Search results for: molecular modelling

Authors: Mohammed Abdullah Basahi

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The objective of the present study was to identify the phylogenetic relationships and determine genetic diversity among Suaeda genotypes growing in Saudi Arabia and to find out whether these could be a potential source for genetic diversity. A set of nineteen genotypes was analyzed using twenty-four ISSR primers. Clear amplified polymorphic DNA products were obtained from the screening of twenty-four ISSR primers on nineteen genotypes that allowed selection of ten primers and the results were reproducible. Nineteen genotypes were revealed a unique profile with ten ISSR primers and thus it can be used for the DNA fingerprinting. Different primers produced a different level of polymorphism among the nineteen genotypes. The number of polymorphic bands per primer varied from 5 to 14 with an average of 8 bands per primer. The results revealed that the genotypes differed for ISSR markers. The genetic similarity based on Nei and Li’s ranged from 0.450 to 0.930. Cluster analysis was conducted based on ISSR data to group the Suaeda genotypes and to construct a dendrogram. Four groups can be distinguished by truncating the dendrogram at GS value of 0.54. ISSR markers showed high level of polymorphism among the genotypes examined. The present study indicates that ISSR markers could be successfully used in genetic characterization and diversity in Suaeda.

Keywords: suaeda, DNA fingerprinting, ISSR, Saudi Arabia

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Authors: Nagasamy Venkatesh Dhandapani, Amged Awad El-Gied

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Cefixime, a BCS class II drug, is insoluble in water but freely soluble in acetone and in alcohol. The aqueous solubility of cefixime in water is poor and exhibits exceptionally slow and intrinsic dissolution rate. In the present study, cefixime and β-Cyclodextrin (β-CD) solid dispersions were prepared with a view to study the effect and influence of β-CD on the solubility and dissolution rate of this poorly aqueous soluble drug. Phase solubility profile revealed that the solubility of cefixime was increased in the presence of β-CD and was classified as A_L-type. Effect of variable, such as drug:carrier ratio, was studied. Physical characterization of the solid dispersion was characterized by Fourier transform infrared spectroscopy (FT-IR) and Differential scanning calorimetry (DSC). These studies revealed that a distinct loss of drug crystallinity in the solid molecular dispersions is ostensibly accounting for enhancement of dissolution rate in distilled water. The drug release from the prepared solid dispersion exhibited a first order kinetics. Solid dispersions of cefixime showed a 6.77 times fold increase in dissolution rate over the pure drug.

Keywords: β-cyclodextrin, cefixime, dissolution, Kneading method, solid dispersions, release kinetics

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Authors: W. Wen, G. Jackson, S. Maskill, D. G. McCartney, W. Sun

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CoNiCrAlY alloys have been widely used as bond coats for thermal barrier coating (TBC) systems because of low cost, improved control of composition, and the feasibility to tailor the coatings microstructures. Coatings are in general very thin structures, and therefore it is impossible to characterize the mechanical responses of the materials via conventional mechanical testing methods. Due to this reason, miniature specimen testing methods, such as the small punch test technique, have been developed. This paper presents some of the recent research in evaluating the mechanical properties of the CoNiCrAlY coatings at room and high temperatures, through the use of small punch testing and the developed miniature specimen tensile testing, applicable to a range of temperature, to investigate the elastic-plastic and creep behavior as well as ductile-brittle transition temperature (DBTT) behavior. An inverse procedure was developed to derive the mechanical properties from such tests for the coating materials. A two-layer specimen test method is also described. The key findings include: 1) the temperature-dependent coating properties can be accurately determined by the miniature tensile testing within a wide range of temperature; 2) consistent DBTTs can be identified by both the SPT and miniature tensile tests (~ 650 °C); and 3) the FE SPT modelling has shown good capability of simulating the early local cracking. In general, the temperature-dependent material behaviors of the CoNiCrAlY coating has been effectively characterized using miniature specimen testing and inverse method.

Keywords: NiCoCrAlY coatings, mechanical properties, DBTT, miniature specimen testing

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Authors: H. Elmsellem, A. Aouniti, S. Radi, A. Chetouani, B. Hammouti

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The synthesis of new organic molecules offers various molecular structures containing heteroatoms and substituents for corrosion protection in acid pickling of metals. The most synthesized compounds are the nitrogen heterocyclic compounds, which are known to be excellent complex or chelate forming substances with metals. The choice of the inhibitor is based on two considerations: first it could be synthesized conveniently from relatively cheap raw materials, secondly, it contains the electron cloud on the aromatic ring or, the electro negative atoms such as nitrogen and oxygen in the relatively long chain compounds. In the present study, (NE)‐2‐methyl‐N‐(thiophen‐2‐ylmethylidene) aniline(T) was synthesized and its inhibiting action on the corrosion of mild steel in 1 M hydrochloric acid was examined by different corrosion methods, such as weight loss, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). The experimental results suggest that this compound is an efficient corrosion inhibitor and the inhibition efficiency increases with the increase in inhibitor concentration. Adsorption of this compound on mild steel surface obeys Langmuir’s isotherm. Correlation between quantum chemical calculations and inhibition efficiency of the investigated compound is discussed using the Density Functional Theory method (DFT).

