Sequence analysis of the second internal Transcribed spacer (ITS2) region of rDNA for species identification of trichostrongylus nematodes isolated from domestic livestock in Iran

Background: Infectivity of herbivores with Trichostrongylus nematodes is widespread in many countries, having a major economic impact on breeding, survivability, and productivity of domestic livestock. This study was carried out on Trichostrongylus species isolated from domestic livestock in order to develop an easy-to-perform method for species identification. Methods: Trichostrongylus isolates were collected from sheep, goat, cattle, and buffaloes in Khuzestan Province, southwest Iran. Primary species identification was carried out based on morphological characterization of male worms. PCR amplification of ITS2-rDNA region was performed on genomic DNA and the products were sequenced. Phylogenetic analysis of the nucleotide sequence data was conducted employing Bayesian Inference approach. Consequently, a restriction fragment length polymorphism (RFLP) profile was designed to differentiate Trichostrongylus species. Results: A consensus sequence of 238 nucleotides was deposited in the GenBank for Iranian isolates of Trichostrongylus species including T. colubriformis, T. capricola, T. probolurus and T. vitrinus. The designated RFLP using restriction enzyme TasI could readily differentiate among species having different ITS2 sequence. The molecular analysis was in concordance with morphological findings. Conclusion: Phylogenetic analysis indicated a close relationship among the sequences obtained in this study and reference sequence of relevant species. ITS2-RFLP with TasI is recommended for molecular differentiation of common Trichostrongylus species

Discrete alpha-skew-Laplace Distribution

Classical discrete distributions rarely support modelling data on the set of whole integers. In this paper, we shall introduce a flexible discrete distribution on this set, which can, in addition, cover bimodal as well as unimodal data sets. The proposed distribution can also be fitted to positive and negative skewed data. The distribution is indeed a discrete counterpart of the continuous alpha-skew-Laplace distribution recently introduced in the literature. The proposed distribution can also be viewed as a weighted version of the discrete Laplace distribution. Several distributional properties of this class such as cumulative distribution function, moment generating function, moments, modality, infinite divisibility and its truncation are studied. A simulation study is also performed. Finally, a real data set is used to show applicability of the new model comparing to several rival models, such as the discrete normal and Skellam distributions

Molecular and morphological characterization of the tapeworm Taenia hydatigena (Pallas, 1766) in sheep from Iran

Although Taenia hydatigena is one of the most prevalent taeniid species of livestock, very little molecular genetic information exists for this parasite. Up to 100 sheep isolates of T. hydatigena were collected from 19 abattoirs located in the provinces of Tehran, Alborz and Kerman. A calibrated microscope was used to measure the larval rostellar hook lengths. Following DNA extraction, fragments of cytochrome c oxidase 1 (CO1) and 12S rRNA genes were amplified by the polymerase chain reaction method and the amplicons were subjected to sequencing. The mean total length of large and small hooks was 203.4 μm and 135.9 μm, respectively. Forty CO1 and 39 12S rRNA sequence haplotypes were obtained in the study. The levels of pairwise nucleotide variation between individual haplotypes of CO1 and 12S rRNA genes were determined to be between 0.3-3.4% and 0.2-2.1%, respectively. The overall nucleotide variation among all the CO1 haplotypes was 9.7%, and for all the 12S rRNA haplotypes it was 10.1%. A significant difference was observed between rostellar hook morphometry and both CO1 and 12S rRNA sequence variability. A significantly high level of genetic variation was observed in the present study. The results showed that the 12S rRNA gene is more variable than CO1. © 2013 Cambridge University Press

Genetic characterization of Echinococcus granulosus in camels, cattle and sheep from the south-east of Iran indicates the presence of the G3 genotype

Echinococcus granulosus, the aetiologic agent of cystic echinococcosis (CE), is one of the most important zoonotic helminthes worldwide. Isolates of the parasite show considerable genetic variation in different intermediate hosts. Several genotypes and species are described in different eco-epidemiological settings. This study investigated E. granulosus genotypes existing in livestock and humans from the province of Kerman, located in south-eastern Iran, using sequencing data of cox1 and nad1 mitochondrial genes. Fifty-eight E. granulosus isolates, including 35 from sheep, 11 from cattle, 9 from camels and 3 from goats, were collected from slaughterhouses throughout Kerman. One human isolate was obtained from a surgical case of CE. Mitochondrial cox1 and nad1 regions were amplified using polymerase chain reaction (PCR) and 38 isolates were sequenced. Genotypes G1 (73.7%), G3 (13.2%) and G6 (13.1%) were identified from the isolates. G1 was the most common genotype from sheep (86.7%), cattle (80%), camels (44.4%) and goats (100%). Sheep, cattle and camels were also found to be infected with the G3 genotype (buffalo strain). The human isolate was identified as the G6 genotype. Results showed that the G3 genotype occurred in different animal hosts in addition to G1 and G6 genotypes. © 2011 Cambridge University Press

