximation used in the mathematical model.

Keywords: PID control, thrust vectoring, parallel manipulators, ROV, underwater, attitude control

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Authors: Erkan Polat, Barlas Ozden Caglayan

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By day-to-day developed techniques, it is possible to pass through larger openings by using smaller beam-column sections. Parallel to this trend, it is aimed to produce not only smaller but also economical and architecturally more attractive beams. This study aims to explain the structural behavior of arch steel beam reinforced by using post-tension cable. Due to the effect of post-stressed cable, the arch beam load carrying capacity increases and an optimized section in a smaller size can be obtained with a better architectural view. It also allows better mechanical and applicational solutions for buildings. For better understanding the behavior of the reinforced beam, steel beam and arch steel beam with post-tensioned cable are all modeled and analyzed by using SAP2000 Finite element computer program and compared with each other. Also, full scale test specimens were prepared to test for figuring out the structural behavior and compare the results with the computer model results. Test results are very promising. The similarity of the results between the test and computer analysis shows us that there are no extra knowledge and effort of engineer is needed to calculate such beams. The predicted (and proved by tests) beam carrying capacity is 35% higher than the unreinforced beam carrying capacity. Even just three full scale tests were completed, it is seen that the ratio (%35) may be increased ahead by adjusting the cable post-tension force of beams in much smaller sizes.

Keywords: arch steel beams, pre-stressed cables, finite element, specimen Test

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Authors: Hana Maresova, Daniel Ecler

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The paper focuses on the use of 3D multi-user virtual environments (MUVE) in language teaching and presents the results of four years of research at the Faculty of Education, Palacký University in Olomouc (Czech Republic). In the form of an experiment, mother tongue language teaching in the 3D virtual worlds Second Life and Kitely (experimental group) and parallel traditional teaching on identical topics representing teacher's interpretation using a textbook (control group) were implemented. The didactic test, which was presented to the experimental and control groups in an identical form before and after the instruction, verified the effect of the instruction in the experimental group by comparing the results obtained by both groups. Within the three components of mother-tongue teaching (vocabulary, literature, style and communication education), the students in the literature group achieved partially better results (statistically significant in the case of items devoted to the area of visualization of the learning topic), while in the case of grammar and style education the respondents of the control group achieved better results. On the basis of the results obtained, we can conclude that the most appropriate use of MUVE can be seen in the teaching of those topics that provide the possibility of dramatization, experiential learning and group involvement and cooperation, on the contrary, with regard to the need to divide students attention between the topic taught and the control of avatar and movement in virtual reality as less suitable for teaching in the area of memorization of the topic or concepts.

Keywords: distance learning, 3D virtual environments, online teaching, language teaching

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Authors: Mehmet Balci, Sakir Tasdemir, Mustafa Altin, Ozlem Bozok

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Our globalizing world has become almost a small village and everyone can access any information at any time. Everyone lets each other know who does whatever in which place. We can learn which social events occur in which place in the world. From the perspective of education, the course notes that a lecturer use in lessons in a university in any state of America can be examined by a student studying in a city of Africa or the Far East. This dizzying communication we have mentioned happened thanks to fast developments in computer technologies and in parallel with this, internet technology. While these developments in the world, has a very large young population and a rapidly evolving electronic communications infrastructure Turkey has been affected by this situation. Researches has shown that almost all young people in Turkey has an account in a social network. Especially becoming common of mobile devices causes data traffic in social networks to increase. In this study, has been surveyed on students in the different age groups and at the Selcuk University Vocational School of Technical Sciences Department of Computer Technology. Student’s opinions about the use of internet and social media has been gotten. Using the Internet and social media skills, purposes, operating frequency, access facilities and tools, social life and effects on vocational education etc. have been explored. Both internet and use of social media positive and negative effects on this department students results have been obtained by the obtained findings evaluating from various aspects. Relations and differences have been found out with statistic.

Keywords: computer technologies, internet use, social network, higher vocational school

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Authors: Abderrahmane Kechich, Othmane Abdelkhalek

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Static converters behave as nonlinear loads that inject harmonic currents into the grid and increase the consumption of the inactive power. On the other hand, the increased use of sensitive equipment requires the application of sinusoidal voltages. As a result, the electrical power quality control has become a major concern in the field of power electronics. In this context, the active power conditioner (UPQC) was developed. It combines both serial and parallel structures; the series filter can protect sensitive loads and compensate for voltage disturbances such as voltage harmonics, voltage dips or flicker when the shunt filter compensates for current disturbances such as current harmonics, reactive currents and imbalance. This double feature is that it is one of the most appropriate devices. Calculating parameters is an important step and in the same time it’s not easy for that reason several researchers based on trial and error method for calculating parameters but this method is not easy for beginners researchers especially what about the controller’s parameters, for that reason this paper gives a mathematical way to calculate of almost all of UPQC parameters away from trial and error method. This paper gives also a new approach for calculating of PI regulators parameters for purpose to have a stable UPQC able to compensate for disturbances acting on the waveform of line voltage and load current in order to improve the electrical power quality.

