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Sample records for analyzer integrating genotype

  1. Molecular methods for bacterial genotyping and analyzed gene regions

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    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  2. Analyzing genotype-by-environment interaction using curvilinear regression

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    Dulce Gamito Santinhos Pereira

    2012-12-01

    Full Text Available In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield is not linear across environments and can be written as a second (or higher order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i a test for parallelism of regression curves; and (ii a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth, and the other with downward-facing concavity (i.e. the yield approaches saturation. Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.. We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials.

  3. Complex Genotype Mixtures Analyzed by Deep Sequencing in Two Different Regions of Hepatitis B Virus.

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    Andrea Caballero

    Full Text Available This study assesses the presence and outcome of genotype mixtures in the polymerase/surface and X/preCore regions of the HBV genome in patients with chronic hepatitis B virus (HBV infection. Thirty samples from ten chronic hepatitis B patients were included. The polymerase/surface and X/preCore regions were analyzed by deep sequencing (UDPS in the first available sample at diagnosis, a pre-treatment sample, and a sample while under treatment. HBV genotype was determined by phylogenesis. Quasispecies complexity was evaluated by mutation frequency and nucleotide diversity. The polymerase/surface and X/preCore regions were validated for genotyping from 113 GenBank reference sequences. UDPS yielded a median of 10,960 sequences per sample (IQR 16,645 in the polymerase/surface region and 11,595 sequences per sample (IQR 14,682 in X/preCore. Genotype mixtures were more common in X/preCore (90% than in polymerase/surface (30% (p<0.001. On X/preCore genotyping, all samples were genotype A, whereas polymerase/surface yielded genotypes A (80%, D (16.7%, and F (3.3% (p = 0.036. Genotype changes in polymerase/surface were observed in four patients during natural quasispecies dynamics and in two patients during treatment. There were no genotype changes in X/preCore. Quasispecies complexity was higher in X/preCore than in polymerase/surface (p = 0.004. The results provide evidence of genotype mixtures and differential genotype proportions in the polymerase/surface and X/preCore regions. The genotype dynamics in HBV infection and the different patterns of quasispecies complexity in the HBV genome suggest a new paradigm for HBV genotype classification.

  4. Complex Genotype Mixtures Analyzed by Deep Sequencing in Two Different Regions of Hepatitis B Virus.

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    Caballero, Andrea; Gregori, Josep; Homs, Maria; Tabernero, David; Gonzalez, Carolina; Quer, Josep; Blasi, Maria; Casillas, Rosario; Nieto, Leonardo; Riveiro-Barciela, Mar; Esteban, Rafael; Buti, Maria; Rodriguez-Frias, Francisco

    2015-01-01

    This study assesses the presence and outcome of genotype mixtures in the polymerase/surface and X/preCore regions of the HBV genome in patients with chronic hepatitis B virus (HBV) infection. Thirty samples from ten chronic hepatitis B patients were included. The polymerase/surface and X/preCore regions were analyzed by deep sequencing (UDPS) in the first available sample at diagnosis, a pre-treatment sample, and a sample while under treatment. HBV genotype was determined by phylogenesis. Quasispecies complexity was evaluated by mutation frequency and nucleotide diversity. The polymerase/surface and X/preCore regions were validated for genotyping from 113 GenBank reference sequences. UDPS yielded a median of 10,960 sequences per sample (IQR 16,645) in the polymerase/surface region and 11,595 sequences per sample (IQR 14,682) in X/preCore. Genotype mixtures were more common in X/preCore (90%) than in polymerase/surface (30%) (pgenotyping, all samples were genotype A, whereas polymerase/surface yielded genotypes A (80%), D (16.7%), and F (3.3%) (p = 0.036). Genotype changes in polymerase/surface were observed in four patients during natural quasispecies dynamics and in two patients during treatment. There were no genotype changes in X/preCore. Quasispecies complexity was higher in X/preCore than in polymerase/surface (p = 0.004). The results provide evidence of genotype mixtures and differential genotype proportions in the polymerase/surface and X/preCore regions. The genotype dynamics in HBV infection and the different patterns of quasispecies complexity in the HBV genome suggest a new paradigm for HBV genotype classification.

  5. Phenotypic and genotypic data integration and exploration through a web-service architecture

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    Nuzzo, Angelo; Riva, Alberto; Bellazzi, Riccardo

    2009-01-01

    Background Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data. Results We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets. Conclusion In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies. PMID:19828081

  6. Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

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    Zhu, Xuli; Jiang, Libo; Ye, Meixia; Sun, Lidan; Gragnoli, Claudia; Wu, Rongling

    2016-05-01

    Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation.

  7. Differentiation and Integration: Guiding Principles for Analyzing Cognitive Change

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    Siegler, Robert S.; Chen, Zhe

    2008-01-01

    Differentiation and integration played large roles within classic developmental theories but have been relegated to obscurity within contemporary theories. However, they may have a useful role to play in modern theories as well, if conceptualized as guiding principles for analyzing change rather than as real-time mechanisms. In the present study,…

  8. CYP2C9 polymorphism in patients with epilepsy: genotypic frequency analyzes andphenytoin adverse reactions correlation

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    Carlos Alexandre Twardowschy

    2011-04-01

    Full Text Available OBJECTIVE: CYP2C9 is a major enzyme in human drug metabolism and the polymorphism observed in the corresponding gene may affect therapeutic outcome during treatment. The distribution of variant CYP2C9 alleles and prevalence of phenytoin adverse reactions were hereby investigated in a population of patients diagnosed with epilepsy. METHOD: Allele-specific PCR analysis was carried out in order to determine frequencies of the two most common variant alleles, CYP2C9*2 and CYP2C9*3 in genomic DNA isolated from 100 epileptic patients. We also analyzed the frequency of phenytoin adverse reactions among those different genotypes groups. The data was presented as mean±standard deviation. RESULTS: The mean age at enrollment was 39.6±10.3 years (range, 17-72 years and duration of epilepsy was 26.5±11.9 years (range 3-48 years. The mean age at epilepsy onset was 13.1±12.4 years (range, 1 month-62 years. Frequencies of CYP2C9*1 (84%, CYP2C9*2 (9% and CYP2C9*3 (7% were similar to other published reports. Phenytoin adverse reactions were usually mild and occurred in 15% patients, without correlation with the CYP2C9 polymorphism (p=0.34. CONCLUSION: Our findings indicate an overall similar distribution of the CYP2C9 alleles in a population of patients diagnosed with epilepsy in the South of Brazil, compared to other samples. This sample of phenytoin users showed no drug related adverse reactions and CYP2C9 allele type correlation. The role of CYP2C9 polymorphism influence on phenytoin adverse reaction remains to be determined since some literature evidence and our data found negative results.

  9. Analyzing Distributed Functions in an Integrated Hazard Analysis

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    Morris, A. Terry; Massie, Michael J.

    2010-01-01

    Large scale integration of today's aerospace systems is achievable through the use of distributed systems. Validating the safety of distributed systems is significantly more difficult as compared to centralized systems because of the complexity of the interactions between simultaneously active components. Integrated hazard analysis (IHA), a process used to identify unacceptable risks and to provide a means of controlling them, can be applied to either centralized or distributed systems. IHA, though, must be tailored to fit the particular system being analyzed. Distributed systems, for instance, must be analyzed for hazards in terms of the functions that rely on them. This paper will describe systems-oriented IHA techniques (as opposed to traditional failure-event or reliability techniques) that should be employed for distributed systems in aerospace environments. Special considerations will be addressed when dealing with specific distributed systems such as active thermal control, electrical power, command and data handling, and software systems (including the interaction with fault management systems). Because of the significance of second-order effects in large scale distributed systems, the paper will also describe how to analyze secondary functions to secondary functions through the use of channelization.

  10. A fully integrated standalone portable cavity ringdown breath acetone analyzer

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    Sun, Meixiu; Jiang, Chenyu; Gong, Zhiyong; Zhao, Xiaomeng; Chen, Zhuying; Wang, Zhennan; Kang, Meiling; Li, Yingxin; Wang, Chuji

    2015-09-01

    Breath analysis is a promising new technique for nonintrusive disease diagnosis and metabolic status monitoring. One challenging issue in using a breath biomarker for potential particular disease screening is to find a quantitative relationship between the concentration of the breath biomarker and clinical diagnostic parameters of the specific disease. In order to address this issue, we need a new instrument that is capable of conducting real-time, online breath analysis with high data throughput, so that a large scale of clinical test (more subjects) can be achieved in a short period of time. In this work, we report a fully integrated, standalone, portable analyzer based on the cavity ringdown spectroscopy technique for near-real time, online breath acetone measurements. The performance of the portable analyzer in measurements of breath acetone was interrogated and validated by using the certificated gas chromatography-mass spectrometry. The results show that this new analyzer is useful for reliable online (online introduction of a breath sample without pre-treatment) breath acetone analysis with high sensitivity (57 ppb) and high data throughput (one data per second). Subsequently, the validated breath analyzer was employed for acetone measurements in 119 human subjects under various situations. The instrument design, packaging, specifications, and future improvements were also described. From an optical ringdown cavity operated by the lab-set electronics reported previously to this fully integrated standalone new instrument, we have enabled a new scientific tool suited for large scales of breath acetone analysis and created an instrument platform that can even be adopted for study of other breath biomarkers by using different lasers and ringdown mirrors covering corresponding spectral fingerprints.

  11. Phen-Gen: combining phenotype and genotype to analyze rare disorders.

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    Javed, Asif; Agrawal, Saloni; Ng, Pauline C

    2014-09-01

    We introduce Phen-Gen, a method that combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders. Simulations revealed that the causal variant was ranked first in 88% of cases when it was a coding variant-a 52% advantage over a genotype-only approach-and Phen-Gen outperformed other existing prediction methods by 13-58%. If disease etiology was unknown, the causal variant was assigned the top rank in 71% of simulations. Phen-Gen is available at http://phen-gen.org/.

  12. Experience analyzing wind data for large-scale integration

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Zhi; Dai, RenChang; Freeman, Lavelle A.; Miller, Nicholas W.; Shao, Miaolei [GEe Energy Consulting Group, Schenectady, NY (United States)

    2010-07-01

    Wind is a major piece of the green energy effort, and will certainly play a more important role in the future power industry. GE Energy has conducted a numer of large-scale renewable integration studies in North America. The objective of these studies is to understand how integrating large amounts of variable energy resources into the supply mix affects grid operation and economics. As part of this effort, various statistical analyses were performed to characterize the variability and uncertainty of wind generation. Based on the results of this characterization, further engineering and economic studies are performed to assess operational requirements, costs, and savings attributable to wind resources. For these analyses, a large amount of input data is usually required, and is often obtained in different formats. These data sets are not very intuitive at first glance, and need extensive effort to be developed into something informative. Based on project experience, different methods have been developed to explore and extrapolate the information hidden within large amounts of raw data. Algorithms and macros have been written to validate and correct data, to create summary information, and to produce derived data sets for further analyses. Informative plots and charts have also been programmed into various applications to provide quick, useful analysis when needed. This article introduces some illustrative and easy-to-analyze ways to look at these data using readily available tools. (orig.)

  13. Genotype × environmental interactions for analyzing adaptability and stability in different clones of Dalbergia sissoo Roxb.

    Institute of Scientific and Technical Information of China (English)

    A.Kumar; A.Bhatt; S.Ravichandran; V.Kumar; S.Dobhal

    2012-01-01

    In total 36 superior clones of Dalbergia sissoo Roxb.,screened from 300 selections conducted in natural and growing range of India and Nepal,were multiplied using single nodal cuttings and established to evaluate genotype×environmental interactions for adaptability and stability at the age of 30 months in three geographical locations in the state of Punjab,India.Clone 124 had maximum adaptability and stability (bi =1.04) to perform exceedingly well over the locations.Clones 36 and 1 were stable with mean regression coefficient of 0.84 and 1.22,respectively.Nonetheless,clone 41 performed exceedingly well for all the characters to attain maximum population mean,and the performance varied substantially across the locations.Therefore,clone 41 was eonsidered as productive but non-adaptive clone.Though some of the clones were sensitive to sites,14 clones for height,16 for collar diameter,12 for DBH and 7 for volume were relatively un-sensitive with higher regression coefficient.Nonetheless,clone 124 was the most stable with average bi value of 1.04 and productive,which could play an important role in future breeding and commercial deployment of stable and productive planting stock of Dalbergia sissoo.

  14. AnalyzeHOLE - An Integrated Wellbore Flow Analysis Tool

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    Halford, Keith

    2009-01-01

    Conventional interpretation of flow logs assumes that hydraulic conductivity is directly proportional to flow change with depth. However, well construction can significantly alter the expected relation between changes in fluid velocity and hydraulic conductivity. Strong hydraulic conductivity contrasts between lithologic intervals can be masked in continuously screened wells. Alternating intervals of screen and blank casing also can greatly complicate the relation between flow and hydraulic properties. More permeable units are not necessarily associated with rapid fluid-velocity increases. Thin, highly permeable units can be misinterpreted as thick and less permeable intervals or not identified at all. These conditions compromise standard flow-log interpretation because vertical flow fields are induced near the wellbore. AnalyzeHOLE, an integrated wellbore analysis tool for simulating flow and transport in wells and aquifer systems, provides a better alternative for simulating and evaluating complex well-aquifer system interaction. A pumping well and adjacent aquifer system are simulated with an axisymmetric, radial geometry in a two-dimensional MODFLOW model. Hydraulic conductivities are distributed by depth and estimated with PEST by minimizing squared differences between simulated and measured flows and drawdowns. Hydraulic conductivity can vary within a lithology but variance is limited with regularization. Transmissivity of the simulated system also can be constrained to estimates from single-well, pumping tests. Water-quality changes in the pumping well are simulated with simple mixing models between zones of differing water quality. These zones are differentiated by backtracking thousands of particles from the well screens with MODPATH. An Excel spreadsheet is used to interface the various components of AnalyzeHOLE by (1) creating model input files, (2) executing MODFLOW, MODPATH, PEST, and supporting FORTRAN routines, and (3) importing and graphically

  15. Port supply chain integration : analyzing biofuel supply chains

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    Stevens, Leonie C. E.; Vis, Iris F. A.

    2016-01-01

    This paper focuses on port supply chain integration to strengthen operational and business performance. We provide a structured and comprehensive method to enable port supply chain integration and demonstrate its applicability to the biofuel supply chain. We define the value proposition, role, activ

  16. Soil chemicals properties and wheat genotype impact on micronutrient and toxic elements content in wheat integral flour

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    Krunoslav Karalić

    2012-02-01

    Full Text Available Aim To determine impact of soil chemical properties and different wheat genotypes in Croatia on micronutrient and toxic elements content in wheat integral flour. Methods Research was conducted and soil samples were collected from two different production areas in the Republic of Croatia: Ovčara and Dalj. Besides soil samples, grain samples of four different Croatian wheat genotypes were also collected and analyzed. In total, 40 samples of soil and 40 samples of wheat grain were analysed for total (aqua regia and plant available (EDTA extraction heavy metal content of Fe, Mn, Zn, Cu, Pb, Cd. Results Determined soil pHKCl ranged from 5.63 to 6.25 at Ovčara and from 6.95 to 7.37 at Dalj sampling sites. The highest total concentration of heavy metals in soil were determined for Fe, followed by Mn, Zn, Cu, Pb and the lowest total concentration wasrecorded for Cd. The highest EDTA concentrations in soil were determined for Mn, than followed by Fe, Cu, Pb, and the lowest EDTA concentration was recorded for Cd. The highest concentration in integral wheat flour was found for Fe, than lower for Mn, Zn, Cu, Pb and the lowest concentration was found for Cd. If consumers in Croatia used daily 203 g of bread made of integral flour, they would take 2.31 to 8.44 µg Cd daily, depending on soil and wheat genotype.Conclusion The analysed soil and winter wheat genotypes have significant impact on potential daily intake of toxic and essentialheavy metals by integral flour or bread.

  17. Integrative methods for analyzing big data in precision medicine.

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    Gligorijević, Vladimir; Malod-Dognin, Noël; Pržulj, Nataša

    2016-03-01

    We provide an overview of recent developments in big data analyses in the context of precision medicine and health informatics. With the advance in technologies capturing molecular and medical data, we entered the area of "Big Data" in biology and medicine. These data offer many opportunities to advance precision medicine. We outline key challenges in precision medicine and present recent advances in data integration-based methods to uncover personalized information from big data produced by various omics studies. We survey recent integrative methods for disease subtyping, biomarkers discovery, and drug repurposing, and list the tools that are available to domain scientists. Given the ever-growing nature of these big data, we highlight key issues that big data integration methods will face.

  18. In vitro application of integrated selection index for screening drought tolerant genotypes in common wheat

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    Ezatollah FARSHADFAR

    2016-10-01

    Full Text Available This experiment was conducted on 20 wheat genotypes during 2010-2011 growing season at the Razi University, Kermanshah, Iran. A completely randomized design with six replications was used for callus induction and a 20 × 2 factorial experiment with three replications was used for response of genotypes to in vitro drought stress. ANOVA exhibited highly significant differences among the genotypes for callus growth rate, relative fresh mass growth, relative growth rate, callus water content, percent of callus chlorosis and proline content under stress condition (15 % PEG. PCA showed that the integrated selection index was correlated with callus growth index, relative fresh mass growth, relative growth rate and proline content indicating that these screening techniques can be useful for selecting drought tolerant genotypes. Screening drought tolerant genotypes and in vitro indicators of drought tolerance using mean rank, standard deviation of ranks and biplot analysis, discriminated genotypes 2, 18 and 10 as the most drought tolerant. Therefore they are recommended to be used as parents for genetic analysis, gene mapping and improvement of drought tolerance.

  19. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

    Science.gov (United States)

    Mungall, Christopher J; McMurry, Julie A; Köhler, Sebastian; Balhoff, James P; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan; Engelstad, Mark; Foster, Erin; Gourdine, J P; Jacobsen, Julius O B; Keith, Dan; Laraway, Bryan; Lewis, Suzanna E; NguyenXuan, Jeremy; Shefchek, Kent; Vasilevsky, Nicole; Yuan, Zhou; Washington, Nicole; Hochheiser, Harry; Groza, Tudor; Smedley, Damian; Robinson, Peter N; Haendel, Melissa A

    2017-01-04

    The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.

  20. Network Based Integrated Analysis of Phenotype-Genotype Data for Prioritization of Candidate Symptom Genes

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    Xing Li

    2014-01-01

    Full Text Available Background. Symptoms and signs (symptoms in brief are the essential clinical manifestations for individualized diagnosis and treatment in traditional Chinese medicine (TCM. To gain insights into the molecular mechanism of symptoms, we develop a computational approach to identify the candidate genes of symptoms. Methods. This paper presents a network-based approach for the integrated analysis of multiple phenotype-genotype data sources and the prediction of the prioritizing genes for the associated symptoms. The method first calculates the similarities between symptoms and diseases based on the symptom-disease relationships retrieved from the PubMed bibliographic database. Then the disease-gene associations and protein-protein interactions are utilized to construct a phenotype-genotype network. The PRINCE algorithm is finally used to rank the potential genes for the associated symptoms. Results. The proposed method gets reliable gene rank list with AUC (area under curve 0.616 in classification. Some novel genes like CALCA, ESR1, and MTHFR were predicted to be associated with headache symptoms, which are not recorded in the benchmark data set, but have been reported in recent published literatures. Conclusions. Our study demonstrated that by integrating phenotype-genotype relationships into a complex network framework it provides an effective approach to identify candidate genes of symptoms.

  1. Integrated Microfluidic Devices for Automated Microarray-Based Gene Expression and Genotyping Analysis

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    Liu, Robin H.; Lodes, Mike; Fuji, H. Sho; Danley, David; McShea, Andrew

    Microarray assays typically involve multistage sample processing and fluidic handling, which are generally labor-intensive and time-consuming. Automation of these processes would improve robustness, reduce run-to-run and operator-to-operator variation, and reduce costs. In this chapter, a fully integrated and self-contained microfluidic biochip device that has been developed to automate the fluidic handling steps for microarray-based gene expression or genotyping analysis is presented. The device consists of a semiconductor-based CustomArray® chip with 12,000 features and a microfluidic cartridge. The CustomArray was manufactured using a semiconductor-based in situ synthesis technology. The micro-fluidic cartridge consists of microfluidic pumps, mixers, valves, fluid channels, and reagent storage chambers. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated in the cartridge to provide pumping of liquid solutions. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross-talk of the stored reagents. Gene expression study of the human leukemia cell line (K562) and genotyping detection and sequencing of influenza A subtypes have been demonstrated using this integrated biochip platform. For gene expression assays, the microfluidic CustomArray device detected sample RNAs with a concentration as low as 0.375 pM. Detection was quantitative over more than three orders of magnitude. Experiment also showed that chip-to-chip variability was low indicating that the integrated microfluidic devices eliminate manual fluidic handling steps that can be a significant source of variability in genomic analysis. The genotyping results showed

  2. Analyzing Developing Country Market Integration using Incomplete Price Data and Cluster Analysis

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    Ansah, I.G.; Gardebroek, Koos; Ihle, R.; Jaletac, M.

    2015-01-01

    Recent global food price developments have spurred renewed interest in analyzing integration of local markets to global markets. A popular approach to quantify market integration is cointegration analysis. However, local market price data often has missing values, outliers, or short and incomplete s

  3. HPV genotyping and site of viral integration in cervical cancers in Indian women.

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    Poulami Das

    Full Text Available Persistent HPV infection plays a major role in cervical cancer. This study was undertaken to identify HPV types in a cohort of Indian women with locally advanced cervical cancer as well as to determine the physical state and/or site of viral integration in the host genome. Pretreatment biopsies (n = 270 from patients were screened for HPV infection by a high throughput HPV genotyping assay based on luminex xMAP technology as well as MY09/11 PCR and SPF1/2 PCR. Overall HPV positivity was observed to be 95%, with HPV16 being most common (63% followed by infection with HPV18. Integration status of the virus was identified using Amplification of Papillomavirus Oncogene Transcripts (APOT assay in a subset of samples positive for HPV16 and/or HPV18 (n = 86 and with an adequate follow-up. The data was correlated with clinical outcome of the patients. Integration of the viral genome was observed in 79% of the cases and a preference for integration into the chromosomal loci 1p, 3q, 6q, 11q, 13q and 20q was seen. Clinical data revealed that the physical state of the virus (integrated or episomal could be an important prognostic marker for cervical cancer.

  4. The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

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    Groza Tudor

    2012-03-01

    Full Text Available Abstract Background Skeletal dysplasias are a rare and heterogeneous group of genetic disorders affecting skeletal development. Patients with skeletal dysplasias suffer from many complex medical issues including degenerative joint disease and neurological complications. Because the data and expertise associated with this field is both sparse and disparate, significant benefits will potentially accrue from the availability of an ontology that provides a shared conceptualisation of the domain knowledge and enables data integration, cross-referencing and advanced reasoning across the relevant but distributed data sources. Results We introduce the design considerations and implementation details of the Bone Dysplasia Ontology. We also describe the different components of the ontology, including a comprehensive and formal representation of the skeletal dysplasia domain as well as the related genotypes and phenotypes. We then briefly describe SKELETOME, a community-driven knowledge curation platform that is underpinned by the Bone Dysplasia Ontology. SKELETOME enables domain experts to use, refine and extend and apply the ontology without any prior ontology engineering experience--to advance the body of knowledge in the skeletal dysplasia field. Conclusions The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain. It provides the means for integrating and annotating clinical and research data, not only at the generic domain knowledge level, but also at the level of individual patient case studies. It enables links between individual cases and publicly available genotype and phenotype resources based on a community-driven curation process that ensures a shared conceptualisation of the domain knowledge and its continuous incremental evolution.

  5. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

    Science.gov (United States)

    Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian; Balhoff, James P.; Borromeo, Charles; Brush, Matthew; Carbon, Seth; Conlin, Tom; Dunn, Nathan; Engelstad, Mark; Foster, Erin; Gourdine, J.P.; Jacobsen, Julius O.B.; Keith, Dan; Laraway, Bryan; Lewis, Suzanna E.; NguyenXuan, Jeremy; Shefchek, Kent; Vasilevsky, Nicole; Yuan, Zhou; Washington, Nicole; Hochheiser, Harry; Groza, Tudor; Smedley, Damian; Robinson, Peter N.; Haendel, Melissa A.

    2017-01-01

    The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype–phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype–phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species. PMID:27899636

  6. An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes.

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    2006-02-01

    Full Text Available An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets--based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes--provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides

  7. Analyzing Integrated Cost-Schedule Risk for Complex Product Systems R&D Projects

    Directory of Open Access Journals (Sweden)

    Zhe Xu

    2014-01-01

    Full Text Available The vast majority of the research efforts in project risk management tend to assess cost risk and schedule risk independently. However, project cost and time are related in reality and the relationship between them should be analyzed directly. We propose an integrated cost and schedule risk assessment model for complex product systems R&D projects. Graphical evaluation review technique (GERT, Monte Carlo simulation, and probability distribution theory are utilized to establish the model. In addition, statistical analysis and regression analysis techniques are employed to analyze simulation outputs. Finally, a complex product systems R&D project as an example is modeled by the proposed approach and the simulation outputs are analyzed to illustrate the effectiveness of the risk assessment model. It seems that integrating cost and schedule risk assessment can provide more reliable risk estimation results.

  8. Tiny Integrated Network Analyzer for Noninvasive Measurements of Electrically Small Antennas

    DEFF Research Database (Denmark)

    Buskgaard, Emil Feldborg; Krøyer, Ben; Tatomirescu, Alexandru

    2016-01-01

    Antenna mismatch and crosstalk are recurring issues in telecommunications. For electrically small antenna systems, these are very hard to measure without affecting the radiation performance of the system and, consequently, the measurement itself. Electrically small antennas are found in many...... applications ranging from consumer electronics to industrial systems. We propose a radically new approach to characterize crosstalk and mismatch based on vector network analysis. By miniaturizing the network analyzer, it can be integrated in the system under test, eliminating the need for cables leaving...... the system. The tiny integrated network analyzer is a stand-alone Arduino-based measurement system that utilizes the transmit signal of the system under test as its reference. It features a power meter with triggering ability, on-board memory, universal serial bus, and easy extendibility with general...

  9. Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

    Science.gov (United States)

    Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

    2016-01-01

    Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).

  10. ANALYZING THE CONSUMER PROFILING FOR IMPROVING EFFORTS OF INTEGRATED MARKETING COMMUNICATION

    Directory of Open Access Journals (Sweden)

    Olimpia OANCEA

    2014-06-01

    Full Text Available In an economy with a strong concurential character, organizations must capitalize the integrated marketing communication in the most effective way, to ensure the creation and maintenance of long-term relationships with current and potential customers. Building and managing the relationships with customers can have a direct and favourable effect on the efficiency of an organization's communication efforts. The integrated marketing communication identifies with the nowadays market dynamics and learns the organizations how easy can be to prosper in an environment where changes occur in an alarming way. Therefore, the purpose of this paper is to analyze the socio-demographic profile of the consumers of bread in Arges County, as well as the preferences and purchasing behaviour at the level of the market segments identified using the K-Means Cluster Analysis method.

  11. Integrative Genomics: Quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data

    Directory of Open Access Journals (Sweden)

    Eric eGamazon

    2013-05-01

    Full Text Available Given recent advances in the generation of high-throughput data such as whole genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent studies show that genome-wide association findings are likely to fall in loci with gene regulatory effects such as expression quantitative trait loci (eQTLs, demonstrating the utility of such integrative approaches. When genotype and gene expression data are available on the same individuals, we developed methods wherein top phenotype-associated genetic variants are prioritized if they are associated, as eQTLs, with gene expression traits that are themselves associated with the phenotype. Yet there has been no method to determine an overall p-value for the findings that arise specifically from the integrative nature of the approach. We propose a computationally feasible permutation method that accounts for the assimilative nature of the method and the correlation structure among gene expression traits and among genotypes. We apply the method to data from a study of cellular sensitivity to etoposide, one of the most widely used chemotherapeutic drugs. To our knowledge, this study is the first statistically sound quantification of the significance of the genotype-phenotype relationships resulting from applying an integrative approach. This method can be easily extended to cases in which gene expression data are replaced by other molecular phenotypes of interest, e.g., microRNA or proteomic data. This study has important implications for studies seeking to expand on genetic association studies by the use of omics data. Finally, we provide an R code to compute the empirical FDR when p-values for the observed and simulated phenotypes are available.

  12. Path-integral methods for analyzing the effects of fluctuations in stochastic hybrid neural networks.

    Science.gov (United States)

    Bressloff, Paul C

    2015-01-01

    We consider applications of path-integral methods to the analysis of a stochastic hybrid model representing a network of synaptically coupled spiking neuronal populations. The state of each local population is described in terms of two stochastic variables, a continuous synaptic variable and a discrete activity variable. The synaptic variables evolve according to piecewise-deterministic dynamics describing, at the population level, synapses driven by spiking activity. The dynamical equations for the synaptic currents are only valid between jumps in spiking activity, and the latter are described by a jump Markov process whose transition rates depend on the synaptic variables. We assume a separation of time scales between fast spiking dynamics with time constant [Formula: see text] and slower synaptic dynamics with time constant τ. This naturally introduces a small positive parameter [Formula: see text], which can be used to develop various asymptotic expansions of the corresponding path-integral representation of the stochastic dynamics. First, we derive a variational principle for maximum-likelihood paths of escape from a metastable state (large deviations in the small noise limit [Formula: see text]). We then show how the path integral provides an efficient method for obtaining a diffusion approximation of the hybrid system for small ϵ. The resulting Langevin equation can be used to analyze the effects of fluctuations within the basin of attraction of a metastable state, that is, ignoring the effects of large deviations. We illustrate this by using the Langevin approximation to analyze the effects of intrinsic noise on pattern formation in a spatially structured hybrid network. In particular, we show how noise enlarges the parameter regime over which patterns occur, in an analogous fashion to PDEs. Finally, we carry out a [Formula: see text]-loop expansion of the path integral, and use this to derive corrections to voltage-based mean-field equations, analogous

  13. Auditory temporal resolution and integration - stages of analyzing time-varying sounds

    DEFF Research Database (Denmark)

    Pedersen, Benjamin

    2007-01-01

    , much is still unknown of how temporal information is analyzed and represented in the auditory system. The PhD lecture concerns the topic of temporal processing in hearing and the topic is approached via four different listening experiments designed to probe several aspects of temporal processing...... scheme: Effects such as attention seem to play an important role in loudness integration, and further, it will be demonstrated that the auditory system can rely on temporal cues at a much finer level of detail than predicted be existing models (temporal details in the time-range of 60 ?s can...

  14. Tiny Integrated Network Analyzer for Noninvasive Measurements of Electrically Small Antennas

    DEFF Research Database (Denmark)

    Buskgaard, Emil Feldborg; Krøyer, Ben; Tatomirescu, Alexandru;

    2016-01-01

    Antenna mismatch and crosstalk are recurring issues in telecommunications. For electrically small antenna systems, these are very hard to measure without affecting the radiation performance of the system and, consequently, the measurement itself. Electrically small antennas are found in many...... the system. The tiny integrated network analyzer is a stand-alone Arduino-based measurement system that utilizes the transmit signal of the system under test as its reference. It features a power meter with triggering ability, on-board memory, universal serial bus, and easy extendibility with general...

  15. An integrative conceptual framework for analyzing customer satisfaction with shopping trip experiences in grocery retailing

    DEFF Research Database (Denmark)

    Esbjerg, Lars; Jensen, Birger Boutrup; Bech-Larsen, Tino

    2012-01-01

    Grocery retailers aim to satisfy customers, and because grocery shopping trips are frequently recurring, they must do socontinuously. Surprisingly, little research has addressed satisfaction with individual grocery shopping trips. This article therefore develops a conceptual framework for analyzing...... customer satisfaction with individual grocery shopping trip experiences within a overall ‘disconfirmation of expectations model’ of customer satisfaction. The contribution of the framework is twofold. First, by focusing on satisfaction with individual grocery shopping trips, previous research...... on satisfaction in the retailing literature. Second, the framework synthesizes and integrates multiple central concepts from different research streams into a common framework for analyzing shopping trip satisfaction. Propositions are derived regarding the relationships among the different concepts...

  16. ITHNA.SYS: An Integrated Thermal Hydraulic and Neutronic Analyzer SYStem for NUR research reactor

    Energy Technology Data Exchange (ETDEWEB)

    Mazidi, S., E-mail: samirmazidi@gmail.com [Division Physique et Applications Nucléaires, Centre de Recherche Nucléaire de Draria (CRND), BP 43 Sebala, Draria, Alger (Algeria); Meftah, B., E-mail: b_meftah@yahoo.com [Division Physique et Applications Nucléaires, Centre de Recherche Nucléaire de Draria (CRND), BP 43 Sebala, Draria, Alger (Algeria); Belgaid, M., E-mail: belgaidm@yahoo.com [Faculté de Physique, Université Houari Boumediene, USTHB, BP 31, Bab Ezzouar, Alger (Algeria); Letaim, F., E-mail: fletaim@yahoo.fr [Faculté des Sciences et Technologies, Université d’El-oued, PO Box 789, El-oued (Algeria); Halilou, A., E-mail: hal_rane@yahoo.fr [Division Réacteur NUR, Centre de Recherche Nucléaire de Draria, BP 43 Sebala, Draria, Alger (Algeria)

    2015-08-15

    Highlights: • We develop a neutronic and thermal hydraulic MTR reactor analyzer. • The analyzer allows a rapid determination of the reactor core parameters. • Some NUR reactor parameters have been analyzed. - Abstract: This paper introduces the Integrated Thermal Hydraulic and Neutronic Analyzer SYStem (ITHNA.SYS) that has been developed for the Algerian research reactor NUR. It is used both as an operating aid tool and as a core physics engineering analysis tool. The system embeds three modules of the MTR-PC software package developed by INVAP SE: the cell calculation code WIMSD, the core calculation code CITVAP and the program TERMIC for thermal hydraulic analysis of a material testing reactor (MTR) core in forced convection. ITHNA.SYS operates both in on-line and off-line modes. In the on-line mode, the system is linked, via the computer parallel port, to the data acquisition console of the reactor control room and allows a real time monitoring of major physical and safety parameters of the NUR core. PC-based ITHNA.SYS provides a viable and convenient way of using an accumulated and often complex reactor physics stock of knowledge and frees the user from the intricacy of adequate reactor core modeling. This guaranties an accurate, though rapid, determination of a variety of neutronic and thermal hydraulic parameters of importance for the operation and safety analysis of the NUR research reactor. Instead of the several hours usually required, the processing time for the determination of such parameters is now reduced to few seconds. Validation of the system was performed with respect to experimental measurements and to calculations using reference codes. ITHNA.SYS can be easily adapted to accommodate other kinds of MTR reactors.

  17. Poorer frontolimbic white matter integrity is associated with chronic cannabis use, FAAH genotype, and increased depressive and apathy symptoms in adolescents and young adults

    Directory of Open Access Journals (Sweden)

    Skyler G. Shollenbarger

    2015-01-01

    Conclusions: Consistent with prior findings, cannabis use was associated with reduced frontolimbic WM integrity. WM integrity was also moderated by FAAH genotype, in that cannabis-using FAAH C/C carriers and A carrying controls had reduced WM integrity compared to control C/C carriers. Observed frontolimbic white matter abnormalities were linked with increased depressive and apathy symptoms in the cannabis users.

  18. Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

    KAUST Repository

    Valdés, Felipe

    2013-03-01

    Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis functions and a collocation testing procedure, thus allowing for a marching-on-in-time (MOT) solution scheme. Unlike dual-source formulations, single-source equations involve space-time domain operator products, for which spatial discretization techniques developed for standalone operators do not apply. Here, the spatial discretization of the single-source time-domain integral equations is achieved by using the high-order divergence-conforming basis functions developed by Graglia alongside the high-order divergence-and quasi curl-conforming (DQCC) basis functions of Valdés The combination of these two sets allows for a well-conditioned mapping from div-to curl-conforming function spaces that fully respects the space-mapping properties of the space-time operators involved. Numerical results corroborate the fact that the proposed procedure guarantees accuracy and stability of the MOT scheme. © 2012 IEEE.

  19. Education and leisure: analyzing the Integrated School Program in Belo Horizonte

    Directory of Open Access Journals (Sweden)

    Marcília de Sousa Silva

    2015-01-01

    Full Text Available This article aims to analyze the concepts of leisure and education that permeate the documents in the Integrated School Program in Belo Horizonte. The analysis was based on the Policy cycle approach and emphasized the contexts of influence and the policy text production. Thus, the formation of the political agenda, the Political Pedagogical Project Program and the Strategic Plan 2010-2030 BH were investigated. The policy context is not organized in a linear fashion; it is a process of groups of interest interaction. With the discourse of coping with school failure, revealed by the students’ yield and flow evaluation indices (approval, repetition and dropout, the Integrated School education documents announce education and leisure as forms of production, strengthening links between public and private. The right to education is restricted to children’s and youth’s access and permanence in school without creating a perspective of universalization and quality. The documents address the leisure with a simplistic view of construction and maintenance of equipment and the idea of activity

  20. Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing

    Science.gov (United States)

    Nieto-Aponte, Leonardo; Ruiz-Ripa, Alicia; Tabernero, David; Gonzalez, Carolina; Gregori, Josep; Vila, Marta; Asensio, Miriam; Garcia-Cehic, Damir; Ruiz, Gerardo; Chen, Qian; Ordeig, Laura; Llorens, Meritxell; Saez, Montserrat; Esteban, Juan I.; Esteban, Rafael; Buti, Maria; Pumarola, Tomas

    2016-01-01

    ABSTRACT The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by

  1. Analyzing the concept of disruptive behavior in healthcare work: an integrative review*

    Directory of Open Access Journals (Sweden)

    Roberta Meneses Oliveira

    Full Text Available Abstract OBJECTIVE To analyze the concept of disruptive behavior in healthcare work. METHOD An integrative review carried out in the theoretical phase of a qualitative research substantiated by the theoretical framework of the Hybrid Model of Concept Development. The search for articles was conducted in the CINAHL, LILACS, PsycINFO, PubMed and SciVerse Scopus databases in 2013. RESULTS 70 scientific articles answered the guiding question and lead to attributes of disruptive behavior, being: incivility, psychological violence and physical/sexual violence; with their main antecedents (intrapersonal, interpersonal and organizational being: personality characteristics, stress and work overload; and consequences of: workers' moral/mental distress, compromised patient safety, labor loss, and disruption of communication, collaboration and teamwork. CONCLUSION Analysis of the disruptive behavior concept in healthcare work showed a construct in its theoretical stage that encompasses different disrespectful conduct adopted by health workers in the hospital context, which deserve the attention of leadership for better recognition and proper handling of cases and their consequences.

  2. Spatial data integration for analyzing the dynamics of Albanian Adriatic shoreline

    Science.gov (United States)

    Arapi, Luan; Nikolli, Pal; Kovaçi, Sander

    2016-04-01

    Shoreline mapping and shoreline change detection are critical subjects for coastal resource management, coastal environmental protection and sustainable coastal development and planning. Coastal changes are attracting more focus since they are important environmental indicators that directly impact coastal economic development and land management. Changes in the shape of shoreline may essentially affect the environment of the coastal zone. These may be caused by natural processes and human activities. The undertaken work focuses on analyzing the Adriatic shoreline dynamics, using spatial temporal data, by taking advantage of Geographic Informatin System (GIS) and Remote Sensing (RS). Shoreline mapping focuses on some specific issues such as mapping methods used to acquire shoreline data, models and database design used to represent shoreline in the spatial database and shoreline -change analysis methods. The study area extends from the mouth of Buna River in the north to Vlora Bay in the south covering a total length of about 220 km. Detection and future assessment of Albanian Adriatic shoreline spatial position is carried out through integration of multi scale resolution of spatial temporal data and different processing methods. We have combined topographic maps at different scales (1:75 000, 1918; 1:50 000, 1937; 1:25 000, 1960, 1986 and 1:10 000, 1995), digital aerial photographs of 2007 year, satellite images of Landsat TM, Landsat ETM+ and field observed GIS data. Generation of spatial data is carried out through vectorization process and image processing. Monitoring the dynamics of shoreline position change requires understanding the coastal processes as well as coastal mapping methods. The net rates of variations in the position of the shoreline are calculated according to transects disposed perpendicularly to the baseline and spaced equally along the coast. Analysis of the relative impact of the natural factors and human activities, it is fundamental

  3. SINDA'85/FLUINT - SYSTEMS IMPROVED NUMERICAL DIFFERENCING ANALYZER AND FLUID INTEGRATOR (CONVEX VERSION)

    Science.gov (United States)

    Cullimore, B.

    1994-01-01

    SINDA, the Systems Improved Numerical Differencing Analyzer, is a software system for solving lumped parameter representations of physical problems governed by diffusion-type equations. SINDA was originally designed for analyzing thermal systems represented in electrical analog, lumped parameter form, although its use may be extended to include other classes of physical systems which can be modeled in this form. As a thermal analyzer, SINDA can handle such interrelated phenomena as sublimation, diffuse radiation within enclosures, transport delay effects, and sensitivity analysis. FLUINT, the FLUid INTegrator, is an advanced one-dimensional fluid analysis program that solves arbitrary fluid flow networks. The working fluids can be single phase vapor, single phase liquid, or two phase. The SINDA'85/FLUINT system permits the mutual influences of thermal and fluid problems to be analyzed. The SINDA system consists of a programming language, a preprocessor, and a subroutine library. The SINDA language is designed for working with lumped parameter representations and finite difference solution techniques. The preprocessor accepts programs written in the SINDA language and converts them into standard FORTRAN. The SINDA library consists of a large number of FORTRAN subroutines that perform a variety of commonly needed actions. The use of these subroutines can greatly reduce the programming effort required to solve many problems. A complete run of a SINDA'85/FLUINT model is a four step process. First, the user's desired model is run through the preprocessor which writes out data files for the processor to read and translates the user's program code. Second, the translated code is compiled. The third step requires linking the user's code with the processor library. Finally, the processor is executed. SINDA'85/FLUINT program features include 20,000 nodes, 100,000 conductors, 100 thermal submodels, and 10 fluid submodels. SINDA'85/FLUINT can also model two phase flow

  4. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    Science.gov (United States)

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage.

  5. Satellite Technology as a Source of Integration. A Comparative Analyze: Europe MERCOSUR

    Science.gov (United States)

    Castillo Argañarás, Luis F.

    2002-01-01

    Satellite technology as a source of integration. A comparative several changes in the field of international law, creating the need to build a new framework for integration and cooperation. analysis between the development of the European Integration for space activities and the first steps towards the same target by the MERCOSUR with a comparative point of view will show the positive and negative side effects of its development up to our present time.

  6. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

    Directory of Open Access Journals (Sweden)

    Druka Arnis

    2008-11-01

    Full Text Available Abstract Background A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. Description Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits. Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. Conclusion By

  7. Analyzing Systems Integration Best Practices and Assessment in DoD Space Systems Acquisition

    Science.gov (United States)

    2009-12-01

    insufficient monitoring of Systems Engineering & Integration (SE&I) progress. Resolving these program and technical maladies first requires an accurate...System Acquisition program, the subject of this thesis is the first step in curing these maladies . Scanning through Government Accountability Office (GAO...design and interface level.‖ (20:11) ―The JPO decided to retain core systems engineering/system integration responsibility. Col. Parkinson had a

  8. Application of a numerical differencing analyzer computer program to a Modular Integrated Utility System

    Science.gov (United States)

    Brandli, A. E.; Donham, C. F.

    1974-01-01

    This paper describes the application of a numerical differencing analyzer computer program to the thermal analyzation of a MIUS model. The MIUS model which was evaluated is one which would be required to support a 648-unit Garden Apartment Complex. This computer program was capable of predicting the thermal performance of this MIUS from the impressed electrical, heating, and cooling loads.

  9. From integrative genomics to systems genetics in the rat to link genotypes to phenotypes

    Science.gov (United States)

    Moreno-Moral, Aida

    2016-01-01

    ABSTRACT Complementary to traditional gene mapping approaches used to identify the hereditary components of complex diseases, integrative genomics and systems genetics have emerged as powerful strategies to decipher the key genetic drivers of molecular pathways that underlie disease. Broadly speaking, integrative genomics aims to link cellular-level traits (such as mRNA expression) to the genome to identify their genetic determinants. With the characterization of several cellular-level traits within the same system, the integrative genomics approach evolved into a more comprehensive study design, called systems genetics, which aims to unravel the complex biological networks and pathways involved in disease, and in turn map their genetic control points. The first fully integrated systems genetics study was carried out in rats, and the results, which revealed conserved trans-acting genetic regulation of a pro-inflammatory network relevant to type 1 diabetes, were translated to humans. Many studies using different organisms subsequently stemmed from this example. The aim of this Review is to describe the most recent advances in the fields of integrative genomics and systems genetics applied in the rat, with a focus on studies of complex diseases ranging from inflammatory to cardiometabolic disorders. We aim to provide the genetics community with a comprehensive insight into how the systems genetics approach came to life, starting from the first integrative genomics strategies [such as expression quantitative trait loci (eQTLs) mapping] and concluding with the most sophisticated gene network-based analyses in multiple systems and disease states. Although not limited to studies that have been directly translated to humans, we will focus particularly on the successful investigations in the rat that have led to primary discoveries of genes and pathways relevant to human disease. PMID:27736746

  10. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments

    NARCIS (Netherlands)

    Duitama, Jorge; Quintero, Juan Camilo; Cruz, Daniel Felipe; Quintero, Constanza; Hubmann, Georg; Foulquié-Moreno, Maria R.; Verstrepen, Kevin J.; Thevelein, Johan M.; Tohme, Joe

    2014-01-01

    Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still

  11. Towards a theoretical framework for analyzing integrated socio-environmental systems

    NARCIS (Netherlands)

    Widlok, T.; Aufgebauer, A.; Bradtmöller, M.; Dikau, R.; Hoffmann, T.; Kretschmer, I.; Panagiotopoulos, K.; Pastoors, A.; Peters, R.; Schäbitz, F.; Schlummer, M.; Solich, M.; Wagner, B.; Weniger, G.C.; Zimmermann, A.

    2012-01-01

    This article addresses two major challenges for an integrated analysis of socio-environmental systems, namely the diversity of contributing disciplines and the wide spectrum of temporal and spatial scales. Archaeology, the geosciences and socio-cultural anthropology provide information relating to a

  12. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples

    Directory of Open Access Journals (Sweden)

    Beier Markus

    2007-08-01

    Full Text Available Abstract Background Genetic variants in immune regulator genes have been associated with numerous diseases, including allergies and cancer. Increasing evidence suggests a substantially elevated disease risk in individuals who carry a combination of disease-relevant single nucleotide polymorphisms (SNPs. For the genotyping of immune regulator genes, such as cytokines, chemokines and transcription factors, an oligonucleotide microarray for the analysis of 99 relevant SNPs was established. Since the microarray design was based on a platform that permits flexible in situ oligonucleotide synthesis, a set of optimally performing probes could be defined by a selection approach that combined computational and experimental aspects. Results While the in silico process eliminated 9% of the initial probe set, which had been picked purely on the basis of potential association with disease, the subsequent experimental validation excluded more than twice as many. The performance of the optimized microarray was demonstrated in a pilot study. The genotypes of 19 hay-fever patients (aged 40–44 with high IgE levels against inhalant antigens were compared to the results obtained with 19 age- and sex-matched controls. For several variants, allele-frequency differences of more than 10% were identified. Conclusion Based on the ability to improve empirically a chip design, the application of candidate-SNP typing represents a viable approach in the context of molecular epidemiological studies.

  13. Analyzing Web 2.0 Integration with Next Generation Networks for Services Rendering

    CERN Document Server

    Lakhtaria, Kamaljit I

    2010-01-01

    The Next Generation Networks (NGN) aims to integrate for IP-based telecom infrastructures and provide most advance & high speed emerging value added services. NGN capable to provide higher innovative services, these services will able to integrate communication and Web service into a single platform. IP Multimedia Subsystem, a NGN leading technology, enables a variety of NGN-compliant communications services to interoperate while being accessed through different kinds of access networks, preferably broadband. IMS–NGN services essential by both consumer and corporate users are by now used to access services, even communications services through the web and web-based communities and social networks, It is key for success of IMS-based services to be provided with efficient web access, so users can benefit from those new services by using web-based applications and user interfaces, not only NGN-IMS User Equipments and SIP protocol. Many Service are under planning which provided only under convergence of ...

  14. Integration of Feedstock Assembly System and Cellulosic Ethanol Conversion Models to Analyze Bioenergy System Performance

    Energy Technology Data Exchange (ETDEWEB)

    Jared M. Abodeely; Douglas S. McCorkle; Kenneth M. Bryden; David J. Muth; Daniel Wendt; Kevin Kenney

    2010-09-01

    Research barriers continue to exist in all phases of the emerging cellulosic ethanol biorefining industry. These barriers include the identification and development of a sustainable and abundant biomass feedstock, the assembly of viable assembly systems formatting the feedstock and moving it from the field (e.g., the forest) to the biorefinery, and improving conversion technologies. Each of these phases of cellulosic ethanol production are fundamentally connected, but computational tools used to support and inform analysis within each phase remain largely disparate. This paper discusses the integration of a feedstock assembly system modeling toolkit and an Aspen Plus® conversion process model. Many important biomass feedstock characteristics, such as composition, moisture, particle size and distribution, ash content, etc. are impacted and most effectively managed within the assembly system, but generally come at an economic cost. This integration of the assembly system and the conversion process modeling tools will facilitate a seamless investigation of the assembly system conversion process interface. Through the integrated framework, the user can design the assembly system for a particular biorefinery by specifying location, feedstock, equipment, and unit operation specifications. The assembly system modeling toolkit then provides economic valuation, and detailed biomass feedstock composition and formatting information. This data is seamlessly and dynamically used to run the Aspen Plus® conversion process model. The model can then be used to investigate the design of systems for cellulosic ethanol production from field to final product.

  15. Analyzing the Heat Transfer Property of Heat Pipe Influenced by Integrated Cooling Apparatus

    Directory of Open Access Journals (Sweden)

    Chen-Ching Ting

    2014-01-01

    Full Text Available Heat pipe with discrete heat transfer property is often called thermal superconductor because it has extremely large thermal conductivity. This special heat transfer property is destroyed by integrating cooling apparatus and further reducing the cooling power of a heat pipe cooler. This paper experimentally studied the heat transfer property of heat pipe influenced by integrated cooling apparatus. To simplify the investigating process, a home-made square heat pipe with the dimensions of L×W×H=10×10×100 mm3 was built with two pieces of copper plates and two pieces of glass plates face to face, respectively. The two pieces of copper plates were constructed with inside walls of capillary structure and the two pieces of glasses were with antifog inside walls for observing the inner phenomenon. Moreover, isothermal circulating cooling water was applied outside the heat pipe instead of cooling fin. The results show that heat vapor in the heat pipe is condensed earlier and cannot reach the remote section of condenser. In other words, the heat transfer property of heat pipe is destroyed by integrating cooling water. This phenomenon causes the unfavorable cooling power of the heat pipe cooler.

  16. An integrated graphic–taxonomic–associative approach to analyze human factors in aviation accidents

    Directory of Open Access Journals (Sweden)

    Gong Lei

    2014-04-01

    Full Text Available Human factors are critical causes of modern aviation accidents. However, existing accident analysis methods encounter limitations in addressing aviation human factors, especially in complex accident scenarios. The existing graphic approaches are effective for describing accident mechanisms within various categories of human factors, but cannot simultaneously describe inadequate human–aircraft–environment interactions and organizational deficiencies effectively, and highly depend on analysts’ skills and experiences. Moreover, the existing methods do not emphasize latent unsafe factors outside accidents. This paper focuses on the above three limitations and proposes an integrated graphic–taxonomic–associative approach. A new graphic model named accident tree (AcciTree, with a two-mode structure and a reaction-based concept, is developed for accident modeling and safety defense identification. The AcciTree model is then integrated with the well-established human factors analysis and classification system (HFACS to enhance both reliability of the graphic part and logicality of the taxonomic part for improving completeness of analysis. An associative hazard analysis technique is further put forward to extend analysis to factors outside accidents, to form extended safety requirements for proactive accident prevention. Two crash examples, a research flight demonstrator by our team and an industrial unmanned aircraft, illustrate that the integrated approach is effective for identifying more unsafe factors and safety requirements.

  17. A new approach to analyze strategy map using an integrated BSC and FUZZY DEMATEL

    Directory of Open Access Journals (Sweden)

    Seyed Abdollah Heydariyeh

    2012-01-01

    Full Text Available Today, with ever-increasing competition in global economic conditions, the necessity of effective implementation of strategy map has become an inevitable and necessary. The strategy map represents a general and structured framework for strategic objectives and plays an important role in forming competitive advantages for organizations. It is important to find important factors influencing strategy map and prioritize them based on suitable factors. In this paper, we propose an integration of BSC and Fuzzy DEMATEL technique to rank different items influencing strategy of a production plan. The proposed technique is implemented for real-world case study of glass production.

  18. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments.

    Science.gov (United States)

    Duitama, Jorge; Quintero, Juan Camilo; Cruz, Daniel Felipe; Quintero, Constanza; Hubmann, Georg; Foulquié-Moreno, Maria R; Verstrepen, Kevin J; Thevelein, Johan M; Tohme, Joe

    2014-04-01

    Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.