High resolution melting technique for molecular epidemiological studies of cystic echinococcosis: Differentiating G1, G3, and G6 genotypes of Echinococcus granulosus sensu lato

Reliable and rapid genotyping of large number of Echinococcus granulosus sensu lato isolates is crucial for understanding the epidemiology and transmission of cystic echinococcosis. We have developed a method for distinguishing and discriminating common genotypes of E. granulosus s.l. (G1, G3, and G6) in Iran. This method is based on polymerase chain reaction coupled with high resolution melting curve (HRM), ramping from 70 to 86 C with fluorescence data acquisition set at 0.1 C increments and continuous fluorescence monitoring. Consistency of this technique was assessed by inter- and intra-assays. Assessment of intra- and inter-assay variability showed low and acceptable coefficient of variations ranging from 0.09 to 0.17 %. Two hundred and eighty E. granulosus s.l. isolates from sheep, cattle, and camel were used to evaluate the applicability and accuracy of the method. The isolates were categorized as G1 (93, 94, and 25 %), G3 (7, 4, and 4 %), and G6 (0, 2, and 71 %) for sheep, cattle, and camel, respectively. HRM results were completely compatible with those obtained from sequencing and rostellar hook measurement. This method proved to be a valuable screening tool for large-scale molecular epidemiological studies. © 2013 Springer-Verlag Berlin Heidelberg

Devon: Deformable Volume Network for Learning Optical Flow

State-of-the-art neural network models estimate large displacement optical flow in multi-resolution and use warping to propagate the estimation between two resolutions. Despite their impressive results, it is known that there are two problems with the approach. First, the multi-resolution estimation of optical flow fails in situations where small objects move fast. Second, warping creates artifacts when occlusion or dis-occlusion happens. In this paper, we propose a new neural network module, Deformable Cost Volume, which alleviates the two problems. Based on this module, we designed the Deformable Volume Network (Devon) which can estimate multi-scale optical flow in a single high resolution. Experiments show Devon is more suitable in handling small objects moving fast and achieves comparable results to the state-of-the-art methods in public benchmarks

Observations of the post shock break-out emission of SN 2011dh with XMM-Newton

After the occurrence of the type cIIb SN 2011dh in the nearby spiral galaxy M 51 numerous observations were performed with different telescopes in various bands ranging from radio to gamma-rays. We analysed the XMM-Newton and Swift observations taken 3 to 30 days after the SN explosion to study the X-ray spectrum of SN 2011dh. We extracted spectra from the XMM-Newton observations, which took place ~7 and 11 days after the SN. In addition, we created integrated Swift/XRT spectra of 3 to 10 days and 11 to 30 days. The spectra are well fitted with a power-law spectrum absorbed with Galactic foreground absorption. In addition, we find a harder spectral component in the first XMM-Newton spectrum taken at t ~ 7 d. This component is also detected in the first Swift spectrum of t = 3 - 10 d. While the persistent power-law component can be explained as inverse Compton emission from radio synchrotron emitting electrons, the harder component is most likely bremsstrahlung emission from the shocked stellar wind. Therefore, the harder X-ray emission that fades away after t ~ 10 d can be interpreted as emission from the shocked circumstellar wind of SN 2011dh.Comment: Accepted for publication as a Research Note in Astronomy and Astrophysic