Keywords: mild steel, Schiff base, inhibition, corrosion, HCl, quantum chemical

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Authors: Suraj Nair, Aravindkumar Vijayalingam, Alexander Perzylo, Alois Knoll

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In the last decade robotics research and development activities have grown rapidly, especially in the domain of service robotics. Integrating service robots into human occupied spaces such as homes, offices, hospitals, etc. has become increasingly worked upon. The primary motive is to ease daily lives of humans by taking over some of the household/office chores. However, several challenges remain in systematically integrating such systems in human shared work-spaces. In addition to sensing and indoor-navigation challenges, programmability of such systems is a major hurdle due to the fact that the potential user cannot be expected to have knowledge in robotics or similar mechatronic systems. In this paper, we propose a cognitive system for service robotics which allows non-expert users to easily model system behaviour in an underspecified manner through abstract tasks and objects associated with them. The system uses domain knowledge expressed in the form of an ontology along with logical reasoning mechanisms to infer all the missing pieces of information required for executing the tasks. Furthermore, the system is also capable of recovering from failed tasks arising due to on-line disturbances by using the knowledge base and inferring alternate methods to execute the same tasks. The system is demonstrated through a coffee fetching scenario in an office environment using a mobile robot equipped with sensors and software capabilities for autonomous navigation and human-interaction through natural language.

Keywords: cognitive robotics, reasoning, service robotics, task based systems

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Authors: Olena Mayboroda, Angel Gonzalez Benito, Jonathan Sabate Del Rio, Marketa Svobodova, Sandra Julich, Herbert Tomaso, Ciara K. O'Sullivan, Ioanis Katakis

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DNA amplification is required for most molecular diagnostic applications but conventional PCR has disadvantages for field testing. Isothermal amplification techniques are being developed to respond to this problem. One of them is the Recombinase Polymerase Amplification (RPA) that operates at isothermal conditions without sacrificing specificity and sensitivity in easy-to-use formats. In this work RPA was used for the optical detection of solid-phase amplification of the potential biowarfare agent Yersinia pestis. Thiolated forward primers were immobilized on the surface of maleimide-activated microtitre plates for the quantitative detection of synthetic and genomic DNA, with elongation occurring only in the presence of the specific template DNA and solution phase reverse primers. Quantitative detection was achieved via the use of biotinylated reverse primers and post-amplification addition of streptavidin-HRP conjugate. The overall time of amplification and detection was less than 1 hour at a constant temperature of 37oC. Single-stranded and double-stranded DNA sequences were detected achieving detection limits of 4.04*10-13 M and 3.14*10-16 M, respectively. The system demonstrated high specificity with negligible responses to non-specific targets.

Keywords: recombinase polymerase amplification, Yersinia pestis, solid-phase detection, ELONA

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Authors: Raja Chinnappan, Huda Alanazi, Shanmugam Easwaramoorthi, Tanveer Mir, Balamurugan Kanagasabai, Ahmed Yaqinuddin, Sandhanasamy Devanesan, Mohamad S. AlSalhi

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Serum albumin (SA) is a highly rich water-soluble protein in plasma. It is known to maintain the living organisms' health and help to maintain the proper liver function, kidney function, and plasma osmolality in the body. Low levels of serum albumin are an indication of liver failure and chronic hepatitis. Therefore, it is important to have a low-cost, accurate and rapid method. In this study, we designed a fluorescent probe, triphenylamine rhodanine-3-acetic acid (mRA), which triggers the fluorescence signal upon binding with serum albumin (SA). mRA is a bifunctional molecule with twisted intramolecular charge transfer (TICT)-induced emission characteristics. An aqueous solution of mRA has an insignificant fluorescence signal; however, when mRA binds to SA, it undergoes TICT and turns on the fluorescence emission. A SA dose-dependent fluorescence signal was performed, and the limit of detection was found to be less than ng/mL. The specific binding of SA was tested from the cross-reactivity study using similar structural or functional proteins.

Keywords: serum albumin, fluorescent sensing probe, liver diseases, twisted intramolecular charge transfer

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Authors: Zineb Ouahdi

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Spirocyclic compound derivatives, with their unique heterocyclic motifs, serve as a continual source of inspiration in the pursuit of developing potential therapeutic agents. These compounds are diverse in their chemical structures; some have fully saturated skeletons, while others are partially unsaturated. Nevertheless, these compounds share a characteristic feature with natural products - the presence of at least one heteroatom in one of their rings. The inclusion of a C = O dipolarophile in pyridazinones imparts an exciting aspect for 1,3-dipolar cycloaddition reactions, the focal point of our study. Our research has involved a detailed theoretical investigation of the reaction between ethyl (Z)-2-bromo-2-(2-(p-tolyl)hydrazono)acetate and 6-methyl-4,5-dihydropyridazine-3(2H)-one. This has been accomplished using the DFT/B3LYP/6-31g(d,p) method, intending to illuminate the chemical pathway of this reaction. The chemical reactivity theories we used for this purpose included FMO, TS, and local and global indices derived from conceptual DFT. The theoretical framework outlined in this study allowed us to propose a reaction mechanism for cycloaddition reactions. It also enabled the identification of the potential activities of the analyzed compounds (P1, P2, P3, P4, P5, and P6) against the major protease of the coronavirus disease (COVID-19). This was achieved using various computational tools, including AutoDock Tools, Autodock Vina, Autodock 4, and PYRX.

Keywords: MEDT, pyridazin, cycloaddition, FMO, DFT, docking

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Authors: Hany M. Abd El-Lateef

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Two novel Schiff bases, 5-bromo-2-[(E)-(pyridin-3-ylimino) methyl] phenol (HBSAP) and 5-bromo-2-[(E)-(quinolin-8-ylimino) methyl] phenol (HBSAQ) have been synthesized. They have been characterized by elemental analysis and spectroscopic techniques (UV–Vis, IR and NMR). Moreover, the molecular structure of HBSAP and HBSAQ compounds are determined by single crystal X-ray diffraction technique. The inhibition activity of HBSAP and HBSAQ for carbon steel in 3.5 %NaCl+0.1 M HCl for both short and long immersion time, at different temperatures (20-50 ºC), was investigated using electrochemistry and surface characterization. The potentiodynamic polarization shows that the inhibitors molecule is more adsorbed on the cathodic sites. Its efficiency increases with increasing inhibitor concentrations (92.8 % at the optimal concentration of 10-3 M for HBSAQ). Adsorption of the inhibitors on the carbon steel surface was found to obey Langmuir’s adsorption isotherm with physical/chemical nature of the adsorption, as it is shown also by scanning electron microscopy. Further, the electronic structural calculations using quantum chemical methods were found to be in a good agreement with the results of the experimental studies.