  19. Analyze and research the integrated navigation technique for GPS and pseudolite

    Science.gov (United States)

    Yuan, Gannan; Gan, Xingli; Li, Zhongyu

    2007-11-01

    To heighten the stability and precision of GPS positioning, the integrated navigation system for GPS and pseudolites (GPS/PL) was set up. The nonlinear equation of pseudo-distance measurement was linearized by Taylor series expansion, but it can't find any influencing factors of the truncation error. A new deducing method of the linear equation of pseudo-distance measurement was put forward, and some influencing factors of the truncation error were found and the nonlinear degree was defined. By the comparison of the nonlinear degree for GPS and pseudolites, the truncation error of pseudolite was found much larger than that of GPS navigation during the linearization. In allusion to the stable flight state of aircrafts, the nonlinear system equations of an integrated navigation system for GPS and pseudolites (GPS/PL) were set up, and the unscented Kalman filter (UKF) was used to estimate the navigation parameters to solve the nonlinear problems of PL. The simulation results showed that the maximum positioning error is 14 meters, and the mean value is 7 meters. Thereby, the pseudolites make the enhancement for the positioning precision and system stability of GPS navigation.

  20. A Bayesian integrated population dynamics model to analyze data for protected species

    Directory of Open Access Journals (Sweden)

    Hoyle, S. D.

    2004-06-01

    Full Text Available Managing wildlife-human interactions demands reliable information about the likely consequences of management actions. This requirement is a general one, whatever the taxonomic group. We describe a method for estimating population dynamics and decision analysis that is generally applicable, extremely flexible, uses data efficiently, and gives answers in a useful format. Our case study involves bycatch of a protected species, the Northeastern Offshore Spotted Dolphin (Stenella attenuata, in the tuna fishery of the eastern Pacific Ocean. Informed decision-making requires quantitative analyses taking all relevant information into account, assessing how bycatch affects these species and how regulations affect the fisheries, and describing the uncertainty in analyses. Bayesian analysis is an ideal framework for delivering information on uncertainty to the decision-making process. It also allows information from other populations or species or expert judgment to be included in the analysis, if appropriate. Integrated analysis attempts to include all relevant data for a population into one analysis by combining analyses, sharing parameters, and simultaneously estimating all parameters, using a combined objective function. It ensures that model assumptions and parameter estimates are consistent throughout the analysis, that uncertainty is propagated through the analysis, and that the correlations among parameters are preserved. Perhaps the most important aspect of integrated analysis is the way it both enables and forces consideration of the system as a whole, so that inconsistencies can be observed and resolved.

  1. A discontinuous galerkin time domain-boundary integral method for analyzing transient electromagnetic scattering

    KAUST Repository

    Li, Ping

    2014-07-01

    This paper presents an algorithm hybridizing discontinuous Galerkin time domain (DGTD) method and time domain boundary integral (BI) algorithm for 3-D open region electromagnetic scattering analysis. The computational domain of DGTD is rigorously truncated by analytically evaluating the incoming numerical flux from the outside of the truncation boundary through BI method based on the Huygens\\' principle. The advantages of the proposed method are that it allows the truncation boundary to be conformal to arbitrary (convex/ concave) scattering objects, well-separated scatters can be truncated by their local meshes without losing the physics (such as coupling/multiple scattering) of the problem, thus reducing the total mesh elements. Furthermore, low frequency waves can be efficiently absorbed, and the field outside the truncation domain can be conveniently calculated using the same BI formulation. Numerical examples are benchmarked to demonstrate the accuracy and versatility of the proposed method.

  2. IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

    Science.gov (United States)

    Maldonado, Emanuel; Sunagar, Kartik; Almeida, Daniela; Vasconcelos, Vitor; Antunes, Agostinho

    2014-01-01

    Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI) software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package), Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs). IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

  3. IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

    Directory of Open Access Journals (Sweden)

    Emanuel Maldonado

    Full Text Available Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package, Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs. IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

  4. A framework for analyzing the impact of data integrity/quality on electricity market operations

    Science.gov (United States)

    Choi, Dae Hyun

    This dissertation examines the impact of data integrity/quality in the supervisory control and data acquisition (SCADA) system on real-time locational marginal price (LMP) in electricity market operations. Measurement noise and/or manipulated sensor errors in a SCADA system may mislead system operators about real-time conditions in a power system, which, in turn, may impact the price signals in real-time power markets. This dissertation serves as a first attempt to analytically investigate the impact of bad/malicious data on electric power market operations. In future power system operations, which will probably involve many more sensors, the impact of sensor data integrity/quality on grid operations will become increasingly important. The first part of this dissertation studies from a market participant's perspective a new class of malicious data attacks on state estimation, which subsequently influences the result of the newly emerging look-ahead dispatch models in the real-time power market. In comparison with prior work of cyber-attack on static dispatch where no inter-temporal ramping constraint is considered, we propose a novel attack strategy, named ramp-induced data (RID) attack, with which the attacker can manipulate the limits of ramp constraints of generators in look-ahead dispatch. It is demonstrated that the proposed attack can lead to financial profits via malicious capacity withholding of selected generators, while being undetected by the existing bad data detection algorithm embedded in today's state estimation software. In the second part, we investigate from a system operator's perspective the sensitivity of locational marginal price (LMP) with respect to data corruption-induced state estimation error in real-time power market. Two data corruption scenarios are considered, in which corrupted continuous data (e.g., the power injection/flow and voltage magnitude) falsify power flow estimate whereas corrupted discrete data (e.g., the on/off status of

  5. Irradiated-Microsphere Gamma Analyzer (IMGA): an integrated system for HTGR coated particle fuel performance assessment

    Energy Technology Data Exchange (ETDEWEB)

    Kania, M.J.; Valentine, K.H.

    1980-02-01

    The Irradiated-Microsphere Gamma Analyzer (IMGA) System, designed and built at ORNL, provides the capability of making statistically accurate failure fraction measurements on irradiated HTGR coated particle fuel. The IMGA records the gamma-ray energy spectra from fuel particles and performs quantitative analyses on these spectra; then, using chemical and physical properties of the gamma emitters it makes a failed-nonfailed decision concerning the ability of the coatings to retain fission products. Actual retention characteristics for the coatings are determined by measuring activity ratios for certain gamma emitters such as /sup 137/Cs//sup 95/Zr and /sup 144/Ce//sup 95/Zr for metallic fission product retention and /sup 134/Cs//sup 137/Cs for an indirect measure of gaseous fission product retention. Data from IMGA (which can be put in the form of n failures observed in N examinations) can be accurately described by the binomial probability distribution model. Using this model, a mathematical relationship between IMGA data (n,N), failure fraction, and confidence level was developed. To determine failure fractions of less than or equal to 1% at confidence levels near 95%, this model dictates that from several hundred to several thousand particles must be examined. The automated particle handler of the IMGA system provides this capability. As a demonstration of failure fraction determination, fuel rod C-3-1 from the OF-2 irradiation capsule was analyzed and failure fraction statistics were applied. Results showed that at the 1% failure fraction level, with a 95% confidence level, the fissile particle batch could not meet requirements; however, the fertile particle exceeded these requirements for the given irradiation temperature and burnup.

  6. Integrative gene network construction to analyze cancer recurrence using semi-supervised learning.

    Directory of Open Access Journals (Sweden)

    Chihyun Park

    Full Text Available BACKGROUND: The prognosis of cancer recurrence is an important research area in bioinformatics and is challenging due to the small sample sizes compared to the vast number of genes. There have been several attempts to predict cancer recurrence. Most studies employed a supervised approach, which uses only a few labeled samples. Semi-supervised learning can be a great alternative to solve this problem. There have been few attempts based on manifold assumptions to reveal the detailed roles of identified cancer genes in recurrence. RESULTS: In order to predict cancer recurrence, we proposed a novel semi-supervised learning algorithm based on a graph regularization approach. We transformed the gene expression data into a graph structure for semi-supervised learning and integrated protein interaction data with the gene expression data to select functionally-related gene pairs. Then, we predicted the recurrence of cancer by applying a regularization approach to the constructed graph containing both labeled and unlabeled nodes. CONCLUSIONS: The average improvement rate of accuracy for three different cancer datasets was 24.9% compared to existing supervised and semi-supervised methods. We performed functional enrichment on the gene networks used for learning. We identified that those gene networks are significantly associated with cancer-recurrence-related biological functions. Our algorithm was developed with standard C++ and is available in Linux and MS Windows formats in the STL library. The executable program is freely available at: http://embio.yonsei.ac.kr/~Park/ssl.php.

  7. An Integrated Approach to Analyzing (Adaptive Comanagement Using the "Politicized" IAD Framework

    Directory of Open Access Journals (Sweden)

    Luke Whaley

    2014-03-01

    Full Text Available Scholars of comanagement are faced with a difficult methodological challenge. As comanagement has evolved and diversified it has increasingly merged with the field of adaptive management and related concepts that derive from resilience thinking and complex adaptive systems theory. In addition to earlier considerations of power sharing, institution building, and trust, the adaptive turn in comanagement has brought attention to the process of social learning and a focus on concepts such as scale, self-organization, and system trajectory. At the same time, a number of scholars are calling for a more integrated approach to studying (adaptive comanagement that is able to situate these normative concepts within a critical understanding of how context and power fundamentally influences the behavior of a system. We propose that the "politicized" version of the Institutional Analysis and Development (IAD Framework, originally developed by Elinor Ostrom and her colleagues, is well suited to addressing this challenge. The framework provides breadth, clarity, and structure by drawing the analyst's attention to the range of variables and questions to be considered when attempting a study of comanagement, the various components of the situation, and the ways in which they interact, and the criteria the analyst may wish to adopt in evaluating the outcomes of the process. Alongside its ability to address contextual factors and power dynamics, the socioeconomic and institutional dimension of the politicized IAD Framework means that it can be used to conduct analyses that result in sound policy recommendations.

  8. Analyzing Web 2.0 Integration with Next Generation Networks for Services Rendering

    Directory of Open Access Journals (Sweden)

    Kamaljit I. Lakhtaria

    2010-08-01

    Full Text Available The Next Generation Networks (NGN aims to integrate for IP-based telecominfrastructures and provide most advance & high speed emerging value added services.NGN capable to provide higher innovative services, these services will able to integratecommunication and Web service into a single platform. IP Multimedia Subsystem, aNGN leading technology, enables a variety of NGN-compliant communications servicesto interoperate while being accessed through different kinds of access networks,preferably broadband. IMS–NGN services essential by both consumer and corporateusers are by now used to access services, even communications services through the weband web-based communities and social networks, It is key for success of IMS-basedservices to be provided with efficient web access, so users can benefit from those newservices by using web-based applications and user interfaces, not only NGN-IMS UserEquipments and SIP protocol. Many Service are under planning which provided onlyunder convergence of IMS & Web 2.0. Convergence between Web 2.0 and NGN-IMScreates and serves new invented innovative, entertainment and information appealing aswell as user centric services and applications. These services merge features from WWWand Communication worlds. On the one hand, interactivity, ubiquity, social orientation,user participation and content generation, etc. are relevant characteristics coming fromWeb 2.0 services. Parallel IMS enables services including multimedia telephony, mediasharing (video-audio, instant messaging with presence and context, online directory,etc. all of them applicable to mobile, fixed or convergent telecom networks. With thispaper, this paper brings out the benefits of adopting web 2.0 technologies for telecomservices. As the services are today mainly driven by the user's needs, and proposed theconcept of unique customizable service interface.

  9. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Directory of Open Access Journals (Sweden)

    Yuguang Zhang

    Full Text Available Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05 at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05 correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05 to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback

  10. A calderón-preconditioned single source combined field integral equation for analyzing scattering from homogeneous penetrable objects

    KAUST Repository

    Valdés, Felipe

    2011-06-01

    A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a single source magnetic field integral equation. The equation is immune to low-frequency and dense-mesh breakdown, and free from spurious resonances. Unlike dual source formulations, this equation involves operator products that cannot be discretized using standard procedures for discretizing standalone electric, magnetic, and combined field operators. Instead, the single source equation proposed here is discretized using a recently developed technique that achieves a well-conditioned mapping from div- to curl-conforming function spaces, thereby fully respecting the space mapping properties of the operators involved, and guaranteeing accuracy and stability. Numerical results show that the proposed equation and discretization technique give rise to rapidly convergent solutions. They also validate the equation\\'s resonant free character. © 2006 IEEE.

  11. Method to synthesize polynomial current waveforms and intensity compensation functions for DFB lasers in digital sweep integration gas analyzers.

    Science.gov (United States)

    Kidd, Gary

    2002-09-01

    With analysis methods using digital sweep integration of the absorbance function, linear current ramps can produce non-linear laser intensity and wavenumber functions from distributed feedback lasers. These non-linear functions produce offset and gain errors in mole fraction estimates on tunable diode laser gas analyzers. A method is described to synthesize polynomial current waveforms and laser intensity compensation functions to give linear wavenumber functions and to minimize the offset error. Quantitative and qualitative results are presented to evaluate reduction in mole fraction errors.

  12. Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention

    Science.gov (United States)

    Fitó, Montserrat; Melander, Olle; Martínez, José Alfredo; Toledo, Estefanía; Carpéné, Christian; Corella, Dolores

    2016-01-01

    Intervention with Mediterranean diet (MedDiet) has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc.) and final cardiovascular phenotypes (stroke, myocardial infarction, etc.) have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition. PMID:27598147

  13. Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention.

    Science.gov (United States)

    Fitó, Montserrat; Melander, Olle; Martínez, José Alfredo; Toledo, Estefanía; Carpéné, Christian; Corella, Dolores

    2016-09-02

    Intervention with Mediterranean diet (MedDiet) has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc.) and final cardiovascular phenotypes (stroke, myocardial infarction, etc.) have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition.

  14. Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention

    Directory of Open Access Journals (Sweden)

    Montserrat Fitó

    2016-09-01

    Full Text Available Intervention with Mediterranean diet (MedDiet has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc. and final cardiovascular phenotypes (stroke, myocardial infarction, etc. have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition.

  15. Automation and integration of polymerase chain reaction with capillary electrophoresis for high throughput genotyping and disease diagnosis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, N.

    1999-02-12

    Genotyping is to detect specific loci in the human genome. These loci provide important information for forensic testing, construction of genetic linkage maps, gene related disease diagnosis and pharmacogenetic research. Genotyping is becoming more and more popular after these loci can be easily amplified by polymerase chain reaction (PCR). Capillary electrophoresis has its unique advantages for DNA analysis due to its fast heat dissipation and ease of automation. Four projects are described in which genotyping is performed by capillary electrophoresis emphasizing different aspects. First, the author demonstrates a principle to determine the genotype based on capillary electrophoresis system. VNTR polymorphism in the human D1S80 locus was studied. Second, the separation of four short tandem repeat (STR) loci vWF, THO1, TPOX and CSF1PO (CTTv) by using poly(ethylene oxide) (PEO) was studied in achieving high resolution and preventing rehybridization of the DNA fragments. Separation under denaturing, non-denaturing conditions and at elevated temperature was discussed. Third, a 250 {micro}m i.d., 365 {micro}m o.d. fused silica capillary was used as the microreactor for PCR. Fourth, direct PCR from blood was studied to simplify the sample preparation for genotyping to minimum.

  16. Pipe3D, a pipeline to analyze Integral Field Spectroscopy Data: I. New fitting philosophy of FIT3D

    Science.gov (United States)

    Sánchez, S. F.; Pérez, E.; Sánchez-Blázquez, P.; González, J. J.; Rosález-Ortega, F. F.; Cano-Dí az, M.; López-Cobá, C.; Marino, R. A.; Gil de Paz, A.; Mollá, M.; López-Sánchez, A. R.; Ascasibar, Y.; Barrera-Ballesteros, J.

    2016-04-01

    We present an improved version of FIT3D, a fitting tool for the analysis of the spectroscopic properties of the stellar populations and the ionized gas derived from moderate resolution spectra of galaxies. This tool was developed to analyze integral field spectroscopy data and it is the basis of Pipe3D, a pipeline used in the analysis of CALIFA, MaNGA, and SAMI data. We describe the philosophy and each step of the fitting procedure. We present an extensive set of simulations in order to estimate the precision and accuracy of the derived parameters for the stellar populations and the ionized gas. We report on the results of those simulations. Finally, we compare the results of the analysis using FIT3D with those provided by other widely used packages, and we find that the parameters derived by FIT3D are fully compatible with those derived using these other tools.

  17. Analyzing the possibility of constructing the air heating system for an integrated solid fuel gasification combined-cycle power plant

    Science.gov (United States)

    Mikula, V. A.; Ryzhkov, A. F.; Val'tsev, N. V.

    2015-11-01

    Combined-cycle power plants operating on solid fuel have presently been implemented only in demonstration projects. One of possible ways for improving such plants consists in making a shift to hybrid process circuits of integrated gasification combined-cycle plants with external firing of solid fuel. A high-temperature air heater serving to heat compressed air is a key element of the hybrid process circuit. The article describes application of a high-temperature recuperative metal air heater in the process circuit of an integrated gasification combined-cycle power plant (IGCC). The available experience with high-temperature air heating is considered, and possible air heater layout arrangements are analyzed along with domestically produced heat-resistant grades of steel suitable for manufacturing such air heater. An alternative (with respect to the traditional one) design is proposed, according to which solid fuel is fired in a noncooled furnace extension, followed by mixing the combustion products with recirculation gases, after which the mixture is fed to a convective air heater. The use of this design makes it possible to achieve considerably smaller capital outlays and operating costs. The data obtained from thermal and aerodynamic calculations of the high-temperature air heater with a thermal capacity of 258 MW for heating air to a temperature of up to 800°C for being used in the hybrid process circuit of a combined-cycle power plant are presented.

  18. Fabrication and characterization of a CNT forest integrated micromechanical resonator for a rarefied gas analyzer in a medium vacuum atmosphere

    Science.gov (United States)

    Sugano, Koji; Matsumoto, Ryu; Tsutsui, Ryota; Kishihara, Hiroyuki; Matsuzuka, Naoki; Yamashita, Ichiro; Uraoka, Yukiharu; Isono, Yoshitada

    2016-07-01

    This study focuses on the development of a multi-walled carbon nanotube (MWCNT) forest integrated micromechanical resonator working as a rarefied gas analyzer for nitrogen (N2) and hydrogen (H2) gases in a medium vacuum atmosphere. The resonant response is detected in the form of changes in the resonant frequency or damping effects, depending on the rarefied gas species. The carbon nanotube (CNT) forest on the resonator enhances the effective specific surface area of the resonator, such that the variation of the resonant frequency and the damping effect based on the gas species increase significantly. We developed the fabrication process for the proposed resonator, which consists of standard micro-electro-mechanical systems (MEMS) processes and high-density CNT synthesis on the resonator mass. The high-density CNT synthesis was realized using multistep alternate coating of two types of ferritin proteins that act as catalytic iron particles. Two devices with different CNT densities were fabricated and characterized to evaluate the effect of the surface area of the CNT forest on the resonant response as a function of gas pressures ranging from 0.011 to 1 Pa for N2 and H2. Considering the damping effect, we found that the device with higher density was able to distinguish N2 and H2 clearly, whereas the device with lower density showed no difference between N2 and H2. We confirmed that a larger surface area showed a higher damping effect. These results were explained based on the kinetic theory of gases. In the case of resonant frequency, the relative resonant frequency shift increased with gas pressure and surface area because of the adsorption of gas molecules on the resonator surfaces. Higher density CNT forest adsorbed more gas molecules on the surfaces. The developed CNT forest integrated micromechanical resonator could successfully detect N2 and H2 gases and distinguish between them under pressures of 1 Pa.

  19. Integrated Path Differential Absorption Lidar Optimizations Based on Pre-Analyzed Atmospheric Data for ASCENDS Mission Applications

    Science.gov (United States)

    Pliutau, Denis; Prasad, Narasimha S.

    2012-01-01

    In this paper a modeling method based on data reductions is investigated which includes pre analyzed MERRA atmospheric fields for quantitative estimates of uncertainties introduced in the integrated path differential absorption methods for the sensing of various molecules including CO2. This approach represents the extension of our existing lidar modeling framework previously developed and allows effective on- and offline wavelength optimizations and weighting function analysis to minimize the interference effects such as those due to temperature sensitivity and water vapor absorption. The new simulation methodology is different from the previous implementation in that it allows analysis of atmospheric effects over annual spans and the entire Earth coverage which was achieved due to the data reduction methods employed. The effectiveness of the proposed simulation approach is demonstrated with application to the mixing ratio retrievals for the future ASCENDS mission. Independent analysis of multiple accuracy limiting factors including the temperature, water vapor interferences, and selected system parameters is further used to identify favorable spectral regions as well as wavelength combinations facilitating the reduction in total errors in the retrieved XCO2 values.

  20. Pipe3D, a pipeline to analyze Integral Field Spectroscopy data: I. New fitting phylosophy of FIT3D

    CERN Document Server

    Sánchez, S F; Sánchez-Blázquez, P; González, J J; Rosález-Ortega, F F; Cano-Díaz, M; López-Cobá, C; Marino, R A; de Paz, A Gil; Mollá, M; López-Sánchez, A R; Ascasibar, Y; Barrera-Ballesteros, J

    2015-01-01

    We present an improved version of FIT3D, a fitting tool for the analysis of the spectroscopic properties of the stellar populations and the ionized gas derived from moderate resolution spectra of galaxies. FIT3D is a tool developed to analyze Integral Field Spectroscopy data and it is the basis of Pipe3D, a pipeline already used in the analysis of datasets like CALIFA, MaNGA, and SAMI. We describe the philosophy behind the fitting procedure, and in detail each of the different steps in the analysis. We present an extensive set of simulations in order to estimate the precision and accuracy of the derived parameters for the stellar populations. In summary, we find that using different stellar population templates we reproduce the mean properties of the stellar population (age, metallicity, and dust attenuation) within ~0.1 dex. A similar approach is adopted for the ionized gas, where a set of simulated emission- line systems was created. Finally, we compare the results of the analysis using FIT3D with those pro...

  1. An integrative approach for analyzing hundreds of neurons in task performing mice using wide-field calcium imaging.

    Science.gov (United States)

    Mohammed, Ali I; Gritton, Howard J; Tseng, Hua-an; Bucklin, Mark E; Yao, Zhaojie; Han, Xue

    2016-02-08

    Advances in neurotechnology have been integral to the investigation of neural circuit function in systems neuroscience. Recent improvements in high performance fluorescent sensors and scientific CMOS cameras enables optical imaging of neural networks at a much larger scale. While exciting technical advances demonstrate the potential of this technique, further improvement in data acquisition and analysis, especially those that allow effective processing of increasingly larger datasets, would greatly promote the application of optical imaging in systems neuroscience. Here we demonstrate the ability of wide-field imaging to capture the concurrent dynamic activity from hundreds to thousands of neurons over millimeters of brain tissue in behaving mice. This system allows the visualization of morphological details at a higher spatial resolution than has been previously achieved using similar functional imaging modalities. To analyze the expansive data sets, we developed software to facilitate rapid downstream data processing. Using this system, we show that a large fraction of anatomically distinct hippocampal neurons respond to discrete environmental stimuli associated with classical conditioning, and that the observed temporal dynamics of transient calcium signals are sufficient for exploring certain spatiotemporal features of large neural networks.

  2. Integrated genome-wide genotyping and gene expression profiling reveals BCL11B as a putative oncogene in acute myeloid leukemia with 14q32 aberrations.

    Science.gov (United States)

    Abbas, Saman; Sanders, Mathijs A; Zeilemaker, Annelieke; Geertsma-Kleinekoort, Wendy M C; Koenders, Jasper E; Kavelaars, Francois G; Abbas, Zabiollah G; Mahamoud, Souad; Chu, Isabel W T; Hoogenboezem, Remco; Peeters, Justine K; van Drunen, Ellen; van Galen, Janneke; Beverloo, H Berna; Löwenberg, Bob; Valk, Peter J M

    2014-05-01

    Acute myeloid leukemia is a neoplasm characterized by recurrent molecular aberrations traditionally demonstrated by cytogenetic analyses. We used high density genome-wide genotyping and gene expression profiling to reveal acquired cryptic abnormalities in acute myeloid leukemia. By genome-wide genotyping of 137 cases of primary acute myeloid leukemia, we disclosed a recurrent focal amplification on chromosome 14q32, which included the genes BCL11B, CCNK, C14orf177 and SETD3, in two cases. In the affected cases, the BCL11B gene showed consistently high mRNA expression, whereas the expression of the other genes was unperturbed. Fluorescence in situ hybridization on 40 cases of acute myeloid leukemia with high BCL11B mRNA expression [2.5-fold above median; 40 out of 530 cases (7.5%)] revealed 14q32 abnormalities in two additional cases. In the four BCL11B-rearranged cases the 14q32 locus was fused to different partner chromosomes. In fact, in two cases, we demonstrated that the focal 14q32 amplifications were integrated into transcriptionally active loci. The translocations involving BCL11B result in increased expression of full-length BCL11B protein. The BCL11B-rearranged acute myeloid leukemias expressed both myeloid and T-cell markers. These biphenotypic acute leukemias all carried FLT3 internal tandem duplications, a characteristic marker of acute myeloid leukemia. BCL11B mRNA expression in acute myeloid leukemia appeared to be strongly associated with expression of other T-cell-specific genes. Myeloid 32D(GCSF-R) cells ectopically expressing Bcl11b showed decreased proliferation rate and less maturation. In conclusion, by an integrated approach involving high-throughput genome-wide genotyping and gene expression profiling we identified BCL11B as a candidate oncogene in acute myeloid leukemia.

  3. A Hierarchical Multi-Unidimensional IRT Approach for Analyzing Sparse, Multi-Group Data for Integrative Data Analysis.

    Science.gov (United States)

    Huo, Yan; de la Torre, Jimmy; Mun, Eun-Young; Kim, Su-Young; Ray, Anne E; Jiao, Yang; White, Helene R

    2015-09-01

    The present paper proposes a hierarchical, multi-unidimensional two-parameter logistic item response theory (2PL-MUIRT) model extended for a large number of groups. The proposed model was motivated by a large-scale integrative data analysis (IDA) study which combined data (N = 24,336) from 24 independent alcohol intervention studies. IDA projects face unique challenges that are different from those encountered in individual studies, such as the need to establish a common scoring metric across studies and to handle missingness in the pooled data. To address these challenges, we developed a Markov chain Monte Carlo (MCMC) algorithm for a hierarchical 2PL-MUIRT model for multiple groups in which not only were the item parameters and latent traits estimated, but the means and covariance structures for multiple dimensions were also estimated across different groups. Compared to a few existing MCMC algorithms for multidimensional IRT models that constrain the item parameters to facilitate estimation of the covariance matrix, we adapted an MCMC algorithm so that we could directly estimate the correlation matrix for the anchor group without any constraints on the item parameters. The feasibility of the MCMC algorithm and the validity of the basic calibration procedure were examined using a simulation study. Results showed that model parameters could be adequately recovered, and estimated latent trait scores closely approximated true latent trait scores. The algorithm was then applied to analyze real data (69 items across 20 studies for 22,608 participants). The posterior predictive model check showed that the model fit all items well, and the correlations between the MCMC scores and original scores were overall quite high. An additional simulation study demonstrated robustness of the MCMC procedures in the context of the high proportion of missingness in data. The Bayesian hierarchical IRT model using the MCMC algorithms developed in the current study has the potential to

  4. A boundary integral approach to analyze the viscous scattering of a pressure wave by a rigid body

    Science.gov (United States)

    Homentcovschi, Dorel; Miles, Ronald N.

    2008-01-01

    The paper provides boundary integral equations for solving the problem of viscous scattering of a pressure wave by a rigid body. By using this mathematical tool uniqueness and existence theorems are proved. Since the boundary conditions are written in terms of velocities, vector boundary integral equations are obtained for solving the problem. The paper introduces single-layer viscous potentials and also a stress tensor. Correspondingly, a viscous double-layer potential is defined. The properties of all these potentials are investigated. By representing the scattered field as a combination of a single-layer viscous potential and a double-layer viscous potential the problem is reduced to the solution of a singular vectorial integral equation of Fredholm type of the second kind. In the case where the stress vector on the boundary is the main quantity of interest the corresponding boundary singular integral equation is proved to have a unique solution. PMID:18709178

  5. A production-quality UNIX Very High Speed Integrated Circuit (VHSIC) Hardware Description Language (VHDL) subset analyzer

    Science.gov (United States)

    Bratton, Randolph M.

    1987-12-01

    This paper describes the design and implementation of the Air Force Institute of Technology's (AFIT's) UNIX-based VHDL Analyzer. The purpose of this tool is to facilitate the introduction of VHDL into the academic environment, which may not be able to use the Department of Defense's VMS-based software. This research emphasized two areas: the criteria for a production-quality software product and the design of an efficient Intermediate Representation (IR) that serves as an interface between the Analyzer and other tools in the AFIT VHDL Environment (AVE). Background on other UNIX VHDL analyzers, as well as other IRs, was presented. A two-part IR, based on Dallen's Patois hardware description language and named the VHDL Intermediate Access (VIA), was designed, and examples were given that illustrate its use. Test results showed that the Analyzer passed over 75 percent of the conformance tests from the VHDL VMS Analyzer Test Suite and performed well in the areas of compile time, memory usage, and disk usage. Recommendations for future research include adding user options to the Analyzer and implementing a design library for VHDL designs.

  6. Development of a Simulation Framework for Analyzing Security of Supply in Integrated Gas and Electric Power Systems

    NARCIS (Netherlands)

    Pambour, Kwabena Addo; Erdener, Burcin Cakir; Bolado-Lavin, Ricardo; Dijkema, Gerhard

    2017-01-01

    Gas and power networks are tightly coupled and interact with each other due to physically interconnected facilities. In an integrated gas and power network, a contingency observed in one system may cause iterative cascading failures, resulting in network wide disruptions. Therefore, understanding th

  7. Using Groupware to Gather and Analyze Intelligence in a Public Setting: Development of Integral Safety Plans in an Electronic Meeting

    NARCIS (Netherlands)

    Rouwette, E.A.J.A.; Vennix, J.A.M.

    2004-01-01

    This chapter focuses on the use of groupware to support local governments in activities in the intelligence cycle. Local governments in The Netherlands have a central role in developing integral safety plans for their district. However, in the implementation of safety plans the contribution of partn

  8. Integrated genotypic analysis of hedgehog-related genes identifies subgroups of keratocystic odontogenic tumor with distinct clinicopathological features.

    Directory of Open Access Journals (Sweden)

    Yasuyuki Shimada

    Full Text Available Keratocystic odontogenic tumor (KCOT arises as part of Gorlin syndrome (GS or as a sporadic lesion. Gene mutations and loss of heterozygosity (LOH of the hedgehog receptor PTCH1 plays an essential role in the pathogenesis of KCOT. However, some KCOT cases lack evidence for gene alteration of PTCH1, suggesting that other genes in the hedgehog pathway may be affected. PTCH2 and SUFU participate in the occurrence of GS-associated tumors, but their roles in KCOT development are unknown. To elucidate the roles of these genes, we enrolled 36 KCOT patients in a study to sequence their entire coding regions of PTCH1, PTCH2 and SUFU. LOH and immunohistochemical expression of these genes, as well as the downstream targets of hedgehog signaling, were examined using surgically-excised KCOT tissues. PTCH1 mutations, including four novel ones, were found in 9 hereditary KCOT patients, but not in sporadic KCOT patients. A pathogenic mutation of PTCH2 or SUFU was not found in any patients. LOH at PTCH1 and SUFU loci correlated with the presence of epithelial budding. KCOT harboring a germline mutation (Type 1 showed nuclear localization of GLI2 and frequent histological findings such as budding and epithelial islands, as well as the highest recurrence rate. KCOT with LOH but without a germline mutation (Type 2 less frequently showed these histological features, and the recurrence rate was lower. KCOT with neither germline mutation nor LOH (Type 3 consisted of two subgroups, Type 3A and 3B, which were characterized by nuclear and cytoplasmic GLI2 localization, respectively. Type 3B rarely exhibited budding and recurrence, behaving as the most amicable entity. The expression patterns of CCND1 and BCL2 tended to correlate with these subgroups. Our data indicates a significant role of PTCH1 and SUFU in the pathogenesis of KCOT, and the genotype-oriented subgroups constitute entities with different potential aggressiveness.

  9. Integrated genotypic analysis of hedgehog-related genes identifies subgroups of keratocystic odontogenic tumor with distinct clinicopathological features.

    Science.gov (United States)

    Shimada, Yasuyuki; Katsube, Ken-ichi; Kabasawa, Yuji; Morita, Kei-ichi; Omura, Ken; Yamaguchi, Akira; Sakamoto, Kei

    2013-01-01

    Keratocystic odontogenic tumor (KCOT) arises as part of Gorlin syndrome (GS) or as a sporadic lesion. Gene mutations and loss of heterozygosity (LOH) of the hedgehog receptor PTCH1 plays an essential role in the pathogenesis of KCOT. However, some KCOT cases lack evidence for gene alteration of PTCH1, suggesting that other genes in the hedgehog pathway may be affected. PTCH2 and SUFU participate in the occurrence of GS-associated tumors, but their roles in KCOT development are unknown. To elucidate the roles of these genes, we enrolled 36 KCOT patients in a study to sequence their entire coding regions of PTCH1, PTCH2 and SUFU. LOH and immunohistochemical expression of these genes, as well as the downstream targets of hedgehog signaling, were examined using surgically-excised KCOT tissues. PTCH1 mutations, including four novel ones, were found in 9 hereditary KCOT patients, but not in sporadic KCOT patients. A pathogenic mutation of PTCH2 or SUFU was not found in any patients. LOH at PTCH1 and SUFU loci correlated with the presence of epithelial budding. KCOT harboring a germline mutation (Type 1) showed nuclear localization of GLI2 and frequent histological findings such as budding and epithelial islands, as well as the highest recurrence rate. KCOT with LOH but without a germline mutation (Type 2) less frequently showed these histological features, and the recurrence rate was lower. KCOT with neither germline mutation nor LOH (Type 3) consisted of two subgroups, Type 3A and 3B, which were characterized by nuclear and cytoplasmic GLI2 localization, respectively. Type 3B rarely exhibited budding and recurrence, behaving as the most amicable entity. The expression patterns of CCND1 and BCL2 tended to correlate with these subgroups. Our data indicates a significant role of PTCH1 and SUFU in the pathogenesis of KCOT, and the genotype-oriented subgroups constitute entities with different potential aggressiveness.

  10. 亚胺培南不敏感大肠埃希菌碳青霉烯酶基因的检测%Analyze the genotypes of carbapenemase in imipenem non-sensitive Escherichia coli

    Institute of Scientific and Technical Information of China (English)

    沈瀚; 宁明哲; 周万青; 曹小利; 张之烽; 张葵

    2013-01-01

    目的 了解碳青霉烯酶基因在亚胺培南不敏感大肠埃希菌中的分布情况.方法 收集亚胺培南不敏感的大肠埃希菌25株,K-B纸片法测定菌株对药物的敏感性;采用EDTA协同试验及改良Hodge试验进行碳青霉烯酶表型检测;PCR法扩增碳青霉烯酶基因并进行序列分析.结果 25株大肠埃希菌呈现泛耐药现象,其中亚胺培南耐药15株,中度敏感10株;改良Hodge试验阳性1 5株,金属酶表型试验全部阴性;15株菌株检出KPC-2酶基因,未检出其它碳青霉烯酶基因.结论 产KPC-2酶是造成该院大肠埃希菌对碳青霉烯类抗菌药物耐药的主要原因.%Objective To analyze the genotypes of carbapenemase among Escherichia coli isolates which is non-sensitive to imipenem. Methods 25 E. coli isolates which were non-sensitive to imipenem were collected, and K-B agar diffusion test were performed to detect the sensitive of these E. coli isolates to antimicrobial agents. Modified Hodge test and EDTA disk synergy test were carried out to screen carbapenemases. And the corresponding carbapenemases encoding genes were further confirmed by PCR amplification along with DNA sequencing. Results All the 25 E. coli isolates displayed extensively drug resistance to the antimicrobial agents tested. Among them, 15 isolates were resistant to imipenem.and 10 isolates were intermediate. All the strains were negative for metal-enzymes indicated by EDTA disk synergy test. Whereas, the 15 imipenem resistant E. coli probably contain class A carbapenemase from the modified Hodge test. And further analysis confirmed that they were the KPC-2 enzymes. Conclusion KPC-2 enzyme is the main carbapenemase responsible for the resistance of E. coli isolates to imipenem in the hospital.

  11. State of art report for critical flow model to analyze a break flow in pressurizer of integral type reactor

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Yeon Moon; Lee, D. J.; Yoon, J. H.; Kim, J. P.; Kim, H. Y

    1999-03-01

    At a critical flow condition, the flow rate can't exceed a maximum value for given upstream conditions and the limited flow rate is called as a critical flow rate. The phenomena of critical flow occur at the discharge of a single phase gas or subcooled water through nozzles and pipes. Among the previous researches on critical flow, many accurate correlations on pressure, temperature and flow rate are represented for the single phase gas. However, for the two phase critical flow, the results of previous work showed that there was a large discrepancy between the analytical and experimental data and the data were in agreement for the limited thermodynamic conditions. Thus, further studies are required to enhance the two phase critical flow model. In the integral reactor, the critical flows of nitrogen gas and subcooled water are expected for the break of gas cylinder pipeline connected to the pressurizer. It requires that the inlet shape of the pipe and the nitrogen gas effect should be considered for the critical flow of integral reactor. The nitrogen gas exist in the pressurizer may affect the flow rate of primary coolant, which has been considered only for a few previous researches. Thus, the evaluation of the effect of the nitrogen on the critical flow gas should be preceded for the proper analysis of the critical flow in the integral reactor. In this report, not only the essences of previous work on critical flow were investigated and summarized but also the effect of nitrogen gas and the inlet shape of the pipe on the critical flow were also investigated. (author)

  12. Desmanthus GENOTYPES

    Directory of Open Access Journals (Sweden)

    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  13. Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

    Science.gov (United States)

    Kim, Yong Tae; Lee, Dohwan; Heo, Hyun Young; Sim, Jeong Eun; Woo, Kwang Man; Kim, Do Hyun; Im, Sung Gap; Seo, Tae Seok

    2016-04-15

    A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1 μL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer.

  14. Effect of genotype, gender and age on sheep meat quality and a case study illustrating integration of knowledge.

    Science.gov (United States)

    Hopkins, D L; Mortimer, S I

    2014-11-01

    Subtle breed differences exist for meat quality traits and the Merino does stand out, although many comparisons are confounded by production site or lack of processing intervention. Despite this, the Merino does seem to have a propensity to produce meat with a higher pH and reduced colour stability under extended ageing. Use of the Merino in a crossbreeding system not only provides benefits from hybrid vigour, but also overcomes the meat quality constraints of pure Merinos. Genetic evaluation for lamb production has enabled impressive genetic gains, but an overemphasis on lean meat production has had to be addressed to counter adverse effects on meat quality traits like eating quality. In this regard, the development of genomic selection has provided a methodology for accurate prediction of genetic merit and applying balanced breeding objectives. The potential for negative meat quality effects has stemmed adoption of non-castration approaches, but ensuring that lamb is young when slaughtered does provide brand integrity.

  15. Development of a Simulation Framework for Analyzing Security of Supply in Integrated Gas and Electric Power Systems

    Directory of Open Access Journals (Sweden)

    Kwabena Addo Pambour

    2017-01-01

    Full Text Available Gas and power networks are tightly coupled and interact with each other due to physically interconnected facilities. In an integrated gas and power network, a contingency observed in one system may cause iterative cascading failures, resulting in network wide disruptions. Therefore, understanding the impacts of the interactions in both systems is crucial for governments, system operators, regulators and operational planners, particularly, to ensure security of supply for the overall energy system. Although simulation has been widely used in the assessment of gas systems as well as power systems, there is a significant gap in simulation models that are able to address the coupling of both systems. In this paper, a simulation framework that models and simulates the gas and power network in an integrated manner is proposed. The framework consists of a transient model for the gas system and a steady state model for the power system based on AC-Optimal Power Flow. The gas and power system model are coupled through an interface which uses the coupling equations to establish the data exchange and coordination between the individual models. The bidirectional interlink between both systems considered in this studies are the fuel gas offtake of gas fired power plants for power generation and the power supply to liquefied natural gas (LNG terminals and electric drivers installed in gas compressor stations and underground gas storage facilities. The simulation framework is implemented into an innovative simulation tool named SAInt (Scenario Analysis Interface for Energy Systems and the capabilities of the tool are demonstrated by performing a contingency analysis for a real world example. Results indicate how a disruption triggered in one system propagates to the other system and affects the operation of critical facilities. In addition, the studies show the importance of using transient gas models for security of supply studies instead of successions of

  16. Pipe3D, a pipeline to analyze Integral Field Spectroscopy Data: II. Analysis sequence and CALIFA dataproducts

    Science.gov (United States)

    Sánchez, S. F.; Pérez, E.; Sánchez-Blázquez, P.; García-Benito, R.; Ibarra-Mede, H. J.; González, J. J.; Rosales-Ortega, F. F.; Sánchez-Menguiano, L.; Ascasibar, Y.; Bitsakis, T.; Law, D.; Cano-Díaz, M.; López-Cobá, C.; Marino, R. A.; Gil de Paz, A.; López-Sánchez, A. R.; Barrera-Ballesteros, J.; Galbany, L.; Mast, D.; Abril-Melgarejo, V.; Roman-Lopes, A.

    2016-04-01

    We present Pipe3D, an analysis pipeline based on the FIT3D fitting tool, developed to explore the properties of the stellar populations and ionized gas of integral field spectroscopy (IFS) data. Pipe3D was created to provide coherent, simple to distribute, and comparable dataproducts, independently of the origin of the data, focused on the data of the most recent IFU surveys (e.g., CALIFA, MaNGA, and SAMI), and the last generation IFS instruments (e.g., MUSE). In this article we describe the different steps involved in the analysis of the data, illustrating them by showing the dataproducts derived for NGC 2916, observed by CALIFA and P-MaNGA. As a practical example of the pipeline we present the complete set of dataproducts derived for the 200 datacubes that comprises the V500 setup of the CALIFA Data Release 2 (DR2), making them freely available through the network. Finally, we explore the hypothesis that the properties of the stellar populations and ionized gas of galaxies at the effective radius are representative of the overall average ones, finding that this is indeed the case.

  17. Integrating statistical and ecophysiological analysis of genotype by environment interaction for grain filling of barley in Mediterranean areas. II. Grain growth

    NARCIS (Netherlands)

    Voltas, J.; Eeuwijk, van F.A.; Araus, J.L.; Romagosa, I.

    1999-01-01

    In Mediterranean areas, grain growth of temperate cereals often progresses under the harmful influence of drought and high temperature. Genotypic responses are mediated by the specific occurrence of these constraints, thus causing genotype by environment (G × E) interaction. Field experiments were c

  18. HBV genotypic variability in Cuba.

    Science.gov (United States)

    Loureiro, Carmen L; Aguilar, Julio C; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  19. Selection of common bean (Phaseolus vulgaris L.) genotypes using a genotype plus genotype x environment interaction biplot.

    Science.gov (United States)

    Corrêa, A M; Teodoro, P E; Gonçalves, M C; Santos, A; Torres, F E

    2016-08-05

    Recently, the genotype plus genotype x environment interaction (GGE) biplot methodology has been used to investigate genotype x environment interactions in several crop species, but has not been applied to the common bean (Phaseolus vulgaris L.) crop in Brazil. The aim of this study was to identify common bean genotypes that exhibit high grain yield and stability in the State of Mato Grosso do Sul, Brazil. We conducted 12 trials from 2000 to 2006 in the municipalities of Aquidauana and Dourados, and evaluated 13 genotypes in a randomized block design with three replications. Grain yield data were subjected to individual and joint analyses of variance. After analyzing the GE interaction, the adaptability and phenotypic stability of the common bean genotypes were analyzed using GGE biplot methodology. The genotypes EMGOPA-201, Xamego, and Aporé are recommended for growing in Mato Grosso do Sul, because they exhibited high grain yield and phenotypic stability.

  20. Analyzing an Integrated Planning Approach Among Planning Scale and Sector A Case Study of Malang City’s Vision as The City of Education

    Directory of Open Access Journals (Sweden)

    Akhmad Amirudin

    2014-04-01

    Full Text Available Integrated planning is more needed by government today because of the complexity of problems and limited resources. Integrated planning can undertake the problems by giving comprehensive solution and provide how much resources are needed to reach the goal. Integrated planning approach is implied to provide better tools to guide actions towards the development of cities, improvement of human conditions, and ultimately a better urbanism. So the research focused on integrated planning in Malang City based on Malang City’s vision, strategic planning, operational planning, budgeting planning in Malang City to achieve Malang City’s vision as the city of Education. In this study, researcher used qualitative method with descriptive research, which is a research process aims to describe the exact nature / something happened and took place on the research conducted. The research purpose is to identify and describe and analyze the process of Malang City Planning Agency integrate other planning scale and sector in developing planning; and to identify, describe and analyze the process of Malang City Planning Agency integrated all stakeholders in Integrated Planning process. This research use descriptive research method. The reason to use descriptive research method in this study because the principle objectives of this study aimed to describe, illustrate in a systematic, factual and accurate statement of the facts and the relationship between phenomenon. Then qualitative method was directed at the individual's background and a holistic (whole. So in this case should not isolate the individual or organization into a variable or hypothesis, but should view it as part of wholeness. The result of this research in the case study of Malang City has shown thatThe case study of Malang City showed that various sectors recognized but did not pay much attention to Malang City’s vision as City of Education in their plans; however, Regional Mid-term Development

  1. An integrated one-step system to extract, analyze and annotate all relevant information from image-based cell screening of chemical libraries.

    Science.gov (United States)

    Rabal, Obdulia; Link, Wolfgang; Serelde, Beatriz G; Bischoff, James R; Oyarzabal, Julen

    2010-04-01

    Here we report the development and validation of a complete solution to manage and analyze the data produced by image-based phenotypic screening campaigns of small-molecule libraries. In one step initial crude images are analyzed for multiple cytological features, statistical analysis is performed and molecules that produce the desired phenotypic profile are identified. A naïve Bayes classifier, integrating chemical and phenotypic spaces, is built and utilized during the process to assess those images initially classified as "fuzzy"-an automated iterative feedback tuning. Simultaneously, all this information is directly annotated in a relational database containing the chemical data. This novel fully automated method was validated by conducting a re-analysis of results from a high-content screening campaign involving 33 992 molecules used to identify inhibitors of the PI3K/Akt signaling pathway. Ninety-two percent of confirmed hits identified by the conventional multistep analysis method were identified using this integrated one-step system as well as 40 new hits, 14.9% of the total, originally false negatives. Ninety-six percent of true negatives were properly recognized too. A web-based access to the database, with customizable data retrieval and visualization tools, facilitates the posterior analysis of annotated cytological features which allows identification of additional phenotypic profiles; thus, further analysis of original crude images is not required.

  2. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies

    Directory of Open Access Journals (Sweden)

    Specht Günther

    2010-03-01

    Full Text Available Abstract Background Mitochondrial DNA (mtDNA is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. Description eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle, security aspects (by using database technology and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs. It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. Conclusions The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

  3. Breeding for specific bioregions: a genotype by environment study of horticultural and nutritional traits integrating breeder and farmer priorities for organic

    NARCIS (Netherlands)

    Renaud, E.N.C.; Lammerts Van Bueren, E.; Maliepaard, C.A.; Paulo, M.J.; Juvik, J.A.; Myers, J.R.

    2010-01-01

    The genotype by environment interaction study of broccoli, amongst others, demonstrates that traits of a cultivar are sometimes ranked differently when grown in an organic production system compared to a conventional system. This has strong implications for breeding strategies. The breeders intervie

  4. Hepatitis C Virus Genotypes

    Directory of Open Access Journals (Sweden)

    Kayhan Azadmanesh

    2005-09-01

    obtained from the patient, followed by composition of a phylogenetic tree, which is presently the 'gold standard' for the detection and identification of the various HCV genotypes and subtypes(29. Investigators of HCV genotyping have used sequence analysis of HCV NS5, core, E1, and 5'-UTRs. This approach, however, is cumbersome and regarded as impractical for routine clinical laboratory settings(30. More convenient methods focus on the amplification of defined regions of the HCV genome by reverse transcription (RT-PCR followed by digestion with restriction enzymes and restriction length polymorphism analysis (RFLP(31, amplification with genotype-specific primers(32, hybridization of genotype-specific probes with the amplified products(33 heteroduplex mobility assay(34, melting curve analysis with fluorescence resonance energy transfer probe(35 and DNA enzyme assays(36. HCV typing can also be done by analyzing the sequences of several regions of the virus genome(37, 38. A commercial kit (InnoLipafor HCV genotyping has been introduced in Europe by Innogenetics (Zwijndre, Belgium, which is based on hybridization of 5'-UTR amplification products with genotype specific probes(39. It has been shown that genotyping methods using 5'- UTR, including InnoLipa, may not discriminate subtype 1a from 1b in 5 to 10% of cases and also may not distinguish between subtypes 2a and 2c(39. Others have used restriction enzymes to determine a restriction fragment length polymorphism. In this method, a PCR amplified DNA fragment is digested into fragments with different lengths by enzymes (restriction endonucleases that recognize cleavage sites specific for each genotype(40. Investigators have used different regions of the HCV genome for restriction fragment length polymorphism, including NS5 and the 5'-UTR(41, 42. Although the 5'-UTR region is sufficiently variable to allow HCV genotypes in most clinical situations, it cannot always characterize HCV subtypes(43 and may fail to trace the origin

  5. Analyzing Orientations

    Science.gov (United States)

    Ruggles, Clive L. N.

    Archaeoastronomical field survey typically involves the measurement of structural orientations (i.e., orientations along and between built structures) in relation to the visible landscape and particularly the surrounding horizon. This chapter focuses on the process of analyzing the astronomical potential of oriented structures, whether in the field or as a desktop appraisal, with the aim of establishing the archaeoastronomical "facts". It does not address questions of data selection (see instead Chap. 25, "Best Practice for Evaluating the Astronomical Significance of Archaeological Sites", 10.1007/978-1-4614-6141-8_25) or interpretation (see Chap. 24, "Nature and Analysis of Material Evidence Relevant to Archaeoastronomy", 10.1007/978-1-4614-6141-8_22). The main necessity is to determine the azimuth, horizon altitude, and declination in the direction "indicated" by any structural orientation. Normally, there are a range of possibilities, reflecting the various errors and uncertainties in estimating the intended (or, at least, the constructed) orientation, and in more formal approaches an attempt is made to assign a probability distribution extending over a spread of declinations. These probability distributions can then be cumulated in order to visualize and analyze the combined data from several orientations, so as to identify any consistent astronomical associations that can then be correlated with the declinations of particular astronomical objects or phenomena at any era in the past. The whole process raises various procedural and methodological issues and does not proceed in isolation from the consideration of corroborative data, which is essential in order to develop viable cultural interpretations.

  6. Comparison of Macular Integrity Assessment (MAIA ™, MP-3, and the Humphrey Field Analyzer in the Evaluation of the Relationship between the Structure and Function of the Macula.

    Directory of Open Access Journals (Sweden)

    Kazuyuki Hirooka

    Full Text Available This study was conducted in order to compare relationships between the macular visual field (VF mean sensitivity measured by MAIATM (Macular Integrity Assessment, MP-3, or Humphry field analyzer (HFA and the ganglion cell and inner plexiform layer (GCA thicknesses.This cross-sectional study examined 73 glaucoma patients and 19 normal subjects. All subjects underwent measurements for GCA thickness by Cirrus HD-OCT and static threshold perimetry using MAIATM, MP-3, or HFA. VF and OCT in the retinal view were used to examine both the global relationship between the VF sensitivity and GCA thickness, and the superior hemiretina and inferior hemiretina. The relationship between the GCA thickness and macular sensitivity was examined by Spearman correlation analysis.For each instrument, statistically significant macular VF sensitivity (dB and GCA thickness relationships were observed using the decibel scale (R = 0.547-0.687, all P < 0.001. The highest correlation for the global (R = 0.682 and the superior hemiretina (R = 0.594 GCA thickness-VF mean sensitivity was observed by the HFA. The highest correlation for the inferior hemiretina (R = 0.687 GCA thickness-VF mean sensitivity was observed by the MP-3. Among the three VF measurement instruments, however, no significant differences were found for the structure-function relationships.All three VF measurement instruments found similar structure-function relationships in the central VF.

  7. Integration and relative value of biomarkers for prediction of MCI to AD progression: Spatial patterns of brain atrophy, cognitive scores, APOE genotype and CSF biomarkers

    Directory of Open Access Journals (Sweden)

    Xiao Da

    2014-01-01

    Full Text Available This study evaluates the individual, as well as relative and joint value of indices obtained from magnetic resonance imaging (MRI patterns of brain atrophy (quantified by the SPARE-AD index, cerebrospinal fluid (CSF biomarkers, APOE genotype, and cognitive performance (ADAS-Cog in progression from mild cognitive impairment (MCI to Alzheimer's disease (AD within a variable follow-up period up to 6 years, using data from the Alzheimer's Disease Neuroimaging Initiative-1 (ADNI-1. SPARE-AD was first established as a highly sensitive and specific MRI-marker of AD vs. cognitively normal (CN subjects (AUC = 0.98. Baseline predictive values of all aforementioned indices were then compared using survival analysis on 381 MCI subjects. SPARE-AD and ADAS-Cog were found to have similar predictive value, and their combination was significantly better than their individual performance. APOE genotype did not significantly improve prediction, although the combination of SPARE-AD, ADAS-Cog and APOE ε4 provided the highest hazard ratio estimates of 17.8 (last vs. first quartile. In a subset of 192 MCI patients who also had CSF biomarkers, the addition of Aβ1–42, t-tau, and p-tau181p to the previous model did not improve predictive value significantly over SPARE-AD and ADAS-Cog combined. Importantly, in amyloid-negative patients with MCI, SPARE-AD had high predictive power of clinical progression. Our findings suggest that SPARE-AD and ADAS-Cog in combination offer the highest predictive power of conversion from MCI to AD, which is improved, albeit not significantly, by APOE genotype. The finding that SPARE-AD in amyloid-negative MCI patients was predictive of clinical progression is not expected under the amyloid hypothesis and merits further investigation.

  8. Integration and relative value of biomarkers for prediction of MCI to AD progression: spatial patterns of brain atrophy, cognitive scores, APOE genotype and CSF biomarkers.