Neural network based simulation of sea-state sequences

The present PhD study, in its first part, uses artificial neural networks (ANNs), an optimization technique called simulated annealing, and statistics to simulate the significant wave height (Hs) and mean zero-up-crossing period ( ) of 3-hourly sea-states of a location in the North East Pacific using a proposed distribution called hepta-parameter spline distribution for the conditional distribution of Hs or given some inputs. Two different seven- network sets of ANNs for the simulation and prediction of Hs and were trained using 20-year observed Hs’s and ’s. The preceding Hs’s and ’s were the most important inputs given to the networks, but the starting day of the simulated period was also necessary. However, the code replaced the day with the corresponding time and the season. The networks were trained by a simulated annealing algorithm and the outputs of the two sets of networks were used for calculating the parameters of the probability density function (pdf) of the proposed hepta-parameter distribution. After the calculation of the seven parameters of the pdf from the network outputs, the Hs and of the future sea-state is predicted by generating random numbers from the corresponding pdf. In another part of the thesis, vertical piles have been studied with the goal of identifying the range of sea-states suitable for the safe pile driving operation. Pile configuration including the non-linear foundation and the gap between the pile and the pile sleeve shims were modeled using the finite elements analysis facilities within ABAQUS. Dynamic analyses of the system for a sea-state characterized by Hs and and modeled as a combination of several wave components were performed. A table of safe and unsafe sea-states was generated by repeating the analysis for various sea-states. If the prediction for a particular sea-state is repeated N times of which n times prove to be safe, then it could be said that the predicted sea-state is safe with the probability of 100(n/N)%. The last part of the thesis deals with the Hs return values. The return value is a widely used measure of wave extremes having an important role in determining the design wave used in the design of maritime structures. In this part, Hs return value was calculated demonstrating another application of the above simulation of future 3-hourly Hs’s. The maxima method for calculating return values was applied in such a way that avoids the conventional need for unrealistic assumptions. The significant wave height return value has also been calculated using the convolution concept from a model presented by Anderson et al. (2001).EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Comparison of clinical findings and rapid streptococcal antigen detection test in the diagnosis of group a Streptococcal (GAS) pharyngitis

Background: Group A β-hemolytic Streptococcal (GAS) pharyngitis is a common illness in children. Diagnosis and proper treatment of group A streptococcal sore throat is important particularly to prevent non-superlative sequel. Clinical findings continue to be used in differentiating streptococcal infection from viral sore throat. Objectives: The aim of this study was to evaluate the accuracy of clinical findings and rapid test in comparison with culture in the diagnosis of group A Streptococcal (GAS) pharyngitis. Patients and Methods: Ninety-four children between 3 to 16 years, who were referred to the pediatric clinic of Rasoul-e-Akram hospital with clinical findings of fever or sore throat were evaluated from October 2006 to May 2007. Clinical findings were recorded and swabs were taken for group A streptococcal cultures and streptococcal rapid antigen detection test. Analysis of statistical significance was performed using the chi-square method. The accuracy of clinical findings and rapid test was compared with the culture method as the gold standard, and sensitivity, specificity, positive predictive values, negative predictive value, positive likelihood ratio (LR+) and negative likelihood ratio (LR-) were calculated. Results: The culture was positive in 38 (40.4) of the 94 evaluated children. The mean age of children was 8 ± 3.7 years. The presence of petechiae, exudate and Lymphadenopathy (LAP) was more likely in children with positive streptococcus culture and rapid test (P value < 0.05). Lymphadenopathy was known to feature the most sensitivity (100), specificity (76.8), and positive predictive value (74.5), negative predictive value (100) and positive likelihood ratio (LR) (4.3) among clinical findings. The results of rapid test showed sensitivity of 89.4, specificity of 100, positive predictive value of 100, and negative predictive value of 93.3 in comparison with culture as the gold standard. In general, the accuracy of rapid test was found higher than subjective clinical findings (P = 0.001) Conclusions: Although LAP had good performance in early diagnosis of GAS, a combination of clinical findings, including tonsillar exudates, petechiae with results of rapid antigen test or culture is necessary for clinician judgment. Throat culture is the gold standard test for detecting group A Streptococcal infection, but rapid test is a good replacement for culture. © 2016, Infectious Diseases and Tropical Medicine Research Center

Safety and Efficacy of MLC601 in Iranian Patients after Stroke: A Double-Blind, Placebo-Controlled Clinical Trial

Objective. To investigate the safety and efficacy of MLC601 (NeuroAid) as a traditional Chinese medicine on motor recovery after ischemic stroke. Methods. This study was a double-blind, placebo-controlled clinical trial on 150 patients with a recent (less than 3 month) ischemic stroke. All patients were given either MLC601 (100 patients) or placebo (50 patients), 4 capsules 3 times a day, as an add-on to standard stroke treatment for 3 months. Results. Sex, age, elapsed time from stroke onset, and risk factors in the treatment group were not significantly different from placebo group at baseline (P > .05). Repeated measures analysis showed that Fugl-Meyer assessment was significantly higher in the treatment group during 12 weeks after stroke (P < .001). Good tolerability to treatment was shown, and adverse events were mild and transient. Conclusion. MLC601 showed better motor recovery than placebo and was safe on top of standard ischemic stroke medications especially in the severe and moderate cases