Keywords: carbon steel, Schiff bases, corrosion inhibition, SEM, electrochemical techniques

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Authors: Marcela Parra-Vargas, Ana Sandoval-Rodriguez, Roberto Rodriguez-Echevarria, Jose Dominguez-Rosales, Juan Armendariz-Borunda

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Non-alcoholic fatty liver disease (NAFLD) is characterized by an excess of hepatic lipids, and it is to author’s best knowledge, the most prevalent chronic liver disorder. Anthocyanin-rich food consumption is linked to health benefits in metabolic disorders associated with obesity and NAFLD, although the precise functional role of anthocyanidin delphinidin (Dp) has yet to be established. The aim of this study was to investigate the effect of the Dp in NAFLD metabolic alterations by evaluating prevention or amelioration of hepatic lipid accumulation, as well as molecular mechanisms in two experimental obesity-related models of NALFD. In vitro: HepG2 cells were incubated with sodium palmitate (PA, 1 mM) to induce lipotoxic damage, and concomitantly treated with Dp (180 uM) for 24 h. Subsequently, total lipid accumulation was measured by colorimetric staining with Oil Red O, and total intrahepatic triglycerides were determined by an enzymatic assay. To assess molecular mechanisms, cells were pre-treated with PA for 24 h and then exposed to Dp for 1 h. In vivo: four-week-old male C57BL/6Nhsd mice were allocated in two main groups. Mice were fed with standard diet (control) or high-fat and high-carbohydrate diet (45% fat, HFD) for 16 wk to induce NAFLD. Then HFD was divided into subgroups: one treated orally with Dp (15 mg/kg bw, HFD-Dp) every day for 4 wk, while HFD group treated with vehicle (DMSO). Weight and fasting glucose were recorded weekly, while dietary ingestion was measured daily. Insulin tolerance test was performed at the end of treatment. Liver histology was evaluated with H&E and Masson’s trichrome stain. RT-PCR was used to evaluate gene expression and Western Blot to determine levels of protein in both experimental models. Parametric data were analyzed with one-way ANOVA and Tukey’s post-hoc test. Kruskal-Wallis and Mann-Whitney U test for non-parametric data, and P < 0.5 were considered significant. Dp prevented hepatic lipid accumulation by PA in HepG2 hepatocytes. Furthermore, Dp down-regulated gene expression of SREBP1c, FAS, and CPT1a without modifying AMPK phosphorylation levels. In vivo, Dp oral administration did not ameliorate lipid metabolic alterations raised by HFD. Adiposity, dietary ingestion, fasting glucose, and insulin sensitivity after Dp treatment remained similar to HFD group. Histological analysis showed hepatic damage in HFD groups and no differences between HFD and HFD-Dp groups were found. Hepatic gene expression of ACC and FAS were not altered by HFD. SREBP1c was similar in both HFD and HFD-Dp groups. No significant changes were observed in SREBP1c, ACC, and FAS adipose tissue gene expression by HFD or Dp treatment. Additionally, immunoblotting analysis revealed no changes in pathway SIRT1-LKB-AMPK and PPAR alpha by both HFD groups compared to control. In conclusion, the antioxidant Dp may provoke beneficial effects in the prevention of hepatic lipid accumulation. Nevertheless, the oral dose administrated in mice that simulated the total intake of anthocyanins consumed daily by humans has no effect as a treatment on hepatic lipid metabolic alterations and histological abnormalities associated with exposure to chronic HFD. A healthy lifestyle with regular intake of antioxidants such as anthocyanins may prevent metabolic alterations in NAFLD.

Keywords: anthocyanins, antioxidants, delphinidin, non-alcoholic fatty liver disease, obesity

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Authors: Supriya Patibanda, Xiaopeng Gong, Krishna N. Jonnalagadda, Ralph Abrahams

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Yttria stabilized zirconia (YSZ) is used as a top coat in thermal barrier coatings in high-temperature turbine/jet engine applications. The mechanical behaviour of YSZ depends on the microstructural features like crack density and porosity, which are a result of coating method. However, experimentally ascertaining their individual effect is difficult due to the inherent challenges involved like material synthesis and handling. The current work deals with the development of a phenomenological model to replicate the tensile behavior of air plasma sprayed YSZ obtained from experiments. Initially, uniaxial tensile experiments were performed on freestanding YSZ coatings of ~300 µm thick for different crack densities and porosities. The coatings exhibited a nonlinear behavior and also a huge variation in strength values. With the obtained experimental tensile curve as a base and crack density and porosity as prime variables, a phenomenological model was developed using ABAQUS interface with new user material defined employing VUMAT sub routine. The relation between the tensile stress and the crack density was empirically established. Further, a parametric study was carried out to investigate the effect of the individual features on the non-linearity in these coatings. This work enables to generate new coating designs by varying the key parameters and predicting the mechanical properties with the help of a simulation, thereby minimizing experiments.