    Science.gov (United States)

    Da, Xiao; Toledo, Jon B; Zee, Jarcy; Wolk, David A; Xie, Sharon X; Ou, Yangming; Shacklett, Amanda; Parmpi, Paraskevi; Shaw, Leslie; Trojanowski, John Q; Davatzikos, Christos

    2014-01-01

    This study evaluates the individual, as well as relative and joint value of indices obtained from magnetic resonance imaging (MRI) patterns of brain atrophy (quantified by the SPARE-AD index), cerebrospinal fluid (CSF) biomarkers, APOE genotype, and cognitive performance (ADAS-Cog) in progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD) within a variable follow-up period up to 6 years, using data from the Alzheimer's Disease Neuroimaging Initiative-1 (ADNI-1). SPARE-AD was first established as a highly sensitive and specific MRI-marker of AD vs. cognitively normal (CN) subjects (AUC = 0.98). Baseline predictive values of all aforementioned indices were then compared using survival analysis on 381 MCI subjects. SPARE-AD and ADAS-Cog were found to have similar predictive value, and their combination was significantly better than their individual performance. APOE genotype did not significantly improve prediction, although the combination of SPARE-AD, ADAS-Cog and APOE ε4 provided the highest hazard ratio estimates of 17.8 (last vs. first quartile). In a subset of 192 MCI patients who also had CSF biomarkers, the addition of Aβ1-42, t-tau, and p-tau181p to the previous model did not improve predictive value significantly over SPARE-AD and ADAS-Cog combined. Importantly, in amyloid-negative patients with MCI, SPARE-AD had high predictive power of clinical progression. Our findings suggest that SPARE-AD and ADAS-Cog in combination offer the highest predictive power of conversion from MCI to AD, which is improved, albeit not significantly, by APOE genotype. The finding that SPARE-AD in amyloid-negative MCI patients was predictive of clinical progression is not expected under the amyloid hypothesis and merits further investigation.

  9. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  10. Analyzing the relationship between genotype and phenotype of common deafness genic in two hereditary hearing loss families%2个耳聋家系中常见耳聋基因的基因型与表型相关性分析

    Institute of Scientific and Technical Information of China (English)

    张华; 陈俞; 赵娟; 胡斌; 皮力东·库亚西

    2012-01-01

    目的:检测耳聋家系中耳聋患者的基因型,结合听力损失程度,分析常见耳聋基因的基因型与表型之间的关系.方法:选取2个耳聋小家系,检测4个耳聋基因的9个位点的突变,同时对家系成员进行纯音测听检查.结果:LGR-1家系中,Ⅰ:1、Ⅰ:2、Ⅰ:4和Ⅱ:5基因型为单杂合突变,表型为轻中度聋;Ⅱ:3和Ⅱ:4基因型为双杂合突变,Ⅱ:2和Ⅲ:1基因型为复合杂合突变,表型均为重度或极重度聋.HXL-2家系中,Ⅰ:1和Ⅰ:2基因型为单杂合突变,表型为轻中度聋;Ⅱ:2、Ⅱ:3、Ⅱ:5和Ⅲ:2基因型为单杂合突变,但表型为重度或极重度聋;Ⅱ:1基因型为双杂合突变,表型为极重度聋;Ⅲ:1基因型为单杂合突变,左耳为中度聋,右耳为中重度聋.结论:单杂合突变患者表型多为轻度或中度聋,而基因型为单杂合突变的重度或极重度聋患者可能存在另外一个没有检测到的突变;基因型为双杂合突变或复合杂合突变的患者,表型多为重度或极重度聋;基因型与听力表型之间存在一定的正相关性.%Objective: To investigate the relationship between genotype and phenotype of common deafness genes by analyzing genotype and degree of hearing loss in deaf patients from deafness pedigrees. Method:Two small deafness pedigrees were selected. Nine locus mutations of four deafness genes were detected, and pure tone aud-iometry on family members were conducted simultaneously. Result: In LGR-1 pedigree, Ⅰ :1. Ⅰ :2, Ⅰ :4, and Ⅱ :5 carried single heterozygous mutation, which manifested by mild moderate deafness in phenotype; while 0 :3 and Ⅱ :4 genotype were double heterozygous mutation, and Ⅱ :2 and Ⅲ :1 genotype were composite mutation, both manifested by severe or profound deafness in phenotype. In HXL-2 pedigree, Ⅰ :1 and Ⅰ :2 carried single hetero-zygous mutation, which manifested by mild-moderate deafness while Ⅱ: 2, Ⅱ : 3, Ⅱ : 5 and Ⅲ : 2 presented with se

  11. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  12. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Ana Paula Oliveira Nogueira

    2011-01-01

    Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

  13. A novel SVM-ID3 hybrid feature selection method to build a disease model for melanoma using integrated genotyping and phenotype data from dbGaP.

    Science.gov (United States)

    Son, Yeşim Aydın; Yücebaş, Sait Can

    2014-01-01

    The relations between Single Nucleotide Polymorphism (SNP) and complex diseases are likely to be non-linear and require analysis of the high dimensional data. Previous studies in the field mostly focus on genotyping and effects of various phenotypes are not considered. To fill this gap a hybrid feature selection model of support vector machine and decision tree has been designed. The designed method is tested on melanoma. We were able to select phenotypic features such as moles and dysplastic nevi, and SNPs those maps to specific genes such as CAMK1D. The performance results of the proposed hybrid model, on melanoma dataset are 79.07% of sensitivity and 0.81 of area under ROC curve.

  14. MICROSATELLITE GENOTYPING USING THE BASESTATION DNA FRAGMENT ANALYZER. (R826603)

    Science.gov (United States)

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  15. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial.

    Science.gov (United States)

    Wang, Gary P; Berry, Charles C; Malani, Nirav; Leboulch, Philippe; Fischer, Alain; Hacein-Bey-Abina, Salima; Cavazzana-Calvo, Marina; Bushman, Frederic D

    2010-06-03

    X-linked severe-combined immunodeficiency (SCID-X1) has been treated by therapeutic gene transfer using gammaretroviral vectors, but insertional activation of proto-oncogenes contributed to leukemia in some patients. Here we report a longitudinal study of gene-corrected progenitor cell populations from 8 patients using 454 pyrosequencing to map vector integration sites, and extensive resampling to allow quantification of clonal abundance. The number of transduced cells infused into patients initially predicted the subsequent diversity of circulating cells. A capture-recapture analysis was used to estimate the size of the gene-corrected cell pool, revealing that less than 1/100th of the infused cells had long-term repopulating activity. Integration sites were clustered even at early time points, often near genes involved in growth control, and several patients harbored expanded cell clones with vectors integrated near the cancer-implicated genes CCND2 and HMGA2, but remain healthy. Integration site tracking also documented that chemotherapy for adverse events resulted in successful control. The longitudinal analysis emphasizes that key features of transduced cell populations--including diversity, integration site clustering, and expansion of some clones--were established early after transplantation. The approaches to sequencing and bioinformatics analysis reported here should be widely useful in assessing the outcome of gene therapy trials.

  16. Genotyping with TaqMAMA.

    Science.gov (United States)

    Li, Baohui; Kadura, Ibrahim; Fu, Dong-Jing; Watson, David E

    2004-02-01

    TaqMAMA combines the quantitative strengths of TaqMan with the allele-specific PCR of MAMA. In this article we develop TaqMAMA as a technique for screening human DNA samples for known genetic polymorphisms. In the first set of experiments, plasmids that model all types of genetic polymorphisms were used to understand the relationship between TaqMAMA primer/template mismatches and their strength of allelic discrimination. These data can be used to improve allelic discrimination of other primer extension genotyping methodologies through directed use of nucleotide mismatches. We used the data to derive a guide for TaqMAMA primer design and DNA strand selection for TaqMAMA genotyping assays. The guide was then used to develop assays for 11 known and novel human genetic polymorphisms. Genotypes were assigned quickly and accurately in all cases. TaqMAMA genotyping assays require minimal development time, have a high probability of success, produce reliable data that are straightforward to analyze, and are very cost-competitive.

  17. Analog multivariate counting analyzers

    CERN Document Server

    Nikitin, A V; Armstrong, T P

    2003-01-01

    Characterizing rates of occurrence of various features of a signal is of great importance in numerous types of physical measurements. Such signal features can be defined as certain discrete coincidence events, e.g. crossings of a signal with a given threshold, or occurrence of extrema of a certain amplitude. We describe measuring rates of such events by means of analog multivariate counting analyzers. Given a continuous scalar or multicomponent (vector) input signal, an analog counting analyzer outputs a continuous signal with the instantaneous magnitude equal to the rate of occurrence of certain coincidence events. The analog nature of the proposed analyzers allows us to reformulate many problems of the traditional counting measurements, and cast them in a form which is readily addressed by methods of differential calculus rather than by algebraic or logical means of digital signal processing. Analog counting analyzers can be easily implemented in discrete or integrated electronic circuits, do not suffer fro...

  18. Breathing patterns of awake rats exposed to acrolein and perfluorisobutylene determined with an integrated system of nose-only exposure and online analyzed multiple monitoring of breathing

    NARCIS (Netherlands)

    Bergers, W.W.A.; Beyersbergen Van Henegouwen, A.G.; Hammer, A.H.; Bruijnzeel, P.L.B.

    1996-01-01

    Studies on changes in breathing patterns of rats due to exposure to acrolein and the Leflon pyrolysis product perfluorisobutylene (PFIB) were performed to evaluate a new developed integrated system of nose- only exposure and multiple monitoring of breathing of up to eight rats. Measurements of breat

  19. Integrating geospatial data and cropping system simulation within a geographic information system to analyze spatial seed cotton yield, water use, and irrigation requirements

    Science.gov (United States)

    The development of sensors that provide geospatial information on crop and soil conditions has been a primary success for precision agriculture. However, further developments are needed to integrate geospatial data into computer algorithms that spatially optimize crop production while considering po...

  20. Genotypic Variation for Salinity Tolerance in Sorghum (Sorghum bicolor (L. Moench Genotypes at Early Growth Stages

    Directory of Open Access Journals (Sweden)

    Tigabu, Endalew

    2013-04-01

    Full Text Available Sorghum (Sorghum bicolor L. Moench is the fifth most economically important crop among cereals in the world. Salinity is an abiotic factor which reduces productivity of sorghum. Exploiting genetic variability to identify salt tolerant genotype is one of the strategies used to overcome salinity. Pot experiment was carried out to evaluate the genetic variation of eleven sorghum genotypes for NaCl salinity response at germination and early seedling stages. The experimental treatments were five NaCl salinity levels (0, 2, 4, 8, and 16 dS m-1 and eleven sorghum genotypes (Gambella1107, Melkam, S-35, ESH-2, Gobye, 97MW6130, Meko, 76T1#23, ICSV-111, Abshir and Teshale. The experimental design was completely randomized design with three replicates.Data was analyzed using SAS (version 9.0 statistical software and means were separated by LSD. Germination rate, final germination percentage, seedling shoot length and seedling root length were measured. The ANOVA for treatments, genotypes and their interaction was found to be highly significant (p<0.001 with regard to all parameters. Genotypes Meko, Gambella1107, ICSV-111 and Melkam were found salt tolerant during germination and seedling growth stages. However, genotypes ESH-2 and Gobye were salt sensitive during both stages. The rest sorghum genotypes were intermediate in their salt tolerance. The study affirmed the presence of wide genotypic variation among the sorghum genotypes for NaCl salt tolerance.

  1. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  2. Integration of phase separation with ultrasound-assisted salt-induced liquid-liquid microextraction for analyzing the fluoroquinones in human body fluids by liquid chromatography.

    Science.gov (United States)

    Wang, Huili; Gao, Ming; Wang, Mei; Zhang, Rongbo; Wang, Wenwei; Dahlgren, Randy A; Wang, Xuedong

    2015-03-15

    Herein, we developed a novel integrated device to perform phase separation based on ultrasound-assisted salt-induced liquid-liquid microextraction for determination of five fluoroquinones (FQs) in human body fluids. The integrated device consisted of three simple HDPE components used to separate the extraction solvent from the aqueous phase prior to retrieving the extractant. A series of extraction parameters were optimized using the response surface method based on central composite design. Optimal conditions consisted of 945μL acetone extraction solvent, pH 2.1, 4.1min stir time, 5.9g Na2SO4, and 4.0min centrifugation. Under optimized conditions, the limits of detection (at S/N=3) were 0.12-0.66μgL(-1), the linear range was 0.5-500μgL(-1) and recoveries were 92.6-110.9% for the five FQs extracted from plasma and urine. The proposed method has several advantages, such as easy construction from inexpensive materials, high extraction efficiency, short extraction time, and compatibility with HPLC analysis. Thus, this method shows excellent prospects for sample pretreatment and analysis of FQs in human body fluids.

  3. Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family

    Directory of Open Access Journals (Sweden)

    Eskandari Sepehr

    2007-10-01

    Full Text Available Abstract Background Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent technological advances, structural coverage of membrane integral proteins continues to be sparse. ConSequently, sequence-based methods represent an important alternative to illuminate functional roles. In this report, we critically examine the ability of several computational methods to provide functional insight within two specific areas. First, can phylogenomic methods accurately describe the functional diversity across a membrane integral protein family? And second, can sequence-based strategies accurately predict key functional sites? Due to the presence of a recently solved structure and a vast amount of experimental mutagenesis data, the neurotransmitter/Na+ symporter (NSS family is an ideal model system to assess the quality of our predictions. Results The raw NSS sequence dataset contains 181 sequences, which have been aligned by various methods. The resultant phylogenetic trees always contain six major subfamilies are consistent with the functional diversity across the family. Moreover, in well-represented subfamilies, phylogenetic clustering recapitulates several nuanced functional distinctions. Functional sites are predicted using six different methods (phylogenetic motifs, two methods that identify subfamily-specific positions, and three different conservation scores. A canonical set of 34 functional sites identified by Yamashita et al. within the recently solved LeuTAa structure is used to assess the quality of the predictions, most of which are predicted by the bioinformatic methods. Remarkably, the importance of these sites is largely confirmed by experimental mutagenesis. Furthermore, the collective set of functional site predictions qualitatively clusters along the proposed transport pathway, further

  4. RUN DMC: An efficient, parallel code for analyzing Radial Velocity Observations using N-body Integrations and Differential Evolution Markov chain Monte Carlo

    CERN Document Server

    Nelson, Benjamin E; Payne, Matthew J

    2013-01-01

    In the 20+ years of Doppler observations of stars, scientists have uncovered a diverse population of extrasolar multi-planet systems. A common technique for characterizing the orbital elements of these planets is Markov chain Monte Carlo (MCMC), using a Keplerian model with random walk proposals and paired with the Metropolis-Hastings algorithm. For approximately a couple of dozen planetary systems with Doppler observations, there are strong planet-planet interactions due to the system being in or near a mean-motion resonance (MMR). An N-body model is often required to accurately describe these systems. Further computational difficulties arise from exploring a high-dimensional parameter space ($\\sim$7 x number of planets) that can have complex parameter correlations. To surmount these challenges, we introduce a differential evolution MCMC (DEMCMC) applied to radial velocity data while incorporating self-consistent N-body integrations. Our Radial velocity Using N-body DEMCMC (RUN DMC) algorithm improves upon t...

  5. Can Clustering in Genotype Space Reveal "Niches"?

    Science.gov (United States)

    D'Andrea, Rafael; Ostling, Annette

    2016-01-01

    Community ecology lacks the success enjoyed by population genetics to quantify the relative roles played by deterministic and stochastic processes. It has been proposed that clustered patterns of abundance in genotype space provide evidence of selection in microbial communities, since no such clustering would arise in the absence of selection. We critique this test for its unrealistic null hypothesis. We show mathematically and with simulations that point mutations alone lead to clustering in genotype space by causing correlations between abundances of similar genotypes. We also show potential deviations from the mutation-only pattern caused by immigration from a source pool. Clustered patterns in genotype space may still be revealing of selection if analyzed quantitatively but only if neutral and selective regimes can be distinguished once mutation and immigration are included in the null model.

  6. Dual beam Doppler FD-OCT system with integrated Dynamic Vessel Analyzer and rotatable beams to measure total retinal blood flow

    Science.gov (United States)

    Doblhoff-Dier, Veronika; Werkmeister, René M.; Gröschl, Martin; Schmetterer, Leopold

    2014-03-01

    We present a method capable of measuring the total retinal blood flow in arteries and veins based on dual beam Fourierdomain Doppler optical coherence tomography (OCT) in combination with a fundus camera based Dynamic Vessel Analyzer. Incorporating a Dynamic vessel analyzer into the system not only gives a live image of the fundus - it also allows determining the vessels' diameter precisely during the OCT measurement, which is necessary for the determination of the blood flow. While dual beam systems with fixed detection plane allow only vessels with certain orientations to be measured, the detection plane of our system can be rotated by 90°. This ensures that the blood's velocity can be measured in all vessels around the optic nerve head. The results of the total blood flow measurements are in the same range as previously published data. Additionally, the high degree of conformity between the measured venous and arterial flow corroborated the system's validity. For larger vessels, the logarithmic values of vessel diameter and blood flow were found to be related linearly with a regression coefficient of around 3, which is in accordance with Murray's law. For smaller vessels (diameter below 60 μm), the values diverge from the linear dependence. The high sensitivity and the good agreement with published data suggest a high potential for examining the retinal blood flow in patients with ocular diseases.

  7. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Cardiovascular Disease Share this page: Was this page helpful? Also ... of choice to decrease the risk of developing cardiovascular disease (CVD) . However, there is a wide variability in ...

  8. Hepatitis B virus genotypes and hepatocellular carcinoma in Thailand

    Institute of Scientific and Technical Information of China (English)

    Pisit Tangkijvanich; Varocha Mahachai; Piyawat Komolmit; Juthatip Fongsaru; Apiradee Theamboonlers; Yong Poovorawan

    2005-01-01

    AIM: The role of hepatitis B virus (HBV) genotypes on the clinical features and prognosis of patients with hepatocellular carcinoma (HCC) is currently unknown. The aim of the present study was to evaluate the distribution of HBV genotypes and their clinical relevance in Thai patients.METHODS: HBV genotypes were determined by PCR-RFLP in stored sera of 93 asymptomatic carriers, 103 patients with chronic hepatitis, 60 patients with cirrhosis and 76patients with HCC. The clinical data were analyzed in relation to the HBV genotype.RESULTS: HBV genotypes C and B were predominant in Thailand, accounting for 73% and 21%, respectively. The distributions of genotypes B and C were similar in HCC patients compared to the other groups. Genotype C was significantly more common in HCC patients who were under 40 years old than genotype B (18% vs 0%, P= 0.03), but was significantly less common in patients older than 60 years (26% vs 56.5%, P= 0.01). The positive rate of hepatitis B e antigen (HBeAg) in patients with genotype C was significantly higher than that in patients with genotype B (71.6% vs 44.4%, P = 0.03 in chronic hepatitis; 56.8% vs 11.1%,P = 0.01 in cirrhosis). There were no differences between HCC patients with genotypes B and C regarding tumor staging by CLIP criteria and the overall median survival. Multivariate analyses showed that HBV genotype was not an independent prognostic factor of survival in HCC patients.CONCLUSION: Patients with genotype C had a higher positive rate of HBeAg and exhibited earlier progression of cirrhosis and HCC than those with genotype B. However,there were no differences in the risk of developing HCC and its prognosis between patients with these genotypes.

  9. Rank correlation among different statistical models in ranking of winter wheat genotypes

    Directory of Open Access Journals (Sweden)

    Mozaffar Roostaei

    2014-04-01

    Full Text Available Several statistical methods have been developed for analyzing genotype × environment (GE interactions in crop breeding programs to identify genotypes with high yield and stability performances. Four statistical methods, including joint regression analysis (JRA, additive mean effects and multiplicative interaction (AMMI analysis, genotype plus GE interaction (GGE biplot analysis, and yield–stability (YSi statistic were used to evaluate GE interaction in 20 winter wheat genotypes grown in 24 environments in Iran. The main objective was to evaluate the rank correlations among the four statistical methods in genotype rankings for yield, stability and yield–stability. Three kinds of genotypic ranks (yield ranks, stability ranks, and yield–stability ranks were determined with each method. The results indicated the presence of GE interaction, suggesting the need for stability analysis. With respect to yield, the genotype rankings by the GGE biplot and AMMI analysis were significantly correlated (P < 0.01. For stability ranking, the rank correlations ranged from 0.53 (GGE–YSi; P < 0.05 to 0.97 (JRA–YSi; P < 0.01. AMMI distance (AMMID was highly correlated (P < 0.01 with variance of regression deviation (S2di in JRA (r = 0.83 and Shukla stability variance (σ2 in YSi (r = 0.86, indicating that these stability indices can be used interchangeably. No correlation was found between yield ranks and stability ranks (AMMID, S2di, σ2, and GGE stability index, indicating that they measure static stability and accordingly could be used if selection is based primarily on stability. For yield–stability, rank correlation coefficients among the statistical methods varied from 0.64 (JRA–YSi; P < 0.01 to 0.89 (AMMI–YSi; P < 0.01, indicating that AMMI and YSi were closely associated in the genotype ranking for integrating yield with stability performance. Based on the results, it can be concluded that YSi was closely correlated with (i JRA in ranking

  10. Geographic distribution of hepatitis C virus genotypes in Brazil

    Directory of Open Access Journals (Sweden)

    Campiotto S.

    2005-01-01

    Full Text Available Brazil is a country of continental dimension with a population of different ethnic backgrounds. Thus, a wide variation in the frequencies of hepatitis C virus (HCV genotypes is expected to occur. To address this point, 1,688 sequential samples from chronic HCV patients were analyzed. HCV-RNA was amplified by the RT-PCR from blood samples collected from 1995 to 2000 at different laboratories located in different cities from all Brazilian States. Samples were collected in tubes containing a gel separator, centrifuged in the site of collection and sent by express mail in a refrigerated container to Laboratório Bioquímico Jardim Paulista, São Paulo, SP, Brazil. HCV- RNA was extracted from serum and submitted to RT and nested PCR using standard procedures. Nested PCR products were submitted to cycle sequencing reactions without prior purification. Sequences were analyzed for genotype determination and the following frequencies were found: 64.9% (1,095 for genotype 1, 4.6% (78 for genotype 2, 30.2% (510 for genotype 3, 0.2% (3 for genotype 4, and 0.1% (2 for genotype 5. The frequencies of HCV genotypes were statistically different among Brazilian regions (P = 0.00017. In all regions, genotype 1 was the most frequent (51.7 to 74.1%, reaching the highest value in the North; genotype 2 was more prevalent in the Center-West region (11.4%, especially in Mato Grosso State (25.8%, while genotype 3 was more common in the South (43.2%. Genotypes 4 and 5 were rarely found and only in the Southeast, in São Paulo State. The present data indicate the need for careful epidemiological surveys throughout Brazil since knowing the frequency and distribution of the genotypes would provide key information for understanding the spread of HCV.

  11. Distribution of HCV genotypes in the metropolitan area of Naples

    Directory of Open Access Journals (Sweden)

    Giuseppe Sodano

    2013-08-01

    Full Text Available The Hepatitis C virus is characterized by high genomic variability that leads to the identification of six different genotypes and many subtypes. In this work, we show the prevalence of genotypes in patients living in the metropolitan area of Naples collected in one year, analyzing differences in the distribution depending on sex and age groups.

  12. Genotyping of FCN and MBL2 polymorphisms using pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans O.; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...... to most other genotyping assays the sequence surrounding the polymorphism provides an internal control making this method highly reliable....

  13. Publishing SNP genotypes of human embryonic stem cell lines: policy statement of the International Stem Cell Forum Ethics Working Party.

    Science.gov (United States)

    Knoppers, Bartha M; Isasi, Rosario; Benvenisty, Nissim; Kim, Ock-Joo; Lomax, Geoffrey; Morris, Clive; Murray, Thomas H; Lee, Eng Hin; Perry, Margery; Richardson, Genevra; Sipp, Douglas; Tanner, Klaus; Wahlström, Jan; de Wert, Guido; Zeng, Fanyi

    2011-09-01

    Novel methods and associated tools permitting individual identification in publicly accessible SNP databases have become a debatable issue. There is growing concern that current technical and ethical safeguards to protect the identities of donors could be insufficient. In the context of human embryonic stem cell research, there are no studies focusing on the probability that an hESC line donor could be identified by analyzing published SNP profiles and associated genotypic and phenotypic information. We present the International Stem Cell Forum (ISCF) Ethics Working Party's Policy Statement on "Publishing SNP Genotypes of Human Embryonic Stem Cell Lines (hESC)". The Statement prospectively addresses issues surrounding the publication of genotypic data and associated annotations of hESC lines in open access databases. It proposes a balanced approach between the goals of open science and data sharing with the respect for fundamental bioethical principles (autonomy, privacy, beneficence, justice and research merit and integrity).

  14. 基于材料各向异性的整体梁裂纹转折分析%Analyzing Crack Turn of Wing-Beam Integrated Structure Based on Anisotropic Mechanical Properties of Aluminum Alloy

    Institute of Scientific and Technical Information of China (English)

    殷之平; 郭今; 黄其青

    2012-01-01

    Sections 1 through 3 of the full paper explain the analysis mentioned in the title. Their core consists of: (1) taking into consideration the differences among mechanical properties of aluminum alloy in the directions of S-T-L, we perform the quasi-static simulation of the crack propagation path of the wing-beam integrated structure with Abaqus/Explicit and its VUMAT subroutine interface; (2) we analyze the quasi-static crack propagation characteristics of the wing-beam integrated structure under residual strength test and then compare the simulation results as shown in Figs. 5, 6 and 7 with the results of experiments performed by us, given in Fig. 2. The comparison results show preliminarily that, in designing a wing-beam integrated structure and analyzing a crack turn with the anisotrop-ic yielding standard, the anisotropie mechanical properties must be considered because it is these properties that cause the 90° turn near the rib of the wing-beam integrated structure under residual strength test.%考虑铝合金材料S-T-L方向材料性能的差异,运用Abaqus/Explicit及其子程序VUMAT进行整体翼梁稳定裂纹扩展路径的准静态模拟,研究了整体翼梁结构在进行剩余强度试验时准静态裂纹扩展特性,并与试验结果进行对比.分析结果显示,考虑材料各向异性损伤失效的材料模型可以很好的描述准静态裂纹扩展,并且可以较好的模拟整体梁裂纹在腹板45°转折和筋条附近90°转折.

  15. Axiom turkey genotyping array

    Science.gov (United States)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  16. 便携式煤矿固定设备集成测试分析仪的设计%Design of portable and integrated analyzer for fixed facilities in coal mines

    Institute of Scientific and Technical Information of China (English)

    程国栋

    2013-01-01

    According to the national industry standard AQ1011-2005,economical equipment operation,this paper presents a portable and integrated analyzer for fixed facilities in coal mines based on USB,to ensure the safety and efficiency of mineral production.The experiments for performance evaluation and for field fault diagnosis of the mine ventilation fans are also completed.Theoretical analysis and industrial field experiments show that the portable and integration analyzer can satisfy testing requirements.%  为确保煤矿安全生产和设备高效经济运行,本文以国家安全生产行业标准AQ1011-2005为依据,研究开发了基于USB总线的便携式煤矿固定设备集成测试分析仪,完成了对仪器的性能评价和对通风机的现场故障诊断实验。通过理论分析和现场实验表明,本文所开发的便携式煤矿固定设备集成测试分析仪具备良好的测试性能,能够满足煤矿现场测试与分析的要求。

  17. Characteristics of general distribution of hepatitis B virus genotypes in China

    Institute of Scientific and Technical Information of China (English)

    Chang-Tai Zhu; Chun-Lei Dong

    2009-01-01

    BACKGROUND:Based on differences in the virus nucleotide sequence, hepatitis B virus (HBV) genotypes are presently divided into genotypes A-H. The geographic distributions of HBV genotypes differ in countries and regions. To determine the general characteristics of their distributions in the mainland of China, we reviewed articles on HBV genotypes published in China. METHODS:The Wanfang Database and the CNKI Database were searched for original articles involving HBV in China, and then the data from the articles were classiifed according to genotype and latitude and analyzed using SPSS 11.0. RESULTS:The main HBV genotypes were C, B and BC, and their rates were 50.99%, 35.58%, 6.07%, respectively;other genotypes were rare. There was a negative correlation between latitude and the rate of genotype B (r=-0.782,P0.05). CONCLUSIONS:In China, HBV genotype C predominates, followed by genotype C and mixed genotype BC; genotypes A, D and others are rare. With an increasing latitude, the distribution of genotype B decreases gradually, while that of genotype C tends to increase. The other genotypes do not show any changes.

  18. Digital Microfluidics Sample Analyzer

    Science.gov (United States)

    Pollack, Michael G.; Srinivasan, Vijay; Eckhardt, Allen; Paik, Philip Y.; Sudarsan, Arjun; Shenderov, Alex; Hua, Zhishan; Pamula, Vamsee K.

    2010-01-01

    Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.

  19. 'Integration'

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2011-01-01

    After a long history dominated by out-migration, Denmark, Norway and Sweden have, in the past 50 years, become immigration societies. This article compares how these Scandinavian welfare societies have sought to incorporate immigrants and refugees into their national communities. It suggests that......, while the countries have adopted disparate policies and ideologies, differences in the actual treatment and attitudes towards immigrants and refugees in everyday life are less clear, due to parallel integration programmes based on strong similarities in the welfare systems and in cultural notions...... of equality in the three societies. Finally, it shows that family relations play a central role in immigrants’ and refugees’ establishment of a new life in the receiving societies, even though the welfare society takes on many of the social and economic functions of the family....

  20. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons...... for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point....

  1. Real-time molecular epidemiology of tuberculosis by direct genotyping of smear-positive clinical specimens.

    Science.gov (United States)

    Alonso, María; Herranz, Marta; Martínez Lirola, Miguel; González-Rivera, Milagros; Bouza, Emilio; García de Viedma, Darío

    2012-05-01

    We applied MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing) to directly analyze the bacilli present in 61 stain-positive specimens from tuberculosis patients. A complete MIRU type (24 loci) was obtained for all but one (no amplification in one locus) of the specimens (98.4%), and the allelic values fully correlated with those obtained from the corresponding cultures. Our study is the first to demonstrate that real-time genotyping of Mycobacterium tuberculosis can be achieved, fully transforming the way in which molecular epidemiology techniques can be integrated into control programs.

  2. Analyzing Spacecraft Telecommunication Systems

    Science.gov (United States)

    Kordon, Mark; Hanks, David; Gladden, Roy; Wood, Eric

    2004-01-01

    Multi-Mission Telecom Analysis Tool (MMTAT) is a C-language computer program for analyzing proposed spacecraft telecommunication systems. MMTAT utilizes parameterized input and computational models that can be run on standard desktop computers to perform fast and accurate analyses of telecommunication links. MMTAT is easy to use and can easily be integrated with other software applications and run as part of almost any computational simulation. It is distributed as either a stand-alone application program with a graphical user interface or a linkable library with a well-defined set of application programming interface (API) calls. As a stand-alone program, MMTAT provides both textual and graphical output. The graphs make it possible to understand, quickly and easily, how telecommunication performance varies with variations in input parameters. A delimited text file that can be read by any spreadsheet program is generated at the end of each run. The API in the linkable-library form of MMTAT enables the user to control simulation software and to change parameters during a simulation run. Results can be retrieved either at the end of a run or by use of a function call at any time step.

  3. Susceptibility of biallelic haplotype and genotype frequencies to genotyping error.

    Science.gov (United States)

    Moskvina, Valentina; Schmidt, Karl Michael

    2006-12-01

    With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.

  4. Genotype × Environment Interaction for Iron Concentration of Rice in Central Java of Indonesia

    Institute of Scientific and Technical Information of China (English)

    Suwarto; Nasrullah

    2011-01-01

    To explore the effect of genotype and genotype × environment interaction on Fe concentration in rice grains,Fe concentrations of 10 genotypes were analyzed across eight paddy field environments during 2007-2008 using the AMMI-biplot method.Experiments were conducted using a randomized completely block design with three replications in eight environments.Results indicated that environment (E),genotype (G) and genotype × environment interaction (GE) significantly affected Fe concentration in rice grains.Environment explained 74.43 % of total (G+E+GE) variation,whereas G and GE captured 5.60% and 19.67%,respectively.Rice genotype Barumun was desirable in terms of the highest ability and stability for Fe concentration in rice grains.Environment in genotype Cilongok was the best representative of the overall environments and the most powerful to discriminate rice genotypes.

  5. Chlamydia trachomatis Genotypes and the Swedish New Variant among Urogenital Chlamydia trachomatis Strains in Finland

    Directory of Open Access Journals (Sweden)

    Suvi Niemi

    2011-01-01

    Full Text Available Our aims were to genotype Chlamydia trachomatis strains present in urogenital samples and to investigate the occurrence of the Swedish new variant of C. trachomatis in Finland. We genotyped 160 C. trachomatis positive samples with ompA real-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%, F (28%, and G (13%. Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype among C. trachomatis strains, the new variant was rarely found in Finland.

  6. Biotyping and genotyping (MLVA16 of Brucella abortus isolated from cattle in Brazil, 1977 to 2008.

    Directory of Open Access Journals (Sweden)

    Sílvia Minharro

    Full Text Available Brucellosis is a worldwide distributed zoonosis that causes important economic losses to animal production. In Brazil, information on the distribution of biovars and genotypes of Brucella spp. is scarce or unavailable. This study aimed (i to biotype and genotype 137 Brazilian cattle isolates (from 1977 to 2008 of B. abortus and (ii to analyze their distribution. B. abortus biovars 1, 2 and 3 (subgroup 3b were confirmed and biovars 4 and 6 were first described in Brazil. Genotyping by the panel 1 revealed two groups, one clustering around genotype 40 and another around genotype 28. Panels 2A and 2B disclosed a high diversity among Brazilian B. abortus strains. Eighty-nine genotypes were found by MLVA16. MLVA16 panel 1 and 2 showed geographic clustering of some genotypes. Biotyping and MLVA16 genotyping of Brazilian B. abortus isolates were useful to better understand the epidemiology of bovine brucellosis in the region.

  7. Hepatitis B virus genotypes and resistance mutations in patients under long term lamivudine therapy: characterization of genotype G in Brazil

    Directory of Open Access Journals (Sweden)

    Brandão Carlos E

    2008-01-01

    Full Text Available Abstract Background Lamivudine is an oral nucleoside analogue widely used for the treatment of chronic hepatitis B. The main limitation of lamivudine use is the selection of resistant mutations that increases with time of utilization. Hepatitis B virus (HBV isolates have been classified into eight genotypes (A to H with distinct geographical distributions. HBV genotypes may also influence pathogenic properties and therapeutic features. Here, we analyzed the HBV genotype distribution and the nature and frequency of lamivudine resistant mutations among 36 patients submitted to lamivudine treatment for 12 to 84 months. Results Half of the patients were homosexual men. Only 4/36 (11% patients were HBV DNA negative. As expected for a Brazilian group, genotypes A (24/32 positive individuals, 75%, D (3/32, 9.3% and F (1/32, 3% were present. One sample was from genotype C, which is a genotype rarely found in Brazil. Three samples were from genotype G, which had not been previously detected in Brazil. Lamivudine resistance mutations were identified in 20/32 (62% HBV DNA positive samples. Mean HBV loads of patients with and without lamivudine resistance mutations were not very different (2.7 × 107 and 6.9 × 107 copies/mL, respectively. Fifteen patients showed the L180M/M204V lamivudine resistant double mutation. The triple mutant rt173V/180M/204V, which acts as a vaccine escape mutant, was found in two individuals. The three isolates of genotype G were entirely sequenced. All three showed the double mutation L180M/M204V and displayed a large genetic divergence when compared with other full-length genotype G isolates. Conclusion A high (55% proportion of patients submitted to long term lamivudine therapy displayed resistant mutations, with elevated viral load. The potential of transmission of such HBV mutants should be monitored. The identification of genotypes C and G, rarely detected in South America, seems to indicate a genotype distribution different

  8. Variability of traits quinoa introduced genotypes (Chenopodium quinoa Willd.)

    OpenAIRE

    Dražić, Slobodan; ŽIVANOVIĆ, Tomislav; Maletić, Radojka; Glamočlija, Đorđe; Žarković, Branka; Dražić, Milena

    2013-01-01

    We analyzed variability and influence of investigated factors on grain yield of quinoa during three year period (2009, 2010, 2011). The experiment was conducted at two locations (Nova Pazova and Surduk), using two introduced genotypes of quinoa: KVL 37 and KVL 52. We detected that location and genotype had important impact. Grain yield varied according to years of study (1224 kg/ha to 1671 kg/ha). Results of regression and correlation analysis indicate on variation of the impact of plant heig...

  9. Use AMMI model to analyze adaptability of rice varieties

    Institute of Scientific and Technical Information of China (English)

    SHENXihang; WANGLei; YANGShihua; XIEFuxian

    1998-01-01

    The adaptability of rice varieties is one of the most concerned questions to rice breeders. In rice breeding, combined variety test and regional trials which included multiple genotypes and environments were conducted to identify the adaptability of new rice varieties. In most regional trials, interaction between genotype and environment is significant, so it is important to analyze the interaction for estimating the adaptability of rice varieties.

  10. STR MARKERS. GENOTYPING APPLICATIONS

    Directory of Open Access Journals (Sweden)

    I. O. Sirbu

    2001-01-01

    Full Text Available STR (short tandem repeats loci consist of short, repetitive sequence elements of 2-8 bp in length. These abundant repeats are well distributed throughout the human genome and are rich source of highly polymorphic markers. There are literally hundreds of STR systems which have been mapped throughout the human genome. Several dozen have been investigated for application to human identity testing. These STR loci are found on almost every chromosome in the genome. They may be amplified using a variety of PCR primers. Tetranucleotide repeats have been most popular among forensic scientists due to their fidelity in PCR amplification although some tri- and pentanucleotide repeats are also in use. In this paper we intend (far from being exhaustive to present a synthesis of the characteristics of these genetic markers and their applications in genotyping, giving as an example the use of the STRs in a paternity testing case.

  11. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

    Science.gov (United States)

    Karangwa, Consolee K.; Sosnovtsev, Stanislav V.

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining “static”) and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification (“static” versus “evolving”), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as “immunotypes”. We propose that “immunotypes” and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population. PMID:28103318

  12. Mendel Meets CSI: Forensic Genotyping as a Method to Teach Genetics & DNA Science

    Science.gov (United States)

    Kurowski, Scotia; Reiss, Rebecca

    2007-01-01

    This article describes a forensic DNA science laboratory exercise for advanced high school and introductory college level biology courses. Students use a commercial genotyping kit and genetic analyzer or gene sequencer to analyze DNA recovered from a fictitious crime scene. DNA profiling and STR genotyping are outlined. DNA extraction, PCR, and…

  13. Development of a candidate method for forensic microbial genotyping using multiplex pyrosequencing combined with a universal biotinylated primer.

    Science.gov (United States)

    Gu, Yan; Mao, Xuhu; Zha, Lagabaiyila; Hou, Yiping; Yun, Libing

    2015-01-01

    Bacterial genotyping can be used for crime scene investigations and contribute to the attribution of biological attacks for microbial forensics. PyroMark ID Pyrosequencer as an accurate detection platform for single nucleotide polymorphisms (SNPs) has been applied to identify and resolve microorganisms involved in closely Escherichia coli O157:H7 (E. coli O157:H7). To explore more applications and improve the efficiency for pyrosequencing in this field, we developed a method integrated multiplex pyrosequencing with a universal primer. Two multiplex pyrosequencing assays with a universal biotinylated primer were designed to analyze five SNPs located in four gene of E. coli O157:H7 strain. The accuracy of the established assays was validated by genotyping reference strain E. coli O157:H7 EDL933 and E. coli K-12. We also demonstrated that two multiplex pyrosequencing assays were specific and sensitive for genotyping closely related E. coli O157 strains. Reproducibility of results and multiplexing capability were evaluated by a comparison of this method with the monoplex pyrosequencing. Furthermore, these two multiplex pyrosequencing assays have been successfully applied to detect 11 E. coli O157 strains isolated from 1504 Chinese livestock samples. This method reduces costs and time consumption in the process of pyrosequencing analysis, and potentially serves as a rapid tool and reliable candidate strategy for the microbial identification and other genotyping application.

  14. AMMI AND GGE BIPLOT ANALYSIS OF BREAD WHEAT GENOTYPES IN THE NORTHERN PART OF ETHIOPIA

    Directory of Open Access Journals (Sweden)

    Fetien Abay

    2013-04-01

    Full Text Available The genotype environment interaction manipulates the selection criteria in a multipurpose crop like wheat. Ten bread wheat genotypes were evaluated at five wheat growing locations of Tigray region in the year 2011. Yield data was analyzed using the additive main effect and multiplication interaction model (AMMI and GGE biplot. The AMMI analysis of variance for grain yield detected significant effects for genotype, location and genotype by location interaction. Location effect was responsible for the greatest part of the variation, followed by genotype and genotype by location interaction effects. Based on AMMI stability value, G4, G10, G8 and G9 were the most stable genotypes, while G1, G2, and G3 were the most responsive genotypes. The GGE biplot also showed G1, G2, G3, and G4 have long vectors and located far away from the biplot origin and hence are considered to have larger contribution to GEI (specifically adapted genotypes. G10 however is widely adapted genotype. The ‘which won where’ feature of the GGE biplot identified G4 as the winning genotype at Samre, Hagereselam, and Atsbi, while G1 winning at Quiha and Wukro. The GGE biplot also identified two bread wheat mega-environments. This indicates that analysis of multi-location trail data using GGE and AMMI model is important for determining visual comparisons, adaptability/stability focusing on overall performance to identify superior genotypes

  15. AMMI AND GGE BIPLOT ANALYSIS OF BREAD WHEAT GENOTYPES IN THE NORTHERN PART OF ETHIOPIA

    Directory of Open Access Journals (Sweden)

    Hintsa G. Hagos

    2013-04-01

    Full Text Available The genotype environment interaction manipulates the selection criteria in a multipurpose crop like wheat. Ten bread wheat genotypes were evaluated at five wheat growing locations of Tigray region in the year 2011. Yield data was analyzed using the additive main effect and multiplication interaction model (AMMI and GGE biplot. The AMMI analysis of variance for grain yield detected significant effects for genotype, location and genotype by location interaction. Location effect was responsible for the greatest part of the variation, followed by genotype and genotype by location interaction effects. Based on AMMI stability value, G4, G10, G8 and G9 were the most stable genotypes, while G1, G2, and G3 were the most responsive genotypes. The GGE biplot also showed G1, G2, G3, and G4 have long vectors and located far away from the biplot origin and hence are considered to have larger contribution to GEI (specifically adapted genotypes. G10 however is widely adapted genotype. The ‘which won where’ feature of the GGE biplot identified G4 as the winning genotype at Samre, Hagereselam, and Atsbi, while G1 winning at Quiha and Wukro. The GGE biplot also identified two bread wheat mega-environments. This indicates that analysis of multi-location trail data using GGE and AMMI model is important for determining visual comparisons, adaptability/stability focusing on overall performance to identify superior genotypes.

  16. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics.

    Science.gov (United States)

    Wei, Dahai; Zeng, Yongyi; Xing, Xiaohua; Liu, Hongzhi; Lin, Minjie; Han, Xiao; Liu, Xiaolong; Liu, Jingfeng

    2016-02-05

    Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify the proteome differences between the HBV genotypes B- and C-induced HCC. In brief, a total of 83 proteins in the surrounding noncancerous tissues and 136 proteins in the cancerous tissues between HBV genotype-B- and genotype-C-induced HCC were identified, respectively. This information revealed that there might be different molecular mechanisms of the tumorigenesis and development of HBV genotypes B- and C-induced HCC. Furthermore, our results indicate that the two proteins ARFIP2 and ANXA1 might be potential biomarkers for distinguishing the HBV genotypes B- and C-induced HCC. Thus, the quantitative proteomic analysis revealed molecular differences between the HBV genotypes B- and C-induced HCC, and might provide fundamental information for further deep study.

  17. Molecular methods for genotyping complex copy number polymorphisms.

    Science.gov (United States)

    Cantsilieris, Stuart; Baird, Paul N; White, Stefan J

    2013-02-01

    Genome structural variation shows remarkable complexity with respect to copy number, sequence content and distribution. While the discovery of copy number polymorphisms (CNP) has increased exponentially in recent years, the transition from discovery to genotyping has proved challenging, particularly for CNPs embedded in complex regions of the genome. CNPs that are collectively common in the population and possess a dynamic range of copy numbers have proved the most difficult to genotype in association studies. This is in some part due to technical limitations of genotyping assays and the sequence properties of the genomic region being analyzed. Here we describe in detail the basis of a number of molecular techniques used to genotype complex CNPs, compare and contrast these approaches for determination of multi-allelic copy number, and discuss the potential application of these techniques in genetic studies.

  18. The Intermodulation Lockin Analyzer

    CERN Document Server

    Tholen, Erik A; Forchheimer, Daniel; Schuler, Vivien; Tholen, Mats O; Hutter, Carsten; Haviland, David B

    2011-01-01

    Nonlinear systems can be probed by driving them with two or more pure tones while measuring the intermodulation products of the drive tones in the response. We describe a digital lock-in analyzer which is designed explicitly for this purpose. The analyzer is implemented on a field-programmable gate array, providing speed in analysis, real-time feedback and stability in operation. The use of the analyzer is demonstrated for Intermodulation Atomic Force Microscopy. A generalization of the intermodulation spectral technique to arbitrary drive waveforms is discussed.

  19. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  20. Analyzing in the Present

    DEFF Research Database (Denmark)

    Revsbæk, Line; Pedersen, Lene Tanggaard

    2015-01-01

    The article presents a notion of “analyzing in the present” as a source of inspiration in analyzing qualitative research materials. The term emerged from extensive listening to interview recordings during everyday commuting to university campus. Paying attention to the way different parts...... of various interviews conveyed diverse significance to the listening researcher at different times became a method of continuously opening up the empirical material in a reflexive, breakdown-oriented process of analysis. We argue that situating analysis in the present of analyzing emphasizes and acknowledges...... the interdependency between researcher and researched. On this basis, we advocate an explicit “open-state-of mind” listening as a key aspect of analyzing qualitative material, often described only as a matter of reading transcribed empirical materials, reading theory, and writing. The article contributes...

  1. Miniature mass analyzer

    CERN Document Server

    Cuna, C; Lupsa, N; Cuna, S; Tuzson, B

    2003-01-01

    The paper presents the concept of different mass analyzers that were specifically designed as small dimension instruments able to detect with great sensitivity and accuracy the main environmental pollutants. The mass spectrometers are very suited instrument for chemical and isotopic analysis, needed in environmental surveillance. Usually, this is done by sampling the soil, air or water followed by laboratory analysis. To avoid drawbacks caused by sample alteration during the sampling process and transport, the 'in situ' analysis is preferred. Theoretically, any type of mass analyzer can be miniaturized, but some are more appropriate than others. Quadrupole mass filter and trap, magnetic sector, time-of-flight and ion cyclotron mass analyzers can be successfully shrunk, for each of them some performances being sacrificed but we must know which parameters are necessary to be kept unchanged. To satisfy the miniaturization criteria of the analyzer, it is necessary to use asymmetrical geometries, with ion beam obl...

  2. Analyzing Microarray Data.

    Science.gov (United States)

    Hung, Jui-Hung; Weng, Zhiping

    2017-03-01

    Because there is no widely used software for analyzing RNA-seq data that has a graphical user interface, this protocol provides an example of analyzing microarray data using Babelomics. This analysis entails performing quantile normalization and then detecting differentially expressed genes associated with the transgenesis of a human oncogene c-Myc in mice. Finally, hierarchical clustering is performed on the differentially expressed genes using the Cluster program, and the results are visualized using TreeView.

  3. On-Demand Urine Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this program (through Phase III) is to develop an analyzer that can be integrated into International Space Station (ISS) toilets to measure key...

  4. Total organic carbon analyzer

    Science.gov (United States)

    Godec, Richard G.; Kosenka, Paul P.; Smith, Brian D.; Hutte, Richard S.; Webb, Johanna V.; Sauer, Richard L.

    The development and testing of a breadboard version of a highly sensitive total-organic-carbon (TOC) analyzer are reported. Attention is given to the system components including the CO2 sensor, oxidation reactor, acidification module, and the sample-inlet system. Research is reported for an experimental reagentless oxidation reactor, and good results are reported for linearity, sensitivity, and selectivity in the CO2 sensor. The TOC analyzer is developed with gravity-independent components and is designed for minimal additions of chemical reagents. The reagentless oxidation reactor is based on electrolysis and UV photolysis and is shown to be potentially useful. The stability of the breadboard instrument is shown to be good on a day-to-day basis, and the analyzer is capable of 5 sample analyses per day for a period of about 80 days. The instrument can provide accurate TOC and TIC measurements over a concentration range of 20 ppb to 50 ppm C.

  5. Analyzing an Aging ISS

    Science.gov (United States)

    Scharf, R.

    2014-01-01

    The ISS External Survey integrates the requirements for photographic and video imagery of the International Space Station (ISS) for the engineering, operations, and science communities. An extensive photographic survey was performed on all Space Shuttle flights to the ISS and continues to be performed daily, though on a level much reduced by the limited available imagery. The acquired video and photo imagery is used for both qualitative and quantitative assessments of external deposition and contamination, surface degradation, dynamic events, and MMOD strikes. Many of these assessments provide important information about ISS surfaces and structural integrity as the ISS ages. The imagery is also used to assess and verify the physical configuration of ISS structure, appendages, and components.

  6. Advances in hematology analyzers.

    Science.gov (United States)

    DeNicola, Dennis B

    2011-05-01

    The complete blood count is one of the basic building blocks of the minimum database in veterinary medicine. Over the past 20 years, there has been a tremendous advancement in the technology of hematology analyzers and their availability to the general practitioner. There are 4 basic methodologies that can be used to generate data for a complete blood count: manual methods, quantitative buffy coat analysis, automated impedance analysis, and flow cytometric analysis. This article will review the principles of these methodologies, discuss some of their advantages and disadvantages, and describe some of the hematology analyzers that are available for the in-house veterinary laboratory.

  7. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  8. Biplot analysis of phenotypic stability in upland cotton genotypes in Mato Grosso.

    Science.gov (United States)

    Farias, F J C; Carvalho, L P; Silva Filho, J L; Teodoro, P E

    2016-05-20

    Seed cotton yield is a trait governed by multiple genes that cause changes in the performance of genotypes depending on the cultivation environment. Breeding programs examine the genotype x environment interaction (GE) using precise statistical methods, such as AMMI (additive main effects and multiplicative interaction) and GGE biplot (genotype main effects + genotype x environment interaction). The AMMI method combines the analysis of variance and principal components, to adjust the main effects (genotypes and environments) and the effects of GE interaction, respectively. The GGE biplot groups the genotype additive effect together with the multiplicative effect of the GE interaction, and submits both of these to the principal components analysis. The aim of this study was to investigate the association between the AMMI and GGE biplot methods and select cotton genotypes that simultaneously showed high productivity of seed cotton and stability in Mato Grosso environments. Trials were conducted with cotton cultivars in eight environments across Mato Grosso State in the 2008/2009 crop season. The experiment used a randomized block design with 16 genotypes and four replicates per genotype x environment combination. Data for seeds cotton productivity were analyzed by AMMI and GGE biplot methods. Both methods were concordant in the discrimination of environments and genotypes for phenotypic stability. The genotypes BRS ARAÇÁ and LD 05 CV had high seed cotton productivity and phenotypic stability, and could be grown in all environments across Mato Grosso State.

  9. The potential of different lime tree (Tilia spp genotypes for phytoextraction of heavy metals

    Directory of Open Access Journals (Sweden)

    Šijačić-Nikolić Mirjana

    2012-01-01

    Full Text Available The research of heavy metals contents (Pb, Mn, Zn, Ni, Fe in soil in the area of the National Park „Fruška gora”, along the highway M21 shows lower values for manganese, zinc and iron than the maximum allowed quantity prescribed by law. For nickel and lead it shows higher values than maximum allowed quantity. The heavy metals contents in leaves of lime tree in 12 analyzed genotypes are far below average values in accordance with ECCE with all genotypes except genotype 7 for lead and genotypes 7 and 8 for iron. The results of analysis of variance components show that out of four components (locality, genotype, locality x genotype and error only the interaction between locality and genotype does not contribute to variance. The contents of Pb, Mn, Fe and Zn in leaves is primarily influenced by genotype while Ni contents may be considered a consequence of locality. The selection of genotypes which is able to uptake greater quantities of heavy metals than other genotypes may serve as a solid basis for phytoextraction of heavy metals as a technology by which heavy metals, metalloids and radionuclides are extracted from environment through usage of suitable species and plant genotypes able to uptake and accumulate the given pollutants in parts of plant tissue. [Projekat Ministarstva nauke Republike Srbije, br. 43007: Studying climate change and its influence on the environment: Impacts, adaptation and mitigation

  10. Portable Fuel Quality Analyzer

    Science.gov (United States)

    2014-01-27

    other transportation industries, such as trucking. The PFQA could also be used in fuel blending operations performed at petroleum, ethanol and biodiesel plants. ...JAN 2014 2. REPORT TYPE Project Summary 3. DATES COVERED 29-07-2013 to 27-01-2014 4. TITLE AND SUBTITLE PORTABLE FUEL QUALITY ANALYZER

  11. Analyzing Workforce Education. Monograph.

    Science.gov (United States)

    Texas Community & Technical Coll. Workforce Education Consortium.