Keywords: UPQC, Shunt active filer, series active filer, PI controller, PWM control, dual-loop control

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Authors: S. Pathak, R. Lazarus

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A 25-year-old male HIV patient (CD4 cells 20/µL and HIV viral load 14200000 copies/ml) with a past medical history of duodenal ulcer, pneumocystis carinii pneumonia, oesophageal candidiasis presented with fever and a seizure to hospital. The only recent travel had been a religious pilgrimage from Singapore to Malaysia 5 days prior; during the trip he sustained skin abrasions. The patient had recently started highly active antiretroviral therapy 2 months prior. Clinical examination was unremarkable other than a temperature of 38.8°C and perianal warts. Laboratory tests showed a leukocyte count 12.5x109 cells/L, haemoglobin 9.4 g/dL, normal biochemistry and a C-reactive protein 121 mg/L. CT head and MRI head were unremarkable and cerebrospinal fluid analysis performed after a delay (due to technical difficulties) of 11 days was unremarkable. Blood cultures (three sets) taken on admission showed Gram-negative rods in the anaerobic bottles only at the end of incubation with culture result confirmed by molecular sequencing showing Helicobacter cinaedi. The patient was treated empirically with ceftriaxone for seven days and this was converted to oral co-amoxiclav for a further seven days after the blood cultures became positive. A Transthoracic echocardiogram was unremarkable. The patient made a full recovery. Helicobacter cinaedi is a gram-negative anaerobic fastidious organism affecting patients with comorbidity. Infection may manifest as cellulitius, colitis or as in this case as bloodstream infection – the latter is often attributed to faeco-oral infection. Laboratory identification requires prolonged culture. Therapeutic options may be limited by resistance to macrolides and fluoroquinolones. The likely pathogen inoculation routes in the case described include gastrointestinal translocation due to proctitis at the site of perianal warts, or breach of the skin via abrasions occurring during the pilgrimage. Such organisms are increasing in prevalence as our patient population ages and patients have multiple comorbidities including HIV. It may be necessary in patients with unexplained fever to prolong incubation of sterile sites including blood in order to identify this unusual fastidious organism.

Keywords: fastidious, Helicobacter cinaedi, HIV, immunocompromised

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Authors: Jean Paul M. Milambo

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Purpose: Aromatase inhibitors (AIs) are indicated in the treatment of hormone-receptive breast cancer in postmenopausal women in various settings. Studies have shown cardiovascular events in some developed countries. To date the data is sparce for evidence-based recommendations in African clinical settings due to lack of cancer registries, capacity building and surveillance systems. Therefore, this study was conducted to assess the feasibility of HyBeacon® probe genotyping adjunctive to standard care for timely prediction and diagnosis of Aromatase inhibitors (AIs) associated adverse events in breast cancer survivors in Africa. Methods: Cross sectional study was conducted to assess the knowledge of POCT among six African countries using online survey and telephonically contacted. Incremental cost effectiveness ratio (ICER) was calculated, using diagnostic accuracy study. This was based on mathematical modeling. Results: One hundred twenty-six participants were considered for analysis (mean age = 61 years; SD = 7.11 years; 95%CI: 60-62 years). Comparison of genotyping from HyBeacon® probe technology to Sanger sequencing showed that sensitivity was reported at 99% (95% CI: 94.55% to 99.97%), specificity at 89.44% (95% CI: 87.25 to 91.38%), PPV at 51% (95%: 43.77 to 58.26%), and NPV at 99.88% (95% CI: 99.31 to 100.00%). Based on the mathematical model, the assumptions revealed that ICER was R7 044.55. Conclusion: POCT using HyBeacon® probe genotyping for AI-associated adverse events maybe cost effective in many African clinical settings. Integration of preventive measures for early detection and prevention guided by different subtype of breast cancer diagnosis with specific clinical, biomedical and genetic screenings may improve cancer survivorship. Feasibility of POCT was demonstrated but the implementation could be achieved by improving the integration of POCT within primary health cares, referral cancer hospitals with capacity building activities at different level of health systems. This finding is pertinent for a future envisioned implementation and global scale-up of POCT-based initiative as part of risk communication strategies with clear management pathways.