Keywords: crack density, finite element method, plasma sprayed coatings, VUMAT

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Authors: Mir Hussain Nawaz, Lyudmila Nedyalkova, Haizhong Zhu, Wael M. Rabeh

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In this study, we aim to biochemically and structurally characterize the interactions of human HK2 with the mitochondria in addition to the role of its N-terminal domain in catalysis and stability of the full-length enzyme. Here, we solved the crystal structure of human HK2 in complex with glucose and glucose-6-phosphate (PDB code: 2NZT), where it is a homodimer with catalytically active N- and C-terminal domains linked by a seven-turn α-helix. Different from the inactive N-terminal domains of isozymes 1 and 3, the N- domain of HK2 not only capable to catalyze a reaction but it is responsible for the thermodynamic stabilizes of the full-length enzyme. Deletion of first α-helix of the N-domain that binds to the mitochondria altered the stability and catalytic activity of the full-length HK2. In addition, we found the linker helix between the N- and C-terminal domains to play an important role in controlling the catalytic activity of the N-terminal domain. HK2 is a major step in the regulation of glucose metabolism in cancer making it an ideal target for the development of new anticancer therapeutics. Characterizing the structural and molecular mechanisms of human HK2 and its role in cancer metabolism will accelerate the design and development of new cancer therapeutics that are safe and cancer specific.

Keywords: cancer metabolism, enzymology, drug discovery, protein stability

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Authors: L. Bouzina, A. Bensafi, M. Duval, C. Mathis, M. Rawiso

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We study the stability and structural properties of mixtures of model nanoparticles and non-adsorbing polymers in the 'protein limit', where the size of polymers exceeds the particle size substantially. We have synthesized in institute (Charles Sadron Strasbourg) model nanoparticles by coating fullerene C60 molecules with low molecular weight polystyrene (PS) chains (6 PS chains with a degree of polymerization close to 25 and 50 are grafted on each fullerene C60 molecule. We will present a Small Angle Neutron scattering (SANS) study of Tetrahydrofuran (THF) solutions involving long polystyrene (PS) chains and fullerene (C60) nanoparticles. Long PS chains and C60 nanoparticles with different arm lengths were synthesized either hydrogenated or deuteriated. They were characterized through Size Exclusion Chromatography (SEC) and Quasielastic Light Scattering (QLS). In this way, the solubility of the C60 nanoparticles in the usual good solvents of PS was controlled. SANS experiments were performed by use of the contrast variation method in order to measure the partial scattering functions related to both components. They allow us to obtain information about the dispersion state of the C60 nanoparticles as well as the average conformation of the long PS chains. Specifically, they show that the addition of long polymer chains leads to the existence of an additional attractive interaction in between soft nanoparticles.

Keywords: fulleren nanoparticles, polymer, small angle neutron scattering, solubility

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Authors: M. Doudi, M. H. Pazandeh, L. Rahimzadeh Torabi

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Bedsores are pressure ulcers that occur on the skin or tissue due to being immobile and lying in bed for extended periods. Bedsores have the potential to progress into open ulcers, increasing the possibility of variety of bacterial infection. Acinetobacter baumannii, a pathogen of considerable clinical importance, exhibited a significant correlation with Bedsores (pressure ulcers) infections, thereby manifesting a wide spectrum of antibiotic resistance. The emergence of drug resistance has led researchers to focus on alternative methods, particularly phage therapy, for tackling bacterial infections. Phage therapy has emerged as a novel therapeutic approach to regulate the activity of these agents. The management of bacterial infections greatly benefits from the clinical utilization of bacteriophages as a valuable antimicrobial intervention. The primary objective of this investigation consisted of isolating and discerning potent bacteriophage capable of targeting multi drug-resistant (MDR) and extensively drug-resistant (XDR) bacteria obtained from pressure ulcers. In present study, analyzed and isolated A. baumannii strains obtained from a cohort of patients suffering from pressure ulcers at Taleghani Hospital in Ahvaz, Iran. An approach that included biochemical and molecular identification techniques was used to determine the taxonomic classification of bacterial isolates at the genus and species levels. The molecular identification process was facilitated by using the 16S rRNA gene in combination with universal primers 27 F, and 1492 R. Bacteriophage was obtained through the isolation process conducted on treatment plant sewage located in Isfahan, Iran. The main goal of this study was to evaluate different characteristics of phage, such as their appearance, range of hosts they can infect, how quickly they can enter a host, their stability at varying temperatures and pH levels, their effectiveness in killing bacteria, the growth pattern of a single phage stage, mapping of enzymatic digestion, and identification of proteomics patterns. The findings demonstrated that an examination was conducted on a sample of 50 specimens, wherein 15 instances of A. baumannii were identified. These microorganisms are the predominant Gram-negative agents known to cause wound infections in individuals suffering from bedsores. The study's findings indicated a high prevalence of antibiotic resistance in the strains isolated from pressure ulcers, excluding the clinical strains that exhibited responsiveness to colistin.According to the findings obtained from assessments of host range and morphological characteristics of bacteriophage VbɸAB-1, it can be concluded that this phage possesses specificity towards A. Baumannii BAH_Glau1001 was classified as a member of the Plasmaviridae family. The bacteriophage mentioned earlier showed the strongest antibacterial effect at a temperature of 18 °C and a pH of 6.5. Through the utilization of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis on protein fragments, it was established that the bacteriophage VbɸAB-1 exhibited a size range between 50 and 75 kilodaltons (KDa). The numerous research findings on the effectiveness of phages and the safety studies conducted suggest that the phages studied in this research can be considered as a practical solution and recommended approach for controlling and treating stubborn pathogens in burn wounds among hospitalized patients.