    This monograph examines the issue of task analysis as used in workplace literacy programs, debating the need for it and how to perform it in a rapidly changing environment. Based on experiences of community colleges in Texas, the report analyzes ways that task analysis can be done and how to implement work force education programs more quickly.…

  12. Analyzing Stereotypes in Media.

    Science.gov (United States)

    Baker, Jackie

    1996-01-01

    A high school film teacher studied how students recognized messages in film, examining how film education could help students identify and analyze racial and gender stereotypes. Comparison of students' attitudes before and after the film course found that the course was successful in raising students' consciousness. (SM)

  13. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  14. Environmental influences on pigeonpea-Fusarium udum interactions and stability of genotypes to Fusarium wilt.

    Directory of Open Access Journals (Sweden)

    Mamta eSharma

    2016-03-01

    Full Text Available Fusarium wilt (Fusarium udum Butler is an important biotic constraint to pigeonpea (Cajanus cajan L. production worldwide. Breeding for fusarium wilt resistance continues to be an integral part of genetic improvement of pigeonpea. Therefore, the study was aimed to identify and validate resistant genotypes to fusarium wilt and determine the magnitude of genotype × environment (G × E interactions through multi-environment and multi-year screening. Total 976 genotypes including germplasm and breeding lines were screened against wilt in wilt sick plot at Patancheru, India. Ninety two genotypes found resistant to wilt were tested further for two more years in wilt sick plot at Patancheru and Pigeonpea Wilt Nursery (PWN comprising of 29 genotypes was constituted. PWN was evaluated at nine locations representing different agro-climatic zones of India for wilt resistance during two crop seasons 2007/08 and 2008/09. Genotypes (G, environment (E and G × E interactions biplot partitioned main effect into G, E and G × E interactions and significant effects (p≤0.001 were obtained for wilt incidence. Genotype contributed 36.51% of resistance variation followed by environment (29.32%. GGE biplot in integration with boxplot and multiple comparison tests enabled us to identify seven stable genotypes (ICPL 20109, ICPL 20096, ICPL 20115, ICPL 20116, ICPL 20102, ICPL 20106 and ICPL 20094 based on their performance across diverse environments. These genotypes have broad based resistance and can be exploited in pigeonpea breeding program.

  15. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

    Kaderali, L. (Lars); Deshpande, A. (Alina); Uribe-Romeo, F. J. (Francisco J.); Schliep, A.; Torney, D. C. (David C.)

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  16. Magnetoresistive emulsion analyzer.

    Science.gov (United States)

    Lin, Gungun; Baraban, Larysa; Han, Luyang; Karnaushenko, Daniil; Makarov, Denys; Cuniberti, Gianaurelio; Schmidt, Oliver G

    2013-01-01

    We realize a magnetoresistive emulsion analyzer capable of detection, multiparametric analysis and sorting of ferrofluid-containing nanoliter-droplets. The operation of the device in a cytometric mode provides high throughput and quantitative information about the dimensions and magnetic content of the emulsion. Our method offers important complementarity to conventional optical approaches involving ferrofluids, and paves the way to the development of novel compact tools for diagnostics and nanomedicine including drug design and screening.

  17. PhosphoSiteAnalyzer

    DEFF Research Database (Denmark)

    Bennetzen, Martin V; Cox, Jürgen; Mann, Matthias

    2012-01-01

    an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility...... and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net ....

  18. IPv6 Protocol Analyzer

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    With the emerging of next generation Intemet protocol (IPv6), it is expected to replace the current version of Internet protocol (IPv4) that will be exhausted in the near future. Besides providing adequate address space, some other new features are included into the new 128 bits of IP such as IP auto configuration, quality of service, simple routing capability, security, mobility and multicasting. The current protocol analyzer will not be able to handle IPv6 packets. This paper will focus on developing protocol analyzer that decodes IPv6 packet. IPv6 protocol analyzer is an application module,which is able to decode the IPv6 packet and provide detail breakdown of the construction of the packet. It has to understand the detail construction of the IPv6, and provide a high level abstraction of bits and bytes of the IPv6 packet.Thus it increases network administrators' understanding of a network protocol,helps he/she in solving protocol related problem in a IPv6 network environment.

  19. Filaggrin genotype determines functional and molecular alterations in skin of patients with atopic dermatitis and ichthyosis vulgaris.

    Directory of Open Access Journals (Sweden)

    Mårten C G Winge

    Full Text Available BACKGROUND: Several common genetic and environmental disease mechanisms are important for the pathophysiology behind atopic dermatitis (AD. Filaggrin (FLG loss-of-function is of great significance for barrier impairment in AD and ichthyosis vulgaris (IV, which is commonly associated with AD. The molecular background is, however, complex and various clusters of genes are altered, including inflammatory and epidermal-differentiation genes. OBJECTIVE: The objective was to study whether the functional and molecular alterations in AD and IV skin depend directly on FLG loss-of-function, and whether FLG genotype determines the type of downstream molecular pathway affected. METHODS AND FINDINGS: Patients with AD/IV (n = 43 and controls (n = 15 were recruited from two Swedish outpatient clinics and a Swedish AD family material with known FLG genotype. They were clinically examined and their medical history recorded using a standardized questionnaire. Blood samples and punch biopsies were taken and trans-epidermal water loss (TEWL and skin pH was assessed with standard techniques. In addition to FLG genotyping, the STS gene was analyzed to exclude X-linked recessive ichthyosis (XLI. Microarrays and quantitative real-time PCR were used to compare differences in gene expression depending on FLG genotype. Several different signalling pathways were altered depending on FLG genotype in patients suffering from AD or AD/IV. Disease severity, TEWL and pH follow FLG deficiency in the skin; and the number of altered genes and pathways are correlated to FLG mRNA expression. CONCLUSIONS: We emphasize further the role of FLG in skin-barrier integrity and the complex compensatory activation of signalling pathways. This involves inflammation, epidermal differentiation, lipid metabolism, cell signalling and adhesion in response to FLG-dependent skin-barrier dysfunction.

  20. Haplotypes versus genotypes on pedigrees

    Directory of Open Access Journals (Sweden)

    Kirkpatrick Bonnie B

    2011-04-01

    Full Text Available Abstract Background Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysis with haplotype data have not yet been developed, and the computational complexity of such problems has been an open question. Furthermore, it is not clear in which scenarios haplotype data would provide better estimates than genotype data for quantities such as recombination rates. Results To answer these questions, a reduction is given from genotype problem instances to haplotype problem instances, and it is shown that solving the haplotype problem yields the solution to the genotype problem, up to constant factors or coefficients. The pedigree analysis problems we will consider are the likelihood, maximum probability haplotype, and minimum recombination haplotype problems. Conclusions Two algorithms are introduced: an exponential-time hidden Markov model (HMM for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data.

  1. Genotyping of FCN and MBL2 Polymorphisms Using Pyrosequencing

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Madsen, Hans Ole; Garred, Peter

    2014-01-01

    Pyrosequencing represents one of the most thorough methods used to analyze polymorphisms. One advantage of using pyrosequencing for genotyping is the ability to identify not only single-nucleotide polymorphisms (SNPs) but also tri-allelic variations, insertions and deletions (InDels). In contrast...

  2. Analyzing Chinese Financial Reporting

    Institute of Scientific and Technical Information of China (English)

    SABRINA; ZHANG

    2008-01-01

    If the world’s capital markets could use a harmonized accounting framework it would not be necessary for a comparison between two or more sets of accounting standards. However,there is much to do before this becomes reality.This article aims to pres- ent a general overview of China’s General Accepted Accounting Principles(GAAP), U.S.General Accepted Accounting Principles and International Financial Reporting Standards(IFRS),and to analyze the differ- ences among IFRS,U.S.GAAP and China GAAP using fixed assets as an example.

  3. Analyzing business models

    DEFF Research Database (Denmark)

    Nielsen, Christian

    2014-01-01

    financial statement. Plumlee (2003) finds for instance that such information imposes significant costs on even expert users such as analysts and fund managers and reduces their use of it. Analysts’ ability to incorporate complex information in their analyses is a decreasing function of its complexity......, because the costs of processing and analyzing it exceed the benefits indicating bounded rationality. Hutton (2002) concludes that the analyst community’s inability to raise important questions on quality of management and the viability of its business model inevitably led to the Enron debacle. There seems...

  4. Mineral/Water Analyzer

    Science.gov (United States)

    1983-01-01

    An x-ray fluorescence spectrometer developed for the Viking Landers by Martin Marietta was modified for geological exploration, water quality monitoring, and aircraft engine maintenance. The aerospace system was highly miniaturized and used very little power. It irradiates the sample causing it to emit x-rays at various energies, then measures the energy levels for sample composition analysis. It was used in oceanographic applications and modified to identify element concentrations in ore samples, on site. The instrument can also analyze the chemical content of water, and detect the sudden development of excessive engine wear.

  5. Study of Various HCV Genotypes in Patients Managing by Referral Clinic in Yazd Province

    Directory of Open Access Journals (Sweden)

    M Pedarzadeh

    2012-02-01

    Full Text Available Introduction: Determining virus genotype is a major factor for initiation of treatment because various kinds of genotypes need different antiviral drugs. Distribution of hepatitis C genotype in the word is variable in each country or even in each province. So we need to determine distribution pattern of hepatitis C genotype in our region. This study was performed in referral clinic of Yazd province. Methods: This was a descriptive study conducted between 2007 and 2010 on patients who were observed by Yazd referral clinic (the clinic for evaluating and management of patients with high risk behaviors. Ninety two patients who had positive RIBA test for hepatitis C infection were randomly selected and entered the study. Genotyping was performed using RT-PCR method. The primer was "universal primer HCV". Prevalence of various genotypes was analyzed according to gender, addiction and co- existence of HCV-HIV infection. Personal information and laboratory results were analyzed using SPSS. Results: The most common genotype in our study was genotype 3a (65% of cases, followed by 1a (35%. Globally 83% of patients were IV drug addict. Genotype distribution in these patients was similar to others. Fifteen patients had co-infection of HCV-HIV, and 47% of them were contaminated by genotype 1a and 53% with 3a. We could not find any patient contaminated with genotypes 2 or 4. No other genotypes except 1 & 3 or mixed genotype infection could be determined in our patients. Twenty three percent of patients had negative PCR despite positive RIBA test. This indicates that self improvement from acute hepatitis C infection in IV drug addict patients is similar to other people. Conclusion: According to the results of our study, about 2/3 of patients were infected by genotype 3a. This kind of chronic hepatitis C shows a better response to treatment comparing genotype 1a (or 1b with shorter duration and lower cost drugs. But despite higher incidence of genotype 3a, we

  6. Relationship between hepatitis C virus genotypes and viral load in Chenzhou,China

    Institute of Scientific and Technical Information of China (English)

    谷斌

    2014-01-01

    Objective To investigate the epidemiological characteristics of hepatitis C and the genotypes of hepatitis C virus(HCV)in Chenzhou,Hunan Province,China,and to analyze the difference in HCV RNA load between genotype 1 patients and non-genotype 1 patients.Methods Sixty hepatitis C patients with positive HCV RNA,who were from Chenzhou and received initial treatment in our hospital from March 2012 to March 2013,were included in the study.HCV RNA load and HCV genotypes were determined,and

  7. Analyzing Aeroelasticity in Turbomachines

    Science.gov (United States)

    Reddy, T. S. R.; Srivastava, R.

    2003-01-01

    ASTROP2-LE is a computer program that predicts flutter and forced responses of blades, vanes, and other components of such turbomachines as fans, compressors, and turbines. ASTROP2-LE is based on the ASTROP2 program, developed previously for analysis of stability of turbomachinery components. In developing ASTROP2- LE, ASTROP2 was modified to include a capability for modeling forced responses. The program was also modified to add a capability for analysis of aeroelasticity with mistuning and unsteady aerodynamic solutions from another program, LINFLX2D, that solves the linearized Euler equations of unsteady two-dimensional flow. Using LINFLX2D to calculate unsteady aerodynamic loads, it is possible to analyze effects of transonic flow on flutter and forced response. ASTROP2-LE can be used to analyze subsonic, transonic, and supersonic aerodynamics and structural mistuning for rotors with blades of differing structural properties. It calculates the aerodynamic damping of a blade system operating in airflow so that stability can be assessed. The code also predicts the magnitudes and frequencies of the unsteady aerodynamic forces on the airfoils of a blade row from incoming wakes. This information can be used in high-cycle fatigue analysis to predict the fatigue lives of the blades.

  8. Field Deployable DNA analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Wheeler, E; Christian, A; Marion, J; Sorensen, K; Arroyo, E; Vrankovich, G; Hara, C; Nguyen, C

    2005-02-09

    This report details the feasibility of a field deployable DNA analyzer. Steps for swabbing cells from surfaces and extracting DNA in an automatable way are presented. Since enzymatic amplification reactions are highly sensitive to environmental contamination, sample preparation is a crucial step to make an autonomous deployable instrument. We perform sample clean up and concentration in a flow through packed bed. For small initial samples, whole genome amplification is performed in the packed bed resulting in enough product for subsequent PCR amplification. In addition to DNA, which can be used to identify a subject, protein is also left behind, the analysis of which can be used to determine exposure to certain substances, such as radionuclides. Our preparative step for DNA analysis left behind the protein complement as a waste stream; we determined to learn if the proteins themselves could be analyzed in a fieldable device. We successfully developed a two-step lateral flow assay for protein analysis and demonstrate a proof of principle assay.

  9. Analyzing the platelet proteome.

    Science.gov (United States)

    García, Angel; Zitzmann, Nicole; Watson, Steve P

    2004-08-01

    During the last 10 years, mass spectrometry (MS) has become a key tool for protein analysis and has underpinned the emerging field of proteomics. Using high-throughput tandem MS/MS following protein separation, it is potentially possible to analyze hundreds to thousands of proteins in a sample at a time. This technology can be used to analyze the protein content (i.e., the proteome) of any cell or tissue and complements the powerful field of genomics. The technology is particularly suitable for platelets because of the absence of a nucleus. Cellular proteins can be separated by either gel-based methods such as two-dimensional gel electrophoresis or one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by liquid chromatography (LC) -MS/MS or by multidimensional LC-MS/MS. Prefractionation techniques, such as subcellular fractionations or immunoprecipitations, can be used to improve the analysis. Each method has particular advantages and disadvantages. Proteomics can be used to compare the proteome of basal and diseased platelets, helping to reveal information on the molecular basis of the disease.

  10. Population samples and genotyping technology.

    Science.gov (United States)

    Mack, S J; Sanchez-Mazas, A; Single, R M; Meyer, D; Hill, J; Dron, H A; Jani, A J; Thomson, G; Erlich, H A

    2007-04-01

    The 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th-IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new high-resolution class I and class II genotype data are being generated for 112 population samples from around the world.

  11. Glutamine synthetase in Durum Wheat: Genotypic Variation and Relationship with Grain Protein Content.

    Science.gov (United States)

    Nigro, Domenica; Fortunato, Stefania; Giove, Stefania L; Paradiso, Annalisa; Gu, Yong Q; Blanco, Antonio; de Pinto, Maria C; Gadaleta, Agata

    2016-01-01

    Grain protein content (GPC), is one of the most important trait in wheat and its characterized by a very complex genetic control. The identification of wheat varieties with high GPC (HGPC), as well as the characterization of central enzymes involved in these processes, are important for more sustainable agricultural practices. In this study, we focused on Glutamine synthetase (GS) as a candidate to study GPC in wheat. We analyzed GS expression and its enzymatic activity in different tissues and phenological stages in 10 durum wheat genotypes with different GPC. Although each genotype performed quite differently from the others, both because their genetic variability and their adaptability to specific environmental conditions, the highest GS activity and expression were found in genotypes with HGPC and vice versa the lowest ones in genotypes with low GPC (LGPC). Moreover, in genotypes contrasting in GPC bred at different nitrogen regimes (0, 60, 140 N Unit/ha) GS behaved differently in diverse organs. Nitrogen supplement increased GS expression and activity in roots of all genotypes, highlighting the key role of this enzyme in nitrogen assimilation and ammonium detoxification in roots. Otherwise, nitrogen treatments decreased GS expression and activity in the leaves of HGPC genotypes and did not affect GS in the leaves of LGPC genotypes. Finally, no changes in GS and soluble protein content occurred at the filling stage in the caryopses of all analyzed genotypes.

  12. Analyzing architecture articles

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In the present study, we express the quality, function, and characteristics of architecture to help people comprehensively understand what architecture is. We also reveal the problems and conflict found in population, land, water resources, pollution, energy, and the organization systems in construction. China’s economy is transforming. We should focus on the cities, architectural environment, energy conservation, emission-reduction, and low-carbon output that will result in successful green development. We should macroscopically and microscopically analyze the development, from the natural environment to the artificial environment; from the relationship between human beings and nature to the combination of social ecology in cities, and farmlands. We must learn to develop and control them harmoniously and scientifically to provide a foundation for the methods used in architecture research.

  13. Analyzing geographic clustered response

    Energy Technology Data Exchange (ETDEWEB)

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1991-08-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm. 21 refs., 15 figs., 2 tabs.

  14. The Phenotype/Genotype Correlation of Lactase Persistence among Omani Adults

    Directory of Open Access Journals (Sweden)

    Abdulrahim Al-Abri

    2013-09-01

    Full Text Available Objective: To examine the correlation of lactase persistence phenotype with genotype in Omani adults.Methods: Lactase persistence phenotype was tested by hydrogen breath test in 52 Omani Adults using the Micro H2 analyzer. Results were checked against genotyping using direct DNA sequencing.Results: Forty one individuals with C/C-13910 and T/T-13915 genotypes had positive breath tests (≥20 ppm; while eight of nine individuals with T/C-13910 or T/G-13915 genotypes had negative breath tests (<20 ppm and two subjects were non-hydrogen producers. The agreement between phenotype and genotype using Kappa value was very good (0.93.Conclusion: Genotyping both T/C-13910 and T/G-13915 alleles can be used to assist diagnosis and predict lactose intolerance in the Omani population.

  15. Pooled DNA genotyping on Affymetrix SNP genotyping arrays

    Directory of Open Access Journals (Sweden)

    Owen Michael J

    2006-02-01

    Full Text Available Abstract Background Genotyping technology has advanced such that genome-wide association studies of complex diseases based upon dense marker maps are now technically feasible. However, the cost of such projects remains high. Pooled DNA genotyping offers the possibility of applying the same technologies at a fraction of the cost, and there is some evidence that certain ultra-high throughput platforms also perform with an acceptable accuracy. However, thus far, this conclusion is based upon published data concerning only a small number of SNPs. Results In the current study we prepared DNA pools from the parents and from the offspring of 30 parent-child trios that have been extensively genotyped by the HapMap project. We analysed the two pools with Affymetrix 10 K Xba 142 2.0 Arrays. The availability of the HapMap data allowed us to validate the performance of 6843 SNPs for which we had both complete individual and pooled genotyping data. Pooled analyses averaged over 5–6 microarrays resulted in highly reproducible results. Moreover, the accuracy of estimating differences in allele frequency between pools using this ultra-high throughput system was comparable with previous reports of pooling based upon lower throughput platforms, with an average error for the predicted allelic frequencies differences between the two pools of 1.37% and with 95% of SNPs showing an error of Conclusion Genotyping thousands of SNPs with DNA pooling using Affymetrix microarrays produces highly accurate results and can be used for genome-wide association studies.

  16. Analyzing Pseudophosphatase Function.

    Science.gov (United States)

    Hinton, Shantá D

    2016-01-01

    Pseudophosphatases regulate signal transduction cascades, but their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this in no way precludes their having other functions as integral elements of signaling networks. Thus, understanding their roles in signaling pathways may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [mitogen-activated protein kinase (MAPK) phospho-serine-threonine/tyrosine binding], which has been linked to tumorigenesis, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase so that the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalians cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). A combination of cellular, molecular, biochemical, and proteomic techniques has served as powerful tools in identifying novel functions of the pseudophosphatase MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the

  17. TEAMS Model Analyzer

    Science.gov (United States)

    Tijidjian, Raffi P.

    2010-01-01

    The TEAMS model analyzer is a supporting tool developed to work with models created with TEAMS (Testability, Engineering, and Maintenance System), which was developed by QSI. In an effort to reduce the time spent in the manual process that each TEAMS modeler must perform in the preparation of reporting for model reviews, a new tool has been developed as an aid to models developed in TEAMS. The software allows for the viewing, reporting, and checking of TEAMS models that are checked into the TEAMS model database. The software allows the user to selectively model in a hierarchical tree outline view that displays the components, failure modes, and ports. The reporting features allow the user to quickly gather statistics about the model, and generate an input/output report pertaining to all of the components. Rules can be automatically validated against the model, with a report generated containing resulting inconsistencies. In addition to reducing manual effort, this software also provides an automated process framework for the Verification and Validation (V&V) effort that will follow development of these models. The aid of such an automated tool would have a significant impact on the V&V process.

  18. Downhole Fluid Analyzer Development

    Energy Technology Data Exchange (ETDEWEB)

    Bill Turner

    2006-11-28

    A novel fiber optic downhole fluid analyzer has been developed for operation in production wells. This device will allow real-time determination of the oil, gas and water fractions of fluids from different zones in a multizone or multilateral completion environment. The device uses near infrared spectroscopy and induced fluorescence measurement to unambiguously determine the oil, water and gas concentrations at all but the highest water cuts. The only downhole components of the system are the fiber optic cable and windows. All of the active components--light sources, sensors, detection electronics and software--will be located at the surface, and will be able to operate multiple downhole probes. Laboratory testing has demonstrated that the sensor can accurately determine oil, water and gas fractions with a less than 5 percent standard error. Once installed in an intelligent completion, this sensor will give the operating company timely information about the fluids arising from various zones or multilaterals in a complex completion pattern, allowing informed decisions to be made on controlling production. The research and development tasks are discussed along with a market analysis.

  19. Bios data analyzer.

    Science.gov (United States)

    Sabelli, H; Sugerman, A; Kovacevic, L; Kauffman, L; Carlson-Sabelli, L; Patel, M; Konecki, J

    2005-10-01

    The Bios Data Analyzer (BDA) is a set of computer programs (CD-ROM, in Sabelli et al., Bios. A Study of Creation, 2005) for new time series analyses that detects and measures creative phenomena, namely diversification, novelty, complexes, nonrandom complexity. We define a process as creative when its time series displays these properties. They are found in heartbeat interval series, the exemplar of bios .just as turbulence is the exemplar of chaos, in many other empirical series (galactic distributions, meteorological, economic and physiological series), in biotic series generated mathematically by the bipolar feedback, and in stochastic noise, but not in chaotic attractors. Differencing, consecutive recurrence and partial autocorrelation indicate nonrandom causation, thereby distinguishing chaos and bios from random and random walk. Embedding plots distinguish causal creative processes (e.g. bios) that include both simple and complex components of variation from stochastic processes (e.g. Brownian noise) that include only complex components, and from chaotic processes that decay from order to randomness as the number of dimensions is increased. Varying bin and dimensionality show that entropy measures symmetry and variety, and that complexity is associated with asymmetry. Trigonometric transformations measure coexisting opposites in time series and demonstrate bipolar, partial, and uncorrelated opposites in empirical processes and bios, supporting the hypothesis that bios is generated by bipolar feedback, a concept which is at variance with standard concepts of polar and complementary opposites.

  20. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  1. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  2. Epidemiology and genetic characterization of hepatitis A virus genotype IIA.

    Science.gov (United States)

    Desbois, Delphine; Couturier, Elisabeth; Mackiewicz, Vincent; Graube, Arielle; Letort, Marie-José; Dussaix, Elisabeth; Roque-Afonso, Anne-Marie

    2010-09-01

    Three hepatitis A virus (HAV) genotypes, I, II, and III, divided into subtypes A and B, infect humans. Genotype I is the most frequently reported, while genotype II is hardly ever isolated, and its genetic diversity is unknown. From 2002 to 2007, a French epidemiological survey of HAV identified 6 IIA isolates, mostly from patients who did not travel abroad. The possible African origin of IIA strains was investigated by screening the 2008 mandatory notification records of HAV infection: 171 HAV strains from travelers to West Africa and Morocco were identified. Genotyping was performed by sequencing of the VP1/2A junction in 68 available sera. Entire P1 and 5' untranslated regions of IIA strains were compared to reference sequences of other genotypes. The screening retrieved 5 imported IIA isolates. An additional autochthonous case and 2 more African cases were identified in 2008 and 2009, respectively. A total of 14 IIA isolates (8 African and 6 autochthonous) were analyzed. IIA sequences presented lower nucleotide and amino acid variability than other genotypes. The highest variability was observed in the N-terminal region of VP1, while for other genotypes the highest variability was observed at the VP1/2A junction. Phylogenetic analysis identified 2 clusters, one gathering all African and two autochthonous cases and a second including only autochthonous isolates. In conclusion, most IIA strains isolated in France are imported by travelers returning from West Africa. However, the unexplained contamination mode of autochthonous cases suggests another, still to be discovered geographical origin or a French reservoir to be explored.

  3. Physiological and Molecular Analysis of Applied Nitrogen in Rice Genotypes

    Institute of Scientific and Technical Information of China (English)

    Khalid Rehman HAKEEM; Ruby CHANDNA; Altaf AHMAD; Muhammad IQBAL

    2012-01-01

    Ten genotypes of rice (Oryza sativa L.) were grown for 30 d in complete nutrient solution with 1 mmol/L (N-insufficient),4 mmol/L (N-moderate) and 10 mmol/L (N-high) nitrogen levels,and nitrogen efficiency (NE) was analyzed.Growth performance,measured in terms of fresh weight,dry weight and lengths of root and shoot,was higher in N-efficient than in N-inefficient rice genotypes at low N level.Of these 10 genotypes,Suraksha was identified as the most N-efficient,while Vivek Dhan the most N-inefficient.To find out the physiological basis of this difference,the nitrate uptake rate of root and the activities of nitrate assimilatory enzymes in leaves of N-efficient and N-inefficient rice genotypes were studied.Uptake experiments revealed the presence of two separate nitrate transporter systems mediating high- and low-affinity nitrate uptake.Interestingly,the nitrate uptake by the roots of Suraksha is mediated by both high- and low-affinity nitrate transporter systems,while that of Vivek Dhan by only low-affinity nitrate transporter system.Study of the activities and expression levels of nitrate assimilatory enzymes in N-efficient and N-inefficient rice genotypes showed that nitrate reductase (NR) and glutamine svnthetase (GS) play important roles in N assimilation under low-nitrogen conditions.

  4. Soft Decision Analyzer

    Science.gov (United States)

    Steele, Glen; Lansdowne, Chatwin; Zucha, Joan; Schlensinger, Adam

    2013-01-01

    The Soft Decision Analyzer (SDA) is an instrument that combines hardware, firmware, and software to perform realtime closed-loop end-to-end statistical analysis of single- or dual- channel serial digital RF communications systems operating in very low signal-to-noise conditions. As an innovation, the unique SDA capabilities allow it to perform analysis of situations where the receiving communication system slips bits due to low signal-to-noise conditions or experiences constellation rotations resulting in channel polarity in versions or channel assignment swaps. SDA s closed-loop detection allows it to instrument a live system and correlate observations with frame, codeword, and packet losses, as well as Quality of Service (QoS) and Quality of Experience (QoE) events. The SDA s abilities are not confined to performing analysis in low signal-to-noise conditions. Its analysis provides in-depth insight of a communication system s receiver performance in a variety of operating conditions. The SDA incorporates two techniques for identifying slips. The first is an examination of content of the received data stream s relation to the transmitted data content and the second is a direct examination of the receiver s recovered clock signals relative to a reference. Both techniques provide benefits in different ways and allow the communication engineer evaluating test results increased confidence and understanding of receiver performance. Direct examination of data contents is performed by two different data techniques, power correlation or a modified Massey correlation, and can be applied to soft decision data widths 1 to 12 bits wide over a correlation depth ranging from 16 to 512 samples. The SDA detects receiver bit slips within a 4 bits window and can handle systems with up to four quadrants (QPSK, SQPSK, and BPSK systems). The SDA continuously monitors correlation results to characterize slips and quadrant change and is capable of performing analysis even when the

  5. Alzheimer's disease: analyzing the missing heritability.

    Directory of Open Access Journals (Sweden)

    Perry G Ridge

    Full Text Available Alzheimer's disease (AD is a complex disorder influenced by environmental and genetic factors. Recent work has identified 11 AD markers in 10 loci. We used Genome-wide Complex Trait Analysis to analyze >2 million SNPs for 10,922 individuals from the Alzheimer's Disease Genetics Consortium to assess the phenotypic variance explained first by known late-onset AD loci, and then by all SNPs in the Alzheimer's Disease Genetics Consortium dataset. In all, 33% of total phenotypic variance is explained by all common SNPs. APOE alone explained 6% and other known markers 2%, meaning more than 25% of phenotypic variance remains unexplained by known markers, but is tagged by common SNPs included on genotyping arrays or imputed with HapMap genotypes. Novel AD markers that explain large amounts of phenotypic variance are likely to be rare and unidentifiable using genome-wide association studies. Based on our findings and the current direction of human genetics research, we suggest specific study designs for future studies to identify the remaining heritability of Alzheimer's disease.

  6. Heads or Tails: Genotyping of Hepatitis C Virus Concerning the 2k/1b Circulating Recombinant Form

    Science.gov (United States)

    Schuermans, Wim; Orlent, Hans; Desombere, Isabelle; Descheemaeker, Patrick; Van Vlierberghe, Hans; Geerts, Anja; Verhelst, Xavier; Reynders, Marijke; Padalko, Elizaveta

    2016-01-01

    As different hepatitis C virus (HCV) genotypes respond differently to initiated therapy, correct HCV genotyping is essential. A potential risk for misclassification of the intergenotypic HCV circulating recombinant form (CRF) 2k/1b strains exists, depending on the genotyping method used. The aim was to investigate the differences in HCV genotyping methods with regard to CRF 2k/1b and to gain insight in the prevalence of the CRF 2k/1b. Genotyping results by Versant HCV Genotype Assay were compared with nonstructural protein 5B (NS5B) sequencing. In total, from November 2001 until March 2015, 3296 serum samples were analyzed by Versant HCV Genotype Assay. As misclassified CRF is harbored among HCV genotype 2, we further focused our search on 142 (4.3%) samples positive for HCV genotype 2. On 116 (81.7%) retrieved samples, the NS5B sequencing was performed. Twelve out of the 116 retrieved samples (10.3%) were classified as CRF 2k/1b by sequencing of the NS5B region. Ten of these 12 samples were originally misclassified as genotype 2a or 2c, while 2 of them were misclassified as genotype 2. Our results show that the current prevalence of CRF 2k/1b is underestimated. The importance of correct HCV genotyping is emphasized, considering the tailored choice of treatment regimen and overall prognosis. PMID:27563879

  7. Comparative evaluation of INNO-LiPA HBV assay, direct DNA sequencing and subtractive PCR-RFLP for genotyping of clinical HBV isolates

    Directory of Open Access Journals (Sweden)

    Hasan Fuad

    2010-05-01

    Full Text Available Abstract Genotypes (A to H of hepatitis B virus (HBV influence liver disease progression and response to antiviral therapy in HBV-infected patients. Several methods have been developed for rapid genotyping of HBV strains. However, some of these methods may not be suitable for developing countries. The performance of INNO-LiPA HBV Genotyping assay (LiPA, direct DNA sequencing and subtractive PCR-RFLP of genotype-specific HBV genome regions were evaluated for accurately determining the HBV genotypes by analyzing sera (n = 80 samples from chronic HBV patients. Both, LiPA and DNA sequencing identified 63, 4 and 13 HBV strains as belonging to genotype D, genotype A and mixed genotype A and D, respectively. On the contrary, the PCR-RFLP-based method correctly identified all 4 genotype A but only 56 of 63 genotype D strains. Seven genotype D strains yielded indeterminate results. DNA sequence comparisons showed that a single nucleotide change in the target region generated an additional restriction site for Nla IV that compromised the accuracy of this method. Furthermore, all the mixed genotype A and D strains were identified only as genotype A strains. The data show that the PCR-RFLP-based method incorrectly identified some genotype D strains and failed to identify mixed genotype infections while LiPA and DNA sequencing yielded accurate results.

  8. The Information Flow Analyzing Based on CPC

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhang; LI Hui

    2005-01-01

    The information flow chart within product life cycle is given out based on collaborative production commerce (CPC) thoughts. In this chart, the separated information systems are integrated by means of enterprise knowledge assets that are promoted by CPC from production knowledge. The information flow in R&D process is analyzed in the environment of virtual R&D group and distributed PDM. In addition, the information flow throughout the manufacturing and marketing process is analyzed in CPC environment.

  9. Evolution and mutations of hepatitis B virus quasispecies in genotype B and C during vertical transmission.

    Science.gov (United States)

    Wu, Quanxin; Xu, Cheng; Li, Junnan; Li, Li; Yan, Guohua; Yue, Liangliang; Zeng, Yi; Huang, Hongfei; Deng, Guohong; Wang, Yuming

    2016-06-01

    Evolution patterns of HBV QS between genotype B and C during vertical transmission are not well understood. In this study, we enrolled 10 HBV infected mother-infant pairs (four pairs with genotype B, four pairs with genotype C, and two with co-infection) without anti-viral therapy. Serum HBV DNA of mothers and infants were sequenced, HBV QS complexity and diversity were analyzed, polymorphisms and mutation sites were recorded, and phylogenetic trees were performed. Our result showed that the QS complexities in P (amino acid), C/PreC (amino acid), and PreS1 (nucleotide) gene were significantly higher in mothers than in infants in pairs with genotype C (P 0.05). Unlike genotype C, QS complexity of P gene (nucleotide) was significantly higher in infants than in mothers (P genotype B, similarly, QS complexities of full-length and other genes (except Pre S2) were also higher in infants than in mothers but without significant differences (P > 0.05). QS diversities of full-length and most genes in genotype B were comparable between mothers and their infants (P > 0.05), in pairs with genotype C, dS of P, X, RT genes, genetic distance of Pre S1 gene (amino acid) and dN of Pre S1 gene were significant higher in mothers than in infants (P genotype B and C during vertical transmission might contribute to distinct prognosis.

  10. Microsatellite-based genotyping of Candida albicans isolated from patients with superficial candidiasis.

    Science.gov (United States)

    Shimizu, Kazue; Hattori, Hisao; Adachi, Hidesada; Oshima, Ryosuke; Horii, Toshinobu; Tanaka, Reiko; Yaguchi, Takashi; Tomita, Yasushi; Akiyama, Masashi; Kawamoto, Fumihiko; Kanbe, Toshio

    2011-01-01

    This study aimed to examine the genotype distribution of Candida albicans and the major genotypes involved in superficial candidiasis. The genotypes of C. albicans isolated from the infection sites of patients with superficial candidiasis (referred to as infection isolates) were analyzed by fragment analysis using 4 microsatellite markers (HIS3, CDC3, CAI and CAIII). Genotypes of the infection isolates were compared with those of C. albicans isolated from oral mucosa of non-candidiasis patients (referred to as oral isolates). Isolates of C. albicans showed 4 major genotypes for HIS3/CAI (" a " for 148 : 148 / 23 : 23," b " for 148 : 160 / 33 : 41," c " for 148 : 164 / 32 : 41 and " d " for 152 : 152 / 18 : 27). The genotypes " a "," b " and " d " were commonly found in oral (4.7, 8.8 and 7.6%, respectively) and infection (6.6, 9.2 and 15.4%, respectively) isolates. No isolates of genotype " c " were isolated from infection sites. The genotype " a " was found in the isolates from patients with genitalia candidiasis. Genotyping of multiple isolates from an individual patient showed that C. albicans from infection sites was genetically homogenous as compared with that of oral isolates, even in the same patient with candidiasis.

  11. Tuberculosis genotyping information management system: enhancing tuberculosis surveillance in the United States.

    Science.gov (United States)

    Ghosh, Smita; Moonan, Patrick K; Cowan, Lauren; Grant, Juliana; Kammerer, Steve; Navin, Thomas R

    2012-06-01

    Molecular characterization of Mycobacterium tuberculosis complex isolates (genotyping) can be used by public health programs to more readily identify tuberculosis (TB) transmission. The Centers for Disease Control and Prevention's National Tuberculosis Genotyping Service has offered M. tuberculosis genotyping for every culture-confirmed case in the United States since 2004. The TB Genotyping Information Management System (TB GIMS), launched in March 2010, is a secure online database containing genotype results linked with case characteristics from the national TB registry for state and local TB programs to access, manage and analyze these data. As of September 2011, TB GIMS contains genotype results for 89% of all culture-positive TB cases for 2010. Over 400 users can generate local and national reports and maps using TB GIMS. Automated alerts on geospatially concentrated cases with matching genotypes that may represent outbreaks are also generated by TB GIMS. TB genotyping results are available to enhance national TB surveillance and apply genotyping results to conduct TB control activities in the United States.

  12. Two-mode clustering of genotype by trait and genotype by environment data

    NARCIS (Netherlands)

    Hageman, J.A.; Malosetti, M.; Eeuwijk, van F.A.

    2012-01-01

    In this paper, we demonstrate the use of two-mode clustering for genotype by trait and genotype by environment data. In contrast to two separate (one mode) clusterings on genotypes or traits/environments, two-mode clustering simultaneously produces homogeneous groups of genotypes and traits/environm

  13. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D;

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES...... well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015015969.......: Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  14. Assessing the impact of differential genotyping errors on rare variant tests of association.

    Science.gov (United States)

    Mayer-Jochimsen, Morgan; Fast, Shannon; Tintle, Nathan L

    2013-01-01

    Genotyping errors are well-known to impact the power and type I error rate in single marker tests of association. Genotyping errors that happen according to the same process in cases and controls are known as non-differential genotyping errors, whereas genotyping errors that occur with different processes in the cases and controls are known as differential genotype errors. For single marker tests, non-differential genotyping errors reduce power, while differential genotyping errors increase the type I error rate. However, little is known about the behavior of the new generation of rare variant tests of association in the presence of genotyping errors. In this manuscript we use a comprehensive simulation study to explore the effects of numerous factors on the type I error rate of rare variant tests of association in the presence of differential genotyping error. We find that increased sample size, decreased minor allele frequency, and an increased number of single nucleotide variants (SNVs) included in the test all increase the type I error rate in the presence of differential genotyping errors. We also find that the greater the relative difference in case-control genotyping error rates the larger the type I error rate. Lastly, as is the case for single marker tests, genotyping errors classifying the common homozygote as the heterozygote inflate the type I error rate significantly more than errors classifying the heterozygote as the common homozygote. In general, our findings are in line with results from single marker tests. To ensure that type I error inflation does not occur when analyzing next-generation sequencing data careful consideration of study design (e.g. use of randomization), caution in meta-analysis and using publicly available controls, and the use of standard quality control metrics is critical.

  15. Hepatitis C virus genotypes distribution and transmission risk factors in Luxembourg from 1991 to 2006

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    AIM: To analyze the Hepatitis C virus (HCV) genotype distribution and transmission risk factors in a population of unselected patients in Luxembourg. METHODS: Epidemiological information (gender, age and transmission risks) were collected from 802patients newly diagnosed for hepatitis C and living in Luxembourg, among whom 228 patients referred from prison. Genotyping using 5'noncoding (5'NC) sequencing was performed. We compared categorical data using the Fisher's exact F-test and odds ratios (OR) were calculated for evaluating association of HCV genotype and risk factors. RESULTS: The sex ratio was predominantly male (2.2) and individuals aged less than 40 years represented 49.6% of the population. Genotype l was predominant (53.4%) followed by genotype 3 (33%). Among risk factors, intravenous drug usage (IVDU) was the most frequently reported (71.4%) followed by medical-related transmission (17.6%) including haernophilia, transfusion recipients and other nosocomial reasons. Genotype 3was significantly associated to IVDU (OR=4.84,P<0.0001= whereas genotype l was significantly associated with a medical procedure (OR = 2.42,P<0.001=.The HCV genotype distribution from inmate patients differed significantly from the rest of the population (Chi-square test with four degrees of freedom, P<0.0001= with a higher frequency of genotype 3 (46.5% vs 27.5%) and a lower frequency of genotype 1 and 4 (44.7% vs 56.8%and 5.3% vs 9.6%,respectively).IVDU was nearly exclusively reported as a risk factor in prison. CONCLUSION: We report the first description of the HCV genotype distribution in Luxembourg. The repartition is similar to other European countries, with one of the highest European prevalence rates of genotype 3 (33%). Since serology screening became available in 1991,IVDU remains the most common way of HCV transmission in Luxembourg.

  16. Integration Algorithm of Bounding-surface Model for Analyzing Cyclic Behaviors of Saturated Clay%饱和粘土循环动力分析边界面模型的积分算法

    Institute of Scientific and Technical Information of China (English)

    张福征; 胡存; 刘海笑

    2012-01-01

    Based on kinematic hardening rule, the bounding-surface plasticity model can be used to predict the dynamic response of saturated clay subject to cyclic loading. The numerical integration of the model is regarded as the means to evaluate offshore marine structures ,such as large-diameter cylindrical structure, the guarantee of bearing performance and dynamic response in the marine environment. The stress conversion method based on SMP rule is adopted to build a bounding-surface model which consider the tensile properties of the soil. Based on generalized trapezoidal rule, the integration algorithm of bounding-surface model is put forward to simulate the tri-axial tensile test and dynamic tri-axial test for the saturated soil. The simulation result basically accords with the geotechnical testing data.%基于运动硬化准则的新型边界面塑性模型,能够预测循环载荷作用下饱和粘土的动力响应,该模型的数值积分格式是合理评估海洋环境下大圆筒结构等近海工程结构承载性能和动力响应的保证.采用基于SMP准则的变换应力法,建立能考虑土体拉伸特性的边界面模型,根据广义梯形法则提出该模型的积分算法,模拟饱和粘土的三轴拉伸试验和动三轴试验,数值结果与土工试验数据吻合较好.

  17. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  18. An integrated in silico approach to analyze the involvement of single amino acid polymorphisms in FANCD1/BRCA2-PALB2 and FANCD1/BRCA2-RAD51 complex.

    Science.gov (United States)

    Doss, C George Priya; Nagasundaram, N

    2014-11-01

    Fanconi anemia (FA) is an autosomal recessive human disease characterized by genomic instability and a marked increase in cancer risk. The importance of FANCD1 gene is manifested by the fact that deleterious amino acid substitutions were found to confer susceptibility to hereditary breast and ovarian cancers. Attaining experimental knowledge about the possible disease-associated substitutions is laborious and time consuming. The recent introduction of genome variation analyzing in silico tools have the capability to identify the deleterious variants in an efficient manner. In this study, we conducted in silico variation analysis of deleterious non-synonymous SNPs at both functional and structural level in the breast cancer and FA susceptibility gene BRCA2/FANCD1. To identify and characterize deleterious mutations in this study, five in silico tools based on two different prediction methods namely pathogenicity prediction (SIFT, PolyPhen, and PANTHER), and protein stability prediction (I-Mutant 2.0 and MuStab) were analyzed. Based on the deleterious scores that overlap in these in silico approaches, and the availability of three-dimensional structures, structure analysis was carried out with the major mutations that occurred in the native protein coded by FANCD1/BRCA2 gene. In this work, we report the results of the first molecular dynamics (MD) simulation study performed to analyze the structural level changes in time scale level with respect to the native and mutated protein complexes (G25R, W31C, W31R in FANCD1/BRCA2-PALB2, and F1524V, V1532F in FANCD1/BRCA2-RAD51). Analysis of the MD trajectories indicated that predicted deleterious variants alter the structural behavior of BRCA2-PALB2 and BRCA2-RAD51 protein complexes. In addition, statistical analysis was employed to test the significance of these in silico tool predictions. Based on these predictions, we conclude that the identification of disease-related SNPs by in silico methods, in combination with MD

  19. Modelo hipercubo integrado a um algoritmo genético para análise de sistemas médicos emergenciais em rodovias The hypercube queuing model integrated to a genetic algorithm to analyze emergency medical systems on highways

    Directory of Open Access Journals (Sweden)

    Ana Paula Iannoni

    2006-04-01

    Full Text Available O modelo hipercubo, conhecido na literatura de problemas de localização de sistemas servidor para cliente, é um modelo baseado em teoria de filas espacialmente distribuídas e aproximações Markovianas. O modelo pode ser modificado para analisar os sistemas de atendimentos emergenciais (SAEs em rodovias, considerando as particularidades da política de despacho destes sistemas. Neste estudo, combinou-se o modelo hipercubo com um algoritmo genético para otimizar a configuração e operação de SAEs em rodovias. A abordagem é efetiva para apoiar decisões relacionadas ao planejamento e operação destes sistemas, por exemplo, em determinar o tamanho ideal para as áreas de cobertura de cada ambulância, de forma a minimizar o tempo médio de resposta aos usuários e o desbalanceamento das cargas de trabalho das ambulâncias. Os resultados computacionais desta abordagem foram analisados utilizando dados reais do sistema Anjos do Asfalto (rodovia Presidente Dutra.The hypercube model, well-known in the literature on problems of server-to-customer localization systems, is based on the spatially distributed queuing theory and Markovian analysis approximations. The model can be modified to analyze Emergency Medical Systems (EMSs on highways, considering the particularities of these systems' dispatching policies. In this study, we combine the hypercube model with a genetic algorithm to optimize the configuration and operation of EMSs on highways. This approach is effective to support planning and operation decisions, such as determining the ideal size of the area each ambulance should cover to minimize not only the average time of response to the user but also ambulance workload imbalances, as well as generating a Pareto efficient boundary between these measures. The computational results of this approach were analyzed using real data Anjos do Asfalto EMS (which covers the Presidente Dutra highway.

  20. Progress in genotyping of Chlamydia trachomatis

    Institute of Scientific and Technical Information of China (English)

    Xia Yong; Xiong Likuan

    2014-01-01

    Objective To review the common genotyping techniques of Chlamydia trachomatis in terms of their principles,characteristics,applications and limitations.Data sources Data used in this review were mainly from English literatures of PubMed database.The search terms were "Chlamydia trachomatis" and "genotyping".Meanwhile,data from World Health Organization were also cited.Study selection Original articles and reviews relevant to present review's theme were selected.Results Different genotyping techniques were applied on different occasions according to their characteristics,especially in epidemiological studies worldwide,which pushed the study of Chlamydia trachomatis forward greatly.In addition,summaries of some epidemiological studies by genotyping were also included in this work for reference and comparison.Conclusions A clear understanding of common genotyping techniques could be helpful to genotype C.trachomatis more appropriately and effectively.Furthermore,more studies on the association of genotypes of Ch/amydia trachomatis with clinical manifestations should be performed.

  1. An integrated system for genetic analysis

    Directory of Open Access Journals (Sweden)

    Duan Xiao

    2006-04-01

    Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

  2. Distribution of hepatitis C virus genotypes in volunteer blood donors from Chengdu, China.

    Science.gov (United States)

    Gong, Tianxiang; Zhao, Xin; Luo, Yijia; Hong, Ying; Li, Shuping; Fu, Xuemei

    2016-07-01

    Hepatitis C virus (HCV) is a significant pathogen of global concern. The virus is usually spread through blood contact, such as transfusion, hemodialysis and injection of illegal drugs. HCV genotypes have a geographic distribution in different areas. In this paper, we focus on the distribution of HCV genotypes from volunteer blood donors in Chengdu. The prevalence of genotypes was analyzed using phylogenetic analysis. Phylogenetic trees were constructed based on the HCV core and NS5B regions from 313 sequences. HCV sequences were classified into six subtypes, and HCV genotypes were determined with the following results: 1b in 283, 2a in 14, 3b in seven, 3a in three, 6a in five and 6u in one. Subtype 1b was the most common and accounted for approximately 90.41 % (283/313), and a virus of subtype 6u was isolated for the first time from the Chengdu area. Genotypes 4 and 5 were not detected.

  3. Analysis on Interaction between Genotype of Four Main Flavonoids of Barley Grain and Environment

    Institute of Scientific and Technical Information of China (English)

    Tao YANG; Chengli DUAN; Yawen ZENG; Juan DU; Shuming YANG; Xiaoying PU; Shengchao YANG

    2012-01-01

    [Objective] This study aimed to analyze the interaction between genotype of flavonoids of barley grain and environment, to increase the flavonoid content of barley grain in cultivation and breeding. [Method] In this study, the content of cate- chin, myricetin, quercetin and kaempferol of barley grain planted in Kunming, Qujing and Baoshan were determined by HPLC, and the genotype, environment, genotype- environment interaction of the flavonoid content of barley grain were analyzed. [Result] According to the experimental results, the genotype variance, environmental variance and G x E interaction variance of catechin and kaempferol contents show the same trend: genotype variation 〉 environmental variation 〉 G × E interaction variation, which all reach a extremely significant level; the genotype variance, envi- ronmental variance and G × E interaction variance of quercetin and total flavonoid contents show the same trend: genetype variation 〉 G × E interaction variation 〉 environmental variation, which all reach a extremely significant level; the genotype variance and environmental variance of myricetin content both reach a extremely sig- nificant level, while the G × E interaction variance reaches a significant level, showing an order of genotype variation 〉 environmental variation 〉 G × E interaction variation; the genotype variance, environmental variance and G x E interaction vari- ance of total flavonoid content show an order of genotype variation 〉 environmental variation 〉 G × E interaction variation. Among different barley varieties, Ziguang- mangluoerling and Kuanyingdamai in Qujing, Kunming and Baoshan have relatively high content of quercetin, while other barley varieties barely contain any quercetin. The grains of Ziguangmangluoerling and Kuanyingdamai are purple, while the grains of other barley varieties are yellow. [Conclusion] Four main flavonoids and the total flavonoids of barley grain are mainly under genetic control and

  4. Genotype by sex and genotype by age interactions with sedentary behavior: the Portuguese Healthy Family Study.

    Directory of Open Access Journals (Sweden)

    Daniel M V Santos

    Full Text Available Sedentary behavior (SB expression and its underlying causal factors have been progressively studied, as it is a major determinant of decreased health quality. In the present study we applied Genotype x Age (GxAge and Genotype x Sex (GxSex interaction methods to determine if the phenotypic expression of different SB traits is influenced by an interaction between genetic architecture and both age and sex. A total of 1345 subjects, comprising 249 fathers, 327 mothers, 334 sons and 325 daughters, from 339 families of The Portuguese Healthy Family Study were included in the analysis. SB traits were assessed by means of a 3-d physical activity recall, the Baecke and IPAQ questionnaires. GxAge and GxSex interactions were analyzed using SOLAR 4.0 software. Sedentary behaviour heritability estimates were not always statistically significant (p>0.05 and ranged from 3% to 27%. The GxSex and GxAge interaction models were significantly better than the single polygenic models for TV (min/day, EEsed (kcal/day, personal computer (PC usage and physical activty (PA tertiles. The GxAge model is also significantly better than the polygenic model for Sed (min/day. For EEsed, PA tertiles, PC and Sed, the GxAge interaction was significant because the genetic correlation between SB environments was significantly different from 1. Further, PC and Sed variance heterogeneity among distinct ages were observed. The GxSex interaction was significant for EEsed due to genetic variance heterogeneity between genders and for PC due to a genetic correlation less than 1 across both sexes. Our results suggest that SB expression may be influenced by the interactions between genotype with both sex and age. Further, different sedentary behaviors seem to have distinct genetic architectures and are differentially affected by age and sex.

  5. Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines

    Science.gov (United States)

    Jahoor, Ahmed; Orabi, Jihad; Andersen, Jeppe R.; Janss, Luc L.; Jensen, Just

    2017-01-01

    Wheat breeding programs generate a large amount of variation which cannot be completely explored because of limited phenotyping throughput. Genomic prediction (GP) has been proposed as a new tool which provides breeding values estimations without the need of phenotyping all the material produced but only a subset of it named training population (TP). However, genotyping of all the accessions under analysis is needed and, therefore, optimizing TP dimension and genotyping strategy is pivotal to implement GP in commercial breeding schemes. Here, we explored the optimum TP size and we integrated pedigree records and genome wide association studies (GWAS) results to optimize the genotyping strategy. A total of 988 advanced wheat breeding lines were genotyped with the Illumina 15K SNPs wheat chip and phenotyped across several years and locations for yield, lodging, and starch content. Cross-validation using the largest possible TP size and all the SNPs available after editing (~11k), yielded predictive abilities (rGP) ranging between 0.5–0.6. In order to explore the Training population size, rGP were computed using progressively smaller TP. These exercises showed that TP of around 700 lines were enough to yield the highest observed rGP. Moreover, rGP were calculated by randomly reducing the SNPs number. This showed that around 1K markers were enough to reach the highest observed rGP. GWAS was used to identify markers associated with the traits analyzed. A GWAS-based selection of SNPs resulted in increased rGP when compared with random selection and few hundreds SNPs were sufficient to obtain the highest observed rGP. For each of these scenarios, advantages of adding the pedigree information were shown. Our results indicate that moderate TP sizes were enough to yield high rGP and that pedigree information and GWAS results can be used to greatly optimize the genotyping strategy. PMID:28081208

  6. Interrelationship of hepatitis C virus genotypes with patient characteristics in Bahrain

    Science.gov (United States)

    Abdulla, Maheeba A; Murad, Eman A; Aljenaidi, Hend A; Aljowder, Duha R; Aljeeran, Omar IK; Farid, Eman; Al Qamish, Jehad R

    2017-01-01

    Aim Hepatitis C virus (HCV) shows genotype-based variation in prevalence across geographical regions. This study was conducted to understand the clinical interrelationship of HCV genotypes with patient characteristics. Methods Medical records of 122 patients positive for HCV RNA test collected during 2013 and 2014 were included for analysis. Only adults were included in the study. HCV RNA extraction and genotyping was done as part of the routine diagnostic requirements. The association of continuous and categorical variables with genotypes was analyzed through analysis of variance and chi-square tests, respectively. Results Of the 122 patients selected, 103 were Bahrainis, 18 non-Bahrainis, and 1 was unregistered. Genotype 1 was the predominant (53%) one, followed by types 3 (23%) and 4 (20%). Classical symptoms, clinical signs, liver function test, and ultrasonographic results were recorded. Cirrhosis and ascites showed significant variation across genotypes. Although alanine transaminase, total bilirubin, and albumin levels were increased, gamma-glutamyltransferase and alkaline phosphatase levels were normal. About 12% of the subjects were alcohol users, 4% were positive for HIV infection and 2.4% were positive for hepatitis B virus infection. The circulating HCV RNA load was at medium-level in the study cohort and showed significant association with the HCV genotypes and subtypes. Patients with genotype 1a had 6 times more load than patients with type 4 (Prelationship of HCV RNA viral load with the severity of liver disease in our cohort.