Keywords: breast cancer, diagnosis, point of care, South Africa, aromatase inhibitors

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Authors: Sajewicz-Krukowska Joanna, Domańska-Blicharz Katarzyna, Tarasiuk Karolina, Marzec-Kotarska Barbara

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Astroviral infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as decreased egg production, breeding disorders, poor weight gain, and even increased mortality. Commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for "white chicks syndrome" associated with increased embryo/chick mortality. The CAstV-mediated pathogenesis in chicken occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV-chicken interactions remain unclear, and there is no information available regarding gene expression changes in the chicken's spleen in response to CAstV infection. We aimed to investigate the molecular background triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of 5 birds each. One group was inoculated with CAstV, and the other was used as the negative control. On 4th dpi, spleen samples were collected and immediately frozen at -70°C for RNA isolation. We analysed transcriptional profiles of the chickens' spleens at the 4th day following infection using RNA-seq to establish differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative real-time PCR (qRT-PCR). A total of 31959 transcripts were identified in response to CAstV infection. Eventually 45 DEGs (p-value<0.05; Log2Foldchange>1)were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on 4 genes (IFIT5, OASL, RASD1, DDX60) confirmed RNAseq results. Top differentially expressed genes belonged to novel putative IFN-induced CAstV restriction factors. Most of the DEGs were associated with RIG-I–like signalling pathway or, more generally, with an innate antiviral response(upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, IFI6, and downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, YWHAB). The study provided a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proved the cell cycle in the spleen and immune signalling in chickens were predominantly affected upon CAstV infection.

Keywords: chicken astrovirus, CastV, RNA-seq, transcriptome, spleen

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Authors: A. Elmajdoub, A. El-Mahmoudy

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The present study was designed to investigate the neurotransmitters that mediate the excitatory response of the circular muscle of final branches of mesenteric artery in bovine calves. Mesentery was dissected and the iliac branches were separated and used. The final mesenteric branches of diameter 400 micrometers and less responded strongly to norepinephrine and moderately to ATP. However, the mesenteric branches of wider diameters were gradually less responsive to norepinephrine and those of diameter 700 micrometers were exclusively nonresponsive. These arteries were strongly responsive to ATP (100 µM). Norepinephrine response was sensitive to phentolamine (3 µM) and prazosin (5 µM) indicating that it is mediated by α1 receptor; while ATP response was sensitive to suramin (200 µM), PPADS (50 µM), but not to cibacron blue (100 µM) indicating that it is mediated via P2X receptor. Further confirmatory experiments were performed including application of α1 and P2X receptor specific agonists which are methoxamine and α,β-methylene ATP. Methoxamine (1 µM) showed effects similar to norepinephrine in final branches and was without effect in wider branches. α,β-methylene ATP (1 µM), exhibited more pronounced effects on both wide and narrow branches but in parallel manner to that of ATP. Agonists for α2 and P2Y receptors as clonidine (10 µM) and 2-meThio ATP (10 µM), respectively, were without effect indicating that involvement of these receptors is unlikely. The neuropeptide-Y (200 nM) did not have any effects on either the narrow or the wide rings. Conclusion: These data may imply that in the most peripheral mesenteric arteries a strong vasopressor power represented by norepinephrine and ATP integration is needed for maintaining peripheral resistance; on the other hand a mild vasopressor power mediated only by ATP is enough to maintain the vascular tone in the relatively central mesenteric branches.

Keywords: ATP, calves, mesenteric artery, norepinephrine

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Authors: Omar Dib, Rita Yaacoub, Luc Eveleigh, Nathalie Locquet, Hussein Dib, Ali Bassal, Christophe B. Y. Cordella

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The potential of front-face fluorescence coupled with chemometric techniques, namely parallel factor analysis (PARAFAC) and multiple linear regression (MLR) as a rapid analysis tool to characterize Lebanese virgin olive oils was investigated. Fluorescence fingerprints were acquired directly on 102 Lebanese virgin olive oil samples in the range of 280-540 nm in excitation and 280-700 nm in emission. A PARAFAC model with seven components was considered optimal with a residual of 99.64% and core consistency value of 78.65. The model revealed seven main fluorescence profiles in olive oil and was mainly associated with tocopherols, polyphenols, chlorophyllic compounds and oxidation/hydrolysis products. 23 MLR regression models based on PARAFAC scores were generated, the majority of which showed a good correlation coefficient (R > 0.7 for 12 predicted variables), thus satisfactory prediction performances. Acid values, peroxide values, and Delta K had the models with the highest predictions, with R values of 0.89, 0.84 and 0.81 respectively. Among fatty acids, linoleic and oleic acids were also highly predicted with R values of 0.8 and 0.76, respectively. Factors contributing to the model's construction were related to common fluorophores found in olive oil, mainly chlorophyll, polyphenols, and oxidation products. This study demonstrates the interest of front-face fluorescence as a promising tool for quality control of Lebanese virgin olive oils.

Keywords: front-face fluorescence, Lebanese virgin olive oils, multiple Linear regressions, PARAFAC analysis

Procedia PDF Downloads 449