Keywords: acinetobacter baumannii, extremely drug- resistant, phage therapy, surgery wound

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Authors: Dawit Gebreegzabher Hagos, Yazezew Kebede Kiro, Mahmud Abdulkader, Henk H. D. F. Schallig, Dawit Wolday

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Rapid and accurate visceral leishmaniasis (VL) diagnosis is needed to initiate prompt treatment to reduce morbidity and mortality. Here, we evaluated the performance of loop-mediated isothermal amplification (LAMP) assay for the diagnosis of VL from blood in an endemic area in Ethiopia. LAMP was positive in 117/122 confirmed VL cases and negative in 149/152 controls, resulting in a sensitivity of 95.9% (95% CI: 90.69–98.66) and a specificity of 98.0% (95% CI: 94.34–99.59), respectively. The sensitivity of the LAMP assay was 95.0% (95% CI: 88.61–98.34) in HIV-negatives and 100% (95% CI: 85.18–100.0) in HIV-positives. Compared with microscopy, LAMP detected 82/87 (94.3%, 95% CI: 87.10–98.11) of the microscopy1 cases and was negative in 11/27 (40.7%, 95% CI: 22.39–61.20) of the microscopy2 cases. Compared with the rK39 serology, LAMP detected 113/120 (94.2%, 95% CI: 88.35–97.62) of the rK391 cases and was negative in 149/154 (96.8%, 95% CI: 92.59–98.94) of the rK392 cases. However, when compared with microscopy only, rK39 detected 83/87 (95.4%, 95% CI: 88.64–98.73) of the microscopy1 cases and negative in only 12/27 (44.4%, 95% CI: 25.48–64.67) of the microscopy– cases. There was an excellent agreement between rK39 and LAMP (Kappa 5 0.91, 95% CI: 0.86–0.96). Furthermore, an algorithm using rK39 followed by LAMP would yield a sensitivity of 99.2% (95%CI: 95.52–99.89) and a specificity of 98.0% (95% CI: 94.34–99.59). The findings demonstrate that the LAMP assay is an accurate and rapid molecular assay for VL diagnosis, including in HIV-1 co-infected patients, in an endemic setting.

Keywords: visceral leishmaniasis, HIV, diagnosis, LAMP, Ethiopia

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Authors: Rajan Vohra, Ravinder Singh Sawhney, Kunwar Partap Singh

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Electrical charge transport through two basic strands thymine and adenine of DNA have been investigated and analyzed using the jellium model approach. The FFT-2D computations have been performed for semi-empirical Extended Huckel Theory using atomistic tool kit to contemplate the charge transport metrics like current and conductance. The envisaged data is further evaluated in terms of transmission spectrum, HOMO-LUMO Gap and number of electrons. We have scrutinized the behavior of the devices in the range of -2V to 2V for a step size of 0.2V. We observe that both thymine and adenine can act as molecular devices when sandwiched between two gold probes. A prominent observation is a drop in HLGs of adenine and thymine when working as a device as compared to their intrinsic values and this is comparative more visible in case of adenine. The current in the thymine based device exhibit linear increase with voltage in spite of having low conductance. Further, the broader transmission peaks represent the strong coupling of electrodes to the scattering molecule (thymine). Moreover, the observed current in case of thymine is almost 3-4 times than that of observed for adenine. The NDR effect has been perceived in case of adenine based device for higher bias voltages and can be utilized in various future electronics applications.

Keywords: adenine, DNA, extended Huckel, thymine, transmission spectra

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Authors: Cristina Isabrl de Oliveira SAntos

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The study aims to investigate how transferrable and effective career conversations could be, in the context of general track Portuguese secondary schools, with the view of improving students’ career competencies. It does so by analysing: 1) the extent to which students’ perceptions of career conversations relate with their existing career competencies, 2) the extent to which each of the parameters; perceptions of career conversations and student career competencies, relate with student situational and personal characteristics, 3) how patterns in perceptions of headteachers and of teachers at a school, regarding the implementation of career conversations, correlate to the views of students regarding career conversations and to school contextual characteristics. Data were collected from 27 secondary schools out of 32 in the same district of Aveiro, in Portugal. Interviews were performed individually, with 27 headteachers, and in groups, with a total of 10 teacher groups and 11 student groups. Survey responses were also collected from742 studentsand 310 teachers. Interview responses were coded and analysed using grounded theory principles. Data from questionnaires is currently beingscrutinised through descriptive statistics with SPSS, and Structural Equation Modelling (SEM). Triangulation during different stages of data analysis uses the principles of retroduction and abduction of the realist evaluation framework. Conclusions from the pilot-study indicate that student perceptions scores on content and relationship in career conversations change according to their career competencies and the type of school. Statistically significant differences in perceptions of career conversations were found for subgroups based on gender and parent educational level.

Keywords: career conversations, career competencies, secondary education, teachers

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Authors: Michael A. Kraus, Navid Pourmoghaddam, Martin Botz, Jens Schneider, Geralt Siebert

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Fragmentation analysis of tempered glass gives insight into the quality of the tempering process and defines a certain degree of safety as well. Different standard such as the European EN 12150-1 or the American ASTM C 1048/CPSC 16 CFR 1201 define a minimum number of fragments required for soda-lime safety glass on the basis of fragmentation test results for classification. This work presents an approach for the glass breakage pattern prediction using a Voronoi Tesselation over Random Fields. The random Voronoi tessellation is trained with and validated against data from several breakage patterns. The fragments in observation areas of 50 mm x 50 mm were used for training and validation. All glass specimen used in this study were commercially available soda-lime glasses at three different thicknesses levels of 4 mm, 8 mm and 12 mm. The results of this work form a Bayesian framework for the training and prediction of breakage patterns of tempered soda-lime glass using a Voronoi Random Field Tesselation. Uncertainties occurring in this process can be well quantified, and several statistical measures of the pattern can be preservation with this method. Within this work it was found, that different Random Fields as basis for the Voronoi Tesselation lead to differently well fitted statistical properties of the glass breakage patterns. As the methodology is derived and kept general, the framework could be also applied to other random tesselations and crack pattern modelling purposes.