  7. AGT M235T genotype/anxiety interaction and gender in the HyperGEN study.

    Directory of Open Access Journals (Sweden)

    Sarah S Knox

    Full Text Available BACKGROUND: Both anxiety and elevated heart rate (HR have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N = 1,002 men and 987 women, was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM with an endophenotype, heart rate (HR in high and low anxious groups. METHODOLOGY: The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, smoking, alcohol consumption, beta blocker medication, body mass index, physical activity and hours of television viewing (sedentary life style. PRINCIPAL FINDINGS: Although there was no main effect of genotype on HR in men or women, high anxious men with the TT genotype had high HR, whereas high anxious men with the MM genotype had low HR. In women, HR was inversely associated with anxiety but there was no interaction with genotype. CONCLUSION/SIGNIFICANCE: The results suggest that high anxiety in men with the TT genotype may increase risk for hypertension whereas the MM genotype may be protective in high anxious men. This type of gene x environment interaction may be one reason why genome wide association studies sometimes fail to replicate. The locus may be important only in combination with certain environmental factors.

  8. Association of adiponectin genotype polymorphisms at positions 45 and 276 with obstructive sleep apnea hypopnea syndrome

    Institute of Scientific and Technical Information of China (English)

    Mei Su; Xilong Zhang; Shicheng Su

    2009-01-01

    Objective: To investigate the relationship between adiponectin genotype polymorphisms and obstructive sleep apnea hypopnea syndrome (OSAHS). Methods: Using the TaqMan polymerase chain reaction(PCR) method, the single nucleotide polymorphisms(SNP)at positions 45 and 276 in the adiponectin gene were determined in Chinese of the Han nationality in the Nanjing district. The OSAHS group consisted of 78 patients, and the control group contained 40 subjects. The association of adiponectin genotype polymorphisms at positions 45 and 276 with obstructive sleep apnea hypopnea syndrome was analyzed. Results: No evidence of a direct association was found between OSAHS and adiponectin genotype SNP at positions 45 and 276(P> 0.05). However, compared with those OSAHS patients having G/T+T/T genotype at position 276, the OSAHS patients with the G/G genotype showed a greater neck circumference(NC), a prolonged duration of the longest apnea event, and elevated levels of blood cholesterol and low-density lipoprotein cholesterol(P < 0.05). Conclusion: No direct association was detected between OSAHS and adiponectin genotype distribution at positions 45 and 276 in Chinese of Han nationality in the Nanjing district. However, OSAHS patients with the adiponectin GIG genotype at position 276 had a larger NC and the longest apnea event compared to those having the adiponectin SNP276 G/T +T/T genotype. This may have an indirect influence on the development of OSAHS.

  9. Genetic parameters and simultaneous selection for root yield, adaptability and stability of cassava genotypes

    Directory of Open Access Journals (Sweden)

    João Tomé de Farias Neto

    2013-12-01

    Full Text Available The objective of this work was to estimate genetic parameters and to evaluate simultaneous selection for root yield and for adaptability and stability of cassava genotypes. The effects of genotypes were assumed as fixed and random, and the mixed model methodology (REML/Blup was used to estimate genetic parameters and the harmonic mean of the relative performance of genotypic values (HMRPGV, for simultaneous selection purposes. Ten genotypes were analyzed in a complete randomized block design, with four replicates. The experiment was carried out in the municipalities of Altamira, Santarém, and Santa Luzia do Pará in the state of Pará, Brazil, in the growing seasons of 2009/2010, 2010/2011, and 2011/2012. Roots were harvested 12 months after planting, in all tested locations. Root yield had low coefficients of genotypic variation (4.25% and broad-sense heritability of individual plots (0.0424, which resulted in low genetic gain. Due to the low genotypic correlation (0.15, genotype classification as to root yield varied according to the environment. Genotypes CPATU 060, CPATU 229, and CPATU 404 stood out as to their yield, adaptability, and stability.

  10. Genotype and ancestry modulate brain's DAT availability in healthy humans.

    Directory of Open Access Journals (Sweden)

    Elena Shumay

    Full Text Available The dopamine transporter (DAT is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3 is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET with [¹¹C]cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms--3-UTR- and intron 8--VNTRs. The main findings are the following: 1 both polymorphisms analyzed as single genetic markers and in combination (haplotype modulate DAT density in midbrain; 2 ethnic background and age influence the strength of these associations; and 3 age-related changes in DAT availability differ in the 3-UTR and intron 8--genotype groups.

  11. Environmental Influences on Pigeonpea-Fusarium udum Interactions and Stability of Genotypes to Fusarium Wilt.

    Science.gov (United States)

    Sharma, Mamta; Ghosh, Raju; Telangre, Rameshwar; Rathore, Abhishek; Saifulla, Muhammad; Mahalinga, Dayananda M; Saxena, Deep R; Jain, Yogendra K

    2016-01-01

    Fusarium wilt (Fusarium udum Butler) is an important biotic constraint to pigeonpea (Cajanus cajan L.) production worldwide. Breeding for fusarium wilt resistance continues to be an integral part of genetic improvement of pigeonpea. Therefore, the study was aimed at identifying and validating resistant genotypes to fusarium wilt and determining the magnitude of genotype × environment (G × E) interactions through multi-environment and multi-year screening. A total of 976 genotypes including germplasm and breeding lines were screened against wilt using wilt sick plot at Patancheru, India. Ninety two genotypes resistant to wilt were tested for a further two years using wilt sick plot at Patancheru. A Pigeonpea Wilt Nursery (PWN) comprising of 29 genotypes was then established. PWN was evaluated at nine locations representing different agro-climatic zones of India for wilt resistance during two crop seasons 2007/08 and 2008/09. Genotypes (G), environment (E), and G × E interactions were examined by biplot which partitioned the main effect into G, E, and G × E interactions with significant levels (p ≤ 0.001) being obtained for wilt incidence. The genotype contributed 36.51% of resistance variation followed by the environment (29.32%). A GGE biplot integrated with a boxplot and multiple comparison tests enabled us to identify seven stable genotypes (ICPL 20109, ICPL 20096, ICPL 20115, ICPL 20116, ICPL 20102, ICPL 20106, and ICPL 20094) based on their performance across diverse environments. These genotypes have broad based resistance and can be exploited in pigeonpea breeding programs.

  12. MLVA Genotyping Characteristics of Human Brucella melitensis Isolated from Ulanqab of Inner Mongolia, China

    Science.gov (United States)

    Liu, Zhi-Guo; Di, Dong-Dong; Wang, Miao; Liu, Ri-Hong; Zhao, Hong-Yan; Piao, Dong-Ri; Tian, Guo-Zhong; Fan, Wei-Xing; Jiang, Hai; Cui, Bu-Yun; Xia, Xian-Zhu

    2017-01-01

    Brucellosis is a serious public health problem in Ulanqab, which is a region located in the middle of the Inner Mongolia Autonomous Region adjacent to Shanxi and Hebei provinces. The disease is prevalent in both the latter provinces and Ulanqab with the highest prevalence of brucellosis occurring in Inner Mongolia. The MLVA-16 scheme is a genotyping tool for assessing genetic diversity and relationships among isolates. Moreover, this genotyping tool can also be applied to epidemiological trace-back investigations. This study reports the occurrence of at least two B. melitensis biovars (1 and 3) in Ulanqab, encompassing 22 and 94 isolates, respectively. B. melitensis biovar 3 was the predominant biovar in the area examined. Panel 1 (MLVA-8) identified three genotypes (42, 63, and 114), with genotype 42 (n = 101) representing 87% of the tested strains. MLVA-11 identified eight genotypes (116, 111, 297, 291, and 342–345) from 116 of the analyzed isolates. All of these isolates were identified as belonging to the East Mediterranean group. Genotype 116 (n = 94) was the predominant genotype and represented 81% of the isolates. The isolates pertaining to this genotype were distributed throughout most of Ulanqab and neighboring regions. The MLVA-16 scheme showed the presence of 69 genotypes, with 46 genotypes being represented by single isolates. This analysis revealed that Ulanqab brucellosis cases had epidemiologically unrelated and sporadic characteristics. The remaining 23 genotypes were shared (between a total of 70 isolates) with each genotype being represented by two to eight isolates. These data indicate that these cases were epidemiologically related. MLVA genotyping confirmed the occurrence of a multipoint outbreak epidemic and intrafamilial brucellosis. Extensive genotype-sharing events were observed among isolates from different regions of Ulanqab and from other provinces of China. These findings suggest either a lack of control of animal movement between

  13. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  14. Rotavirus genotypes in Belarus, 2008-2012.

    Science.gov (United States)

    Semeiko, Galina V; Yermalovich, Marina A; Poliakova, Nadezhda; Mijatovic-Rustempasic, Slavica; Kerin, Tara K; Wasley, Annemarie; Videbaek, Dovile; Gentsch, Jon R; Bowen, Michael D; Samoilovich, Elena O

    2014-12-01

    This study describes group A rotavirus (RVA) genotype prevalence in Belarus from 2008 to 2012. In 2008, data from 3 sites in Belarus (Brest, Mogilev, Minsk) indicated that G4P[8] was the predominant genotype. Data from Minsk (2008-2012) showed that G4P[8] was the predominant RVA genotype in all years except in 2011 when G3P[8] was most frequently detected. Other RVA genotypes common in Europe (G1P[8], G2P[4]) were detected each year of the study. This study reveals the dominance of genotype G4P[8] in Belarus and helps to establish the baseline genotype prevalence prior to RVA vaccine introduction in the country.

  15. Multiattribute Response of Maize Genotypes Tested in Different Coastal Regions of Brazil

    Directory of Open Access Journals (Sweden)

    Lúcio Borges de Araújo

    2011-01-01

    Full Text Available This work applies the three mode principal components analysis to analyze simultaneously the multiple attributes; to fit of models with additive main effects and multiplicative interaction effects (AMMI models and the regressions models on sites (SREG models; to evaluate, respectively, the multivariate response of the genotype × environment interaction and the mean response of 36 genotypes of corn tested in 4 locations in Brazil. The results were presented by joint plots to identify the best genotypes for their adaptability and performance in the set of attributes.

  16. Evaluating the impact of genotype errors on rare variant tests of association.

    Science.gov (United States)

    Cook, Kaitlyn; Benitez, Alejandra; Fu, Casey; Tintle, Nathan

    2014-01-01

    The new class of rare variant tests has usually been evaluated assuming perfect genotype information. In reality, rare variant genotypes may be incorrect, and so rare variant tests should be robust to imperfect data. Errors and uncertainty in SNP genotyping are already known to dramatically impact statistical power for single marker tests on common variants and, in some cases, inflate the type I error rate. Recent results show that uncertainty in genotype calls derived from sequencing reads are dependent on several factors, including read depth, calling algorithm, number of alleles present in the sample, and the frequency at which an allele segregates in the population. We have recently proposed a general framework for the evaluation and investigation of rare variant tests of association, classifying most rare variant tests into one of two broad categories (length or joint tests). We use this framework to relate factors affecting genotype uncertainty to the power and type I error rate of rare variant tests. We find that non-differential genotype errors (an error process that occurs independent of phenotype) decrease power, with larger decreases for extremely rare variants, and for the common homozygote to heterozygote error. Differential genotype errors (an error process that is associated with phenotype status), lead to inflated type I error rates which are more likely to occur at sites with more common homozygote to heterozygote errors than vice versa. Finally, our work suggests that certain rare variant tests and study designs may be more robust to the inclusion of genotype errors. Further work is needed to directly integrate genotype calling algorithm decisions, study costs and test statistic choices to provide comprehensive design and analysis advice which appropriately accounts for the impact of genotype errors.

  17. Life History Traits and Population Growth of Greenhouse Whitefly (Trialeurodes vaporariorum Westwood on Different Tomato Genotypes

    Directory of Open Access Journals (Sweden)

    Mirjana Prijović

    2013-12-01

    Full Text Available The effects of five tomato genotypes (cv. Narvik and hybrids NS-6, Tamaris, Alliance and Marko on the survival, reproduction, development and population growth of the greenhouse whitefly Trialeurodes vaporariorum were examined. A laboratory population of T. vaporariorum had been reared on tobacco plants for three years before the study. Females that laid eggs on the genotype Marko lived significantly longer and their offspring needed significantly shorter periods to develop than females on the genotype Narvik. The highest gross and net fecundity rates were found in females on the genotype Marko (36.74 eggs/ female and 27.93 eggs/female, respectively and they differed significantly from the corresponding rates of females living on the genotype NS-6 (18.55 eggs/female and 15.33 eggs/ female, who had the lowest fecundity rates. The highest gross and net fertility rates were also found in females on the genotype Marko (31.24 adults/female and 23.73 adults/female, and they were significantly higher than those of females living on NS-6 (14.85 adults/female and 12.53 adults/female. Besides, net fertility rate of the females living on the genotype Narvik (13.80 adults/female was also significantly lower than the rate of females on Marko. The instantaneous rates of increase showed no significant difference over a 10-day interval following the start of oviposition, while the increase rate was significantly higher on the genotype Marko after 12, 14 and 16 days, compared to the genotype NS-6. Eighteen, 20 and 22 days after the beginning of oviposition, the instantaneous rate of increase on the genotype Marko was significantly higher than it was on NS-6 and Narvik. Our data provide a basis for further research aiming to improve programs of integrated management of greenhouse whitefly.

  18. Justification for setting the individual animal genotype call rate threshold at eighty-five percent.

    Science.gov (United States)

    Purfield, D C; McClure, M; Berry, D P

    2016-11-01

    Data quality of SNP arrays impacts the accuracy and precision of downstream data analyses. One such quality control measure often imposed is a threshold on individual animal call rate. Different call rate thresholds have been applied across studies; little is known, however, about the impact of these thresholds on the quality of the genotype data. The objective of the present study was to investigate the effect of different call rate thresholds on the integrity of the genotypes but also to quantify the contribution of different factors to the variability in animal call rate. Data included 142,342 samples genotyped on a custom Illumina genotype panel from 141,591 dairy and beef cattle; the number of Illumina SNP on the panel was 14,371. The mean animal call rate across all samples was 99.09%; 487 animals had both a low call rate (call rate (≥99%) after resampling and regenotyping. Several factors were associated ( call rate including animal sex, the sampling herd, the date of genotyping, the genotyping plate, and the plate well. The genotype and allele concordance between the genotypes of the 487 low- and high-call rate individuals improved at a diminishing rate as mean animal call rate increased. Mean genotype and allele concordance rates of 0.987 and 0.997, respectively, existed when animal call rate was between 85 and 90%, increasing to 0.998 and 0.999, respectively, when animal call rate was between 95 and call rate animals increased when animal call rate improved; an allele concordance rate of 1.00 was achieved when animal call rate was between 85 and call rate animals improved as animal call rate increased; the mean genotype concordance rate of the imputed nonobserved SNP was 0.41 when animal call rate was call rate was between 95 and call rate was call rate threshold of 85%.

  19. Distribution of hepatitis B virus genotypes: Phylogenetic analysis and virological characteristics of Genotype C circulating among HBV carriers in Kolkata, Eastern India

    Institute of Scientific and Technical Information of China (English)

    Arup Banerjee; Sibnarayan Datta; Partha K Chandra; Susanta Roychowdhury; Chinmoy Kumar Panda; Runu Chakravarty

    2006-01-01

    AIM: To evaluate the genotype distribution of hepatitis B virus (HBV) in Eastern India and to clarify the phylogenetic origin and virological characteristics of the recently identified genotype C in this region.METHODS: Genotype determination, T1762/A1764mutation in the basal core promoter (BCP) and A1896mutation in the precore region of 230 subjects were determined by restriction fragment length polymorphism method (RFLP) and the result was confirmed by direct sequencing.RESULTS: The predominant genotypes D (HBV/D) and A (HBV/A) were detected in 131/230 (57%) and 57/230(25%) samples. In addition, genotype C (HBV/C) was detected in 42/230 (18%) isolates. Surface gene region was sequenced from 45 isolates (27 HBV/C, 9 HBV/A and 9 HBV/D). Phylogenetic analysis revealed that all of the HBV/C sequences clustered with South East Asian subgenotype (HBV/Cs). The sequence data showed remarkable similarity with a Thai strain (AF068756) (99.5%± 0.4% nucleotide identities) in 90% of the genotype C strains analyzed. T1762/A1764 mutation in BCP region, associated with high ALT was significantly higher in HBeAg negative isolates than HBeAg positive isolates.Frequency of A1896 mutation leading to HBeAg negativity was low.CONCLUSION: The present study reports the genotypic distribution and the characteristics of partial genome sequences of HBV/C isolates from Eastern India. Low genetic diversity and confinement of HBV/C in Eastern India possibly indicate a recent, limited, spread in this region. Genotype C with T1762/A1764 mutation has been reported to increase the risk for hepatocellular carcinoma; therefore genotype C carriers in Eastern India should be carefully monitored.

  20. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots

    Directory of Open Access Journals (Sweden)

    Justice Kipkorir Rono

    2016-01-01

    Full Text Available The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI and genotype plus genotype by environment (GGE biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P<0.05 affected by environments (E, genotypes (G and genotype by environment interaction (GEI. GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield.

  1. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots

    Science.gov (United States)

    Cheruiyot, Erick Kimutai; Othira, Jacktone Odongo; Njuguna, Virginia Wanjiku; Macharia, Joseph Kinyoro; Owuoche, James; Oyier, Moses; Kange, Alex Machio

    2016-01-01

    The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P < 0.05) affected by environments (E), genotypes (G) and genotype by environment interaction (GEI). GGE biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield. PMID:27777968

  2. Analyzing visual signals as visual scenes.

    Science.gov (United States)

    Allen, William L; Higham, James P

    2013-07-01

    The study of visual signal design is gaining momentum as techniques for studying signals become more sophisticated and more freely available. In this paper we discuss methods for analyzing the color and form of visual signals, for integrating signal components into visual scenes, and for producing visual signal stimuli for use in psychophysical experiments. Our recommended methods aim to be rigorous, detailed, quantitative, objective, and where possible based on the perceptual representation of the intended signal receiver(s). As methods for analyzing signal color and luminance have been outlined in previous publications we focus on analyzing form information by discussing how statistical shape analysis (SSA) methods can be used to analyze signal shape, and spatial filtering to analyze repetitive patterns. We also suggest the use of vector-based approaches for integrating multiple signal components. In our opinion elliptical Fourier analysis (EFA) is the most promising technique for shape quantification but we await the results of empirical comparison of techniques and the development of new shape analysis methods based on the cognitive and perceptual representations of receivers. Our manuscript should serve as an introductory guide to those interested in measuring visual signals, and while our examples focus on primate signals, the methods are applicable to quantifying visual signals in most taxa.

  3. Soft Decision Analyzer and Method

    Science.gov (United States)

    Steele, Glen F. (Inventor); Lansdowne, Chatwin (Inventor); Zucha, Joan P. (Inventor); Schlesinger, Adam M. (Inventor)

    2016-01-01

    A soft decision analyzer system is operable to interconnect soft decision communication equipment and analyze the operation thereof to detect symbol wise alignment between a test data stream and a reference data stream in a variety of operating conditions.

  4. 在高钾血症实验中电解质分析仪的应用对机能学整合课程作用的探讨%Hyperkalemia Electrolyte Analyzer Used in the Experiments to Explore the Role of Function to Integrate Course

    Institute of Scientific and Technical Information of China (English)

    安英; 陈雪; 徐博; 赵丽晶; 沈楠

    2015-01-01

    机能学实验整合课程中高钾血症及救治实验是重要内容,在高钾血症及救治实验中电解质分析仪的应用,使学生摆脱了模型制备方法和血钾测定的束缚,能够更加直观的感受高钾血症对个体的影响以及救治诊疗过程,提升了实验教学效果.本文探讨电解质分析仪在机能学整合实验中的应用的重要性及及其在机能学整合课程教学效果提高中发挥的作用.%Function to the integration of high potassium hematic disease and treatment experiment is an important content, in hyperkalemia and treatment experiment, the application of electrolyte analyzer to make the students get rid of the preparation methods and models for the determination of potassium, can more intuitive feelings hyperkalemia impact on individuals as well as the treatment for diagnosis and treatment process, improve the experiment teaching effects. This paper discuss the application of electrolyte analyzer in function to integrate experiment and the importance of and its function to integrate the teaching effect to improve its role.

  5. Organization theory. Analyzing health care organizations.

    Science.gov (United States)

    Cors, W K

    1997-02-01

    Organization theory (OT) is a tool that can be applied to analyze and understand health care organizations. Transaction cost theory is used to explain, in a unifying fashion, the myriad changes being undertaken by different groups of constituencies in health care. Agency theory is applied to aligning economic incentives needed to ensure Integrated Delivery System (IDS) success. By using tools such as OT, a clearer understanding of organizational changes is possible.

  6. Identification of novel Coxiella burnetii genotypes from Ethiopian ticks.

    Directory of Open Access Journals (Sweden)

    Kinga M Sulyok

    Full Text Available BACKGROUND: Coxiella burnetii, the etiologic agent of Q fever, is a highly infectious zoonotic bacterium. Genetic information about the strains of this worldwide distributed agent circulating on the African continent is limited. The aim of the present study was the genetic characterization of C. burnetii DNA samples detected in ticks collected from Ethiopian cattle and their comparison with other genotypes found previously in other parts of the world. METHODOLOGY/PRINCIPAL FINDINGS: A total of 296 tick samples were screened by real-time PCR targeting the IS1111 region of C. burnetii genome and from the 32 positive samples, 8 cases with sufficient C. burnetii DNA load (Amblyomma cohaerens, n = 6; A. variegatum, n = 2 were characterized by multispacer sequence typing (MST and multiple-locus variable-number tandem repeat analysis (MLVA. One novel sequence type (ST, the proposed ST52, was identified by MST. The MLVA-6 discriminated the proposed ST52 into two newly identified MLVA genotypes: type 24 or AH was detected in both Amblyomma species while type 26 or AI was found only in A. cohaerens. CONCLUSIONS/SIGNIFICANCE: Both the MST and MLVA genotypes of the present work are closely related to previously described genotypes found primarily in cattle samples from different parts of the globe. This finding is congruent with the source hosts of the analyzed Ethiopian ticks, as these were also collected from cattle. The present study provides genotype information of C. burnetii from this seldom studied East-African region as well as further evidence for the presumed host-specific adaptation of this agent.

  7. iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

    Directory of Open Access Journals (Sweden)

    Lim Yun Ping

    2006-12-01

    Full Text Available Abstract Background The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations. Results To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded. Conclusion The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.

  8. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D;

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES...... dietary, physical activity, or drug based interventions. Gene by treatment interaction models were fitted to individual participant data from all studies included in this review, using allele dose coding for genetic effects and a common set of covariates. Study level interactions were combined using...... random effect models. Metaregression and subgroup analysis were used to assess sources of study heterogeneity. RESULTS: We identified eight eligible randomised controlled trials for the systematic review and meta-analysis (n=9563). Overall, differential changes in body mass index, body weight, and waist...

  9. Hepatitis B virus genotypes and mutations in the basal core promoter and pre-core/core in chronically infected patients in southern Brazil: a cross-sectional study of HBV genotypes and mutations in chronic carriers

    Directory of Open Access Journals (Sweden)

    Flávia Miryan Martins Almeida de Mello

    2014-12-01

    Full Text Available Introduction In Brazil, little data exist regarding the distribution of genotypes in relation to basal core promoter (BCP and precore/core mutations among chronic hepatitis B virus (HBV carriers from different regions of the country. The aim of this study was to identify HBV genotypes and the frequency of mutations at the BCP and precore/core region among the prevalent genotypes in chronic carriers from southern Brazil. Methods Nested-polymerase chain reaction (nested-PCR products amplified from the S-polymerase gene, BCP and precore/core region from 54 samples were sequenced and analyzed. Results Phylogenetic analysis of the S-polymerase gene sequences showed that 66.7% (36/54 of the patients were infected with genotype D (D1, D2, D3, 25.9% (14/54 with genotype A (A1, A2, 5.6% (3/54 with subgenotype C2, and 2% (1/54 with genotype E. A comparison of virological characteristics showed significant differences between genotypes A, C and D. The comparison between HBeAg status and the G1896A stop codon mutation in patients with genotype D revealed a relationship between HBV G1896A precore mutants and genotype D and hepatitis B e antigen (HBeAg seroconversion. Genotype D had a higher prevalence of the G1896A mutation and the presence of a thymine at position 1858. Genotype A was associated with a higher prevalence of the G1862T mutation and the presence of a cytosine at position 1858. Conclusions HBV genotype D (D3 is predominant in HBV chronic carriers from southern Brazil. The presence of mutations in the BCP and precore/core region was correlated with the HBV genotype and HBeAg negative status.

  10. An adolescent female having hepatocellular carcinoma associated with hepatitis B virus genotype H with a deletion mutation in the pre-S2 region.

    Science.gov (United States)

    Oba, Utako; Koga, Yuhki; Hoshina, Takayuki; Suminoe, Aiko; Abe, Kenji; Hayashida, Makoto; Taguchi, Tomoaki; Hara, Toshiro

    2015-04-01

    The genotypes of hepatitis B virus (HBV) have a distinct geographical distribution, with HBV genotype H being very rare in East Asia, including Japan. We herein report the case of a 12-year-old Japanese female with hepatocellular carcinoma (HCC) who exhibited HBV genotype H. Notably, the HBV isolated from the patient had a deletion mutation in the pre-S2 region. The genome of HBV genotype H in the patient with HCC has not been analyzed in detail. The deletion mutations in the pre-S2 region, which may play an important role in hepatocarcinogenesis in children, can also present in genotype H.

  11. Hepatitis B virus genotypes:an overview

    Institute of Scientific and Technical Information of China (English)

    Mamun-Al Mahtab; Salimur Rahman; Mobin Khan; Fazal Karim

    2008-01-01

    BACKGROUND: Hepatitis B virus (HBV) infection is a major cause of mortality and morbidity globally. The quest continues to identify viral factors that inlfuence disease progression and severity as well as responses to treatment of HBV infection. Based on variations in HBV, the virus has been divided into a number of genotypes. DATA SOURCES: Review of published literature on HBV genotypes. RESULTS: HBV genotypes are likely to be important in determining the severity and progression of HBV-induced liver disease as well as responses to different anti-viral agents. CONCLUSION: Although HBV genotyping is not yet recommended for routine use in treating HBV infection, available data suggest that, as in hepatitis C virus infection, HBV genotyping is also likely to become a routine investigation for HBV treatment, perhaps in the not too distant future.

  12. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  13. Interpreting genotype × environment interactions for grain yield of rainfed durum wheat in Iran

    Institute of Scientific and Technical Information of China (English)

    Reza Mohammadi; Ezatollah Farshadfar; Ahmed Amri

    2015-01-01

    Clustering genotype × environment (GE) interactions and understanding the causes of GE interactions are among the most important tasks in crop breeding programs. Pattern analysis (cluster and ordination techniques) was applied to analyze GE interactions for grain yield of 24 durum wheat (Triticum turgidum L. var. durum) genotypes (breeding lines and old and new cultivars) along with a popular bread wheat (Triticum aestivum) cultivar grown in 21 different rainfed environments during the 2010–2013 cropping seasons. To investigate the causes of GE interaction, several genotypic and environmental covariables were used. In a combined ANOVA, environment was the predominant source of variation, accounting for 81.2%of the total sum of squares (TSS), and the remaining TSS due to the GE interaction effect was almost seven times that of the genetic effect. Cluster analysis separated the environments into four groups with similar discriminating ability among genotypes, and genotypes into five groups with similar patterns in yield performance. Pattern analysis confirmed two major environmental clusters (cold and warm), and allowed the discrimination and characterization of genotype adaptation. Within the cold-environment cluster, several subclusters were identified. The breeding lines were most adapted to moderate and warm environments, whereas the old varieties were adapted to cold environments. The results indicated that winter rainfall and plant height were among the environmental and genotypic covariables, respectively, that contributed most to GE interaction for grain yield in rainfed durum wheat.

  14. Interpreting genotype × environment interactions for grain yield of rainfed durum wheat in Iran

    Institute of Scientific and Technical Information of China (English)

    Reza Mohammadi; Ezatollah Farshadfar; Ahmed Amri

    2015-01-01

    Clustering genotype × environment(GE) interactions and understanding the causes of GE interactions are among the most important tasks in crop breeding programs. Pattern analysis(cluster and ordination techniques) was applied to analyze GE interactions for grain yield of 24 durum wheat(Triticum turgidum L. var. durum) genotypes(breeding lines and old and new cultivars) along with a popular bread wheat(Triticum aestivum) cultivar grown in 21 different rainfed environments during the 2010–2013 cropping seasons. To investigate the causes of GE interaction, several genotypic and environmental covariables were used. In a combined ANOVA, environment was the predominant source of variation,accounting for 81.2% of the total sum of squares(TSS), and the remaining TSS due to the GE interaction effect was almost seven times that of the genetic effect. Cluster analysis separated the environments into four groups with similar discriminating ability among genotypes, and genotypes into five groups with similar patterns in yield performance.Pattern analysis confirmed two major environmental clusters(cold and warm), and allowed the discrimination and characterization of genotype adaptation. Within the cold-environment cluster, several subclusters were identified. The breeding lines were most adapted to moderate and warm environments, whereas the old varieties were adapted to cold environments. The results indicated that winter rainfall and plant height were among the environmental and genotypic covariables, respectively, that contributed most to GE interaction for grain yield in rainfed durum wheat.

  15. A preliminary study on correlation between adiponectin genotype polymorphisms and obstructive sleep apnea hypopnea syndrome

    Institute of Scientific and Technical Information of China (English)

    CAO Juan; SU Shi-cheng; HUANG Han-peng; DING Ning; YIN Min; HUANG Mao; ZHANG Xi-long

    2012-01-01

    Background Obstructive sleep apnea hypopnea syndrome (OSAHS) is regarded as a disease with strong genetic background and associated with hypoadiponectinemia.It is worthwhile to investigate the possible correlation between the single nucleotide polymorphisms (SNPs) in the adiponectin gene and OSAHS.Methods With the TaqMan polymerase chain reaction (PCR) method,the SNPs at positions 45 and 276 in the adiponectin gene were determined in Chinese of Han nationality in Nanjing district consisting of 103 OSAHS patients (OSAHS group) and 67 normal controls (control group).The association of adiponectin genotype polymorphisms at positions 45 and 276 with OSAHS was analyzed.Results No evidence of a direct association was found between OSAHS and adiponectin genotype SNP at positions 45 and 276 (P >0.05).However,compared with those OSAHS patients having G/T+T/T genotype at position 276,the OSAHS patients with G/G genotype showed a longer neck circumference,a prolonged duration of the longest apnea event,and an elevated level of blood cholesterol and low-density lipoprotein cholesterol (P <0.05).Conclusions No direct association was suggested between OSAHS and adiponectin genotype distribution at positions 45 and 276 in Chinese of Han nationality in Nanjing district.However,in OSAHS patients,those with adiponectin G/G genotype at position 276,seemed to have a higher potential risk in development of OSAHS than those having adiponectin SNP276 G/T +T/T genotype.

  16. Screening selected genotypes of cowpea [Vigna unguiculata (L.) Walp.] for salt tolerance during seedling growth stage.

    Science.gov (United States)

    Gogile, A; Andargie, M; Muthuswamy, M

    2013-07-15

    The environmental stress such as, salinity (soil or water) are serious obstacles for field crops especially in the arid and semi-arid parts of the world. This study was conducted to assess the potential for salt tolerance of cowpea genotypes during the seedling stage. The experimental treatments were 9 cowpea genotypes and 4 NaCl concentrations (0, 50, 100 and 200 mM) and they were tested in greenhouse. The experimental design was completely randomized design in factorial combination with three replications. Data analysis was carried out using SAS (version 9.1) statistical software. Seedling shoots and root traits, seedling shoots and root weight, number of leaves and total biological yield were evaluated. The analyzed data revealed highly significant (p cowpea genotypes, treatments and their interactions. It is found that salt stress significantly decreased root length, shoot length, seedling shoot and root weight of cowpea genotypes. The extent of decrease varied with genotypes and salt concentrations. Most genotypes were highly susceptible to 200 mM NaCl concentration. The correlation analysis revealed positive and significant association among most of the parameters. Genotypes 210856, 211557 and Asebot were better salt tolerant. The study revealed the presence of broad intra specific genetic variation in cowpea varieties for salt stress with respect to their early biomass production.

  17. Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data using Barcode Genotypes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent Rosenbaum; Grarup, Niels;

    2014-01-01

    of the method on simulated data. We find that even with only a small number of barcode genotypes, Wunderbar is capable of identifying mislabeled samples and sample mix-ups with high sensitivity and specificity, even with a high genotyping error rate and even in the presence of dependency between the individual...... barcode genotypes. To detect mislabeled samples we calculate the probability that the discordance between genotypes in the data and in the independent genotypes can be attributed to random (non-mislabeling) genotyping errors. To identify mix-ups we calculate the probability of identifying the set......Abstract—Undetected mislabeled samples may affect the results of genotype studies, particular when rare genetic variants are investigated. Mislabeled samples are often not detected during quality control and if they are detected, they are normally discarded due to a lack of a reliable method...

  18. Analyzing Valuation Practices through Contracts

    DEFF Research Database (Denmark)

    Tesnière, Germain; Labatut, Julie; Boxenbaum, Eva

    This paper seeks to analyze the most recent changes in how societies value animals. We analyze this topic through the prism of contracts between breeding companies and farmers. Focusing on new valuation practices and qualification of breeding animals, we question the evaluation of difficult...

  19. Analyzing data files in SWAN

    CERN Document Server

    Gajam, Niharika

    2016-01-01

    Traditionally analyzing data happens via batch-processing and interactive work on the terminal. The project aims to provide another way of analyzing data files: A cloud-based approach. It aims to make it a productive and interactive environment through the combination of FCC and SWAN software.

  20. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  1. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

    Directory of Open Access Journals (Sweden)

    Vaishali P. Waman

    2016-08-01

    Full Text Available Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae. There are four serotypes of Dengue Virus (DENV-1 to DENV-4, each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis

  2. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes

    Science.gov (United States)

    Waman, Vaishali P.; Kolekar, Pandurang; Ramtirthkar, Mukund R.; Kale, Mohan M.

    2016-01-01

    Background Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. Methods Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. Results DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. Discussion Complete genome-based analysis revealed that the

  3. Flavonoid profile of green asparagus genotypes.

    Science.gov (United States)

    Fuentes-Alventosa, J M; Jaramillo, S; Rodríguez-Gutiérrez, G; Cermeño, P; Espejo, J A; Jiménez-Araujo, A; Guillén-Bejarano, R; Fernández-Bolaños, J; Rodríguez-Arcos, R

    2008-08-27

    The determination of flavonoid profiles from different genotypes of triguero asparagus and their comparison to those from green asparagus commercial hybrids was the main goal of this study. The samples consisted of 32 commercial hybrids and 65 genotypes from the Huetor-Tajar population variety (triguero). The analysis of individual flavonoids by HPLC-DAD-MS has allowed the determination of eight naturally occurring flavonol derivatives in several genotypes of triguero asparagus. Those compounds included mono-, di-, and triglycosides of three flavonols, that is, quercetin, isorhamnetin, and kaempferol. The detailed analysis of the flavonoid profiles revealed significant differences among the distinct genotypes. These have been classified in three distinct groups as the result of a k-means clustering analysis, two of them containing both commercial hybrids and triguero asparagus and another cluster constituted by 21 genotypes of triguero asparagus, which contain several key flavonol derivatives able to differentiate them. Hence, the triglycosides tentatively identified as quercetin-3-rhamnosyl-rutinoside, isorhamnetin-3-rhamnosyl-rutinoside, and isorhamnetin-3-O-glucoside have been detected only in the genotypes grouped in the above-mentioned cluster. On the other hand, the compound tentatively identified as isorhamnetin-3-glucosyl-rutinoside was present in most genotypes of triguero asparagus, whereas it has not been detected in any of the commercial hybrids.

  4. HPV Genotyping 9G Membrane Test

    Directory of Open Access Journals (Sweden)

    Danishmalik Rafiq Sayyed

    2013-11-01

    Full Text Available The results of the genital human papillomavirus (HPV detection in 439 cervical samples by cervical cytology were compared with sequencing analysis and a newly developed HPV genotyping 9G membrane test. The excellent sensitivity and specificity of the HPV genotyping 9G membrane test was assured by a signal to noise ratio of more than 300 and a target hybridization to non-target hybridization ratio of 300 ~ 400 at 25 °C. The final results can be obtained in 29 min by simple loading of the hybridization and washing solutions and scanning the membranes without any drying steps or special handling. The 100% identical results of the HPV genotyping 9G membrane test with sequencing results in 439 clinical samples demonstrate significant clinical application for this test. HPV genotyping 9G membrane tests can identify and discriminate five HR-HPV genotypes which are prevalent in almost 87% of cervical cancer cases. Its simple handling makes the HPV genotyping 9G membrane test a very convenient platform for accurate HPV genotyping.

  5. Understanding salt tolerance mechanisms in wheat genotypes by exploring antioxidant enzymes

    DEFF Research Database (Denmark)

    Amjad, M.; Akhtar, J.; Haq, M.A.;

    2014-01-01

    The activities of antioxidant enzymes were analyzed in six wheat genotypes under different concentrations of NaCl (0, 100 and 200 mM). Plants were harvested after either 15 or 30 days of salt stress. The most salt tolerant genotype (SARC-1) maintained lower Na+ and higher relative growth rate (RGR....... Additionally, glutathione reductase (GR) activity was decreased in salt sensitive (S-9189 and S-9476) than salt tolerant (SARC-1) genotypes. Under salt stress conditions a negative relationship between SOD and leaf Na+, and a positive between SOD and shoot fresh weight (SFW), were observed. The higher...... efficiency of antioxidant enzymes of tolerant genotypes could be considered as one of the factors involved in salt tolerance of wheat....

  6. Genotype x environment interactions for seed yield and its components in sesame (Sesame indicum L..

    Directory of Open Access Journals (Sweden)

    Kumaresan.D and N. Nadarajan

    2010-07-01

    Full Text Available A study was conducted to analyze the genotype by environment (GxE interaction effect on yield and its components insesame grown in three environments by using AMMI analysis. The mean square were significant for genotypes, environments,GxE interaction for the characters viz., number of capsules, 1000 seed weight and single plant yield. The genotypes namelyPSR 2007 x Co1, Si 42 x Co 1, Si 42 x VRI 1, AHT 123 x VRI 1, B 203 x SVPR 1 and YLM 4030 x SVPR 1 recorded highmean but low interaction effect which are desirable for releasing as stable hybrids. The genotypes OMT 30 x VRI 1, OMT 30x SVPR 1 and DPI 1424 x VRI 1 exhibited high interaction effect and are suitable for specific environments

  7. ANALYZE Users' Guide

    Energy Technology Data Exchange (ETDEWEB)

    Azevedo, S.

    1982-10-01

    This report is a reproduction of the visuals that were used in the ANALYZE Users' Guide lectures of the videotaped LLNL Continuing Education Course CE2018-H, State Space Lectures. The course was given in Spring 1982 through the EE Department Education Office. Since ANALYZE is menu-driven, interactive, and has self-explanatory questions (sort of), these visuals and the two 50-minute videotapes are the only documentation which comes with the code. More information about the algorithms contained in ANALYZE can be obtained from the IEEE book on Programs for Digital Signal Processing.

  8. Molecular Characterization of Acanthamoeba spp. Occurring in Water Bodies and Patients in Poland and Redefinition of Polish T16 Genotype.

    Science.gov (United States)

    Adamska, Małgorzata

    2016-01-01

    Acanthamoeba genus is divided into 20 genotypes (T1-T20) on the basis of the gene encoding 18S rRNA sequence. Using of at least 2 kbp gene fragments is strongly recommended to identify new genotypes and 5% difference is commonly used as a criterion of new genotypes, however, this value is questionable. In this paper, Polish Acanthamoeba strains described earlier on the basis of ~850 bp Ami fragment of 18S rRNA gene as T4, T11 and a new T16 genotype, have been analyzed using near-complete sequence of the gene. This analysis was needed because the Ami fragment does not reveal full variability within 18S rRNA gene. Phylogenetic analysis based on Ami fragment is biased by artifacts in the construction of the tree, so the fragment should not be used for identification of new putative Acanthamoeba genotypes. The analysis confirmed that the Polish sequences represent T4 and T11 genotypes and that the strains described earlier as T16 genotype are in fact a new subgroup of the T20 genotype and that this genotype should be divided into two subgroups: T20a (two strains described by [J. Eukaryot. Microbiol. 62 (2015) 69]) and T20b (11 Polish strains described in this study). The T20b subgroup was isolated from both clinical samples and water bodies used by people as bathing places and there is a risk of infection for humans during contact with water.

  9. Molecular analysis of hepatitis B virus isolates in Mexico: Predominant circulation of hepatitis B virus genotype H

    Institute of Scientific and Technical Information of China (English)

    Cosme Alvarado-Esquivel; Erwin Sablon; Carlos Jesús Conde-González; Luis Juárez-Figueroa; Lilia Ruiz-Maya; Sergio Aguilar-Benavides

    2006-01-01

    AIM:To determine the genotypes in Mexican hepatitis B virus (HBV) isolates and characterize their precore and core promoter mutations.METHODS: Forty-nine HBV isolates of Mexico obtained from sera of 15 hepatitis patients, 6 hemodialysis patients, 20 men seeking HIV testing, and 8 AIDS patients were analyzed. HBV isolates were amplified by PCR,and genotyped by line probe assay (INNO-LiPA HBV Genotyping; INNOGENETICS N V, Ghent, Belgium).HBV genotype confirmation was performed by DNA sequencing part of the sAg region. Precore and core promoter mutation characterization was performed by line probe assay (INNO-LiPA HBV PreCore; INNOGENETICS N.V.; Ghent, Belgium).RESULTS: Overall, HBV genotype H was found in 37(75.5%) out of the 49 isolates studied. HBV genotypes G, A, and D were found in 5 (10.2%), 4 (8.2%), and 3(6.1%) isolates, respectively. HBV genotype H was predominant in isolates from hemodialysis patients (100%),hepatitis patients (80%), and men seeking HIV testing (75%), and accounted for half of infections in AIDS patients (50%). Six (12.2%) out of the 49 HBV isolates showed both wild type and mutant populations at precore codon 28. These mixed wild type and precore murant populations were observed in one HBV genotype A isolate and in all HBV genotype G isolates. A dual variant core promoter mutation was observed in 1 (2%) of the isolates, which was genotype H.CONCLUSION: HBV genotype H is highly predominant in HBV isolates of Mexico followed by genotypes G, A and D. A low frequency of precore and core promoter mutations is observed in HBV Mexican isolates.

  10. HCV genotype-specific correlation with serum markers: Higher predictability for genotype 4a

    Directory of Open Access Journals (Sweden)

    Asad Sultan

    2011-06-01

    Full Text Available Abstract Background Several factors have been proposed to assess the clinical outcome of HCV infection. The correlation of HCV genotypes to possible serum markers in clinical prediction is still controversial. The main objective of this study was to determine the existence of any correlation between HCV genotypes to viral load and different clinical serum markers. Methods We performed a prospective cross-sectional and observational study. About 3160 serum HCV RNA positive patients were chosen from 4020 randomly selected anti-HCV positive patients. Statistical analysis was performed using the SPSS 16 software package. ROC (receiver operating characteristics curves were used to compare diagnostic values of serum markers to predict genotypes. Results The most prevalent genotype was 3a (73.9% followed by 1a (10.7%, 4a (6.4% and 3b (6.1% in Pakistani population. No correlation was found between viral load and serum markers for genotype 3a in a large no. of sample (n = 2336. While significant correlation was observed between viral load and AST in genotype 3b, ALP with viral load and ALT for genotype 1a. Patients with genotype 4a showed a significant inverse correlation with viral load and Hb level and AST with ALP. For genotype 4a, AUC (area under the curve of ALT, ALP, AST, bilirubin, Hb level and viral load was 0.790, 0.763, 0.454, 0.664, 0.458 and 0.872 respectively. Conclusions In conclusion, there was a significant variable response of HCV genotypes with serum markers. Severity of disease is independent of serum marker level in genotype 3a, while the liver damage in genotype 4a may associate with viral cytopathic effect as well as the immune-mediated process. An index using six serum markers may correctly predict genotype 4a in patients with ≥75% accuracy.

  11. C2Analyzer:Co-target-Co-function Analyzer

    Institute of Scientific and Technical Information of China (English)

    Md Aftabuddin; Chittabrata Mal; Arindam Deb; Sudip Kundu

    2014-01-01

    MicroRNAs (miRNAs) interact with their target mRNAs and regulate biological pro-cesses at post-transcriptional level. While one miRNA can target many mRNAs, a single mRNA can also be targeted by a set of miRNAs. The targeted mRNAs may be involved in different bio-logical processes that are described by gene ontology (GO) terms. The major challenges involved in analyzing these multitude regulations include identification of the combinatorial regulation of miR-NAs as well as determination of the co-functionally-enriched miRNA pairs. The C2Analyzer:Co-target-Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched. For a given set of GO term(s), it can also identify the set of miRNAs whose targets are enriched in the given GO term(s). Moreover, C2Analyzer can also identify the co-targeting miRNA pairs, their targets and GO processes, which they are involved in. The miRNA-miRNA co-functional relationship can also be saved as a .txt file, which can be used to further visualize the co-functional network by using other software like Cytoscape. C2Analyzer is freely available at www.bioinformatics.org/c2analyzer.

  12. Aspects of the Genotype-Environment Interaction at the Japanese Quail (Coturnix-Coturnix Japonica

    Directory of Open Access Journals (Sweden)

    Teofil Oroian

    2010-05-01

    Full Text Available We analyzed the problems of genotype-environment interaction at three Coturnix Coturnix Japonica varieties. The environment where the experiment took place is perfect identically for all the activities, to ensure that the observed differences at the followed traits to be strictly attributed to the genotype differences. We analyzed the body weight, eggs weight, eggs large and small diameter, yolk and egg white weight, egg-shell weight. The data were statistically interpreted using the average and dispersal indices estimation, and the significance testing using Student test.

  13. Mars & Multi-Planetary Electrical Environment Spectrum Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Our objective is to develop MENSA as a highly integrated planetary radio and digital spectrum analyzer cubesat payload that can be deployed as a satellite instrument...

  14. Hepatitis C virus genotypes in Pakistan: a systemic review

    Directory of Open Access Journals (Sweden)

    Ali Ijaz

    2011-09-01

    Full Text Available Abstract Background and aim Phylogenetic analysis has led to the classification of hepatitis C virus (HCV into 1-6 major genotypes. HCV genotypes have different biological properties, clinical outcome and response to antiviral treatment and provide important clues for studying the epidemiology, transmission and pathogenesis. This article deepens the current molecular information about the geographical distribution of HCV genotypes and subgenotypes in population of four provinces of Pakistan. 34 published papers (1996-2011 related to prevalence of HCV genotypes/serotypes and subgenotypes in Pakistan were searched. Result HCV genotype/s distribution from all 34 studies was observed in 28,400 HCV infected individuals in the following pattern: 1,999 (7.03% cases of genotype 1; 1,085 (3.81% cases of genotype 2; 22,429 (78.96% cases of genotype 3; 453 (1.59% cases of genotype 4; 29 (0.10% cases of genotype 5; 37 (0.13% cases of genotype 6; 1,429 (5.03% cases of mixed genotypes, and 939 (3.30% cases of untypeable genotypes. Overall, genotype 3a was the predominant genotype with a rate of 55.10%, followed by genotype 1a, 3b and mixed genotype with a rate of 10.25%, 8.20%, and 5.08%, respectively; and genotypes 4, 5 and 6 were rare. Genotype 3 occurred predominately in all the provinces of Pakistan. Second more frequently genotype was genotype 1 in Punjab province and untypeable genotypes in Sindh, Khyber Pakhtunkhwa and Balochistan provinces.

  15. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  16. Analyzing the Biology on the System Level

    Institute of Scientific and Technical Information of China (English)

    Wei Tong

    2004-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology-systemic structures, dynamics, control methods, and design principles.

  17. Analyzing PICL trace data with MEDEA

    Energy Technology Data Exchange (ETDEWEB)

    Merlo, A.P. [Pavia Univ. (Italy). Dipt di Informatica e Sistemistica; Worley, P.H. [Oak Ridge National Lab., TN (United States)

    1993-11-01

    Execution traces and performance statistics can be collected for parallel applications on a variety of multiprocessor platforms by using the Portable Instrumented Communication Library (PICL). The static and dynamic performance characteristics of performance data can be analyzed easily and effectively with the facilities provided within the MEasurements Description Evaluation and Analysis tool (MEDEA). This report describes the integration of the PICL trace file format into MEDEA. A case study is then outlined that uses PICL and MEDEA to characterize the performance of a parallel benchmark code executed on different hardware platforms and using different parallel algorithms and communication protocols.

  18. Genotype instability during long-term subculture of lymphoblastoid cell lines.

    Science.gov (United States)

    Oh, Ji Hee; Kim, Young Jin; Moon, Sanghoon; Nam, Hye-Young; Jeon, Jae-Pil; Lee, Jong Ho; Lee, Jong-Young; Cho, Yoon Shin

    2013-01-01

    Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. To evaluate genotypic errors caused by EBV integration into human chromosomes, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix 500K SNP array set. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (50 passages). Analysis of concordance on a chromosome-by-chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs.

  19. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  20. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie;

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years Udgivelsesdato...

  1. ApoE (Apolipoprotein E) Genotyping

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? APOE Genotyping, Alzheimer Disease Share this page: Was this page helpful? Formal ... help in the diagnosis of probable late onset Alzheimer disease (AD) in symptomatic adults. It is called susceptibility ...

  2. HPV genotypes concordance between sex partners.

    Science.gov (United States)

    Benevolo, M; Mottolese, M; Marandino, F; Carosi, M; Diodoro, M G; Sentinelli, S; Visca, P; Rollo, F; Mariani, L; Vocaturo, G; Sindico, R; Di Giannuario, D; Perrone Donnorso, R; Pellicciotta, M; Vocaturo, A

    2007-12-01

    The HPV genotype concordance in the sexual couples could support the sexual viral transmission of HPV infection. The present study contains a case-report of a stable Italian sex couple harbouring the same five HPV genotypes in their genital samples. The female partner, affected by vulvar condilomatosis, evidenced positivity in her cervicovaginal scraping with high risk HPV DNA Hybrid Capture 2 test and was negative at liquid-based performed Pap Test and at colposcopic examination. The male partner was clinically healthy regarding his external genitalia. In both male and female genital scrapings, the following HPV genotypes were detected by means of a PCR-based assay: 6, 16, 53, 73 and 84. This considerably high genotype concordance does not appear to be casual and supports, in our opinion, the hypothesis that genital HPV types are sexually transmitted agents

  3. Counsel the genotype, treat the phenotype

    NARCIS (Netherlands)

    van der Zwaag, Paul A.; van Tintelen, J. Peter

    2011-01-01

    This editorial refers to 'Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure' by S. Waldmuller et al., published in this issue on pages 1185-1192.

  4. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie;

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years....

  5. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

  6. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Science.gov (United States)

    Mascher, Martin; Wu, Shuangye; Amand, Paul St; Stein, Nils; Poland, Jesse

    2013-01-01

    The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing

  7. Apolipoprotein E genotype in patients with Alzheimer's disease

    Institute of Scientific and Technical Information of China (English)

    罗本燕; 陈智; 张艳艳; 潘小平; 李霞; 陈峰

    2003-01-01

    Objective To explore the frequency and significance of ApoE gene polymorphisms in patients with sporadic Alzheimer's disease (AD).Methods Single nucleotide polymorphisms of the ApoE gene were analyzed in 32 cases of AD and 26 controls, using PCR and gene sequencing.Results The single nucleotide polymorphism of ApoE gene 462C/G was significantly associated with AD (P<0.05).Conclusions The 462C/G polymorphism might be a specific genotype in Chinese patients with sporadic AD.

  8. Operating System Performance Analyzer for Embedded Systems

    Directory of Open Access Journals (Sweden)

    Shahzada Khayyam Nisar

    2011-11-01

    Full Text Available RTOS provides a number of services to an embedded system designs such as case management, memory management, and Resource Management to build a program. Choosing the best OS for an embedded system is based on the available OS for system designers and their previous knowledge and experience. This can cause an imbalance between the OS and embedded systems. RTOS performance analysis is critical in the design and integration of embedded software to ensure that limits the application meet at runtime. To select an appropriate operating system for an embedded system for a particular application, the OS services to be analyzed. These OS services are identified by parameters to establish performance metrics. Performance Metrics selected include context switching, Preemption time and interrupt latency. Performance Metrics are analyzed to choose the right OS for an embedded system for a particular application.

  9. CRIE: An automated analyzer for Chinese texts.

    Science.gov (United States)

    Sung, Yao-Ting; Chang, Tao-Hsing; Lin, Wei-Chun; Hsieh, Kuan-Sheng; Chang, Kuo-En

    2016-12-01

    Textual analysis has been applied to various fields, such as discourse analysis, corpus studies, text leveling, and automated essay evaluation. Several tools have been developed for analyzing texts written in alphabetic languages such as English and Spanish. However, currently there is no tool available for analyzing Chinese-language texts. This article introduces a tool for the automated analysis of simplified and traditional Chinese texts, called the Chinese Readability Index Explorer (CRIE). Composed of four subsystems and incorporating 82 multilevel linguistic features, CRIE is able to conduct the major tasks of segmentation, syntactic parsing, and feature extraction. Furthermore, the integration of linguistic features with machine learning models enables CRIE to provide leveling and diagnostic information for texts in language arts, texts for learning Chinese as a foreign language, and texts with domain knowledge. The usage and validation of the functions provided by CRIE are also introduced.

  10. Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data.

    Science.gov (United States)

    Watson, Christopher M; Crinnion, Laura A; Gurgel-Gianetti, Juliana; Harrison, Sally M; Daly, Catherine; Antanavicuite, Agne; Lascelles, Carolina; Markham, Alexander F; Pena, Sergio D J; Bonthron, David T; Carr, Ian M

    2015-09-01

    Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease-causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome-wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.

  11. On-Demand Urine Analyzer

    Science.gov (United States)

    Farquharson, Stuart; Inscore, Frank; Shende, Chetan

    2010-01-01

    A lab-on-a-chip was developed that is capable of extracting biochemical indicators from urine samples and generating their surface-enhanced Raman spectra (SERS) so that the indicators can be quantified and identified. The development was motivated by the need to monitor and assess the effects of extended weightlessness, which include space motion sickness and loss of bone and muscle mass. The results may lead to developments of effective exercise programs and drug regimes that would maintain astronaut health. The analyzer containing the lab-on-a- chip includes materials to extract 3- methylhistidine (a muscle-loss indicator) and Risedronate (a bone-loss indicator) from the urine sample and detect them at the required concentrations using a Raman analyzer. The lab-on- a-chip has both an extractive material and a SERS-active material. The analyzer could be used to monitor the onset of diseases, such as osteoporosis.

  12. Analyzing the Grammar of English

    CERN Document Server

    Teschner, Richard V

    2007-01-01

    Analyzing the Grammar of English offers a descriptive analysis of the indispensable elements of English grammar. Designed to be covered in one semester, this textbook starts from scratch and takes nothing for granted beyond a reading and speaking knowledge of English. Extensively revised to function better in skills-building classes, it includes more interspersed exercises that promptly test what is taught, simplified and clarified explanations, greatly expanded and more diverse activities, and a new glossary of over 200 technical terms.Analyzing the Grammar of English is the only English gram

  13. An update on chemistry analyzers.

    Science.gov (United States)

    Vap, L M; Mitzner, B

    1996-09-01

    This update of six chemistry analyzers available to the clinician discusses several points that should be considered prior to the purchase of equipment. General topics include how to best match an instrument to clinic needs and the indirect costs associated with instrument operation. Quality assurance recommendations are discussed and common terms are defined. Specific instrument features, principles of operation, performance, and costs are presented. The information provided offers potential purchasers an objective approach to the evaluation of a chemistry analyzer for the veterinary clinic.

  14. A European database of Fusarium graminearum and F. culmorum trichothecene genotypes

    Directory of Open Access Journals (Sweden)

    Matias ePasquali

    2016-04-01

    Full Text Available Fusarium species, particularly Fusarium graminearum and F. culmorum, are the main cause of trichothecene type B contamination in cereals. Data on the distribution of Fusarium trichothecene genotypes in cereals in Europe are scattered in time and space. Furthermore, a common core set of related variables (sampling method, host cultivar, previous crop, etc. that would allow more effective analysis of factors influencing the spatial and temporal population distribution, is lacking. Consequently, based on the available data, it is difficult to identify factors influencing chemotype distribution and spread at the European level. Here we describe the results of a collaborative integrated work which aims 1 to characterize the trichothecene genotypes of strains from three Fusarium species, collected over the period 2000-2013, and 2 to enhance the standardization of epidemiological data collection.Information on host plant, country of origin, sampling location, year of sampling and previous crop of 1147 F. graminearum, 479 F. culmorum and 3 F. cortaderiae strains obtained from 17 European countries was compiled and a map of trichothecene type B genotype distribution was plotted for each species. All information on the strains was collected in a freely accessible and updatable database (www.catalogueeu.luxmcc.lu, which will serve as a starting point for epidemiological analysis of potential spatial and temporal trichothecene genotype shifts in Europe.The analysis of the currently available European dataset showed that in F. graminearum, the predominant genotype was 15-acetyldeoxynivalenol (15-ADON (82.9%, followed by 3-acetyldeoxynivalenol (3-ADON (13.6% and nivalenol (NIV (3.5%. In F. culmorum, the prevalent genotype was 3-ADON (59.9%, while the NIV genotype accounted for the remaining 40.1%. Both geographical and temporal patterns of trichothecene genotypes distribution were identified.

  15. Adaptability and Stability Study of Selected Sweet Sorghum Genotypes for Ethanol Production under Different Environments Using AMMI Analysis and GGE Biplots.

    Science.gov (United States)

    Rono, Justice Kipkorir; Cheruiyot, Erick Kimutai; Othira, Jacktone Odongo; Njuguna, Virginia Wanjiku; Macharia, Joseph Kinyoro; Owuoche, James; Oyier, Moses; Kange, Alex Machio

    2016-01-01

    The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P biplot showed high yielding genotypes EUSS10, ACFC003/12, SS14, and EUSS11 for cane yield; EUSS10, EUSS11, and SS14 for juice yield; and EUSS10, SS04, SS14, and ACFC003/12 for ethanol yield. Genotype SS14 showed high general adaptability for cane, juice, and ethanol yield.

  16. Correlation between the Chemical and Genetic Relationships among Thymus saturejoides Genotypes Cultured under in vitro and in vivo Environments.

    Science.gov (United States)

    Nordine, Aicha; Udupa, Sripada M; Iraqi, Driss; Meksem, Khalid; Hmamouchi, Mohamed; ElMeskaoui, Abdelmalek

    2016-04-01

    In this study, the in vitro and in vivo essential oil (EO) composition and genetic variability in six micropropagated genotypes of Thymus saturejoides Coss., a Mediterranean medicinal and aromatic plant, were analyzed by GC/MS and randomly amplified polymorphic DNA (RAPD). Yield and composition of the EO varied between genotypes. Cluster analysis based on RAPD data and EO grouped the six genotypes in three groups in both culture conditions, thus showing considerable intraspecific genetic and chemical variations. Applying the Mantel test, the result showed a significant correlation between the two proximity matrices RAPD and EO obtained from in vitro genotypes, whereas this correlation was not observed when using the EO obtained from the in vivo genotypes.

  17. Strategies for Analyzing Tone Languages

    Science.gov (United States)

    Coupe, Alexander R.

    2014-01-01

    This paper outlines a method of auditory and acoustic analysis for determining the tonemes of a language starting from scratch, drawing on the author's experience of recording and analyzing tone languages of north-east India. The methodology is applied to a preliminary analysis of tone in the Thang dialect of Khiamniungan, a virtually undocumented…

  18. The Convertible Arbitrage Strategy Analyzed

    NARCIS (Netherlands)

    Loncarski, I.; Ter Horst, J.R.; Veld, C.H.

    2006-01-01

    This paper analyzes convertible bond arbitrage on the Canadian market for the period 1998 to 2004.Convertible bond arbitrage is the combination of a long position in convertible bonds and a short position in the underlying stocks. Convertible arbitrage has been one of the most successful strategies

  19. FORTRAN Static Source Code Analyzer

    Science.gov (United States)

    Merwarth, P.

    1984-01-01

    FORTRAN Static Source Code Analyzer program, SAP (DEC VAX version), automatically gathers statistics on occurrences of statements and structures within FORTRAN program and provides reports of those statistics. Provisions made for weighting each statistic and provide an overall figure of complexity.

  20. Analyzing Classroom Instruction in Reading.

    Science.gov (United States)

    Rutherford, William L.

    A method for analyzing instructional techniques employed during reading group instruction is reported, and the characteristics of the effective reading teacher are discussed. Teaching effectiveness is divided into two categories: (1) how the teacher acts and interacts with children on a personal level and (2) how the teacher performs his…

  1. Analyzing Software Piracy in Education.

    Science.gov (United States)

    Lesisko, Lee James

    This study analyzes the controversy of software piracy in education. It begins with a real world scenario that presents the setting and context of the problem. The legalities and background of software piracy are explained and true court cases are briefly examined. Discussion then focuses on explaining why individuals and organizations pirate…

  2. Blood Group ABO Genotyping in Paternity Testing.

    Science.gov (United States)

    Bugert, Peter; Rink, Gabriele; Kemp, Katharina; Klüter, Harald

    2012-06-01

    BACKGROUND: The ABO blood groups result from DNA sequence variations, predominantly single nucleotide and insertion/deletion polymorphisms (SNPs and indels), in the ABO gene encoding a glycosyltransferase. The ABO blood groups A(1), A(2), B and O predominantly result from the wild type allele A1 and the major gene variants that are characterized by four diallelic markers (261G>del, 802G>A, 803G>C, 1061C>del). Here, we were interested to evaluate the impact of ABO genotyping compared to ABO phenotyping in paternity testing. METHODS: The major ABO alleles were determined by PCR amplification with sequence-specific primers (PCR-SSP) in a representative sample of 1,335 blood donors. The genotypes were compared to the ABO blood groups registered in the blood donor files. Then, the ABO phenotypes and genotypes were determined in 95 paternity trio cases that have been investigated by 12 short tandem repeat (STR) markers before. We compared statistical parameters (PL, paternity likelihood; PE, power of exclusion) of both blood grouping approaches. RESULTS: The prevalence of the major ABO alleles and genotypes corresponded to the expected occurrence of ABO blood groups in a Caucasian population. The low resolution genotyping of 4 diallelic markers revealed a correct genotype-phenotype correlation in 1,331 of 1,335 samples (99.7%). In 60 paternity trios with confirmed paternity of the alleged father based on STR analysis both PL and PE of the ABO genotype was significantly higher than of the ABO phenotype. In 12 of 35 exclusion cases (34.3%) the ABO genotype also excluded the alleged father, whereas the ABO phenotype excluded the alleged father only in 7 cases (20%). CONCLUSION: In paternity testing ABO genotyping is superior to ABO phenotyping with regard to PL and PE, however, ABO genotyping is not sufficient for valid paternity testing. Due to the much lower mutation rate compared to STR markers, blood group SNPs in addition to anonymous SNPs could be considered for

  3. ACE DD genotype is unfavorable to Korean short-term muscle power athletes.

    Science.gov (United States)

    Kim, C-H; Cho, J-Y; Jeon, J Y; Koh, Y G; Kim, Y-M; Kim, H-J; Park, M; Um, H-S; Kim, C

    2010-01-01

    The purpose of this study was to test the hypothesis that the ACE DD genotype is unfavorably associated with the ultimate power-oriented performance. To test the hypothesis we recruited a total of 848 subjects including 55 international level power-oriented athletes (High-performance), 100 national level power-oriented athletes (Mid-performance) and 693 healthy controls (Control) in Korea. Then the distributions of ACE polymorphism throughout these groups were analyzed. As a result, there was a gradual decrease of frequencies of the DD genotype with advancing levels of performance (Control vs. Mid-performance vs. High-performance=17.2% vs. 10.0% vs. 5.5%, p=0.002). Also, the frequencies of D allele decreased gradually with advancing levels of performance (Control vs. Mid-performance vs. High-performance=42.6% vs. 35.0% vs. 30.9%, pDD genotype and the D allele. This finding gave 3.83 times lower probability of success in power-oriented sports for individuals with the DD genotype than those with the II+ ID genotype. In conclusion, these results indicate that Korean power-oriented athletes with a lower frequency of the DD genotype had a lower probability of success in power-oriented sports.

  4. Ergosterol concentration and variability in genotype-by-pathogen interaction for grain mold resistance in sorghum.

    Science.gov (United States)

    Mpofu, Leo T; McLaren, Neal W

    2014-08-01

    A lack of understanding of host-by-pathogen relations can hinder the success of breeding for resistance to a major disease. Fungal strain pathogenicity has to be understood from the virulence it can cause on susceptible genotypes and host resistance indicates which genotypes have resistance genes. Where the two worlds meet lies the place where researchers match the prevalent pathogen in the area of production with resistant varieties. This paper uses ergosterol concentration analysis as a measure of fungal biomass accumulation to assess levels of resistance in host genotypes. 11 sorghum genotypes were inoculated with 5 strains of fungi that are known to be associated with grain mold disease of sorghum. The resulting interaction was analyzed using GGE Biplot analysis and Cluster analysis which showed that none of the genotypes were resistant to Phoma sorghina and Curvularia lunata. Three genotypes were resistant to Fusarium thapsinum. One fungal strain (Alternaria alternata) does not contribute any significant damage in the grain mold disease. Fusarium graminearum causes very little grain mold disease. There was no correlation between the fungal strains. Visual scoring did not correlate with ergosterol accumulation. Resistance to grain mold in sorghum is shown to be due to vertical or specific resistance genes. Sorghum breeders should, therefore, identify predominant fungal strains in their localities and then locate and tag these resistance genes in their germplasm and pyramid them in commercial varieties.

  5. Phenotype/genotype correlations in Gaucher disease type 1: Clinical and therapeutic implications

    Energy Technology Data Exchange (ETDEWEB)

    Sibille, A.; Eng, C.M.; Kim, S.J.; Pastores, G. (Mount Sinai School of Medicine, New York, NY (United States)); Grabowski, G.A. (Mount Sinai School of Medicine, New York, NY (United States) Univ. of Cincinnati, OH (United States))

    1993-06-01

    Gaucher disease is the most frequent lysosomal storage disease and the most prevalent genetic disease among Ashkenazi Jews. Gaucher disease type 1 is characterized by marked variability of the phenotype and by the absence of neuronopathic involvement. To test the hypothesis that this phenotypic variability was due to genetic compounds of several different mutant alleles, 161 symptomatic patients with Gaucher disease type 1 (> 90% Ashkenazi Jewish) were analyzed for clinical involvement, and their genotypes were determined. Qualitative and quantitative measures of disease involvement included age at onset of the disease manifestations, hepatic and splenic volumes, age at splenectomy, and severity of bony disease. High statistically significant differences (P < .005) were found in each clinical parameter in patients with the N370S/N370S genotype compared with those patients with the N370S/84GG, N370S/L444P, and N370/ genotypes. The symptomatic N370S homozygotes had onset of their disease two to three decades later than patients with the other genotypes. In addition, patients with the latter genotypes have much more severely involved livers, spleens, and bones and had a higher incidence of splenectomy at an earlier age. These predictive genotype analyses provide the basis for genetic care delivery and therapeutic recommendations in patients affected with Gaucher disease type 1. 38 refs., 1 fig., 4 tabs.

  6. Variability of some traits of flax seed in respect to genotype and climatic conditions

    Directory of Open Access Journals (Sweden)

    Maletić Radojka

    2006-01-01

    Full Text Available Beside its multiple use in oil producing and feed industry, flax seed is used also in pharmaceutical industry as additional medicinal component, whether as mono component or in tea mixtures. Results of a two-year cultivation of several flax genotypes are analyzed. The highest yield of seed in both study years was achieved in genotype "Z" and the lowest in standard cultivar "Mira". In regard to germination energy and total germination, the best value was determined for genotype "B" and the lowest for standard cultivar "Mira". The greatest swelling of flax seeds was established for genotype "B", and the least in the case of genotype "Z". Climatic conditions in the year of cultivation had effects on yield and quality of flax seed. During 2001. the year with high rainfall, higher yields were produced in all tested genotypes, and better germination energy, total germination and mass of 100 seeds established. In seed obtained in 2002, when average temperatures were higher, number of swollen seeds was higher. .

  7. A new genotype of Cryptosporidium from giant panda (Ailuropoda melanoleuca) in China.

    Science.gov (United States)

    Liu, Xuehan; He, Tingmei; Zhong, Zhijun; Zhang, Hemin; Wang, Rongjun; Dong, Haiju; Wang, Chengdong; Li, Desheng; Deng, Jiabo; Peng, Guangneng; Zhang, Longxian

    2013-10-01

    Fifty-seven fecal samples were collected from giant pandas (Ailuropoda melanoleuca) in the China Conservation and Research Centre for the Giant Panda (CCRCGP) in Sichuan and examined for Cryptosporidium oocysts by Sheather's sugar flotation technique. An 18-year-old male giant panda was Cryptosporidium positive, with oocysts of an average size of 4.60×3.99 μm (n=50). The isolate was genetically analyzed using the partial 18S rRNA, 70 kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein (COWP) and actin genes. Multi-locus genetic characterization indicated that the present isolate was different from known Cryptosporidium species and genotypes. The closest relative was the Cryptosporidium bear genotype, with 11, 10, and 6 nucleotide differences in the 18S rRNA, HSP70, and actin genes, respectively. Significant differences were also observed in the COWP gene compared to Cryptosporidium mongoose genotype. The homology to the bear genotype at the 18S rRNA locus was 98.6%, which is comparable to that between Cryptosporidium parvum and Cryptosporidium hominis (99.2%), or between Cryptosporidium muris and Cryptosporidium andersoni (99.4%). Therefore, the Cryptosporidium in giant pandas in this study is considered as a new genotype: the Cryptosporidium giant panda genotype.

  8. Effect of genotype and genotype by environment interaction on total cyanide content, fresh root, and starch yield in farmer-preferred cassava landraces in Tanzania.

    Science.gov (United States)

    Mtunguja, Mariam K; Laswai, Henry S; Kanju, Edward; Ndunguru, Joseph; Muzanila, Yasinta C

    2016-11-01

    High starch yield is the most important trait for commercialized cassava starch production. Furthermore, cyanide present in cassava roots poses a health challenge in the use of cassava for food. Cassava genotypes have varying maturity periods that are also environmental dependent. This study aimed at identifying suitable cultivars and optimum time of harvest to maximize starch production across three environments. The study found significant difference between genotypes, locations, harvest period, and all the interactions (P ≤ 0.001) for all traits analyzed. Kiroba recorded high starch yields of 17.4, 12.7, and 8.2 t ha(-1) at Chambezi, Amani, and Magadu, respectively. Kilusungu recorded highest cyanide content of 300-400 ppm across all locations but Kiroba recorded highest values of 800 ppm, 15 months after planting at Chambezi. Genotype by environment (GGE) biplot analysis revealed that Kiroba was a superior cultivar in terms of starch yield. Kilusungu recorded highest cyanide content and average starch yield, therefore suitable for use in starch production. The study confirmed effect of genotype and genotype by environment interaction, Kiroba cultivar was superior in terms of starch yield and maximum starch yield was obtained at 9 months after planting. Nyamkagile and Kibandameno had the lowest cyanide content across all environments.

  9. Evolutionary analysis of rubella viruses in mainland China during 2010-2012: endemic circulation of genotype 1E and introductions of genotype 2B.

    Science.gov (United States)

    Zhu, Zhen; Rivailler, Pierre; Abernathy, Emily; Cui, Aili; Zhang, Yan; Mao, Naiyin; Xu, Songtao; Zhou, Shujie; Lei, Yue; Wang, Yan; Zheng, Huanying; He, Jilan; Chen, Ying; Li, Chongshan; Bo, Fang; Zhao, Chunfang; Chen, Meng; Lu, Peishan; Li, Fangcai; Gu, Suyi; Gao, Hui; Guo, Yu; Chen, Hui; Feng, Daxing; Wang, Shuang; Tang, Xiaomin; Lei, Yake; Feng, Yan; Deng, Lili; Gong, Tian; Fan, Lixia; Xu, Wenbo; Icenogle, Joseph

    2015-01-23

    Rubella remains a significant burden in mainland China. In this report, 667 viruses collected in 24 of 31 provinces of mainland China during 2010-2012 were sequenced and analyzed, significantly extending previous reports on limited numbers of viruses collected before 2010. Only viruses of genotypes 1E and 2B were found. Genotype 1E viruses were found in all 24 provinces. Genotype 1E viruses were likely introduced into mainland China around 1997 and endemic transmission of primarily one lineage became established. Viruses reported here from 2010-2012 are largely in a single cluster within this lineage. Genotype 2B viruses were rarely detected in China prior to 2010. This report documents a previously undetected 2B lineage, which likely became endemic in eastern provinces of China between 2010 and 2012. Bayesian analyses were performed to estimate the evolutionary rates and dates of appearance of the genotype 1E and 2B viral linages in China. A skyline plot of viral population diversity did not provide evidence of reduction of diversity as a result of vaccination, but should be useful as a baseline for such reductions as vaccination programs for rubella become widespread in mainland China.

  10. A European Database of Fusarium graminearum and F-culmorum Trichothecene Genotypes

    DEFF Research Database (Denmark)

    Pasquali, Matias; Beyer, Marco; Logrieco, Antonio;

    2016-01-01

    Fusarium species, particularly Fusarium graminearum and F culmorum, are the main cause of trichothecene type B contamination in cereals. Data on the distribution of Fusarium trichothecene genotypes in cereals in Europe are scattered in time and space. Furthermore, a common core set of related...... and spread at the European level. Here we describe the results of a collaborative integrated work which aims (1) to characterize the trichothecene genotypes of strains from three Fusarium species, collected over the period 2000-2013 and (2) to enhance the standardization of epidemiological data collection...

  11. Introduction: why analyze single cells?

    Science.gov (United States)

    Di Carlo, Dino; Tse, Henry Tat Kwong; Gossett, Daniel R

    2012-01-01

    Powerful methods in molecular biology are abundant; however, in many fields including hematology, stem cell biology, tissue engineering, and cancer biology, data from tools and assays that analyze the average signals from many cells may not yield the desired result because the cells of interest may be in the minority-their behavior masked by the majority-or because the dynamics of the populations of interest are offset in time. Accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. In this chapter, we discuss the rationale for performing analyses on individual cells in more depth, cover the fields of study in which single-cell behavior is yielding new insights into biological and clinical questions, and speculate on how single-cell analysis will be critical in the future.

  12. Methods for Analyzing Social Media

    DEFF Research Database (Denmark)

    Jensen, Jakob Linaa; [Ukendt], editors

    2013-01-01

    Social media is becoming increasingly attractive for users. It is a fast way to communicate ideas and a key source of information. It is therefore one of the most influential mediums of communication of our time and an important area for audience research. The growth of social media invites many...... new questions such as: How can we analyze social media? Can we use traditional audience research methods and apply them to online content? Which new research strategies have been developed? Which ethical research issues and controversies do we have to pay attention to? This book focuses on research...... strategies and methods for analyzing social media and will be of interest to researchers and practitioners using social media, as well as those wanting to keep up to date with the subject....

  13. GENETIC DIVERGENCE AMONG Passiflora cristalina Vanderpl & Zappi. GENOTYPES BASED ON FLOWER AND FRUIT CHARACTERISTICS

    Directory of Open Access Journals (Sweden)

    GREICIELE FARIAS DA SILVEIRA

    Full Text Available ABSTRACT This study aimed to evaluate the genetic divergence among Passiflora cristalina genotypes and quantify the relative contribution of 30 flower and fruit characteristics, seeking to support the preservation and characterization of genetic resources of the species for preservation and use in future breeding programs. We evaluated 150 fruit and 150 flowers collected in 15 genotypes with naturally occurring in the municipality of Alta Floresta, MT. The characterization of genotypes was performed through 30 morphological characteristics of flowers and fruits, 21 of these for flower and 9 for fruit. Data were evaluated using the principal components and cluster methods obtained by UPGMA method from the similarity matrix (Euclidian mean distance, using the Genes software. By principal component analysis, it has been found that the first three components have absorbed 52.11% of the accumulated variation. The characteristics that most contributed to the discrimination of genotypes were fresh fruit weight, stigma length, length of corona filaments, fruit width, petal width and pulp weight, which are more responsive for the selection of P.cristalina genotypes. Smaller contributions to diversity were obtained from anther width, bract width and fruit length. The smallest contributions for diversity were obtained from the following characteristics: anther width, bract width and fruit length. Through UPGMA clustering method, it was found that there is a large genetic divergence among genotypes analyzed because all genotypes were grouped with over 50% of dissimilarity. This study identified genotypes 4, 5 and 9 as the most divergent and therefore the most suitable for breeding in future breeding programs and genetic conservation of the species.

  14. SNP genotypes of olfactory receptor genes associated with olfactory ability in German Shepherd dogs.

    Science.gov (United States)

    Yang, M; Geng, G-J; Zhang, W; Cui, L; Zhang, H-X; Zheng, J-L

    2016-04-01

    To find out the relationship between SNP genotypes of canine olfactory receptor genes and olfactory ability, 28 males and 20 females from German Shepherd dogs in police service were scored by odor detection tests and analyzed using the Beckman GenomeLab SNPstream. The representative 22 SNP loci from the exonic regions of 12 olfactory receptor genes were investigated, and three kinds of odor (human, ice drug and trinitrotoluene) were detected. The results showed that the SNP genotypes at the OR10H1-like:c.632C>T, OR10H1-like:c.770A>T, OR2K2-like:c.518G>A, OR4C11-like:c.511T>G and OR4C11-like:c.692G>A loci had a statistically significant effect on the scenting abilities (P dogs (P T, OR10H1-like:c.770A>T, OR4C11-like:c.511T>G and OR4C11-like:c.692G>A (P dogs with genotype CC at the OR10H1-like:c.632C>T, genotype AA at the OR10H1-like:c.770A>T, genotype TT at the OR4C11-like:c.511T>G and genotype GG at the OR4C11-like:c.692G>A loci did better at detecting the ice drug. We concluded that there was linkage between certain SNP genotypes and the olfactory ability of dogs and that SNP genotypes might be useful in determining dogs' scenting potential.

  15. Analyzing viewpoint diversity in twitter

    OpenAIRE

    2013-01-01

    Information diversity has a long tradition in human history. Recently there have been claims that diversity is diminishing in information available in social networks. On the other hand, some studies suggest that diversity is actually quite high in social networks such as Twitter. However these studies only focus on the concept of source diversity and they only focus on American users. In this paper we analyze different dimensions of diversity. We also provide an experimental design in which ...

  16. Analyzing ion distributions around DNA.

    Science.gov (United States)

    Lavery, Richard; Maddocks, John H; Pasi, Marco; Zakrzewska, Krystyna

    2014-07-01

    We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.

  17. Remote Laser Diffraction PSD Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2000-06-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified "off-the-shelf" classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a "hot cell" (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable - making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives.

  18. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

    Science.gov (United States)

    Cheung, Mike W.-L.; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists—and probably the most crucial one—is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study. PMID:27242639

  19. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach.

    Science.gov (United States)

    Cheung, Mike W-L; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists-and probably the most crucial one-is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  20. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

    Directory of Open Access Journals (Sweden)

    Mike W.-L. Cheung

    2016-05-01

    Full Text Available Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists – and probably the most crucial one – is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  1. Exhaustive Analysis of a Genotype Space Comprising 10(15 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation.

    Directory of Open Access Journals (Sweden)

    Sayed-Rzgar Hosseini

    2015-08-01

    Full Text Available All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, sustaining life by extracting energy from extracellular nutrients. Here we study metabolism's potential for innovation by analyzing an exhaustive genotype-phenotype map for a space of 10(15 metabolisms that encodes all possible subsets of 51 reactions in central carbon metabolism. Using flux balance analysis, we predict the viability of these metabolisms on 10 different carbon sources which give rise to 1024 potential metabolic phenotypes. Although viable metabolisms with any one phenotype comprise a tiny fraction of genotype space, their absolute numbers exceed 10(9 for some phenotypes. Metabolisms with any one phenotype typically form a single network of genotypes that extends far or all the way through metabolic genotype space, where any two genotypes can be reached from each other through a series of single reaction changes. The minimal distance of genotype networks associated with different phenotypes is small, such that one can reach metabolisms with novel phenotypes--viable on new carbon sources--through one or few genotypic changes. Exceptions to these principles exist for those metabolisms whose complexity (number of reactions is close to the minimum needed for viability. Increasing metabolic complexity enhances the potential for both evolutionary conservation and evolutionary innovation.

  2. The genotypic structure of a multi-host bumblebee parasite suggests a role for ecological niche overlap.

    Directory of Open Access Journals (Sweden)

    Rahel M Salathé

    Full Text Available The genotypic structure of parasite populations is an important determinant of ecological and evolutionary dynamics of host-parasite interactions with consequences for pest management and disease control. Genotypic structure is especially interesting where multiple hosts co-exist and share parasites. We here analyze the natural genotypic distribution of Crithidia bombi, a trypanosomatid parasite of bumblebees (Bombus spp., in two ecologically different habitats over a time period of three years. Using an algorithm to reconstruct genotypes in cases of multiple infections, and combining these with directly identified genotypes from single infections, we find a striking diversity of infection for both data sets, with almost all multi-locus genotypes being unique, and are inferring that around half of the total infections are resulting from multiple strains. Our analyses further suggest a mixture of clonality and sexuality in natural populations of this parasite species. Finally, we ask whether parasite genotypes are associated with host species (the phylogenetic hypothesis or whether ecological factors (niche overlap in flower choice shape the distribution of parasite genotypes (the ecological hypothesis. Redundancy analysis demonstrates that in the region with relatively high parasite prevalence, both host species identity and niche overlap are equally important factors shaping the distribution of parasite strains, whereas in the region with lower parasite prevalence, niche overlap more strongly contributes to the distribution observed. Overall, our study underlines the importance of ecological factors in shaping the natural dynamics of host-parasite systems.

  3. The contributions of the tissue inhibitor of metalloproteinase-1 genotypes to triple negative breast cancer risk.

    Science.gov (United States)

    Chang, Wen-Shin; Liu, Liang-Chih; Hsiao, Chieh-Lun; Su, Chen-Hsien; Wang, Hwei-Chung; Ji, Hong-Xue; Tsai, Chia-Wen; Maa, Ming-Chei; Bau, Da-Tian

    2016-03-01

    The tissue inhibitors of metalloproteinases (TIMPs) are a family of multifunctional proteins which have been shown to be upregulated in various types of cancers. However, the contribution of TIMPs in breast cancer is not fully understood, not to mention triple negative breast cancer (TNBC). This study's aim was to evaluate the contribution of TIMP-1 rs4898, rs6609533, and rs2070584 genotypes to the risk of breast cancer, especially the subtype of TNBC. The contributions of these TIMP-1 genotypes to cancer risk were examined among 1232 breast cancer patients and 1232 healthy controls, and several clinicopathologic factors were also analyzed. The results showed that the percentages of CC, CT, and TT of TIMP-1 rs4898 were differentially distributed at 28.5%, 33.1% and 38.4% in the breast cancer patient group and 34.5%, 41.0% and 24.5% in the control group, respectively (P for trend = 7.99*10(-13)). It was also found that the CC genotype carriers were of increased risk for breast cancer (odds ratio = 1.90, 95% confidence interval = 1.55-2.33, P = 0.0001) than the TT genotype carriers. In addition, we analyzed the allelic frequency distributions of all three TIMP-1s, and the results showed that the C allele of TIMP-1 rs4898 contributes to an increase in breast cancer susceptibility (P = 2.41*10(-12)). On the other hand, there was no difference found in the distribution of genotypic or allelic frequencies among the patients and the controls for TIMP-1 rs6609533 and rs2070584. Thus, it is our conclusion that the CC genotype of TIMP-1 rs4898 compared to the TT wild-type genotype may increase the risk for breast cancer, especially TNBC in Taiwan, and may serve as an early detective and predictive marker.

  4. Validation of cross-genotype neutralization by hepatitis B virus-specific monoclonal antibodies by in vitro and in vivo infection.

    Science.gov (United States)

    Hamada-Tsutsumi, Susumu; Iio, Etsuko; Watanabe, Tsunamasa; Murakami, Shuko; Isogawa, Masanori; Iijima, Sayuki; Inoue, Takako; Matsunami, Kayoko; Tajiri, Kazuto; Ozawa, Tatsuhiko; Kishi, Hiroyuki; Muraguchi, Atsushi; Joh, Takashi; Tanaka, Yasuhito

    2015-01-01

    Vaccines based on hepatitis B virus (HBV) genotype A have been used worldwide for immunoprophylaxis and are thought to prevent infections by non-A HBV strains effectively, whereas, vaccines generated from genotype C have been used in several Asian countries, including Japan and Korea, where HBV genotype C is prevalent. However, acute hepatitis B caused by HBV genotype A infection has been increasing in Japan and little is known about the efficacy of immunization with genotype C-based vaccines against non-C infection. We have isolated human monoclonal antibodies (mAbs) from individuals who were immunized with the genotype C-based vaccine. In this study, the efficacies of these two mAbs, HB0116 and HB0478, were analyzed using in vivo and in vitro models of HBV infection. Intravenous inoculation of HBV genotype C into chimeric mice with human hepatocytes resulted in the establishment of HBV infection after five weeks, whereas preincubation of the inocula with HB0116 or HB0478 protected chimeric mice from genotype C infection completely. Interestingly, both HB0116 and HB0478 were found to block completely genotype A infection. Moreover, infection by a genotype C strain with an immune escape substitution of amino acid 145 in the hepatitis B surface protein was also completely inhibited by incubation with HB0478. Finally, in vitro analysis of dose dependency revealed that the amounts of HB0478 required for complete protection against genotype C and genotype A infection were 5.5 mIU and 55 mIU, respectively. These results suggested that genotype C-based vaccines have ability to induce cross-genotype immunity against HBV infection.

  5. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  6. Cellular apoptosis induced by replication of hepatitis B virus: possible link between viral genotype and clinical outcome

    Directory of Open Access Journals (Sweden)

    Zhang Jianhua

    2007-10-01

    Full Text Available Abstract HBV remains one of the major pathogens of liver diseases but the outcomes as inflammation, cirrhosis and cancer of the liver are greatly related to different viral genotypes. The aim of this study was to assess the pro-apoptotic effect of HBSP from three HBV genotypes on liver derived cells. HepG2 cells were applied in our system and transfected by HBV genotype A, B, and C. Cells were observed under phase contrast microscope, stained by apoptosis marker and analyzed by flow cytometre. HBSP expression was detected by western blot assay. BH3 sequences were aligned and analyzed by Vector NTI. HBV genotypes A, B, and C transfected cells displayed evidence of cell death which was further proved as apoptosis. Natural expression of a pro-apoptotic protein HBSP was detected during genomes transfection. The different apoptotic effects were correlated to the HBSP expression from each genome. Alignment and analysis of the BH3 domains from the three genomes revealed slight variance which might also contribute to the result. Our results suggested that variant HBSP expression and BH3 sequence of HBV genotypes may be involved in differential apoptotic effect in transfected cells. Detailed analysis of the role of HBV genotypes in cellular apoptotic process should provide molecular information on the reported clinical outcome of infection by different HBV genotypes.

  7. The Aqueduct Global Flood Analyzer

    Science.gov (United States)

    Iceland, Charles

    2015-04-01

    As population growth and economic growth take place, and as climate change accelerates, many regions across the globe are finding themselves increasingly vulnerable to flooding. A recent OECD study of the exposure of the world's large port cities to coastal flooding found that 40 million people were exposed to a 1 in 100 year coastal flood event in 2005, and the total value of exposed assets was about US 3,000 billion, or 5% of global GDP. By the 2070s, those numbers were estimated to increase to 150 million people and US 35,000 billion, or roughly 9% of projected global GDP. Impoverished people in developing countries are particularly at risk because they often live in flood-prone areas and lack the resources to respond. WRI and its Dutch partners - Deltares, IVM-VU University Amsterdam, Utrecht University, and PBL Netherlands Environmental Assessment Agency - are in the initial stages of developing a robust set of river flood and coastal storm surge risk measures that show the extent of flooding under a variety of scenarios (both current and future), together with the projected human and economic impacts of these flood scenarios. These flood risk data and information will be accessible via an online, easy-to-use Aqueduct Global Flood Analyzer. We will also investigate the viability, benefits, and costs of a wide array of flood risk reduction measures that could be implemented in a variety of geographic and socio-economic settings. Together, the activities we propose have the potential for saving hundreds of thousands of lives and strengthening the resiliency and security of many millions more, especially those who are most vulnerable. Mr. Iceland will present Version 1.0 of the Aqueduct Global Flood Analyzer and provide a preview of additional elements of the Analyzer to be released in the coming years.

  8. Another look at Bayesian analysis of AMMI models for genotype-environment data

    NARCIS (Netherlands)

    Josse, J.; Eeuwijk, van F.A.; Piepho, H.P.; Denis, J.B.

    2014-01-01

    Linear–bilinear models are frequently used to analyze two-way data such as genotype-by-environment data. A well-known example of this class of models is the additive main effects and multiplicative interaction effects model (AMMI). We propose a new Bayesian treatment of such models offering a proper

  9. Combinations of genetic data in a study of neuroblastoma risk genotypes

    DEFF Research Database (Denmark)

    Capasso, Mario; Calabrese, Francesco Maria; Iolascon, Achille;

    2014-01-01

    Analysis of combinations of genetic changes that occur exclusively in patients may be a supplementary strategy to the single-locus strategy used in many genetic studies. The genotypes of 16 SNPs within susceptibility loci for neuroblastoma (NB) were analyzed in a previous study. In the present st...

  10. Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays

    Institute of Scientific and Technical Information of China (English)

    Edward; M.; Smith; Jack; Littrell; Michael; Olivier

    2007-01-01

    High-throughput SNP genotyping platforms use automated genotype calling algo- rithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been opti- mized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be ad- visable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

  11. Method for analyzing microbial communities

    Science.gov (United States)

    Zhou, Jizhong [Oak Ridge, TN; Wu, Liyou [Oak Ridge, TN

    2010-07-20

    The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

  12. Fuel analyzer; Analisador de combustiveis

    Energy Technology Data Exchange (ETDEWEB)

    Cozzolino, Roberval [RS Motors, Indaiatuba, SP (Brazil)

    2008-07-01

    The current technology 'COMBUSTIMETRO' aims to examine the fuel through performance of the engine, as the role of the fuel is to produce energy for the combustion engine in the form of which is directly proportional to the quality and type of fuel. The 'COMBUSTIMETRO' has an engine that always keeps the same entry of air, fuel and fixed point of ignition. His operation is monitored by sensors (Sonda Lambda, RPM and Gases Analyzer) connected to a processor that performs calculations and records the information, generate reports and graphs. (author)

  13. Orodental phenotype and genotype findings in all subtypes of hypophosphatasia

    Directory of Open Access Journals (Sweden)

    Clauss François

    2009-02-01

    Full Text Available Abstract Background Hypophosphatasia (HP is a rare inherited disorder characterized by a wide spectrum of defects in mineralized tissues and caused by deficiency in the tissue non-specific alkaline phosphatase gene (ALPL. The symptoms are highly variable in their clinical expression, and relate to numerous mutations in this gene. The first clinical sign of the disease is often a premature loss of deciduous teeth, mostly in the moderate forms. Aim The purpose of this study was to document the oral features of HP patients and to relate theses features to the six recognized forms of HP in 5 patients with known genotype and to investigate the genotype-phenotype correlations. Methods Clinical and radiographic examinations were carried out. We collected medical and dental history in the kindred and biochemical data. Finally, mutations in the ALPL gene were tested by DNA sequencing in SESEP laboratory. Results We have for the first time related the known dental anomalies which occur as integral features of HP to the recognized clinical forms of HP. We also pointed out striking dental abnormalities which were never described in association with this rare disease. Accurate genotype-phenotype severity correlations were observed. Conclusion This work allowed us to compare orodental manifestations in all the clinical forms of HP within the patient's sample. According to the severity of the disorder, some dental defects were infrequent, while other were always present. The long term prognosis of the permanent teeth varies from a patient to another. As premature loss of primary teeth is often the first, and sometimes the only visible symptom of the milder forms, the paediatric dentist plays a critical role in the detection and diagnosis of the disease.

  14. Spontaneous viral clearance, viral load, and genotype distribution of hepatitis C virus (HCV) in HIV-infected patients with anti-HCV antibodies in Europe

    DEFF Research Database (Denmark)

    Soriano, Vincent; Mocroft, Amanda; Rockstroh, Juergen

    2008-01-01

    for hepatitis B surface antigen (HBsAg) were more likely to have spontaneously cleared HCV than were those negative for HBsAg (43% vs. 21%; aOR, 2.91 [95% CI, 1.94-4.38]). Of patients with HCV viremia, 786 (53%) carried HCV genotype 1, and 53 (4%), 440 (29%), and 217 (15%) carried HCV genotype 2, 3, and 4...... in IDUs and, conversely, was less common in HBsAg-positive patients. Of the patients with HCV viremia analyzed, 53% were found to carry HCV genotype 1, and this genotype was associated with greater serum HCV RNA levels....

  15. Thermal and evolved gas analyzer

    Science.gov (United States)

    Williams, M. S.; Boynton, W. V.; James, R. L.; Verts, W. T.; Bailey, S. H.; Hamara, D. K.

    1998-01-01

    The Thermal and Evolved Gas Analyzer (TEGA) instrument will perform calorimetry and evolved gas analysis on soil samples collected from the Martian surface. TEGA is one of three instruments, along with a robotic arm, that form the Mars Volatile and Climate Survey (MVACS) payload. The other instruments are a stereo surface imager, built by Peter Smith of the University of Arizona and a meteorological station, built by JPL. The MVACS lander will investigate a Martian landing site at approximately 70 deg south latitude. Launch will take place from Kennedy Space Center in January, 1999. The TEGA project started in February, 1996. In the intervening 24 months, a flight instrument concept has been designed, prototyped, built as an engineering model and flight model, and tested. The instrument performs laboratory-quality differential-scanning calorimetry (DSC) over the temperature range of Mars ambient to 1400K. Low-temperature volatiles (water and carbon dioxide ices) and the carbonates will be analyzed in this temperature range. Carbonates melt and evolve carbon dioxide at temperatures above 600 C. Evolved oxygen (down to a concentration of 1 ppm) is detected, and C02 and water vapor and the isotopic variations of C02 and water vapor are detected and their concentrations measured. The isotopic composition provides important tests of the theory of solar system formation.

  16. VOSA: A VO SED Analyzer

    Science.gov (United States)

    Rodrigo, C.; Bayo, A.; Solano, E.

    2017-03-01

    VOSA (VO Sed Analyzer, http://svo2.cab.inta-csic.es/theory/vosa) is a public web-tool developed by the Spanish Virtual Observatory (http://svo.cab.inta-csic.es/) and designed to help users to (1) build Spectral Energy Distributions (SEDs) combining private photometric measurements with data available in VO services, (2) obtain relevant properties of these objects (distance, extinction, etc) from VO catalogs, (3) analyze them comparing observed photometry with synthetic photometry from different collections of theoretical models or observational templates, using different techniques (chi-square minimization, Bayesian analysis) to estimate physical parameters of the observed objects (teff, logg, metallicity, stellar radius/distance ratio, infrared excess, etc), and use these results to (4) estimate masses and ages via interpolation of collections of isochrones and evolutionary tracks from the VO. In particular, VOSA offers the advantage of deriving physical parameters using all the available photometric information instead of a restricted subset of colors. The results can be downloaded in different formats or sent to other VO tools using SAMP. We have upgraded VOSA to provide access to Gaia photometry and give a homogeneous estimation of the physical parameters of thousands of objects at a time. This upgrade has required the implementation of a new computation paradigm, including a distributed environment, the capability of submitting and processing jobs in an asynchronous way, the use of parallelized computing to speed up processes (˜ ten times faster) and a new design of the web interface.

  17. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    OpenAIRE

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicoch...

  18. Genotypic distribution of HHV-8 in AIDS individuals without and with Kaposi sarcoma: Is genotype B associated with better prognosis of AIDS-KS?

    Science.gov (United States)

    Tozetto-Mendoza, Tania Regina; Ibrahim, Karim Yaqub; Tateno, Adriana Fumie; Oliveira, Cristiane Mendes de; Sumita, Laura Massami; Sanchez, Maria Carmem Arroyo; Luna, Expedito José; Pierrotti, Ligia Camara; Drexler, Jan Felix; Braz-Silva, Paulo Henrique; Pannuti, Claudio Sérgio; Romano, Camila Malta

    2016-11-01

    AIDS-associated Kaposi's sarcoma (AIDS-KS) caused by human herpes virus 8 (HHV-8) is the most severe and resistant form of KS tumor. Our aim was to verify whether there is an association between HHV-8 variability and development of AIDS-KS in Brazil by comparing the HHV-8 variability between individuals without and with KS. Saliva samples and blood, when available, were analyzed by polymerase chain reaction (PCR) techniques for detection of the fragments of ORF K1 of HHV-8, which were then genotyped and analyzed regarding the genetic variability. Our study described 106 positive cases for HHV-8 in the saliva from 751 AIDS patients without previous KS. In addition, we performed a phylogenetic analysis of HHV-8 in 34 of the 106 AIDS patients without KS and in 33 of the 37 patients with active KS. The distribution of HHV-8 genotypes A, B, C, and F in AIDS individuals was indistinguishable by comparing non-KS and KS groups, as well as regarding ethnicity. Considering the KS group, genotype B was associated with better prognosis of KS tumor. Interestingly, we found a particular profile of diversity within clade C and 2 recombinant patterns of HHV-8 in the saliva of AIDS individuals without KS. We emphasize the need to achieve standard genotyping protocol for ORF K1 amplification, thus allowing for substantial detection of HHV-8 variants. Our findings can shed light on the role of HHV-8 variability in the pathogenesis of AIDS-KS.

  19. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A

    2015-01-01

    Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...... samples for genotyping COMT val158met (rs4680). All subjects underwent clinical evaluations and neurocognitive assessment of decision-making, working memory, and impulsivity. The Val/Val COMT genotype was associated with the largest percentage of subjects with gambling disorder (31.8%), a rate...

  20. ABO Genotyping of Complete Hydatidiform Moles

    Directory of Open Access Journals (Sweden)

    R. A. Fisher

    1993-01-01

    Full Text Available It has been suggested that the ABO blood group of a patient and her partner influence the clinical outcome for patients having a pregnancy with a complete hydatidiform mole (CHM. Since CHM lack red blood Cells, it has not previously been possible to type CHM serologically and investigate the relationship between the blood group of the CHM and that of the patient. In the present study we have demonstrated the feasibility of using molecular genotyping to determine the ABO genotype of CHM, the ABO genotype being consistent with the androgenetic origin of CHM in all cases. In the series of 48 cases of CHM, the requirement for chemotherapy was not significantly different in those patients with a CHM of like blood group compared with those with a CHM of unlike blood group.

  1. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  2. An Application of Molecular Genotyping in Mice

    Directory of Open Access Journals (Sweden)

    Underkoffler Lara A.

    2003-01-01

    Full Text Available Microsatellite markers are simple sequence repeats within the mammalian genome that can be used for identifying disease loci, mapping genes of interest as well as studying segregation patterns related to meiotic nondisjunction. Different strains of mice have variable CA repeat lengths and PCR based methods can be used to identify them, thus allowing for specific genotypes to be assigned. Molecular genotyping offers such identification at any developmental stage, which allows for a broad range of anomalies to be studied. We studied chromosomal segregation in relation to nondisjunction in early-gestation mouse embryos using molecular genotyping. Information on the parental origin as well as the number of chromosomes a given progeny carried was obtained in our analysis.

  3. Genotypic diversity and virulence factors of Streptococcus mutans in caries-free and caries-active individuals

    OpenAIRE

    Miula Portelinha Braga; Augusta Piovesan; Natália Valarini; Sandra Mara Maciel; Flaviana Bombarda de Andrade; Regina Célia Poli-Frederico

    2013-01-01

    The objective of this study was to analyze the genotypic diversity, frequency of serotypes and the detection of mutacins from Streptococcus mutans isolates in caries-free and caries-active individuals.A total of 260 S. mutans isolated from 28 individuals with and without dental caries were subjected to AP-PCR and PCR screening of glucosyltransferase B, mutacin and serotype genes, which showed the presence of. 70 different genotypes. There was no statistically significant association between t...

  4. Human papilloma virus genotypes in women from Nayarit, Mexico, with squamous intraepithelial lesions and cervical cancer

    Science.gov (United States)

    Ortega-Cervantes, Laura; Aguilar-Lemarroy, Adriana; Rojas-García, Aurora Elizabeth; Barrón-Vivanco, Briscia Socorro; Vallejo-Ruiz, Verónica; León, David Cantú-De; Hernández, Yael Yvette Bernal; Jáuregui-Martínez, Armando; Medina-Díaz, Irma Martha

    2016-01-01

    Objective In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). Methodology Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test. Data analyses were performed using Stata ver. 8.0 statistical software. Results Of the samples analyzed, 91.2%, HPV DNA was detected. Of these positive samples, 82% were High-risk (HR) viral types. The most prevalent HPV genotypes identified were 16, 58, 31, 18, and 70. Forty two percent of participants had a single infection, while 23 and 26% of participants were infected with two or more HPV genotypes, respectively. HPV 16 was the most prevalent genotype identified and was frequently present as a co-infection with HPV types 18, 51, 52, 59, 66, or 70. Conclusion Women <20 years of age were most often infected with HPV, and the HPV Quadrivalent vaccine (types 16, 18, 6, and 11), currently available in Mexico, no confers protection against a subset of the HPV genotypes identified in the present study (58, 31, 70, and 35). Thus, it is important evaluate the geographical distribution of specific HPV genotypes in all health of center across Mexico in order to implement a successful vaccination program and to diagnose CC in its early stages. PMID:27610056

  5. Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: now and next.

    Science.gov (United States)

    Weniger, Thomas; Krawczyk, Justina; Supply, Philip; Harmsen, Dag; Niemann, Stefan

    2012-06-01

    Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible, and discriminatory typing method. Here, we review new sets of specialized web based bioinformatics tools that have become available for analyzing MLVA data especially in combination with other, complementary genotyping markers (polyphasic analysis). Currently, there are only two databases available that are not restricted to store one kind of genotyping data only, namely SITVIT/SpolDB4 and MIRU-VNTRplus. SITVIT/SpolDB4 (http://www.pasteur-guadeloupe.fr:8081/SITVITDemo) contains spoligotyping data from a large number of strains of diverse origin. However, besides options to query the data, the actual version of SITVIT/SpolDB4 offers no functionality for more complex analysis e.g. tree-based analysis. In comparison, the MIRU-VNTRplus web application (http://www.miru-vntrplus.org), represents a freely accessible service that enables users to analyze genotyping data of their strains alone or in comparison with a currently limited but well characterized reference database of strains representing the major MTBC lineages. Data (MLVA-, spoligotype-, large sequence polymorphism, and single nucleotide polymorphism) can be visualized and analyzed using just one genotyping method or a weighted combination of several markers. A variety of analysis tools are available such as creation of phylogenetic and minimum spanning trees, semi-automated phylogenetic lineage identification based on comparison with the reference database and mapping of geographic information. To facilitate scientific communication, a universal, expanding genotype nomenclature (MLVA MtbC15

  6. Role of cytochrome P450 genotype in the steps toward personalized drug therapy

    Directory of Open Access Journals (Sweden)

    Cavallari LH

    2011-11-01

    Full Text Available Larisa H Cavallari1,2, Hyunyoung Jeong1,2, Adam Bress11Department of Pharmacy Practice, 2Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USAAbstract: Genetic polymorphism for cytochrome 450 (P450 enzymes leads to interindividual variability in the plasma concentrations of many drugs. In some cases, P450 genotype results in decreased enzyme activity and an increased risk for adverse drug effects. For example, individuals with the CYP2D6 loss-of-function genotype are at increased risk for ventricular arrhythmia if treated with usual does of thioridazine. In other cases, P450 genotype may influence the dose of a drug required to achieve a desired effect. This is the case with warfarin, with lower doses often necessary in carriers of a variant CYP2C9*2 or *3 allele to avoid supratherapeutic anticoagulation. When a prodrug, such as clopidogrel or codeine, must undergo hepatic biotransformation to its active form, a loss-of-function P450 genotype leads to reduced concentrations of the active drug and decreased drug efficacy. In contrast, patients with multiple CYP2D6 gene copies are at risk for opioid-related toxicity if treated with usual doses of codeine-containing analgesics. At least 25 drugs contain information in their US Food and Drug Administration-approved labeling regarding P450 genotype. The CYP2C9, CYP2C19, and CYP2D6 genes are the P450 genes most often cited. To date, integration of P450 genetic information into clinical decision making is limited. However, some institutions are beginning to embrace routine P450 genotyping to assist in the treatment of their patients. Genotyping for P450 variants may carry less risk for discrimination compared with genotyping for disease-associated variants. As such, P450 genotyping is likely to lead the way in the clinical implementation of pharmacogenomics. This review discusses variability in the CYP2C9, CYP2C19, and CYP2D6 genes and the

  7. Coaxial charged particle energy analyzer

    Science.gov (United States)

    Kelly, Michael A. (Inventor); Bryson, III, Charles E. (Inventor); Wu, Warren (Inventor)

    2011-01-01

    A non-dispersive electrostatic energy analyzer for electrons and other charged particles having a generally coaxial structure of a sequentially arranged sections of an electrostatic lens to focus the beam through an iris and preferably including an ellipsoidally shaped input grid for collimating a wide acceptance beam from a charged-particle source, an electrostatic high-pass filter including a planar exit grid, and an electrostatic low-pass filter. The low-pass filter is configured to reflect low-energy particles back towards a charged particle detector located within the low-pass filter. Each section comprises multiple tubular or conical electrodes arranged about the central axis. The voltages on the lens are scanned to place a selected energy band of the accepted beam at a selected energy at the iris. Voltages on the high-pass and low-pass filters remain substantially fixed during the scan.

  8. Compact Microwave Fourier Spectrum Analyzer

    Science.gov (United States)

    Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry

    2009-01-01

    A compact photonic microwave Fourier spectrum analyzer [a Fourier-transform microwave spectrometer, (FTMWS)] with no moving parts has been proposed for use in remote sensing of weak, natural microwave emissions from the surfaces and atmospheres of planets to enable remote analysis and determination of chemical composition and abundances of critical molecular constituents in space. The instrument is based on a Bessel beam (light modes with non-zero angular momenta) fiber-optic elements. It features low power consumption, low mass, and high resolution, without a need for any cryogenics, beyond what is achievable by the current state-of-the-art in space instruments. The instrument can also be used in a wide-band scatterometer mode in active radar systems.