Keywords: glass breakage predicition, Voronoi Random Field Tessellation, fragmentation analysis, Bayesian parameter identification

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Authors: Jyothi Nagraj, Sudeshna Mukherjee, Rajdeep Chowdhury

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Autophagy has recently been linked with cancer cell survival post drug insult contributing to acquisition of resistance. However, the molecular signaling governing autophagic survival response is poorly explored. In our study, in osteosarcoma (OS) cells cisplatin shock was found to activate both MAPK and autophagy signaling. An activation of JNK and autophagy acted as pro-survival strategy, while ERK1/2 triggered apoptotic signals upon cisplatin stress. An increased sensitivity of the cells to cisplatin was obtained with simultaneous inhibition of both autophagy and JNK pathway. Furthermore, we observed that the autophagic stimulation upon drug stress regulates other developmentally active signaling pathways like the Hippo pathway in OS cells. Cisplatin resistant cells were thereafter developed by repetitive drug exposure followed by clonal selection. Basal levels of autophagy were found to be high in resistant cells to. However, the signaling mechanism leading to autophagic up-regulation and its regulatory effect differed in OS cells upon attaining drug resistance. Our results provide valuable clues to regulatory dynamics of autophagy that can be considered for development of improved therapeutic strategy against resistant type cancers.

Keywords: JNK, autophagy, drug resistance, cancer

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Authors: Davies Obaromi, Qin Yongsong, James Ndege, Azeez Adeboye, Akinwumi Odeyemi

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The basic model usually used in disease mapping, is the Besag, York and Mollie (BYM) model and which combines the spatially structured and spatially unstructured priors as random effects. Bayesian Conditional Autoregressive (CAR) model is a disease mapping method that is commonly used for smoothening the relative risk of any disease as used in the Besag, York and Mollie (BYM) model. This model (CAR), which is also usually assigned as a prior to one of the spatial random effects in the BYM model, successfully uses information from adjacent sites to improve estimates for individual sites. To our knowledge, there are some unrealistic or counter-intuitive consequences on the posterior covariance matrix of the CAR prior for the spatial random effects. In the conventional BYM (Besag, York and Mollie) model, the spatially structured and the unstructured random components cannot be seen independently, and which challenges the prior definitions for the hyperparameters of the two random effects. Therefore, the main objective of this study is to construct and utilize an extended Bayesian spatial CAR model for studying tuberculosis patterns in the Eastern Cape Province of South Africa, and then compare for flexibility with some existing CAR models. The results of the study revealed the flexibility and robustness of this alternative extended CAR to the commonly used CAR models by comparison, using the deviance information criteria. The extended Bayesian spatial CAR model is proved to be a useful and robust tool for disease modeling and as a prior for the structured spatial random effects because of the inclusion of an extra hyperparameter.

Keywords: Besag2, CAR models, disease mapping, INLA, spatial models

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Authors: Maryam Vaezjalali, Koroush Rahimian, Maryam Asli, Tahmineh Kandelouei, Foad Davoodbeglou, Amir H. Kashi

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Objectives: The present study was conducted to assess the HBV molecular profiles including genotypes, subgenotypes, subtypes & mutations in hepatitis B genes. Materials/Patients and Methods: This study was conducted on 229 intravenous drug users who referred to three Drop- in-Centers and a hospital in Tehran. HBV DNA was extracted from HBsAg positive serum samples and amplified by Nested PCR. HBV genotype, subgenotypes, subtype and genes mutation were determined by direct sequencing. Phylogenetic tree was constructed using neighbor- joining (NJ) method. Statistical analyses were carried out by SPSS 20. Results: HBV DNA was found in 3 HBsAg positive cases. Phylogenetic tree of derived HBV DNAs showed the existence of genotype D (subgenotype D1, subtype ayw2). Also immune escape mutations were determined in S gene. Conclusion: There were a few variations and genotypes and subtypes among infected intravenous drug users. This study showed the predominance of genotype D among intravenous drug users. Our study concurs with other reports from Iran, that all showing currently only genotype D is the only detectable genotype in Iran.

Keywords: drug users, genotype, HBV, phylogenetic tree

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Authors: Selena Gutiérrez, Araceli Martínez

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One of the most important challenges worldwide, scientific and technological, is to have a sustainable energy source; friendly to the environment and widely available. Currently, the 85% of the energy used comes from the fossil sources. Another important environmental problem is that several rubber products (tires, gloves, hoses, among others) are discarded practically without any treatment. In nature, the degradation of such products will take at least 500 years. In 2009, the worldwide rubber production was about 23.6 million tons. In order to solve this problems, our research focus in an alternative synthesis of biofuels in a two-step approach: The metathesis degradation of industrial rubber (models of rubber waste), and the oligomers transesterification. Thus, cis-1,4-polybutadiene (Mn= 9.1x105, Mw/Mn= 2.2) and styrene-butadiene block copolymers with 30% (Mn= 1.61x105; Mw/Mn= 1.3) and 21% wt styrene (Mn= 1.92x105; Mw/Mn= 1.4) were degraded via metathesis with soybean oil as chain transfer agent (CTA) and green solvent; using [(PCy3)2Cl2Ru=CHPh] and [(1,3-diphenyl-4,5-dihydroimidazol-2-ylidene)(PCy3)Ru=CHPh] catalysts. Afterwards, the products were transesterified by basic homogeneous catalysis. Before transesterification, the polystyrene microblocks (Mn= 16,761; Mw/Mn= 1.2) were isolated. Finally, the biofuels obtained (BO) were purified, characterized and showed similar properties to standards biodiesel (SB) (Norms: EN 14214-03 and ASTM D6751-02), i.e. (SB / BO): molecular weight [Daltons] (570 / 543-596), density [g/cm3] (0.86-0.90 / 0.88), kinematic viscosity [mm2/s] (1.90-6.0 / 3.5-4.5), iodine (97 / 97-98) and cetane number (Min.47 / 56-58).