  9. The Mouse Universal Genotyping Array: From Substrains to Subspecies

    Directory of Open Access Journals (Sweden)

    Andrew P. Morgan

    2016-02-01

    Full Text Available Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus. The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.

  10. Analyzing and mining automated imaging experiments.

    Science.gov (United States)

    Berlage, Thomas

    2007-04-01

    Image mining is the application of computer-based techniques that extract and exploit information from large image sets to support human users in generating knowledge from these sources. This review focuses on biomedical applications of this technique, in particular automated imaging at the cellular level. Due to increasing automation and the availability of integrated instruments, biomedical users are becoming increasingly confronted with the problem of analyzing such data. Image database applications need to combine data management, image analysis and visual data mining. The main point of such a system is a software layer that represents objects within an image and the ability to use a large spectrum of quantitative and symbolic object features. Image analysis needs to be adapted to each particular experiment; therefore, 'end user programming' will be desired to make the technology more widely applicable.

  11. Integrated translational genomics for analysis of complex traits in sorghum

    Science.gov (United States)

    We will report on the integration of sequencing and genotype data from natural variation (by whole genome resequencing [wgs] or genotype by sequencing [gbs]), transcriptome (RNA-seq) and mutant analysis (also by wgs) with the goal of identifying genes controlling important agronomic traits and tran...

  12. The Integrated Hazard Analysis Integrator

    Science.gov (United States)

    Morris, A. Terry; Massie, Michael J.

    2009-01-01

    Hazard analysis addresses hazards that arise in the design, development, manufacturing, construction, facilities, transportation, operations and disposal activities associated with hardware, software, maintenance, operations and environments. An integrated hazard is an event or condition that is caused by or controlled by multiple systems, elements, or subsystems. Integrated hazard analysis (IHA) is especially daunting and ambitious for large, complex systems such as NASA s Constellation program which incorporates program, systems and element components that impact others (International Space Station, public, International Partners, etc.). An appropriate IHA should identify all hazards, causes, controls and verifications used to mitigate the risk of catastrophic loss of crew, vehicle and/or mission. Unfortunately, in the current age of increased technology dependence, there is the tendency to sometimes overlook the necessary and sufficient qualifications of the integrator, that is, the person/team that identifies the parts, analyzes the architectural structure, aligns the analysis with the program plan and then communicates/coordinates with large and small components, each contributing necessary hardware, software and/or information to prevent catastrophic loss. As viewed from both Challenger and Columbia accidents, lack of appropriate communication, management errors and lack of resources dedicated to safety were cited as major contributors to these fatalities. From the accident reports, it would appear that the organizational impact of managers, integrators and safety personnel contributes more significantly to mission success and mission failure than purely technological components. If this is so, then organizations who sincerely desire mission success must put as much effort in selecting managers and integrators as they do when designing the hardware, writing the software code and analyzing competitive proposals. This paper will discuss the necessary and

  13. Detection of bovine leukemia virus and identification of its genotype in Mongolian cattle.

    Science.gov (United States)

    Ochirkhuu, Nyamsuren; Konnai, Satoru; Odbileg, Raadan; Nishimori, Asami; Okagawa, Tomohiro; Murata, Shiro; Ohashi, Kazuhiko

    2016-04-01

    Epidemiological studies have indicated that bovine leukemia virus (BLV) infection is globally distributed. However, no information regarding the disease and genetic diversity of the virus in the cattle of Mongolia is currently available. In this study, the prevalence of BLV was assessed using PCR, and the genetic diversity was analyzed through DNA sequencing. Of the 517 samples tested, 20 positives were identified. Phylogenetic analysis showed that six, one, and four isolates were classified into genotype 4, 7, and 1, respectively. Most isolates were clustered with isolates from Eastern Europe and Russia. This study is the first to investigate the BLV genotype in Mongolia.

  14. GGE biplot analysis of yield stability and test location representativeness in proso millet (Panicum miliaceum L.) genotypes

    Institute of Scientific and Technical Information of China (English)

    ZHANG Pan-pan; ZHENG Dian-feng; FENG Bai-li; SONG Hui; KE Xi-wang; JIN Xi-jun; YIN Li-hua; LIU Yang; QU Yang; SU Wang; FENG Nai-jie

    2016-01-01

    The experiments were conducted for three consecutive years across 14 locations using 9 non-waxy proso milet genotypes and 16 locations using 7 waxy proso milet genotypes in China. The objectives of this study were to analyze yield stability and adaptability of proso milets and to evaluate the discrimination and representativeness of locations by analysis of vari-ance (ANOVA) and genotype and genotype by environment interaction (GGE) biplot methods. Grain yields of proso milet genotypes were signiifcantly inlfuenced by environment (E), genotype (G) and their interaction (G×E) (P<0.1%). G×E inter-action effect was six times higher than G effect in non-waxy group and seven times in waxy group. N04-339 in non-waxy and Neimi 6 (NM6) in waxy showed higher grain yields and stability compared with other genotypes. Also, Neimi 9 (NM9, a non-waxy cultivar) and 90322-2-33 (a waxy cultivar) showed higher adaptability in 7 and in 11 locations, respectively. For non-waxy, Dalat, Inner Mongolia (E2) and Wuzhai, Shanxi (E5) were the best sites among al the locations for maximizing the variance among candidate cultivars, and Yanchi, Ningxia (E10) had the best representativeness. Wuzhai, Shanxi (e9) and Yanchi, Ningxia (e14) were the best representative locations, and Baicheng, Jilin (e2) was better discriminating location than others for waxy genotypes. Based on our results, E10 and e14 have enhanced efifciency and accuracy for non-waxy genotypes and waxy genotypes selection, respectively in national regional test of proso milet varieties.

  15. Genotype Analysis of Bacillus anthracis Strains Circulating in Bangladesh.

    Science.gov (United States)

    Rume, Farzana Islam; Affuso, Alessia; Serrecchia, Luigina; Rondinone, Valeria; Manzulli, Viviana; Campese, Emanuele; Di Taranto, Pietro; Biswas, Paritosh Kumar; Ahsan, Chowdhury Rafiqul; Yasmin, Mahmuda; Fasanella, Antonio; Hugh-Jones, Martin

    2016-01-01

    In Bangladesh, anthrax, caused by the bacterium Bacillus anthracis, is considered an endemic disease affecting ruminants with sporadic zoonotic occurrences in humans. Due to the lack of knowledge about risks from an incorrect removal of infected carcasses, the disease is not properly monitored, and because of the socio-economic conditions, the situation is under-reported and under-diagnosed. For sensitive species, anthrax represents a fatal outcome with sudden death and sometimes bleeding from natural orifices. The most common source of infection for ruminants is ingestion of spores during grazing in contaminated pastures or through grass and water contaminated with anthrax spores. Domestic cattle, sheep and goats can also become infected through contaminated bone meal (used as feed) originating from anthrax-infected carcasses. The present investigation was conducted to isolate B. anthracis organisms from 169 samples (73 soil, 1 tissue, 4 bone and 91 bone meal samples) collected from 12 different districts of Bangladesh. The sampling was carried out from 2012 to 2015. Twelve samples resulted positive for B. anthracis. Biomolecular analyses were conducted starting from the Canonical Single Nucleotide Polymorphism (CanSNP) to analyze the phylogenetic origin of strains. The analysis of genotype, obtained through the Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) with the analysis of 15 Variable Number Tandem Repeats (VNTR), demonstrated four different genotypes: two of them were previously identified in the district of Sirajganj. The sub-genotyping, conducted with Single Nucleotide Repeats analysis, revealed the presence of eight subgenotypes. The data of the present study concluded that there was no observed correlation between imported cattle feed and anthrax occurrence in Bangladesh and that the remarkable genetic variations of B. anthracis were found in the soil of numerous outbreaks in this country.

  16. Distribution and molecular evolution of bacillus anthracis genotypes in Namibia.

    Directory of Open Access Journals (Sweden)

    Wolfgang Beyer

    Full Text Available The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks. In Namibia, anthrax outbreaks occur annually in the Etosha National Park (ENP and on private game and livestock farms. We genotyped 384 B. anthracis isolates collected between 1983-2010 to identify the possible epidemiological correlations of anthrax outbreaks within and outside the ENP and to analyze genetic relationships between isolates from domestic and wild animals. The isolates came from 20 animal species and from the environment and were genotyped using a 31-marker multi-locus-VNTR-analysis (MLVA and, in part, by twelve single nucleotide polymorphism (SNP markers and four single nucleotide repeat (SNR markers. A total of 37 genotypes (GT were identified by MLVA, belonging to four SNP-groups. All GTs belonged to the A-branch in the cluster- and SNP-analyses. Thirteen GTs were found only outside the ENP, 18 only within the ENP and 6 both inside and outside. Genetic distances between isolates increased with increasing time between isolations. However, genetic distance between isolates at the beginning and end of the study period was relatively small, indicating that while the majority of GTs were only found sporadically, three genetically close GTs, accounting for more than four fifths of all the ENP isolates, appeared dominant throughout the study period. Genetic distances among isolates were significantly greater for isolates from different host species, but this effect was small, suggesting that while species-specific ecological factors may affect exposure processes, transmission cycles in different host species are still highly interrelated. The MLVA data were further used to establish a model of the probable evolution of GTs within the endemic region of the ENP. SNR-analysis was helpful in correlating an isolate with its source but did not elucidate

  17. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  18. Analyzing and modeling heterogeneous behavior

    Science.gov (United States)

    Lin, Zhiting; Wu, Xiaoqing; He, Dongyue; Zhu, Qiang; Ni, Jixiang

    2016-05-01

    Recently, it was pointed out that the non-Poisson statistics with heavy tail existed in many scenarios of human behaviors. But most of these studies claimed that power-law characterized diverse aspects of human mobility patterns. In this paper, we suggest that human behavior may not be driven by identical mechanisms and can be modeled as a Semi-Markov Modulated Process. To verify our suggestion and model, we analyzed a total of 1,619,934 records of library visitations (including undergraduate and graduate students). It is found that the distribution of visitation intervals is well fitted with three sections of lines instead of the traditional power law distribution in log-log scale. The results confirm that some human behaviors cannot be simply expressed as power law or any other simple functions. At the same time, we divided the data into groups and extracted period bursty events. Through careful analysis in different groups, we drew a conclusion that aggregate behavior might be composed of heterogeneous behaviors, and even the behaviors of the same type tended to be different in different period. The aggregate behavior is supposed to be formed by "heterogeneous groups". We performed a series of experiments. Simulation results showed that we just needed to set up two states Semi-Markov Modulated Process to construct proper representation of heterogeneous behavior.

  19. Thomson parabola ion energy analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Cobble, James A [Los Alamos National Laboratory; Flippo, Kirk A [Los Alamos National Laboratory; Letzring, Samuel A [Los Alamos National Laboratory; Lopez, Frank E [Los Alamos National Laboratory; Offermann, Dustin T [Los Alamos National Laboratory; Oertel, John A [Los Alamos National Laboratory; Mastrosimone, Dino [UNIV OF ROCHESTER

    2010-01-01

    A new, versatile Thomson parabola ion energy (TPIE) analyzer has been designed and constructed for use at the OMEGA-EP facility. Multi-MeV ions from EP targets are transmitted through a W pinhole into a (5- or 8-kG) magnetic field and subsequently through a parallel electric field of up to 30 kV/cm. The ion drift region may have a user-selected length of 10, 50, or 80 cm. With the highest fields, 500-Me V C{sup 6+} and C{sup 5+} may be resolved. TPIE is TIM-mounted at OMEGA-EP and is qualified in all existing TIMs. The instrument runs on pressure-interlocked 15-VDC power available in EP TIM carts. It may be inserted to within several inches of the target to attain sufficient flux for a measurement. For additional flux control, the user may select a square-aperture W pinhole of 0.004-inch or 0.010-inch. The detector consists of CR-39 backed by an image plate. The fully relativistic design code and design features are discussed. Ion spectral results from first use at OMEGA-EP are expected.

  20. Analyzing Agricultural Agglomeration in China

    Directory of Open Access Journals (Sweden)

    Erling Li

    2017-02-01

    Full Text Available There has been little scholarly research on Chinese agriculture’s geographic pattern of agglomeration and its evolutionary mechanisms, which are essential to sustainable development in China. By calculating the barycenter coordinates, the Gini coefficient, spatial autocorrelation and specialization indices for 11 crops during 1981–2012, we analyze the evolutionary pattern and mechanisms of agricultural agglomeration. We argue that the degree of spatial concentration of Chinese planting has been gradually increasing and that regional specialization and diversification have progressively been strengthened. Furthermore, Chinese crop production is moving from the eastern provinces to the central and western provinces. This is in contrast to Chinese manufacturing growth which has continued to be concentrated in the coastal and southeastern regions. In Northeast China, the Sanjiang and Songnen plains have become agricultural clustering regions, and the earlier domination of aquaculture and rice production in Southeast China has gradually decreased. In summary, this paper provides a political economy framework for understanding the regionalization of Chinese agriculture, focusing on the interaction among the objectives, decisionmaking behavior, path dependencies and spatial effects.

  1. A single-nucleotide-polymorphism-based genotyping assay for simultaneous detection of different carbendazim-resistant genotypes in the Fusarium graminearum species complex

    Science.gov (United States)

    Zhang, Hao; Brankovics, Balázs; van der Lee, Theo A.J.; Waalwijk, Cees; van Diepeningen, Anne A.D.; Xu, Jin; Xu, Jingsheng

    2016-01-01

    The occurrence resistance to methyl benzimidazole carbamates (MBC)-fungicides in the Fusarium graminearum species complex (FGSC) is becoming a serious problem in the control of Fusarium head blight in China. The resistance is caused by point mutations in the β2-tubulingene. So far, five resistant genotypes (F167Y, E198Q, E198L, E198K and F200Y) have been reported in the field. To establish a high-throughput method for rapid detection of all the five mutations simultaneously, an efficient single-nucleotide-polymorphism-based genotyping method was developed based on the Luminex xMAP system. One pair of amplification primers and five allele specific primer extension probes were designed and optimized to specially distinguish the different genotypes within one single reaction. This method has good extensibility and can be combined with previous reported probes to form a highly integrated tool for species, trichothecene chemotype and MBC resistance detection. Using this method, carbendazim resistant FGSC isolates from Jiangsu, Anhui and Sichuan Province in China were identified. High and moderate frequencies of resistance were observed in Jiangsu and Anhui Province, respectively. Carbendazim resistance in F. asiaticum is only observed in the 3ADON genotype. Overall, our method proved to be useful for early detection of MBC resistance in the field and the result aids in the choice of fungicide type. PMID:27812414

  2. Relationship between Glucocorticoid-induced Osteoporosis and Vitamine D Receptor Genotypes

    Institute of Scientific and Technical Information of China (English)

    李裕明; 徐琳; 沈凌迅; 余立凯; 陈璐璐

    2002-01-01

    Summary: By means of polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) assay, the association between vitamine D receptor (VDR) genotypes and bone min-eral density (BMD) in the patients receiving long-term glucocorticoid therapy was studied. Theclinical data and blood of 71 patients with rheumatosis who received long-term glucocorticoid ther-apy were collected. BMD was measured by dual-energy X-ray absorptimometry. VDR gene frag-ment (about 185 bp) was amplified by PCR from the extracted genomic DNA, then digested withrestriction endonuclease Bsm I. The genotypes were evaluated based on the fragment length fol-lowing endonuclease digestion and the association between genotypes and BMD or Z-score valueswas analyzed. Among the 71 cases, the detected genotypes were Bb and bb with the distributionfrequency being 11.3 % and 88. 7 % respectively. The distribution frequency of the alleles was inagreement with the Hardy-Weinberg equilibrium. There was no significant difference between thetwo genotypes in age, gender, body mass index (BMI), disease duration, disease types, time ofglucocorticoid administration and cumulative dosage (P>0.05). Osteoporosis rate of the patientswith Bb or bb genotype was 37. 5 % and 33. 3 % respectively, with the difference being not signif-icant (x2=0. 05, P=0. 8). The BMD and Z-score values at lumbar spine and femur in two geno-types were not similar, but the difference had no significant (P>0. 05). The distribution frequen-cy of bb type of VDR genotypes in Hah populations of China was more prevalent, followed by Bband bb types in turn. In the patients receiving long-term glucocorticoid therapy, there was no sig-nificant difference in BMD between Bb and bb genotypes. The data suggest that the VDR geno-types may not be means of identifying patients at greater risk of glucocorticoid-induced osteoporo-sis, which await to be further confirmed by a large sample size.

  3. Use of supplementary genotypes in AMMI analysis.

    Science.gov (United States)

    Pacheco, R M; Duarte, J B; Vencovsky, R; Pinheiro, J B; Oliveira, A B

    2005-03-01

    Improving stability of crop yield in a target production environment is an important breeding objective. It is well known that selection for better stability generally results in lower mean yields and, conversely, that selection for higher mean yields may lead to poorer stability. This paper explores the equivalence between the singular value decomposition used in AMMI analysis and the spectral decomposition used in principal components analysis. This equivalence enables scores of a "supplementary genotype" made up of the highest yield value within each environment to be obtained, and these may serve as the ideal check treatment for selection purposes. These scores are used to (1) display this check in a biplot graph, thereby providing a qualitative comparison with the real genotypes related to their interaction with environments; (2) obtain estimates of the squared distances from the projection of each real genotype to the projection of the "supplementary treatment", thereby allowing conclusions to be made on the yield stability of each real genotype. This procedure was effective in identifying the most stable soybean cultivars in an example shown for illustration.

  4. Genotype by environment interaction in maize breeding

    Directory of Open Access Journals (Sweden)

    Babić Milosav

    2008-01-01

    Full Text Available Because proximity measures occur in pairs where both, similarity and dissimilarity measures exploit the same type of information, companion classification and ordination techniques can be applied. They complement each other in analysis of genotype by environment interaction (GxE data. Choice of method, companion diagnostics and graphical presentation are required within each of methodologies. By clustering of 12 genotypes into 5 groups, 96.26% of variability for genotypes contained in original data is kept. By applying same analysis for environments, 96.45% of variability contained in original data matrix is kept with grouping of 31 environments into 11 groups. Caused by genotypes and environments grouping 78.10% of GxE variability contained in original data matrix remained in analysis of such two-way reduced data. Based on shown results, it is not possible to define smaller growing regions. Clustering of environment can be useful not only for defining mega environments but also for smaller growing regions defining only in combination with some of additional analysis (AMMI, discrimination analysis, correspondent analysis etc.. In such kind of analysis experience of investigator would be of great importance. Choice of test sites for breeding programme can be made based on obtained grouping to a limited extent (rather for restructuring existing test sites network in order to obtain 'better' information with same number of test sites then for its rationalization with number of test sites decreasing.

  5. Polyembryony in non-apomictic citrus genotypes

    Science.gov (United States)

    Aleza, Pablo; Juárez, José; Ollitrault, Patrick; Navarro, Luis

    2010-01-01

    Background and Aims Adventitious embryony from nucellar cells is the mechanism leading to apomixis in Citrus sp. However, singular cases of polyembryony have been reported in non-apomictic genotypes as a consequence of 2x × 4x hybridizations and in vitro culture of isolated nucelli. The origin of the plants arising from the aforementioned processes remains unclear. Methods The genetic structure (ploidy and allelic constitution with microsatellite markers) of plants obtained from polyembryonic seeds arising from 2x × 4x sexual hybridizations and those regenerated from nucellus culture in vitro was systematically analysed in different non-apomictic citrus genotypes. Histological studies were also conducted to try to identify the initiation process underlying polyembryony. Key Results All plants obtained from the same undeveloped seed in 2x × 4x hybridizations resulted from cleavage of the original zygotic embryo. Also, the plants obtained from in vitro nucellus culture were recovered by somatic embryogenesis from cells that shared the same genotype as the zygotic embryos of the same seed. Conclusions It appears that in non-apomictic citrus genotypes, proembryos or embryogenic cells are formed by cleavage of the zygotic embryos and that the development of these adventitious embryos, normally hampered, can take place in vivo or in vitro as a result of two different mechanisms that prevent the dominance of the initial zygotic embryo. PMID:20675656

  6. Analyzing rare diseases terms in biomedical terminologies

    Directory of Open Access Journals (Sweden)

    Erika Pasceri

    2012-03-01

    Full Text Available Rare disease patients too often face common problems, including the lack of access to correct diagnosis, lack of quality information on the disease, lack of scientific knowledge of the disease, inequities and difficulties in access to treatment and care. These things could be changed by implementing a comprehensive approach to rare diseases, increasing international cooperation in scientific research, by gaining and sharing scientific knowledge about and by developing tools for extracting and sharing knowledge. A significant aspect to analyze is the organization of knowledge in the biomedical field for the proper management and recovery of health information. For these purposes, the sources needed have been acquired from the Office of Rare Diseases Research, the National Organization of Rare Disorders and Orphanet, organizations that provide information to patients and physicians and facilitate the exchange of information among different actors involved in this field. The present paper shows the representation of rare diseases terms in biomedical terminologies such as MeSH, ICD-10, SNOMED CT and OMIM, leveraging the fact that these terminologies are integrated in the UMLS. At the first level, it was analyzed the overlap among sources and at a second level, the presence of rare diseases terms in target sources included in UMLS, working at the term and concept level. We found that MeSH has the best representation of rare diseases terms.

  7. Lactase non-persistent genotype influences milk consumption and gastrointestinal symptoms in Northern Russians

    Directory of Open Access Journals (Sweden)

    Khabarova Yulia

    2011-11-01

    Full Text Available Abstract Background Milk is an important source of nutrients. The consumption of milk, however, may cause abdominal complaints in lactose intolerant individuals. The frequency of -13910C/C genotype is known to be high among Northern Russians, exceeding the prevalence in northern Europe. In our study we tested two hypotheses: 1 subjects with lactase non-persistent genotype (-13910C/C have more gastrointestinal (GI symptoms associated with milk 2 subjects with lactase non-persistence avoid using milk. Methods In total, 518 students aged 17 to 26 years were randomly selected from different departments in the Northern State Medical University (NSMU for genotyping the lactase activity-defining -13910C/T variant. All subjects filled in a questionnaire covering their personal data, self-reported GI symptoms and milk consumption habits. Results Northern Russians consume very small amounts of milk daily. Among carriers of the lactase non-persistent (LNP genotype there were 10 percentage units of milk-consumers fewer than among lactase-persistent (LP subjects (p = 0.03. Complaints of GI disorders caused by milk were different between the genotypes (p = 0.02. Among all types of food analyzed only milk was associated with increased GI symptoms among subjects with the LNP genotype (OR = 1.95, CI 1.03-3.69 Conclusions Subjects with -13910C/C have more GI symptoms from milk. Subjects with lactase non-persistent genotype avoid using milk. In the case of increasing milk consumption symptoms may increase the need for medical consultation. It is thus important either for people themselves or for health care staff to be aware of lactase persistence/non-persistence.

  8. 6 HCV genotyping 9G test and its comparison with VERSANT HCV genotype 2.0 assay (LiPA) for the hepatitis C virus genotyping.

    Science.gov (United States)

    Chantratita, Wasun; Song, Keum-Soo; GunHo, Choi; Pongthanapisith, Viroj; Thongbaiphet, Nipa; Wongtabtim, Garanyuta; Pasomsub, Ekawat; Angkanavin, Kanokwan; Nimse, Satish Balasaheb; Sonawane, Mukesh Digambar; Warkad, Shrikant Dasharath; Kim, Taisun

    2017-01-01

    In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

  9. 心理健康教育咨询与学校社会工作合力作用模式初探--基于我国部分民族高校的分析%A Trying Discussion for Analyzing the Possible Integration of Mental Health Education Counseling and School Social Work-Based on some Universities for Nationalities

    Institute of Scientific and Technical Information of China (English)

    范琳俐; 郝世亮

    2013-01-01

    学校社会工作以“人在环境”的理念为理论基点,其作用逻辑异于学生心理健康教育咨询工作模式,但两者核心价值理念相容、工作目标一致。本文从分析民族院校心理健康教育咨询方法的实践及其困境入手,探讨心理教育咨询方法同学校社会工作方法相结合以构建更为完善的民族院校大学生心理健康工作体系的可能模式。%School social work take the"person in the environment"concept as the theoretical basis, and the logic of action is different from the students' psychological health education, but both of theirs core values and work objective are compatible with each other. The article take the Mental Health Education Practice and difficulties of universities for nationalities as a analyzing start, then discussing the possible for creating a comprehensive architecture which can integrate the advantages of the approach of psychological education consulting and method of school social work.

  10. Prevalence of Porphyromonas gingivalis fimA genotypes in Japanese children.

    Science.gov (United States)

    Hayashi, Fumiko; Okada, Mitsugi; Oda, Yuki; Kojima, Taro; Kozai, Katsuyuki

    2012-03-01

    Porphyromonas gingivalis FimA fimbriae have been classified into 6 genotypes (types I-V and Ib) based on the diversity of the fimA genes encoding the fimbrial subunits. We investigated the prevalence of fimA genotype in Japanese children. Dental plaque specimens were obtained from 400 subjects (age; 2 to 15 years), including 134 with healthy gingiva, 239 with gingivitis and 27 with periodontitis, and then analyzed by polymerase chain reaction. P. gingivalis was detected in 1.5%, 10.0% and 29.6% of these subjects, respectively. Significant differences were observed with regard to P. gingivalis infection among the groups [chi-squared analysis: gingivitis vs. healthy, P gingivitis. Our results suggest that the presence of P. gingivalis is associated with periodontal diseases, and that the type II, IV and Ib/II combination are the most common among fimA genotypes.

  11. Vitamin C and reducing sugars in the world collection of Capsicum baccatum L. genotypes.

    Science.gov (United States)

    Perla, Venu; Nimmakayala, Padma; Nadimi, Marjan; Alaparthi, Suresh; Hankins, Gerald R; Ebert, Andreas W; Reddy, Umesh K

    2016-07-01

    This study aimed to analyze 123 genotypes of Capsicum baccatum L. originating from 22 countries, at two stages of fruit development, for vitamin C content and its relationship with reducing sugars in fruit pericarp. Among the parametric population, vitamin C and reducing sugar concentrations ranged between 2.54 to 50.44 and 41-700mgg(-1) DW of pericarp, respectively. Overall, 14 genotypes accumulated 50-500% of the RDA of vitamin C in each 2g of fruit pericarp on a dry weight basis. Compared with ripened fruits, matured (unripened) fruits contained higher vitamin C and lower reducing sugars. About 44% variation in the vitamin C content could be ascribed to levels of reducing sugars. For the first time, this study provides comprehensive data on vitamin C in the world collection of C. baccatum genotypes that could serve as a key resource for food research in future.

  12. Objects in Films: analyzing signs

    Directory of Open Access Journals (Sweden)

    GAMBARATO, Renira Rampazzo

    2009-12-01

    Full Text Available The focus of this essay is the analysis of daily objects as signs in films. Objects from everyday life acquire several functions in films: they can be solely used as scene objects or to support a particular film style. Other objects are specially chosen to translate a character’s interior state of mind or the filmmaker’s aesthetical or ethical commitment to narrative concepts. In order to understand such functions and commitments, we developed a methodology for film analysis which focuses on the objects. Object interpretation, as the starting point of film analysis, is not a new approach. For instance, French film critic André Bazin proposed that use of object interpretation in the 1950s. Similarly, German film theorist Siegfried Kracauer stated it in the 1960s. However, there is currently no existing analytical model to use when engaging in object interpretation in film. This methodology searches for the most representative objects in films which involves both quantitative and qualitative analysis; we consider the number of times each object appears in a film (quantitative analysis as well as the context of their appearance, i.e. the type of shot used and how that creates either a larger or smaller relevance and/or expressiveness (qualitative analysis. In addition to the criteria of relevance and expressiveness, we also analyze the functionality of an object by exploring details and specifying the role various objects play in films. This research was developed at Concordia University, Montreal, Canada and was supported by the Foreign Affairs and International Trade, Canada (DFAIT.

  13. Identification of zoonotic genotypes of Giardia duodenalis.

    Science.gov (United States)

    Sprong, Hein; Cacciò, Simone M; van der Giessen, Joke W B

    2009-12-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG) of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic

  14. Bioaccumulation and degradation of atrazine in several Chinese ryegrass genotypes.

    Science.gov (United States)

    Sui, Ying; Yang, Hong

    2013-12-01

    Soil pollution with herbicides is a global problem. Before phytoremediation technology is developed for the plant-based clean-up of polluted soils, investigation of potential plants that can be used to accumulate and degrade herbicides is a critical step. In this study, three selected genotypes of ryegrass were comprehensively analyzed with regard to the atrazine accumulation, degradation and toxicological response. Under the conditions of soil with 0.8 mg kg(-1) atrazine, the maximum value for atrazine accumulation was 2.70 mg kg(-1) in shoots and 0.58 mg kg(-1) in roots. The residue of atrazine in soil with ryegrass cultivation was much lower than that in soil without ryegrass cultivation. Also, the content of atrazine residues in the rhizosphere was significantly lower than that in the non-rhizosphere soil. Activities of several enzymes (urease, invertase, polyphenol oxidase, acid phosphatase and alkaline phosphatase) in soil were assayed. These enzymes were depressed by atrazine but activated by ryegrass cultivation, even in the presence of atrazine. Finally, comparative studies have been conducted on the ryegrass genotypes in response to atrazine. They showed different capacities of degradation and bioaccumulation of atrazine. One of the grass cultivars Changjiang II (CJ) had better growth and higher levels of chlorophyll, but displayed less oxidative injury than two others, Abode (AB) and Jiewei (JW), under atrazine exposure.

  15. Subgenotype reclassification of genotype B hepatitis B virus

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    Shi Weifeng

    2012-08-01

    Full Text Available Abstract Background Nine subgenotypes from genotype B have been identified for hepatitis B virus (HBV. However, these subgenotypes were less conclusive as they were often designated based on a few representative strains. In addition, subgenotype B6 was designated twice for viruses of different origin. Methods All complete genome sequences of genotype B HBV were phylogenetically analyzed. Sequence divergences between different potential subgenotypes were also assessed. Results Both phylogenetic and sequence divergence analyses supported the designation of subgenotypes B1, B2, B4, and B6 (from Arctic. However, sequence divergences between previously designated B3, B5, B7, B8, B9 and another B6 (from China were mostly less than 4%. In addition, subgenotype B3 did not form a monophyly. Conclusion Current evidence failed to classify original B5, B7, B8, B9, and B6 (from China as subgenotypes. Instead, they could be considered as a quasi-subgenotype B3 of Southeast Asian and Chinese origin. In addition, previously designated B6 (from Arctic should be renamed as B5 for continuous numbering. This novel classification is well supported by both the phylogeny and sequence divergence of > 4%.

  16. Microfluidic hydrogel arrays for direct genotyping of clinical samples.

    Science.gov (United States)

    Jung, Yun Kyung; Kim, Jungkyu; Mathies, Richard A

    2016-05-15

    A microfluidic hydrogel DNA microarray is developed to overcome the limitations of conventional planar microarrays such as low sensitivity, long overnight hybridization time, lack of a melting verification of proper hybrid, and complicated sample preparation process for genotyping of clinical samples. Unlike our previous prototype hydrogel array which can analyze only single-stranded DNA (ssDNA) targets, the device is the first of its type to allow direct multiplexed single nucleotide polymorphism (SNP) detection of human clinical samples comprising double-stranded DNA (dsDNA). This advance is made possible by incorporating a streptavidin (SA) hydrogel capture/purification element in a double T-junction at the start of the linear hydrogel array structure and fabricating ten different probe DNAs-entrapped hydrogels in microfluidic channels. The purified or unpurified polymerase chain reaction (PCR) products labeled with a fluorophore and a biotin are electrophoresed through the SA hydrogel for binding and purification. After electrophoretic washing, the fluorophore-labeled DNA strand is then thermally released for hybridization capture by its complementary probe gel element. We demonstrate the precise and rapid discrimination of the genotypes of five different clinical targets by melting curve analysis based on temperature-gradient electrophoresis within 3h, which is at least 3-fold decrease in incubation time compared to conventional microarrays. In addition, a 1.7 pg (0.024 femtomoles) limit of detection for clinical samples is achieved which is ~100-fold better sensitivity than planar microarrays.

  17. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...

  18. Viral hepatitis B, C infection and genotype distribution among cholangiocarcinoma patients in northeast Thailand.

    Science.gov (United States)

    Barusrux, Sahapat; Nanok, Chaiyachet; Puthisawas, Watcharapong; Pairojkul, Chawalit; Poovorawan, Yong

    2012-01-01

    The prevalence of HBV and HCV infection among 295 cholangiocarcinoma (CCA) patients in northeast Thailand was analyzed. Hepatitis B surface antigen (HBsAg) was detected in 8.8% (26/295 cases) and antibodies to HCV (anti-HCV) in 2.7% (8/295 cases) of CCA cases. Screening for HBV DNA was performed in 15 of 26 HBV seropositive cases and genotypes could be determined in all 15. HBV genotypes C and B were detected in 73.3% (11/15 cases) and 26.7% (4/15 cases), respectively. HCV RNA was detected in 87.5% (7/8 cases) of anti-HCV positive cases. Specifically, 57.1% (4/7 cases) were HCV genotype 1a and 42.9% (3/7 cases) were HCV genotype 3a. The prevalence of infection and genotype distribution of both HCV and HBV among CCA in northeast Thailand is comparable to that in the general population, suggesting that HCV and HBV infections are, if at all, not serious risk factors for CCA.

  19. GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS

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    Amran Muis

    2016-02-01

    Full Text Available The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and  genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

  20. Genotype by environment interaction for seed yield per plant in rapeseed using AMMI model

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    Ana Marjanović-Jeromela

    2011-02-01

    Full Text Available The objective of this study was to assess genotype by environment interaction for seed yield per plant in rapeseed cultivars grown in Northern Serbia by the AMMI (additive main effects and multiplicative interaction model. The study comprised 19 rapeseed genotypes, analyzed in seven years through field trials arranged in a randomized complete block design, with three replicates. Seed yield per plant of the tested cultivars varied from 1.82 to 19.47 g throughout the seven seasons, with an average of 7.41 g. In the variance analysis, 72.49% of the total yield variation was explained by environment, 7.71% by differences between genotypes, and 19.09% by genotype by environment interaction. On the biplot, cultivars with high yield genetic potential had positive correlation with the seasons with optimal growing conditions, while the cultivars with lower yield potential were correlated to the years with unfavorable conditions. Seed yield per plant is highly influenced by environmental factors, which indicates the adaptability of specific genotypes to specific seasons.

  1. Enterovirus-71 genotype C isolated in Peru between 2006 and 2009.

    Science.gov (United States)

    Huaman, Jose L; Carrion, Gladys; Ampuero, Julia S; Ocaña, Victor; Laguna-Torres, V Alberto; Hontz, Robert D

    2016-12-01

    Enterovirus-71 (EV71) was first isolated in California, United States in 1969, belongs to the genus Enterovirus, family Picornaviridae. Although infection normally causes mild, often undiagnosed illness, it can cause central nervous system infections that could turn fatal. Based on VP1 gene analysis, EV71 has been classified into six separate genotypes. Although the molecular epidemiology of EV71 has been well described via studies originating from Asia and Europe, it is mostly unknown in South America. From our study, four EV71 isolates from Peru were characterized using phylogenetic methods to determine their relationship with known reference strains. These four Peruvian EV71 isolates from between 2006 and 2009 were analyzed by RT-PCR using primers capable of amplifying the entire VP1 gene. Reference strains representing all six known genotypes were used to determine any recognizable phylogenetic relationships. In fact, all of our isolates clustered together within the genotype C1 lineage- separate from Asian, European, North American, and Australian strains. We present evidence that EV71 genotype C1 exists in Peru, and this is the first such report documenting EV71 genotype C1 circulating in South America. Gathering additional isolates will help elucidate a more complete global epidemiological picture of EV71 infections.

  2. Naturally occurring genotype 2b/1a hepatitis C virus in the United States

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    Striker Rob

    2011-10-01

    Full Text Available Abstract Background Hepatitis C Virus (HCV infected patients are frequently repeatedly exposed to the virus, but very few recombinants between two genotypes have been reported. Findings We describe the discovery of an HCV recombinant using a method developed in a United States clinical lab for HCV genotyping that employs sequencing of both 5' and 3' portions of the HCV genome. Over twelve months, 133 consecutive isolates were analyzed, and a virus from one patient was found with discordant 5' and 3' sequences suggesting it was a genotype 2b/1a recombinant. We ruled out a mixed infection and mapped a recombination point near the NS2/3 cleavage site. Conclusions This unique HCV recombinant virus described shares some features with other recombinant viruses although it is the only reported recombinant of a genotype 2 with a subtype 1a. This recombinant represents a conundrum for current clinical treatment guidelines, including treatment with protease inhibitors. This recombinant is also challenging to detect by the most commonly employed methods of genotyping that are directed primarily at the 5' structural portion of the HCV genome.

  3. Genetic variability of hepatitis B virus in Uruguay: D/F, A/F genotype recombinants.

    Science.gov (United States)

    Lopez, L; Flichman, D; Mojsiejczuk, L; Gonzalez, M V; Uriarte, R; Campos, R; Cristina, J; Garcia-Aguirre, Laura

    2015-09-01

    Hepatitis B virus (HBV) infection is a serious global health problem. Approximately 2 billion people worldwide have been infected, and approximately 350 million individuals currently suffer from HBV-induced chronic liver infection, which causes 600,000 deaths annually from chronic hepatitis, cirrhosis and hepatocellular carcinoma. HBV is classified in eight genotypes (A-H), and two more have been proposed (I-J). In this paper, complete genome sequences of nine Uruguayan HBV are reported. Five samples belong to genotype F1b and one to genotype A2. Three HBV recombinants were detected: A1/F1b, A2/F1b and D3/F1b. The following mutations were detected: a G1896A substitution, a 33-nucleotide deletion from position 2896 to 2928 in the Pre-S1 region involving Pre-S1 residues 3-13, a 33-nt deletion in the Pre-S1 region involving nt 2913-2945 and Pre-S1 residues 9-19. More F genotypes strains than expected were detected in this study, supporting the hypothesis that there are more people of indigenous origin than declared in our population. Also, one third of the samples analyzed were recombinants. This cannot be explained by the low HBV prevalence in Uruguay, but a high HBV infection rate in drug addicts and dialysis patients could act in favor of multiple-genotype HBV infections that could lead to recombination.

  4. Replication of a chronic hepatitis B virus genotype F1b construct.

    Science.gov (United States)

    Hernández, Sergio; Jiménez, Gustavo; Alarcón, Valentina; Prieto, Cristian; Muñoz, Francisca; Riquelme, Constanza; Venegas, Mauricio; Brahm, Javier; Loyola, Alejandra; Villanueva, Rodrigo A

    2016-03-01

    Genotype F is one of the less-studied genotypes of human hepatitis B virus, although it is widely distributed in regions of Central and South American. Our previous studies have shown that HBV genotype F is prevalent in Chile, and phylogenetic analysis of its full-length sequence amplified from the sera of chronically infected patients identified it as HBV subgenotype F1b. We have previously reported the full-length sequence of a HBV molecular clone obtained from a patient chronically infected with genotype F1b. In this report, we established a system to study HBV replication based on hepatoma cell lines transfected with full-length monomers of the HBV genome. Culture supernatants were analyzed after transfection and found to contain both HBsAg and HBeAg viral antigens. Consistently, fractionated cell extracts revealed the presence of viral replication, with both cytoplasmic and nuclear DNA intermediates. Analysis of HBV-transfected cells by indirect immunofluorescence or immunoelectron microscopy revealed the expression of viral antigens and cytoplasmic viral particles, respectively. To test the functionality of the ongoing viral replication further at the level of chromatinized cccDNA, transfected cells were treated with a histone deacetylase inhibitor, and this resulted in increased viral replication. This correlated with changes posttranslational modifications of histones at viral promoters. Thus, the development of this viral replication system for HBV genotype F will facilitate studies on the regulation of viral replication and the identification of new antiviral drugs.

  5. Mycobacterium tuberculosis strains of the Beijing genotype are rarely observed in tuberculosis patients in South America

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    Viviana Ritacco

    2008-08-01

    Full Text Available The frequency of the Beijing genotype of Mycobacterium tuberculosis as a cause of tuberculosis (TB in South America was determined by analyzing genotypes of strains isolated from patients that had been diagnosed with the disease between 1997 and 2003 in seven countries of the subcontinent. In total, 19 of the 1,202 (1.6% TB cases carried Beijing isolates, including 11 of the 185 patients from Peru (5.9%, five of the 512 patients from Argentina (1.0%, two of the 252 Brazilian cases (0.8%, one of the 166 patients from Paraguay (0.6% and none of the samples obtained from Chile (35, Colombia (36 and Ecuador (16. Except for two patients that were East Asian immigrants, all cases with Beijing strains were native South Americans. No association was found between carrying a strain with the Beijing genotype and having drug or multi-drug resistant disease. Our data show that presently transmission of M. tuberculosis strains of the Beijing genotype is not frequent in Latin America. In addition, the lack of association of drug resistant TB and infection with M. tuberculosis of the Beijing genotype observed presently demands efforts to define better the contribution of the virulence and lack of response to treatment to the growing spread of Beijing strains observed in other parts of the world.

  6. Comparative Transcriptomic Analysis of Salt Adaptation in Roots of Contrasting Medicago truncatula Genotypes

    Institute of Scientific and Technical Information of China (English)

    Ons Zahaf; Anouck Diet; Mounawer Badri; Ana Zabalza; Esther M.González; Hervé Delacroix; Véronique Gruber; Florian Frugier; Martin Crespi; Sandrine Blanchet; Axel de Zélicourt; Beno(i)t Alunni; Julie Plet; Carole Laffont; Laura de Lorenzo; Sandrine Imbeaud; Jean-Laurent Ichanté

    2012-01-01

    Evolutionary diversity can be driven by the interaction of plants with different environments.Molecular bases involved in ecological adaptations to abiotic constraints can be explored using genomic tools.Legumes are major crops worldwide and soil salinity is a main stress affecting yield in these plants.We analyzed in the Medicago truncatula legume the root transcriptome of two genotypes having contrasting responses to salt stress:TN1.11,sampled in a salty Tunisian soil,and the reference Jemalong A17 genotype.TN1.11 plants show increased root growth under salt stress as well as a differential accumulation of sodium ions when compared to A17.Transcriptomic analysis revealed specific gene clusters preferentially regulated by salt in root apices of TN1.11,notably those related to the auxin pathway and to changes in histone variant isoforms.Many genes encoding transcription factors (TFs) were also differentially regulated between the two genotypes in response to salt.Among those selected for functional studies,overexpression in roots of the A17 genotype of the bHLH-type TF most differentially regulated between genotypes improved significantly root growth under salt stress.Despite the global complexity of the differential transcriptional responses,we propose that an increase in this bHLH TF expression may be linked to the adaptation of M.truncatula to saline soil environments.

  7. Genotype MTBDR plus assay for molecular detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis

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    Soniya Sharma

    2014-01-01

    Full Text Available Aim: This study was performed for the rapid identification of Mycobacterium tuberculosis complex and its resistance to rifampicin and isoniazid, directly from the sputum samples of pulmonary tuberculosis patients. Materials and Methods: A commercially available genotype MTBDR plus assay was used for the identification and detection of mutations in Mycobacterial isolates. A total of 100 sputum samples of pulmonary tuberculosis patients were analyzed by using the genotype MTBDR plus assay. The MTBDR plus assay is designed to detect the mutations in the hotspot region of rpoB gene, katG and regulatory region of inhA gene. Results: The genotype MTBDR plus assay detected 22% multidrug resistant (MDR, 2% rifampicin (RMP monoresistant and 1% isoniazid (INH monoresistant isolates. In 22 MDR isolates, the codons most frequently involved in RMP-associated mutations were codon 531 (54.55%, 516 (31.82% and 526 (13.63%, and 90.90% of MDR isolates showed KatG S315T mutations and 9.1% showed inhA C-15T mutations associated with INH resistance. Conclusion: The new genotype MTBDR plus assay represents a rapid, reliable tool for the detection of MDR-TB, wherein results are obtained in 5 h allowing early and appropriate treatment, which is essential to cut the transmission path and reduce the spread of MDR-TB. The genotype MTBDR plus assay can readily be included in a routine laboratory work for the early diagnosis and control of MDR-TB.

  8. FT-IR Characterization of Pollen Biochemistry, Viability, and Germination Capacity in Saintpaulia H. Wendl. Genotypes

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    Erzsebet Buta

    2015-01-01

    Full Text Available FT-IR characterization of pollen biochemistry was analyzed to detect possible connection with the viability (by staining with potassium iodide, 25% and the germination capacity (on solid nutrient medium, in 15 Saintpaulia genotypes. Vibrational spectroscopy indicates that the pollen of S. ionantha genotype “Red Velvet” is rich in proteins, lipids, triglycerides, and esters and has a viability of 88.4% and a low germination capacity (27.16%. For S. ionantha “Jolly Red” and “Lucky Ladybug” genotypes, pollen showed high viability (88.81–91.49% and low germination capacity (23.02–9.17%, even though the pollen is rich in carbohydrates. S. ionantha “Aloha Orchid” genotype has the highest percentage of viability (94.32% and germination capacity (45.73% and a rich content of carbohydrates and polygalacturonic acids. In S. rupicola and S. ionantha genotypes, the rich content of polygalacturonic acids, lipids, and carbohydrates favourably influenced the germination capacity. Spectroscopic result indicates, through different absorbance band intensity, a possible link between biochemical composition, viability, and germination capacity of Saintpaulia pollen. To determine exactly the relation between biochemistry and biological processes, it is necessary to initiate quantitative researches.

  9. Identification of superior chrysanthemum genotypes based on phenological traits and postproduction longevity

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    M. Hassanpour Asil

    2014-07-01

    Full Text Available Chrysanthemum is one of the most important ornamental and medicinal plants in the world. In this study, diversity among 50 genotypes of chrysanthemum morifolium was analyzed using phenologic and morphologic traits. The variation between studied genotypes showed a significant difference for all traits and coefficient of genetic variations for most traits was greater than 40%. The highest general heritability belonged to days to bud coloring (h2=90.59% and post-production longevity (h2=88.3%. The lowest heritability (h2=6.05% was related to disc floret opening. In multiple linear stepwise regression for flower longevity as the dependent variable, such traits as number of days to bud coloring, days to full bloom and pollen shed entered the model. Therefore, vegetative growth period and behavior of florets affect post-production longevity. On the other hand, cluster analysis according to the morphological traits using Ward method classified all the studied genotypes into six groups. In this classification, two genotypes of “Afrooz” and ‘Unknown1’, with short vegetative period, late pollen shed and high post-production longevity were classified into a separate cluster. The findings of this research showed that the studied Chrysanthemum genotypes have desirable genetic potential, and depending on the objectives, most of them could be used in breeding programs to improve different traits.

  10. DD genotype of ACE gene in boys: may it be a risk factor for minimal change nephrotic syndrome?

    Science.gov (United States)

    Alasehirli, Belgin; Balat, Ayşe; Büyükçelik, Mithat

    2012-01-01

    It has been shown that angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism affects the circulating and cellular levels of ACE and may be a risk factor in several renal diseases. We analyzed the association of ACE gene I/D polymorphism with the clinical presentation of minimal change nephrotic syndrome (MCNS) in a Turkish child population. This study consisted of 97 children with MCNS and 144 healthy controls. Genotyping of ACE gene was performed using polymerase chain reaction (PCR). The distributions of ACE genotypes were II in 13%, ID in 49%, and DD in 38% in patient group, and 9%, 49%, and 42% in control group, respectively. The frequency of the D allele was 63% and that of the I allele was 37% in patients. There were no relevant differences in the allele frequencies and genotypes of ACE I/D polymorphism between patients and controls. However, DD genotype was higher in boys in children with MCNS (78.4%. vs. 50.0%, p = 0.004). The frequencies of DD genotype and D allele in boys were 7.25 and 2.56 times higher than II genotype and I allele in the patient group, respectively. We suggest that DD genotype in boys may be one of the risk factors for MCNS.

  11. Evaluation of sugarcane genotypes and production environments in Paraná by GGE biplot and AMMI analysis

    Directory of Open Access Journals (Sweden)

    Pedro Henrique Costa de Mattos

    2013-04-01

    Full Text Available The purpose of this study was to evaluate sugarcane genotypes for the trait tons of sugar per hectare (TSH, stratifying five production environments in the state of Paraná. The performance of 20 genotypes and 2 standard cultivars was analyzed in three consecutive growing seasons by the statistical methods AMMI and GGE Biplot. The GGE Biplot grouped the locations into two megaenvironments and indicated the best-performing genotypes for each one, facilitating the selection of superior genotypes. Another advantage of GGEBiplot is the definition of an ideal genotype (G and environment (E, serving as reference for the evaluation of genotypes and choice of environments with greater GE interaction. Both models indicated RB006970, RB855156 and RB855453 as the genotypes with highest TSH and São Pedro do Ivai as the environment with the greatest GE interaction. Both approaches explained a high percentage of the sum of squares, with a slight advantage of AMMI over GGE Biplot analysis.

  12. Microsatellite analysis of Damask rose (Rosa damascena Mill. accessions from various regions in Iran reveals multiple genotypes

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    Naghavi Mohammad

    2007-03-01

    Full Text Available Abstract Background Damask roses (Rosa damascena Mill. are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran. Results All microsatellite markers showed a high level of polymorphism (5–15 alleles per microsatellite marker, with an average of 9.11 alleles per locus. Cluster analysis of genetic similarities revealed that these microsatellites identified a total of nine different genotypes. The genotype from Isfahan province, which is the major production area, was by far the most common genotype (27/40 accessions. It was identical to the Bulgarian genotype. Other genotypes (each represented by 1–4 accessions were collected from minor production areas in several provinces, notably in the mountainous Northwest of Iran. Conclusion This is the first study that uncovered genetic diversity within Damask rose. Our results will guide new collection activities to establish larger collections and manage the Iranian Damask rose genetic resources. The genotypes identified here may be directly useful for breeding.

  13. Determination of HBV Genotypes among Hbs Ag Positive Blood Donors in Tehran, Iran Using PCR-RFLP

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    S Milani

    2009-03-01

    Full Text Available Background: Hepatitis B virus (HBV is one of the major causative agents of acute and chronic liver disease worldwide and is believed to be responsible for a million deaths annually. On the basis of a comparison of complete genomic se­quences, HBV has been classified into eight genotypes A-H which show a geographical distribution. Some genotypes are associ­ated with different clinical outcomes. Identification of HBV genotypes is important to begin and follow up the treat­ment."nMethods: In this cross-sectional study, the serum samples of blood donors were collected from Tehran Blood Transfusion Cen­ters in period during "2005-2006". Sera of 55 blood donors who were positive for hepatitis B surface antigen were se­lected. DNA was extracted using commercial kit and the S gene sequence was amplified by nested-PCR. PCR products were then analyzed for restriction enzymes that would be genotype specific."nResults: Genotype D was found the only type in all HBV DNA positive serum samples, in Tehran."nConclusion: Genotype D is dominant among Tehran's blood donors, which is consistent with Iran and the Middle East domi­nant genotype.  

  14. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  15. Effects of using phenotypic means and genotypic values in GGE biplot analyses on genotype by environment studies on tropical maize (Zea mays).

    Science.gov (United States)

    Granato, I S C; Fritsche-Neto, R; Resende, M D V; Silva, F F

    2016-10-05

    The objective of this study was to examine the effects of the type and intensity of nutritional stress, and of the statistical treatment of the data, on the genotype x environment (G x E) interaction for tropical maize (Zea mays). For this purpose, 39 hybrid combinations were evaluated under low- and high-nitrogen and -phosphorus availability. The plants were harvested at the V6 stage, and the shoot dry mass was estimated. The variance components and genetic values were assessed using the restricted maximum likelihood/best linear unbiased prediction method, and subsequently analyzed using the GGE biplot method. We observed differences in the performances of the hybrids depending on both the type and intensity of nutritional stress. The results of relationship between environments depended on whether genotypic values or phenotypic means were used. The selection of tropical maize genotypes against nutritional stress should be performed for each nutrient availability level within each type of nutritional stress. The use of phenotypic means for this purpose provides greater reliability than do genotypic values for the analysis of the G x E interaction using GGE biplot.

  16. Electromechanical integrated magnetic gear

    OpenAIRE

    Xiu-hong Hao; Hong-fei Zhang; Ji-de Men

    2016-01-01

    This study proposes a new type of magnetic gear, namely, the electromechanical integrated magnetic gear, that integrates the traditional field-modulated magnetic gear, drive, and control. The topology and operating principle of the electromechanical integrated magnetic gear are described in detail in this article, and the constraints of parameter design and speed ratio of electromechanical integrated magnetic gear are presented. Moreover, magnetic field distribution is analyzed with the finit...

  17. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna;

    2013-01-01

    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer.......Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  18. Increased transmission of Mycobacterium tuberculosis Beijing genotype strains associated with resistance to streptomycin: a population-based study.