Keywords: biofuels, industrial rubber, metathesis, vegetable oils

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Authors: Gordon Newlove Asamoah

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This study’s objective is to determine the impact of the African Continental Free Trade Area (AfCFTA) on Ghana using computable general equilibrium (CGE) modelling. The trade data for the simulation was drawn from the standard GTAP database version 10. The study estimated the Ad valorem equivalent (AVE) of Non-Tariff Measures (NTMs) for the Ghanaian sectors which were used for the analysis. Simulations were performed to remove import tariffs and export taxes for 90% of the tariff lines as well as 50% of the NTMs for all the AfCFTA participating countries. The NTMs' reduction was simulated using these two mechanisms: iceberg costs, also known as import augmenting technological change (AMS), and exporter costs (AXS). The study finds that removing the tariffs and NTMs in the AfCFTA regions has a positive impact on Ghana’s GDP, export and import volumes, terms of trade and welfare as measured by the equivalent variations. However, Ghana recorded a deficit of US$4766.69 million as a trade balance due to its high importation bills. This is not by chance, as Ghana is an importer of high-value-added goods but an exporter of basic agricultural raw materials with low export earnings. The study also finds much larger positive impacts for the AfCFTA regions for both importers and exporters when the NTMs that work as iceberg costs and export costs are reduced. It further finds that by reducing the export cost that increases the cost of intermediate inputs, trade among the AfCFTA regions (intra-AfCFTA trade) is enhanced.

Keywords: impact, AfCFTA, NTMs, Ghana, CGE

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Authors: Lukman Thalib, Luis Furuya-Kanamori, Rachel Walker, Brigid Gillespie, Suhail Doi

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Background and objectives: There are many topical treatments available for Pressure Injury (PI) treatment, yet there is a lack of evidence with regards to the most effective treatment. The objective of this study was to compare the effect of various topical treatments and identify the best treatment choice(s) for PI healing. Methods: Network meta-analysis of published randomized controlled trials that compared the two or more of the following dressing groups: basic, foam, active, hydroactive, and other wound dressings. The outcome complete healing following treatment and the generalised pair-wise modelling framework was used to generate mixed treatment effects against hydroactive wound dressing, currently the standard of treatment for PIs. All treatments were then ranked by their point estimates. Main Results: 40 studies (1,757 participants) comparing 5 dressing groups were included in the analysis. All dressings groups ranked better than basic (i.e. saline gauze or similar inert dressing). The foam (RR 1.18; 95%CI 0.95-1.48) and active wound dressing (RR 1.16; 95%CI 0.92-1.47) ranked better than hydroactive wound dressing in terms of healing of PIs when the latter was used as the reference group. Conclusion & Recommendations: There was considerable uncertainty around the estimates, yet, the use of hydroactive wound dressings appear to perform better than basic dressings. Foam and active wound dressing groups show promise and need further investigation. High-quality research on clinical effectiveness of the topical treatments are warranted to identify if foam and active wound dressings do provide advantages over hydroactive dressings.

Keywords: Net work Meta Analysis, Pressure Injury, Dresssing, Pressure Ulcer

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Authors: R. Suresh, Pavan Kumar Nimmagadda, Ming Zo Tan, Shane Hart, Sharp Ugwuocha

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Polycrystalline diamond compact (PDC) drill bits are extensively used in the oil and gas industry as well as the mining industry. Industry engineers continually improve upon PDC drill bit designs and hydraulic conditions. Optimized injection nozzles play a key role in improving the drilling performance and efficiency of these ever changing PDC drill bits. In the first part of this study, computational fluid dynamics (CFD) modelling is performed to investigate the hydrodynamic characteristics of drilling fluid flow around the PDC drill bit. An Open-source CFD software – OpenFOAM simulates the flow around the drill bit, based on the field input data. A specifically developed console application integrates the entire CFD process including, domain extraction, meshing, and solving governing equations and post-processing. The results from the OpenFOAM solver are then compared with that of the ANSYS Fluent software. The data from both software programs agree. The second part of the paper describes the parametric study of the PDC drill bit nozzle to determine the effect of parameters such as number of nozzles, nozzle velocity, nozzle radial position and orientations on the flow field characteristics and bit washing patterns. After analyzing a series of nozzle configurations, the best configuration is identified and recommendations are made for modifying the PDC bit design.

Keywords: ANSYS Fluent, computational fluid dynamics, nozzle configuration, OpenFOAM, PDC dill bit

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Authors: Patsarawadee Paojinda, Waranya Imprasittichai, Sudaratana R. Krungkrai, Nirianne Marie Q. Palacpac, Toshihiro Horii, Jerapan Krungkrai

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Fusion of the last two enzymes in the pyrimidine biosynthetic pathway in the inversed order by having COOH-terminal orotate phosphoribosyltransferase (OPRT) and NH2-terminal orotidine 5'-monophosphate decarboxylase (OMPDC), as OMPDC-OPRT, are described in many organisms. Here, we produced gene fusions of Plasmodium falciparum OMPDC-OPRT and expressed the bifunctional protein in Escherichia coli. The enzyme was purified to homogeneity using affinity and anion-exchange chromatography, exhibited enzymatic activities and functioned as a dimer. The activities, although unstable, can be stabilized by its substrate and product during purification and long-term storage. Furthermore, the enzyme expressed a perfect catalytic efficiency (kcat/Km). The kcat was selectively enhanced up to 3 orders of magnitude, while the Km was not much affected and remained at low µM levels when compared to the monofunctional enzymes. The fusion of the two enzymes, creating a “super-enzyme” with perfect catalytic power and more flexibility, reflects cryptic relationship of enzymatic reactivaties and metabolic functions on molecular evolution.

Keywords: bifunctional enzyme, orotate phosphoribosyltransferase, orotidine 5'-monophosphate decarboxylase, plasmodium falciparum

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Authors: Sandeep Kaur, Jenny Vuong, Marcel Julliard, Sean O'Donoghue

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Time-series data are useful for modelling as they can enable model-evaluation. However, when reconstructing models from phosphoproteomic data, often non-exact methods are utilised, as the knowledge regarding the network structure, such as, which kinases and phosphatases lead to the observed phosphorylation state, is incomplete. Thus, such reactions are often hypothesised, which gives rise to uncertainty. Here, we propose a framework, implemented via a web-based tool (as an extension to Minardo), which given time-series phosphoproteomic datasets, can generate κ models. The incompleteness and uncertainty in the generated model and reactions are clearly presented to the user via the visual method. Furthermore, we demonstrate, via a toy EGF signalling model, the use of algorithmic verification to verify κ models. Manually formulated requirements were evaluated with regards to the model, leading to the highlighting of the nodes causing unsatisfiability (i.e. error causing nodes). We aim to integrate such methods into our web-based tool and demonstrate how the identified erroneous nodes can be presented to the user via the visual method. Thus, in this research we present a framework, to enable a user to explore phosphorylation proteomic time-series data in the context of models. The observer can visualise which reactions in the model are highly uncertain, and which nodes cause incorrect simulation outputs. A tool such as this enables an end-user to determine the empirical analysis to perform, to reduce uncertainty in the presented model - thus enabling a better understanding of the underlying system.

Keywords: κ-models, model verification, time-series phosphoproteomic datasets, uncertainty and error visualisation

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Authors: Jeremiah Madzimure

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In order to stay competitive in business and improve performance, Small and Medium Enterprises (SMEs) need to make use of business networking and logistics integration. Strategic networking and logistics integration in business companies have become critical as they allow supplier partnering, exchange of vital information/ access to valuable resources allowing innovation, gaining access to additional resources, sharing risks and costs which is required for enhancing company performance. The purpose of this study was to examine the influence of strategic networks and logistics integration on company performance: the case of small and medium enterprises in South Africa. A quantitative research design was adopted in this study, and 137 SMEs owners and managers completed and returned the survey questionnaire. Confirmatory Factor Analysis (CFA) was conducted using the Analysis of Moment Structures (AMOS), version 24.0 to assess psychometric properties of the measurement scales. Path modelling techniques were used to test the proposed hypothesis. Three research hypotheses were postulated. The results indicate that strategic networks had a positive and significant influence on logistics integration and company performance. As well logistics integration had a strong positive and significant influence on company performance. This study provides a useful model for analysing the relationship between strategic networks and logistics integration on company performance. Moreover, the findings of the study provide useful insights into how SMEs should benefit from business networking and logistics integration so as to improve their performance. The implications of the study are discussed, and finally, limitations and recommendations are indicated.

Keywords: strategic networking, logistics integration, company performance, SMEs

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Authors: Renu Yadav, Sanjeev Kumar

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In northern India, chickpea (Cicer arietinum L.) come across with terminal high-temperature stress during reproductive stage which leads to reduced yield. Hence, stable production of chickpea will depend on the development of new methods like ‘priming’ which allow improved adaptation to the drought and heat stress. In the present experiment, 11-day chickpea seedling was primed with mild drought stress and put on recovery stage by irrigating and finally 30-day seedlings were exposed to heat stress 38°C (4 hours), 35°C (8 hours) and 32°C (12 hours). To study the effect of combinatorial stress, heat and drought stress was applied simultaneously. Analyses of various physiological parameters like membrane damage assay, photosynthetic pigments, antioxidative enzyme, total sugars were estimated at all stages. To study the effect of heat stress on the metabolites of the plants, GC-MS and HPLC were performed, while at transcriptional level Real-Time PCR of predicted heat stress-related genes was done. It was concluded that the heat stress significantly affected the chickpea plant at physiological and molecular level in all the five varieties. Results also show less damaging effect in primed plants by increasing the activity of antioxidative enzymes and increased expression of heat shock proteins and heat shock factors.

Keywords: chickpea, combinatorial stress, heat stress, oxidative stress, priming, RT-PCR

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Authors: Nermin Isik, Ozlem Derinbay Ekici

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Bovine coccidiosis is a protozoan disease caused by various species of Eimeria and most signs of disease are chronic or subclinical. The aim of this study was to determine the prevalence of Eimeria spp. in calves in Konya, in Turkey. The study, conducted from January- February 2015, involved 240 faecal samples of calves in the age groups of <1 month, 1-3 months and >3 months in Konya city centre, in Turkey. In a retrospective study from these faecal samples of calves submitted to the University of Selcuk, Faculty of Veterinary Medicine, Laboratory of Parasitology were evaluated regarding the prevalence of Eimeria spp. Faecal samples were examined by Fulleborn saturated salt floatation technique. Eimeria oocysts were found in 8.33% of all samples. The positivity rates in each of the age groups were different. According to the age groups (<1 month, 1-3 months and >3 months), the Eimeria spp. were determined as 0.83, 22.73 and 7.41%, respectively. After examination of stool, detected oocysts were sporulated in 2.5% potassium dichromate at 22º C and species were identified as E. cylindrica, E. zuernii, E. ellipsoidalis, E. subspherica, E. bovis, E. auburnensis, E. canadensis, E. illinoisensis and E. brasiliensis in infected calves. In conclusion, the highest prevalence was observed in the age group of 1-3 months. The presence of Eimeria species in calves demonstrated for the first time in the Konya region in Turkey. Other etiologic agents should also be investigated in calves more seriously. Further molecular epidemiological studies should be performed in this community.

Keywords: Eimeria spp., calves, diarrhea, bovine coccidiosis

Procedia PDF Downloads 537