    Directory of Open Access Journals (Sweden)

    Tran N Buu

    Full Text Available BACKGROUND: Studies have shown that the Mycobacterium tuberculosis Beijing genotype is an emerging pathogen that is frequently associated with drug resistance. This suggests that drug resistant Beijing strains have a relatively high transmission fitness compared to other drug-resistant strains. METHODS AND FINDINGS: We studied the relative transmission fitness of the Beijing genotype in relation to anti-tuberculosis drug resistance in a population-based study of smear-positive tuberculosis patients prospectively recruited and studied over a 4-year period in rural Vietnam. Transmission fitness was analyzed by clustering of cases on basis of three DNA typing methods. Of 2531 included patients, 2207 (87% were eligible for analysis of whom 936 (42% were in a DNA fingerprint cluster. The clustering rate varied by genotype with 292/786 (37% for the Beijing genotype, 527/802 (67% for the East-African Indian (EAI genotype, and 117/619 (19% for other genotypes. Clustering was associated with the EAI compared to the Beijing genotype (adjusted odds ratio (OR(adj 3.4: 95% CI 2.8-4.4. Patients infected with streptomycin-resistant strains were less frequently clustered than patients infected with streptomycin-susceptible strains when these were of the EAI genotype (OR(adj 0.6, 95% CI 0.4-0.9, while this pattern was reversed for strains of the Beijing genotype (OR(adj 1.3, 95% CI 1.0-1.8, p for difference 0.002. The strong association between Beijing and MDR-TB (OR(adj 7.2; 95% CI 4.2-12.3 existed only if streptomycin resistance was present. CONCLUSIONS: Beijing genotype strains showed less overall transmissibility than EAI strains, but when comparisons were made within genotypes, Beijing strains showed increased transmission fitness when streptomycin-resistant, while the reverse was observed for EAI strains. The association between MDR-TB and Beijing genotype in this population was strongly dependent on resistance to streptomycin. Streptomycin resistance may

  19. Genotypic diversity and virulence factors of Streptococcus mutans in caries-free and caries-active individuals

    Directory of Open Access Journals (Sweden)

    Miula Portelinha Braga

    2013-04-01

    Full Text Available The objective of this study was to analyze the genotypic diversity, frequency of serotypes and the detection of mutacins from Streptococcus mutans isolates in caries-free and caries-active individuals.A total of 260 S. mutans isolated from 28 individuals with and without dental caries were subjected to AP-PCR and PCR screening of glucosyltransferase B, mutacin and serotype genes, which showed the presence of. 70 different genotypes. There was no statistically significant association between the presence of genes for serotypes and mutacins with dental caries. However, there was a statistically significant and a strong association between the higher genotypic diversity in the subjects with caries (r = 0.72, p = 0.001. There was an increase in the number of genotypes with increasing age (p <0.01.

  20. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  1. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid...

  2. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  3. IDENTIFICATION OF BETA-LACTOGLOBULIN AND KAPPACASEIN GENOTYPES IN CATTLE

    Directory of Open Access Journals (Sweden)

    R.A. VĂTĂŞESCU-BALCAN

    2013-12-01

    Full Text Available Beta-lactoglobulin (b-Lg and kappa-casein (k-Cn are two of the most important proteins in the mammals’ milk synthesized by the epithelial cells of the mammary glands. They play a crucial role in the milk quality and coagulation process (production of cheese and butter. The PCR-RFLP test was performed to distinguish the different alleles in a population of Romanian Black Spotted cattle, a dairy breed. Genetic polymorphism was detected by digestion with the endonucleases Hae III (b-Lg and Hinf I (k-Cn, followed by electrophoresis in agarose high resolution gel stained with ethidium bromide. Fifty DNA samples from Romanian Black Spotted breed were analyzed for A and B variants. This simple PCR-RFLP test makes feasible the inclusion of b-Lg and k- Cn genotypes in breeding plans and cattle selection.

  4. Genotypic variability and relationships between mite infestation levels, mite damage, grooming intensity, and removal of Varroa destructor mites in selected strains of worker honey bees (Apis mellifera L.).

    Science.gov (United States)

    Guzman-Novoa, Ernesto; Emsen, Berna; Unger, Peter; Espinosa-Montaño, Laura G; Petukhova, Tatiana

    2012-07-01

    The objective of this study was to demonstrate genotypic variability and analyze the relationships between the infestation levels of the parasitic mite Varroa destructor in honey bee (Apis mellifera) colonies, the rate of damage of fallen mites, and the intensity with which bees of different genotypes groom themselves to remove mites from their bodies. Sets of paired genotypes that are presumably susceptible and resistant to the varroa mite were compared at the colony level for number of mites falling on sticky papers and for proportion of damaged mites. They were also compared at the individual level for intensity of grooming and mite removal success. Bees from the "resistant" colonies had lower mite population rates (up to 15 fold) and higher percentages of damaged mites (up to 9 fold) than bees from the "susceptible" genotypes. At the individual level, bees from the "resistant" genotypes performed significantly more instances of intense grooming (up to 4 fold), and a significantly higher number of mites were dislodged from the bees' bodies by intense grooming than by light grooming (up to 7 fold) in all genotypes. The odds of mite removal were high and significant for all "resistant" genotypes when compared with the "susceptible" genotypes. The results of this study strongly suggest that grooming behavior and the intensity with which bees perform it, is an important component in the resistance of some honey bee genotypes to the growth of varroa mite populations. The implications of these results are discussed.

  5. A single Legionella pneumophila genotype in the freshwater system in a ship experiencing three separate outbreaks of legionellosis in 6 years

    Directory of Open Access Journals (Sweden)

    Catrine Ahlen

    2016-08-01

    Full Text Available Background: Recurrent legionella outbreaks at one and the same location are common. We have identified a single Legionella pneumophila genotype associated with recurrent Legionella outbreaks over 6 years. Methods: Field emergency surveys following Legionella outbreaks were performed on a vessel in 2008, 2009 and 2013. Water samples from both the distribution and technical parts of the potable water system were analyzed with respect to L. pneumophila [Real-Time PCR, cultivation, serotyping and genotyping (PFGE] and free-living amoebae, (FLA. Results: Legionella pneumophila serogroup 1 was present in the ship's potable water system during every outbreak. Genotyping of the 2008 survey material showed two separate PFGE genotypes while those in 2009 and 2013 demonstrated the presence of only one of the two genotypes. FLA with intracellular L. pneumophila of the same genotype were also detected. Analyses of the freshwater system on a ship following three separate Legionella outbreaks, for L. pneumophila and FLAs, revealed a single L. pneumophila genotype and FLA (Hartmanella. Conclusions: It is reasonable to assume that the L. pneumophila genotype detected in the freshwater system was the causal agent in the outbreaks onboard. Persistence of an apparently low-pathogenic L. pneumophila genotype and FLA in a potable water system represent a potential risk for recurrent outbreaks.

  6. Correlation between genotypes of tRNA-linked short tandem repeats in Entamoeba nuttalli isolates and the geographical distribution of host rhesus macaques.

    Science.gov (United States)

    Feng, Meng; Komiyama, Tomoyoshi; Yanagi, Tetsuo; Cheng, Xunjia; Sherchand, Jeevan B; Tachibana, Hiroshi

    2014-01-01

    Several polymorphic markers, including serine-rich protein genes, have been used for the genotyping of isolates from the morphologically indistinguishable protozoan parasites Entamoeba histolytica, Entamoeba dispar, and Entamoeba nuttalli. Genotypes of tRNA-linked short tandem repeats (STRs) are highly polymorphic, but the correlation with geographical distribution is unknown. We have recently isolated 15 E. nuttalli strains from wild rhesus macaques in four locations in Kathmandu Valley, Nepal. The sequences of the serine-rich protein genes of the E. nuttalli strains differed among the four locations. In this study, we analyzed tRNA-linked STRs in six loci of the 15 strains. Two genotypes were found in loci N-K2, R-R, and S(TGA)-D, three in locus S-Q, and five in locus D-A. In locus A-L, one major genotype and ten minor genotypes were found, resulting in mixtures of two to six genotypes in eight strains. By combination of the main genotypes in the six loci, the 15 strains were divided into nine genotypes. The genotypes observed in E. nuttalli strains were quite different from those in E. histolytica and E. dispar. A phylogenetic tree constructed from tRNA-linked STRs in the six loci reflected the different places of isolation. These results suggest that sequence diversity of tRNA-linked STRs in E. nuttalli occurs with relatively high frequency and might be a marker of geographical distribution of host rhesus macaques, even in limited areas.

  7. A single Legionella pneumophila genotype in the freshwater system in a ship experiencing three separate outbreaks of legionellosis in 6 years

    Science.gov (United States)

    Ahlen, Catrine; Aas, Marianne; Krusnell, Jadwiga; Iversen, Ole-Jan

    2016-01-01

    Background Recurrent legionella outbreaks at one and the same location are common. We have identified a single Legionella pneumophila genotype associated with recurrent Legionella outbreaks over 6 years. Methods Field emergency surveys following Legionella outbreaks were performed on a vessel in 2008, 2009 and 2013. Water samples from both the distribution and technical parts of the potable water system were analyzed with respect to L. pneumophila [Real-Time PCR, cultivation, serotyping and genotyping (PFGE)] and free-living amoebae, (FLA). Results Legionella pneumophila serogroup 1 was present in the ship's potable water system during every outbreak. Genotyping of the 2008 survey material showed two separate PFGE genotypes while those in 2009 and 2013 demonstrated the presence of only one of the two genotypes. FLA with intracellular L. pneumophila of the same genotype were also detected. Analyses of the freshwater system on a ship following three separate Legionella outbreaks, for L. pneumophila and FLAs, revealed a single L. pneumophila genotype and FLA (Hartmanella). Conclusions It is reasonable to assume that the L. pneumophila genotype detected in the freshwater system was the causal agent in the outbreaks onboard. Persistence of an apparently low-pathogenic L. pneumophila genotype and FLA in a potable water system represent a potential risk for recurrent outbreaks. PMID:27515183

  8. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... was significantly higher for both MinERR and MaxLRT compared with EP and random genotyping methods (either across or within family), for all the proportions of genotyped animals. Power to detect significant QTL (α = 0.01) with 20% genotyping for MinERR and MaxLRT was 80 and 75% of that obtained with complete...... that combining the phenotypic and genotypic information in selective genotyping (e.g. MinERR and MaxLRT) is better than using only the EPs and the combined methods can be considered as alternative approaches to decrease genotyping costs, with unbiased QTL effects, decreased sampling variance of the QTL variance...

  9. Strongyloides stercoralis genotypes in humans in Cambodia.

    Science.gov (United States)

    Schär, Fabian; Guo, Li; Streit, Adrian; Khieu, Virak; Muth, Sinuon; Marti, Hanspeter; Odermatt, Peter

    2014-06-01

    Little is known about the genetic variability of the soil-transmitted nematode, Strongyloides stercoralis, in humans. We sequenced portions of the small subunit rDNA (SSU), including the hyper variable regions (HVR) I and IV from S. stercoralis larvae derived from individuals living in a rural setting in Cambodia. We identified three polymorphic positions, including a previously reported one within the HVR I. HVR IV was invariable. Six different SSU alleles existed in our sample. Although different genotypes of S. stercoralis were found in the same individuals, no heterozygous larvae were found. This indicates that there is no or very little interbreeding between the different genotypes. Further studies are needed to examine if this is because sexual reproduction, which is facultative, is rare in our study area's S. stercoralis population or because what is considered to be S. stercoralis today is actually a complex of closely related species or subspecies.

  10. Genotypic linkages of gene segments of rotaviruses circulating in pediatric patients with acute gastroenteritis in Thailand.

    Science.gov (United States)

    Chaimongkol, Natthawan; Khamrin, Pattara; Malasao, Rungnapa; Thongprachum, Aksara; Ushijima, Hiroshi; Maneekarn, Niwat

    2012-10-01

    Rotavirus is a major cause of morbidity and mortality of infants and young children with diarrhea throughout the world. In Thailand, extensive studies of rotavirus infections have been reported continually and rotavirus diarrhea remains a common illness. To monitor the epidemiological situation of rotavirus in Chiang Mai, Thailand, surveillance of rotavirus circulating in pediatric patients was conducted. A total of 160 fecal specimens collected from children hospitalized with diarrhea were tested for rotaviruses groups A, B, and C by RT-PCR and their genotypes were identified by multiplex PCR and nucleotide sequencing. Group A rotavirus was detected at 29.4% but none of group B and C was found in this study. Molecular characterizations of G- and P-genotypes revealed three different G-P combinations, G1P[8] was the most predominant genotype with the prevalence of 72.3% followed by G2P[4] at 19.2%, and G3P[8] at 8.5%. Phylogenetic analyses of VP7 and VP4 genes of the representative strains detected in the present study, G1, G2, G3, and P[4] and P[8], respectively, revealed that G1 belonged to G1-Ic and G1-II, G2 belonged to G2-II, and G3 belonged to G3-III-S4 lineages while P[4] and P[8] were identified as P[4]-V and P[8]-III lineages. Analyses of VP6, NSP4, and NSP5 genes demonstrated that these representative strains belonged to genotypes I1 and I2, E1 and E2, and H1 and H2, respectively. Analyzing the association of G- and P-genotypes with I, E, H genotypes revealed unique patterns of genotypic linkage. The G1P[8] and G3P[8] were intimately linked with I1, E1, H1 genotypes and displayed the genetic features of G1-P[8]-I1-E1-H1 and G3-P[8]-I1-E1-H1, respectively, while G2P[4] was closely linked to I2, E2, H2 genotypes and showed the genetic pattern of G2-P[4]-I2-E2-H2. This study provides epidemiological information and insight into the genetic background of rotaviruses circulating in pediatric patients in Chiang Mai, Thailand.

  11. Hepatitis C virus genotyping in Greece: unexpected high prevalence of genotype 5a in a Greek island.

    Science.gov (United States)

    Karatapanis, Stylianos; Tsoplou, Panagiota; Papastergiou, Vasilios; Vasiageorgi, Aggeliki; Stampori, Maria; Saitis, Ioannis; Tsitsopoulos, Eustathios; Lisgos, Phillipos; Skorda, Lamprini; Ketikoglou, Ioannis; Goulis, Ioannis

    2012-02-01

    Hepatitis C virus (HCV) genotype 5 (G5) is a rare genotype reported mainly in South Africa. However, increasing data suggest the sporadic presence of this genotype in different European countries. To assess the epidemiology of HCV-G5 in Greece, genotyping was performed in 973 consecutive patients infected with HCV, referred to 7 hepatology centers throughout Greece, from January 2005 to December 2009. Genotype 5a (19 patients, 1.9%) was the fifth most prevalent genotype after genotype 1 (408 patients, 41.9%), genotype 3 (318 patients, 32.7%), genotype 4 (158 patients, 16.2%), and genotype 2 (70 patients, 7.2%). The majority of patients infected with G5 (16/19,84.2%) were referred to the General Hospital of Rhodes, an island in south-east Greece. The HCV genotype distribution in that particular island, indicates a particularly high G5 prevalence of 12.8%, after genotype 1 (40%), genotype 3 (28%), and genotype 4 (15%). Among the patients from Rhodes infected with G5 (n = 16), 13 (81.2%) were females. The mean age was 62.3 ± 6.5 years, significantly older than the patients infected with other HCV genotypes (mean age 40.6 ± 7.2, P < 0.0001). Nine out of the 16 cases (56.2%) presented features of high pre-treatment viral loads. Advanced liver fibrosis (Metavir F3-F4) was found in four out of five performed liver biopsies. Ten patients received treatment with pegylated interferon plus ribavirin and a sustained viral response were achieved in six cases. The source of infection is unknown but parenteral iatrogenic routes of transmission seem to have contributed significantly to the spread of genotype 5a in this region.

  12. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  13. DR_SEQAN: a PC/Windows-based software to evaluate drug resistance using human immunodeficiency virus type 1 genotypes

    Directory of Open Access Journals (Sweden)

    Menéndez-Arias Luis

    2006-03-01

    Full Text Available Abstract Background Genotypic assays based on DNA sequencing of part or the whole reverse transcriptase (RT- and protease (PR-coding regions of the human immunodeficiency virus type 1 (HIV-1 genome have become part of the routine clinical management of HIV-infected individuals. However, the results are difficult to interpret due to complex interactions between mutations found in viral genes. Results DR_SEQAN is a tool to analyze RT and PR sequences. The program output includes a list containing all of the amino acid changes found in the query sequence in comparison with the sequence of a wild-type HIV-1 strain. Translation of codons containing nucleotide mixtures can result in potential ambiguities or heterogeneities in the amino acid sequence. The program identifies all possible combinations of 2 or 3 amino acids that derive from translation of triplets containing nucleotide mixtures. In addition, when ambiguities affect codons relevant for drug resistance, DR_SEQAN allows the user to select the appropriate mutation to be considered by the program's drug resistance interpretation algorithm. Resistance is predicted using a rule-based algorithm, whose efficiency and accuracy has been tested with a large set of drug susceptibility data. Drug resistance predictions given by DR_SEQAN were consistent with phenotypic data and coherent with predictions provided by other publicly available algorithms. In addition, the program output provides two tables showing published drug susceptibility data and references for mutations and combinations of mutations found in the analyzed sequence. These data are retrieved from an integrated relational database, implemented in Microsoft Access, which includes two sets of non-redundant core tables (one for combinations of mutations in the PR and the other for combinations in the RT. Conclusion DR_SEQAN is an easy to use off-line application that provides expert advice on HIV genotypic resistance interpretation. It is

  14. Accuracy of the TRUGENE HIV-1 Genotyping Kit

    Science.gov (United States)

    Grant, Robert M.; Kuritzkes, Daniel R.; Johnson, Victoria A.; Mellors, John W.; Sullivan, John L.; Swanstrom, Ronald; D'Aquila, Richard T.; Van Gorder, Mark; Holodniy, Mark; Lloyd, Jr., Robert M.; Reid, Caroline; Morgan, Gillian F.; Winslow, Dean L.

    2003-01-01

    Drug resistance and poor virological responses are associated with well-characterized mutations in the viral reading frames that encode the proteins that are targeted by currently available antiretroviral drugs. An integrated system was developed that includes target gene amplification, DNA sequencing chemistry (TRUGENE HIV-1 Genotyping Kit), and hardware and interpretative software (the OpenGene DNA Sequencing System) for detection of mutations in the human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase sequences. The integrated system incorporates reverse transcription-PCR from extracted HIV-1 RNA, a coupled amplification and sequencing step (CLIP), polyacrylamide gel electrophoresis, semiautomated analysis of data, and generation of an interpretative report. To assess the accuracy and robustness of the assay system, 270 coded plasma specimens derived from nine patients were sent to six laboratories for blinded analysis. All specimens contained HIV-1 subtype B viruses. Results of 270 independent assays were compared to “gold standard” consensus sequences of the virus populations determined by sequence analysis of 16 to 20 clones of viral DNA amplicons derived from two independent PCRs using primers not used in the kit. The accuracy of the integrated system for nucleotide base identification was 98.7%, and the accuracy for codon identification at 54 sites associated with drug resistance was 97.6%. In a separate analysis of plasma spiked with infectious molecular clones, the assay reproducibly detected all 72 different drug resistance mutations that were evaluated. There were no significant differences in accuracy between laboratories, between technologists, between kit lots, or between days. This integrated assay system for the detection of HIV-1 drug resistance mutations has a high degree of accuracy and reproducibility in several laboratories. PMID:12682149

  15. Hepatitis B virus taxonomy and hepatitis B virus genotypes

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepatitis B virus (HBV) is a member of the hepadnavirus family. Hepadnaviruses can be found in both mammals (orthohepadnaviruses) and birds (avihepadnaviruses).The genetic variability of HBV is very high. There are eight genotypes of HBV and three clades of HBV isolates from apes that appear to be additional genotypes of HBV. Most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarises current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field,updates several recent reviews on HBV genotypes and subgenotypes.

  16. Proifle, spectrum and signiifcance of hepatitis B virus genotypes in chronic HBV-infected patients in Yunnan, China

    Institute of Scientific and Technical Information of China (English)

    Jing You; Bao-Zhang Tang; Hutcha Sriplung; Virasakdi Chongsuvivatwong; Alan Geater; Lin Zhuang; Jun-Hua Huang; Hong-Ying Chen; Lan Yu

    2008-01-01

    BACKGROUND:There are signiifcant variations in the geographical distribution of hepatitis B virus (HBV) genotypes throughout the world, and some genotypes are associated with different clinical outcomes. Eight genotypes of human HBV (designated A-H) have been reported. The present study was designed to examine the distribution of HBV genotypes among patients at various stages of chronic type B liver disease in Yunnan Province, China, and to explore its signiifcance and the relationship of HBV genotype with gender and age, clinical spectrum of chronic HBV infection, and viral replicative activity. METHODS:Serum samples from 126 patients with chronic HBV infection from Yunnan Province, including 26 chronic asymptomatic HBV carriers (ASC), 61 patients with chronic hepatitis B (CHB) (21 mild, 30 moderate and 10 severe), 20 patients with chronic fulminant hepatic failure (CFHF), 12 patients with HBV-related liver cirrhosis (LC) and 7 patients with HBV-related hepatocellular carcinoma (HCC) were analyzed using reverse dot blot (RDB) methodology, which is based on the reverse hybridization principle for HBV genotyping. The relations of HBV genotype with gender and age, clinical patterns, and serological data of the patients were analyzed. RESULTS: In this series, genotypes A, B, C, and D were found. 38.1%patients (48/126) belonged to B, 54.8%(69/126) to C, 0.8%(1/126) to D, 1.6%(2/126) to a mixture of B and C, and 1.6%(2/126) to a mixture of A and C. 3.2%patients (4/126) had unknown genotypes. No other genotypes (E, F, G, and H) were found. Genotypes B and C were predominant. There was a statistically signiifcant difference in the distributions of genotypes C and B (χ2=7.04, P=0.008), and C was the dominant genotype in all patient categories. The rate of genotype B in the mild CHB group was signiifcantly higher than that in the moderate and severe groups (χ2=12.16, P=0.0001; χ2=11.98, P=0.001, respectively), the ASC group (χ2=5.46, P=0.02), the CFHF group (χ2

  17. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  18. Identification of zoonotic genotypes of Giardia duodenalis.

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    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  19. Analyzing modified unimodular gravity via Lagrange multipliers

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    Sáez-Gómez, Diego

    2016-06-01

    The so-called unimodular version of general relativity is revisited. Unimodular gravity is constructed by fixing the determinant of the metric, which leads to the trace-free part of the equations instead of the usual Einstein field equations. Then a cosmological constant naturally arises as an integration constant. While unimodular gravity turns out to be equivalent to general relativity (GR) at the classical level, it provides important differences at the quantum level. Here we extend the unimodular constraint to some extensions of general relativity that have drawn a lot of attention over the last years—f (R ) gravity (or its scalar-tensor picture) and Gauss-Bonnet gravity. The corresponding unimodular version of such theories is constructed as well as the conformal transformation that relates the Einstein and Jordan frames for these nonminimally coupled theories. From the classical point of view, the unimodular versions of such extensions are completely equivalent to their originals, but an effective cosmological constant arises naturally, which may provide a richer description of the evolution of the Universe. Here we analyze the case of Starobisnky inflation and compare it with the original one.

  20. PSAIA – Protein Structure and Interaction Analyzer

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    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  1. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

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    Hu Shunling

    2011-03-01

    Full Text Available Abstract Background Six nucleotide (nt insertion in the 5'-noncoding region (NCR of the nucleoprotein (NP gene of Newcaslte disease virus (NDV is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX. Results In order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates. Conclusions The unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

  2. Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity.

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    Espinoza, Luis Luna; Beserra, Laila A R; Soares, Rodrigo M; Gregori, Fabio

    2016-12-01

    Avian nephritis virus (ANV), which belongs to the family Astroviridae, is associated with different clinical manifestations (including enteric disorders). Despite being frequently found in the avian industry worldwide, information regarding genetic features of these viruses in Brazil is scarce. Therefore, sixty fecal sample pools (5-6 birds of the same flock), representing 60 poultry farms from six Brazilian States, were screened using an astrovirus-specific hemi-nested-PCR assay targeting the conserved ORF1b gene, followed by nucleotide sequencing of amplified products. PCR and phylogenetic analysis confirmed the detection of 21 positive samples to ANV (35 %). In order to investigate the genetic diversity represented by these viruses, amplification, cloning and phylogenetic analysis of the deduced amino acid sequence of ORF2 gene were attempted. Eight samples were successfully cloned (generating 32 clones in total) and sequenced. Based on phylogenetic analysis of ORF2, sequences defined in this study were classified into three genotypes: genotype 5, which has already been described in birds, and two other novel genotypes, tentatively named genotype 8 and 9, all of which occurred in single or mixed infections. Moreover, high intra-genotypic diversity and co-circulation of distinct strains in a same host population were observed. This study revealed the presence of new strains of ANV in Brazilian poultry and their circulation in commercial chicken flocks.

  3. Endophytic bacteria in plant tissue culture: differences between easy- and difficult-to-propagate Prunus avium genotypes.

    Science.gov (United States)

    Quambusch, Mona; Pirttilä, Anna Maria; Tejesvi, Mysore V; Winkelmann, Traud; Bartsch, Melanie

    2014-05-01

    The endophytic bacterial communities of six Prunus avium L. genotypes differing in their growth patterns during in vitro propagation were identified by culture-dependent and culture-independent methods. Five morphologically distinct isolates from tissue culture material were identified by 16S rDNA sequence analysis. To detect and analyze the uncultivable fraction of endophytic bacteria, a clone library was established from the amplified 16S rDNA of total plant extract. Bacterial diversity within the clone libraries was analyzed by amplified ribosomal rDNA restriction analysis and by sequencing a clone for each identified operational taxonomic unit. The most abundant bacterial group was Mycobacterium sp., which was identified in the clone libraries of all analyzed Prunus genotypes. Other dominant bacterial genera identified in the easy-to-propagate genotypes were Rhodopseudomonas sp. and Microbacterium sp. Thus, the community structures in the easy- and difficult-to-propagate cherry genotypes differed significantly. The bacterial genera, which were previously reported to have plant growth-promoting effects, were detected only in genotypes with high propagation success, indicating a possible positive impact of these bacteria on in vitro propagation of P. avium, which was proven in an inoculation experiment.

  4. HPV Genotyping from the high risk mRNA Aptima assay- a direct approach using DNA from Aptima sample tubes.

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    Lillsunde Larsson, G; Kaliff, M; Bergengren, L; Karlsson, M G; Helenius, G

    2016-09-01

    The underlying cause of cervical cancer is an infection with the human papilloma virus (HPV) and HPV testing can be used for cervical cancer screening. The Aptima HPV assay from Hologic is an mRNA HPV test used to identify clinically relevant infections but the method does not discriminate between the different high risk genotypes. The aim of the current study was to evaluate if analyzed Aptima sample transfer tubes could be used as a source for HPV genotyping, using sample DNA. Study samples (n=108); were HPV-tested with mRNA Aptima assay and in parallel DNA was extracted and genotyped with Anyplex II HPV28. Analyzed mRNA Aptima tubes were thereafter used as source for a second DNA extraction and genotyping. Using mRNA Aptima result as reference, 90% of the samples (35/39) were high risk positive with the Anyplex II HPV28. Cohen's kappa 0.78 (95% CI: 0.66-0.90), sensitivity 0.90 (95% CI: 0.76-0.97) and specificity 0.90 (95% CI: 0.80-0.96). Two discordant samples carried low-risk genotypes (HPV 82 and HPV 44) and two were negative. DNA-genotyping results, in parallel to and after mRNA testing, were compared and differed significantly (McNemar test: P=0.021) possibly due to sample extraction volume difference. Cohen's kappa 0.81 (95% CI: 0.70-0.92), sensitivity 0.85 (95% CI: 0.74-0.93) and specificity 0.98 (95% CI: 0.88-1.00). In conclusion, analyzed mRNA Aptima sample tubes could be used as a source for DNA HPV genotyping. The sample volume used for extraction needs to be further explored.

  5. Prevalence of transfusion transmitted virus (TTV genotypes among HCC patients in Qaluobia governorate

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    Salim Rabab F

    2007-12-01

    Full Text Available Abstract Background Transfusion Transmitted virus (TTV is a novel single-stranded DNA virus that was identified in patients with post-transfusion hepatitis of non-A-G type. Clinical significance of TTV infection was analyzed in Egyptian hepatocellular carcinoma (HCC patients. The present study attempted to clarify these issues in Egypt, particularly in Qaluobia governorate, a country known for its high endemicity of liver disease and hepatotropic viruses. Methods TTV are determined in the serum of 60 samples obtained from HCC and liver cirrhosis (LC patients and 30 healthy individuals. TTV DNA is amplified by nested-PCR with TTV-specific mixed primers derived from the conserved open reading frame 1 (ORF1 region followed by digestion with restriction enzyme. Using the enzymes HaeIII, DraI, EcoRI and PstI, we are able to distinguish between the four TTV genotypes. Results The positive rate of TTV detection was 46.7%, 40% and 36.7% among HCC, LC patients and healthy individuals respectively. The more prevalence genotype was detected in the positive serum samples was genotype 1 (35.7% in HCC patients, (50% in LC and (63.3% in healthy individuals, Genotype 5 (21.4%, (25.5% and (18.2% in HCC, LC and healthy individuals respectively. Discussion This study indicates that TTV is commonly present in adult patients with HCC and LC as well as healthy individuals. The most prevalence TTV genotype is genotype 1. It seems that the infection neither contribute to the severity of liver disease no to the causation of HCC.

  6. Correlation of Primary Hepatocellular Carcinoma with HBV Genotypes, Subgenotypes and Gene Mutations in Gansu Province

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    Objective To investigate the occurrence of basal core promoter (BCP) and pre-C mutations in patients with hepatitis B virus (HBV) infection in Gansu Province, China, and to analyze the correlation of HBV mutation and HBV genotype with primary hepatocellular carcinoma (HCC). Methods PCR-RFLP was applied to detect HBV subgenotypes, and the presence of the pre-C and BCP mutations in 62 patients with HCC, 70 patients with hepatitis B induced liver cirrhosis (LC) and 90 patients with chronic hepatitis B (CHB). Results In HCC patients, genotype C was the major genotype (70.97%). The pre-C mutation was found in 59.68%, 31.43% and 16.67% patients with HCC, LC and CHB, respectively. The frequency of BCP mutations was signiifcantly different between patients with HCC, LC and CHB (74.19%, 51.43% and 37.78%, respectively;χ2=30.727, 19.540, respectively,P < 0.01). Patients in HCC group had a higher incidence of pre-C as well as BCP mutations compared to the other groups. The prevalence of pre-C and BCP mutations was signiifcantly higher in patients with genotype C1 (44.32% and 69.32%, respectively) compared to patients with other subgenotypes (P < 0.05). Conclusions The incidence of pre-C and BCP mutations increases with disease progression. Pre-C and BCP mutations frequently occur in patients with genotype C1. HBV genotype C, pre-C mutations and BCP mutations are closely related to the occurrence of HCC.

  7. Lewis blood genotypes of peptic ulcer and gastric cancer patients in Taiwan

    Institute of Scientific and Technical Information of China (English)

    Chi-Jung Yei; Jan-Gowth Chang; Mu-Chin Shih; Sheng-Fung Lin; Chao-Sung Chang; Fu-Tsong Ko; Kuang-Yang Lin; Ta-Chin Liu

    2005-01-01

    AIM: The Lewis b (Leb) antigen has been implicated as a possible binding site for attachment of Helicobacter pylori (H pylori)to gastric mucosa. However, studies both supporting and denying this association have been reported in the literature. Differences in secretor (Se)genotype have been suggested as a possible reason for previous discrepancies. Therefore, we investigated the relationship between Le and Se genotypes and H pylori infection rates in people with peptic ulcer or gastric cancer.METHODS: Peripheral blood samples were obtained from 347 patients with endoscopic evidence of peptic ulcer disease (235 cases of duodenal ulcer, 62 of gastric ulcer,and 50 of combined duodenal ulcer/gastric ulcer) and 51patients with gastric cancer on endoscopy. Peripheral blood specimens from 101 unrelated normal volunteers were used as controls. Lewis phenotype was determined using an antibody method, whereas Le and Se genotypes were determined by DNA amplification and restriction enzyme analysis. Gastric or duodenal biopsies taken from patients with endoscopic evidence of peptic ulcer or gastric cancer were cultured for H pylori. Isolates were identified as H pylori by morphology and production of urease and catalase. The H pylori infection status was also evaluated by rapid urease test (CLO test), and urea breath test (13C-UBT). Results of studies were analyzed by chi-square test (taken as significant).RESULTS: H pyloriwas isolated from 83.7% (303/347)of patients with peptic ulcer disease. Statistical analysis did not show any significant difference in Lewis phenotype or genotype between patients with and without H pylori infection. No significant association was found between Lewis genotype and peptic ulcer or gastric cancer.CONCLUSION: Lewis blood genotype or phenotype may not play a role in the pathogenesis of H pyloriinfection.However, bacterial strain differences and the presence of more than one attachment mechanism may limit the value of epidemiological studies in

  8. Effect of cryogenic grinding on volatile and fatty oil constituents of cumin (Cuminum cyminum L.) genotypes.

    Science.gov (United States)

    Sharma, L K; Agarwal, D; Rathore, S S; Malhotra, S K; Saxena, S N

    2016-06-01

    Effect of cryogenic grinding on recovery of volatile oil, fatty oil percentage and their constituents in two cumin (Cuminum cyminum L.) genotypes have been analyzed. Cryogenic grinding not only retains the volatiles but enhanced the recovery by 33.9 % in GC 4 and 43.5 % in RZ 209. A significant increase (29.9 %) over normal grinding in oil percentage was also observed in genotype RZ 209. This increase was, however, less (15.4 %) in genotype GC 4. Nineteen major compounds were identified in the essential oil of both genotypes. The two grinding techniques had significant effects on dependent variables, viz., volatile oil and monoterpenes. Cuminaldehyde was the main constituent in both genotypes, content of which increased from 48.2 to 56.1 % in GC 4 on cryo grinding. Content of terpines were found to decrease in cryo ground samples of GC 4 and either decrease or no change was found in RZ 209. Organoleptic test showed more pleasant aroma in cryo ground seeds of both the genotypes. Significant increase was also reported in fatty oil yield due to cryogenic grinding. Fatty acid methyl ester (FAME) analysis showed oleic acid as major FAME content of which increased from 88.1 to 94.9 % in RZ 209 and from 88.2 to 90.1 % in GC 4 on cryogenic grinding. Other prominent FAME were palmitic, palmitoleic and stearic acid. Results indicated commercial potential of cryogenic grinding technology for cumin in general and spices in particular for better retention of flavour and quality in spices.

  9. Evaluation of High Resolution Melting for MTHFR C677T Genotyping in Congenital Heart Disease.

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    Ying Wang

    Full Text Available High resolution melting (HRM is a simple, flexible and low-cost mutation screening technique. The methylenetetrahydrofolate reductase (MTHFR gene encoding a critical enzyme, potentially affects susceptibility to some congenital defects like congenital heart disease (CHD. We evaluate the performance of HRM for genotyping of the MTHFR gene C677T locus in CHD cases and healthy controls of Chinese Han population.A total of 315 blood samples from 147 CHD patients (male72, female 75 and 168 healthy controls (male 92, female 76 were enrolled in the study. HRM was utilized to genotype MTHFR C677T locus of all the samples. The results were compared to that of PCR-RFLP and Sanger sequencing. The association of the MTHFR C677T genotypes and the risk of CHD was analyzed using odds ratio with their 95% confidence interval (CIs from unconditional logistic regression.All the samples were successfully genotyped by HRM within 1 hour and 30 minutes while at least 6 hours were needed for PCR-RFLP and sequencing. The genotypes of MTHFR C677T CC, CT, and TT were 9.52%, 49.66%, and 40.82% in CHD group but 29.17%, 50% and 20.83% in control group, which were identical using both methods of HRM and PCR-RFLP, demonstrating the sensitivity and specificity of HRM were all 100%.MTHFR C677T is a potential risk factor for CHD in our local residents of Shandong province in China. HRM is a fast, sensitive, specific and reliable method for clinical application of genotyping.

  10. Global surveillance of emerging Influenza virus genotypes by mass spectrometry.

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    Rangarajan Sampath

    Full Text Available BACKGROUND: Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS technology. METHODS AND PRINCIPAL FINDINGS: Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 isolates. Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period (1999-2006 showed correct identification of the viral species and subtypes with >97% sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100% concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons (2005-2006 showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution. CONCLUSION/SIGNIFICANCE: Thus, rapid RT-PCR/ESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identify mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high-throughput method promises to become an integral component of influenza surveillance.

  11. The human leukocyte antigen genotype has a modest effect on the insulin gene polymorphism-associated susceptibility to type 1 diabetes in the Finnish population.

    Science.gov (United States)

    Laine, A P; Hermann, R; Knip, M; Simell, O; Akerblom, H K; Ilonen, J

    2004-01-01

    In addition to the known human leukocyte antigen (HLA)-associated risk, polymorphisms of insulin gene region show association with type 1 diabetes. We analyzed possible interactions between the HLA class II genotypes and -2221 MspI (insulin) INS gene polymorphism in Finnish population, using a series of 1331 diabetic children and 2222 healthy newborns. C/C genotype was increased among diabetic children compared to the controls (83.2 vs 70.1%). This genotype was slightly more common in diabetic children with low or moderate HLA-associated risk than in those with high risk, but INS gene effect was clear in all major HLA-risk genotypes and, thus, can be used as an additional risk prediction marker, irrespective of HLA genotypes.

  12. Molecular biological analysis of genotyping and phylogeny of severe acute respiratory syndrome associated coronavirus

    Institute of Scientific and Technical Information of China (English)

    王志刚; 李兰娟; 罗芸; 张俊彦; 王敏雅; 程苏云; 张严峻; 王晓萌; 卢亦愚; 吴南屏; 梅玲玲; 王赞信

    2004-01-01

    Background SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS) which has been associated with outbreaks of SARS in Guangdong, Hong Kong and Beijing of China, and other regions worldwide. SARS-CoV from human has shown some variations but its origin is still unknown. The genotyping and phylogeny of SARS-CoV were analyzed and reported in this paper. Methods Full or partial genomes of 44 SARS-CoV strains were collected from GenBank. The genotype, single nucleotide polymorphism and phylogeny of these SARS-CoV strains were analyzed by molecular biological, bioinformatic and epidemiological methods. Conclusion The results mentioned above suggest that SARS-CoV is responding to host immunological pressures and experiencing variation which provide clues, information and evidence of molecular biology for the clinical pathology, vaccine developing and epidemic investigation.

  13. Phylogenetic Analysis of Human Parvovirus B19 Sequences from Eleven Different Countries Confirms the Predominance of Genotype 1 and Suggests the Spread of Genotype 3b▿

    Science.gov (United States)

    Hübschen, Judith M.; Mihneva, Zefira; Mentis, Andreas F.; Schneider, François; Aboudy, Yair; Grossman, Zehava; Rudich, Hagit; Kasymbekova, Kalia; Sarv, Inna; Nedeljkovic, Jasminka; Tahita, Marc C.; Tarnagda, Zekiba; Ouedraogo, Jean-Bosco; Gerasimova, A. G.; Moskaleva, T. N.; Tikhonova, Nina T.; Chitadze, Nazibrola; Forbi, J. C.; Faneye, Adedayo O.; Otegbayo, Jesse A.; Charpentier, Emilie; Muller, Claude P.

    2009-01-01

    Phylogenetic analysis of 166 human parvovirus B19 sequences from 11 different countries attributed 91.57% to genotype 1, 5.42% to genotype 3b, and 3.01% to genotype 3a. Very similar viruses of genotype 1 circulated widely in Europe and Israel. Genotype 3b seems to show an increasing spread outside of Africa. PMID:19741071

  14. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

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    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  15. MARKER ASSISTED SELECTION FOR RESPONSE ATTACK OF VENTURIA INAEQUALIS IN DIFFERENT APPLE GENOTYPES

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    Bianca PATRASCU

    2006-08-01

    Full Text Available Apple scab caused by Venturia inaequalis, is an important disease, spread worldwide, having a major negative impact in apple production. In this study, there were analyzed four apple cultivars (Liberty, Florina, Starkrimson, Golden Spur, used as genitors in a diallel cross, and their seedlings. In the field, plants selection was done after presence or absence of the scab on leaves, and afterwards, phenotipically selection was completed by marker assisted selection. The molecular analysis conducted with the markers AL-07, AM-19 and U1400, detects the presence of the Vf gene, introgressed from Malus floribunda 821, which confers resistance to the pathogen, in the parental cultivars Liberty and Florina, and in all the F1 hybrids belonging these two genitors. Starkrimson and Golden Spur were susceptible scab parents with recessive homozygous genotype (vfvf, while Liberty and Florina were identified as heterozygous scab resistant parents with genotype (Vfvf. From the 60 apple seedlings analyzed, grouped in six combinations after their genitors (in each combinations were selected ten hybrids, among them five resistant and five susceptible to apple scab attack 28 were resistant and heterozygous for Vf gene (Vfvf and 32 were susceptible to scab with recessive homozygous genotypes (vfvf, being obtained almost Mendelian ratio for response to the pathogen, 50% resistant: 50% susceptible. Seedlings belonging to Starkrimson x Golden Spur were only recessive homozygous genotype (vfvf, and in combination resistant x resistant (Liberty x Florina were identified susceptible and resistant offspring, but at last, only with heterozygous for Vf gene (Vfvf and no one with dominant homozygous genotypes (VfVf.

  16. The molecular basis of beta-thalassemia intermedia in southern China: genotypic heterogeneity and phenotypic diversity

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    Sun Manna

    2010-02-01

    Full Text Available Abstract Background The clinical syndrome of thalassemia intermedia (TI results from the β-globin genotypes in combination with factors to produce fetal haemoglobin (HbF and/or co-inheritance of α-thalassemia. However, very little is currently known of the molecular basis of Chinese TI patients. Methods We systematically analyzed and characterized β-globin genotypes, α-thalassemia determinants, and known primary genetic modifiers linked to the production of HbF and the aggravation of α/β imbalance in 117 Chinese TI patients. Genotype-phenotype correlations were analyzed based on retrospective clinical observations. Results A total of 117 TI patients were divided into two major groups, namely heterozygous β-thalassemia (n = 20 in which 14 were characterized as having a mild TI with the Hb levels of 68-95 g/L except for five co-inherited αααanti-3.7 triplication and one carried a dominant mutation; and β-thalassemia homozygotes or compound heterozygotes for β-thalassemia and other β-globin defects in which the β+-thalassemia mutation was the most common (49/97, hemoglobin E (HbE variants was second (27/97, and deletional hereditary persistence of fetal hemoglobin (HPFH or δβ-thalassemia was third (11/97. Two novel mutations, Term CD+32(A→C and Cap+39(C→T, have been detected. Conclusions Chinese TI patients showed considerable heterogeneity, both phenotypically and genotypically. The clinical outcomes of our TI patients were mostly explained by the genotypes linked to the β- and α-globin gene cluster. However, for a group of 14 patients (13 β0/βN and 1 β+/βN with known heterozygous mutations of β-thalassemia and three with homozygous β-thalassemia (β0/β0, the existence of other causative genetic determinants is remaining to be molecularly defined.

  17. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

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    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  18. Phenolics, phytic acid, and phytase in Canadian-grown low-tannin faba bean (Vicia faba L.) genotypes.

    Science.gov (United States)

    Oomah, B Dave; Luc, Geneviéve; Leprelle, Claire; Drover, John C G; Harrison, Judith E; Olson, Mark

    2011-04-27

    Thirteen low-tannin faba bean genotypes grown at two locations in north central Alberta in 2009 were evaluated to investigate the variation in seed characteristics, phenolic and phytate contents, and phytase and antioxidant activities and to elucidate the relationship of these components as a breeding strategy. Seed characteristics including color were predominantly genotype dependent. The faba bean genotypes with total phenolic content ranging from 5.5 to 41.8 mg of catechin equiv/g of sample was linearly related to tannin content and the best predictor of antioxidant activity. Phytic acid content and phytase activity varied significantly among genotypes and between locations, ranging from 5.9 to 15.1 g/kg and from 1606 to 2154 FTU/kg sample, respectively. Multivariate data analysis performed on 19 components analyzed in this study using principal component analysis (PCA) and cluster analysis demonstrate that differences in seed characteristics, phenolic components, phytic acid, and phytase are major factors in segregating faba bean genotypes. The relatively low phytic acid content and high phytase activity of these low-tannin faba bean genotypes are beneficial/essential traits for their use in human and animal nutrition.

  19. KE and EE Genotypes of ICAM-1 Gene K469E Polymorphism Is Associated with Severe Preeclampsia

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    Ehsan Tabatabai

    2014-01-01

    Full Text Available Background. Preeclampsia (PE is one of the most important complications of pregnancy that is associated with significant mortality and morbidity in mother and fetus. Since the etiologic factors in its development are still unclear, we aimed to examine the intercellular adhesion molecule-1 (ICAM-1 gene K469E polymorphism in preeclamptic and control healthy women. Materials and Methods. Genetic polymorphism was analyzed in 192 PE and 186 healthy control women. PCR-RFLP method was used to identify K469E polymorphism. Results. The frequency of KK, KE, and EE genotypes of ICAM-1 gene was not different between PE patients and healthy pregnant women. Whereas, the frequency of KE and EE genotypes was significantly higher in severe PE than mild PE women and control group, and the risk of severe PE was 2.4-fold higher in subjects with KE genotype (OR, 2.4 [95% CI, 1 to 5.9]; P=0.03 and 3.3-fold higher in subjects with EE genotype (OR, 3.3 [95% CI, 1.2 to 9]; P=0.015 compared to individuals with KK genotype. Conclusion. We concluded that KE and EE genotypes of K469E polymorphism could increase risk of severe PE.

  20. Evaluation of glycoprotein B genotypes and load of CMV infecting blood leukocytes on prognosis of AIDS patients

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    Aldo Albuquerque Cunha

    2011-04-01

    Full Text Available BACKGROUND: Cytomegalovirus (CMV remains an important pathogen to immunocompromised patients even in the era of HAART. The present study aimed at evaluating the influence of CMV viral load and its gB genotypes on AIDS patients' outcome. METHODS: Blood samples of 101 AIDS patients were collected and tested for HIV load, CD4 - cell count and opportunistic pathogens, including CMV. Semi-nested PCRs were run to detect CMV genome and in the positive samples, gB genotyping and CMV load were established using enzymatic restriction and real time PCR, respectively. All patients were clinically followed for four years. RESULTS: In thirty patients (31% CMV was detected and all fatal cases (n = 5 occurred in this group of patients (p = 0.007, but only two patients had CMV disease (1.9%. However, viral load was not statistically associated with any analyzed parameter. The most frequently observed CMV genotype was gB2 (45.16% followed by gB3 (35.48%. gB2 genotype was more frequently found in patients with CD4-cell counts under 200 cells/mm³ (p = 0.0017, and almost all fatal cases (80% had gB2 genotype. CONCLUSIONS: Our study suggests that CMV and its polymorphisms in biologically relevant genes, such as the gB encoding ORF, may still influence the prognosis and outcome of AIDS patients. The gB2 genotype was associated to patient's bad outcome.

  1. Application of Microarray-Based Method for Functional SNP Genotyping in the Risk of Gastric Carcinoma in Chinese Population

    Institute of Scientific and Technical Information of China (English)

    Song Li; Meiju Ji; Peng Hou; Nongyue He; Hong Chen

    2006-01-01

    High-throughput SNP detection microarrays were used here to explore the relationship between 5,10-methylenetetrahydrofolate reductase (MTHFR) gene polymorphism C677T and the risk of gastric carcinoma among population in Jiangsu region, by genotyping the specimens from 170 patients with gastric carcinoma and 140 age- and sexmatched control subjects. PCR products were spotted onto a 3-aminopropyltriethoxysilane coated glass slide to fabricate a microarray, then interrogated by hybridization with dual-color probes (Cy3, Cy5) to determine the SNP genotype of each sample, and the relation between the genotypes and the risk of gastric carcinoma was analyzed. The frequencies of C677T genotype were CC(47.9%), CT(40%), CT(12.1%) in control group and CC(35.9%), CT(45.9%), TT(18.2%) in gastric carcinoma group, respectively. The individuals with 677CT+TT genotype group or 677TT had a 1.67-fold (95% CI: 1.06-2.64)or 2.67-fold (95% CI: 1.382-5.341) increased risk to develop gastric carcinoma compared with those having 677CC genotype.It was shown that the single nucleotide polymorphisms in the MTHFR gene are associated with the risk of gastric carcinoma in the Chinese population.

  2. Prevalence of lactase persistent/non-persistent genotypes and milk consumption in a young population in north-west Russia

    Institute of Scientific and Technical Information of China (English)

    Yulia Khabarova; Suvi Torniainen; Hanna Nurmi; Irm J(a)rvel(a); Mauri Isokoski; Kari Mattila

    2009-01-01

    AIM: To estimate the prevalence of the lactasenon-persistent genotype (C/C-13910) in a northernRussian population in accordance with ethnicity, and toevaluate self-reported milk consumption depending onlactase activity. METHODS: Blood samples for genotyping lactaseactivity, defining the C/T-13910 variant by polymerasechain reaction, and direct sequencing were taken from231 medical students of Russian origin aged 17-26 years.We analyzed milk product consumption by questionnairewhich was specially designed for the estimation of milkconsumption and abdominal complaints. RESULTS: We found that the prevalence of theC/C-13190 genotype in the northern Russian populationwas 35.6%. The other genotypes nearby C/T-13910and associated with lactase activity were not present inthe study population. The consumption of milk amongpeople with the non-persistent genotype tended to belower than among the lactose tolerant subjects, but wasnot statistically significant. CONCLUSION: An investigation of the lactase persistentgenotype in a northern Russian population has notbeen performed before. The genotype did not affect theconsumption of milk products in this population whichcould be explained by low consumption of milk productsamong the entire study population.

  3. The distribution of hepatitis B virus genotypes in Thailand.

    Science.gov (United States)

    Louisirirotchanakul, Suda; Olinger, Christophe M; Arunkaewchaemsri, Panida; Poovorawan, Yong; Kanoksinsombat, Chinda; Thongme, Chittima; Sa-Nguanmoo, Pattaratida; Krasae, Sasithorn; Theamboonlert, Apiradee; Oota, Sineenart; Fongsatitkul, Ladda; Puapairoj, Chintana; Promwong, Charuporn; Weber, Bernard

    2012-10-01

    Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.

  4. Prevalence of hepatitis C virus (HCV) genotypes in Balochistan.

    Science.gov (United States)

    Afridi, Sarwat; Naeem, Muhammad; Hussain, Abid; Kakar, Naseebullah; Babar, Masroor Ellahi; Ahmad, Jamil

    2009-07-01

    A molecular study was conducted to investigate the prevalence of Hepatitis C virus genotypes in HCV infected population of Balochistan. Forty HCV seropositive samples belonging to seven different locations of Balochistan were collected from different health care centres. Qualitative analysis of these samples using PCR resulted in 28 positive samples. The PCR positive samples were subjected to genotyping using the method described by Ohno et al (J Clin Microbiol 35:201-202, 1997) with minor modifications. Genotyping of 28 samples revealed three different genotypes including 3a, 3b and 1a. The most prevalent genotype was 3a with rate of 50% followed by genotype 3b and 1a, respectively. Nine samples remained untyped, suggesting the need of further investigation of genotypes in this region. It has been proposed that sequencing of these samples may be helpful to unreveal these genotypes and further epidemiology of HCV genotypes. Further more, extensive and large scale studies are needed to understand the epidemiology of HCV genotypes, as no such study has been carried in this province.

  5. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    SHI JinXiu; WANG Ying; HUANG Wei

    2009-01-01

    With the completion of Human Genome Project, International HapMap Project and the publication of copy number variation in human genome, a great number of accurate, rapid, and cost-effective tech-nologies for SNP analysis have been developed, promoting the research of the complex diseases. This article presents a review of widely used genotyping techniques, and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai (CHGCs).

  6. Celer: an Efficient Program for Genotype Elimination

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    Nicoletta De Francesco

    2010-08-01

    Full Text Available This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis. Removing superfluous genotypes that do not respect the Mendelian inheritance laws can speed up the linkage analysis. We have described in a formal way the Mendelian consistency problem and algorithms known in literature. The formalization helped to polish the algorithms and to find efficient data structures. The performance of the tool has been tested on a wide range of benchmarks. The results are promising if compared to other programs that treat Mendelian consistency.

  7. Development and application of genotyping technologies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    With the completion of Human Genome Project,International HapMap Project and the publication of copy number variation in human genome,a great number of accurate,rapid,and cost-effective technologies for SNP analysis have been developed,promoting the research of the complex diseases.This article presents a review of widely used genotyping techniques,and the progress and prospect in the study of complex diseases in terms of the projects and achievements of Chinese National Human Genome Center at Shanghai(CHGCs).

  8. Mucopolysaccharidosis IVA: correlation between genotype, phenotype and keratan sulfate levels.

    Science.gov (United States)

    Dũng, Vũ Chí; Tomatsu, Shunji; Montaño, Adriana M; Gottesman, Gary; Bober, Michael B; Mackenzie, William; Maeda, Miho; Mitchell, Grant A; Suzuki, Yasuyuki; Orii, Tadao

    2013-01-01

    Mucopolysaccharidosis IVA (MPS IVA) is caused by deficiency of N-acetylgalactosamine-6-sulfate sulfatase (GALNS), leading to systemic skeletal dysplasia because of excessive storage of keratan sulfate (KS) in chondrocytes. In an effort to determine a precise prognosis and personalized treatment, we aim to characterize clinical, biochemical, and molecular findings in MPS IVA patients, and to seek correlations between genotype, phenotype, and blood and urine KS levels. Mutation screening of GALNS gene was performed in 55 MPS IVA patients (severe: 36, attenuated: 13, undefined: 6) by genomic PCR followed by direct sequence analysis. Plasma and urine KS levels were measured by ELISA method. Genotype/phenotype/KS correlations were assessed when data were available. Fifty-three different mutations including 19 novel ones (41 missense, 2 nonsense, 4 small deletions, 1 insertion, and 5 splice-site) were identified in 55 patients and accounted for 93.6% of the analyzed mutant alleles. Thirty-nine mutations were associated with a severe phenotype and ten mutations with an attenuated one. Blood and urine KS concentrations in MPS IVA patients were age-dependent and markedly higher than those in age-matched normal controls. Plasma and urine KS levels in MPS IVA patients with the severe phenotype were higher than in those with an attenuated form. This study provides evidence for extensive allelic heterogeneity of MPS IVA. Accumulation of mutations as well as clinical descriptions and KS levels allows us to predict clinical severity more precisely and should be used for evaluation of responses to potential treatment options.

  9. Algorithmic approach to high-throughput molecular screening for alpha interferon-resistant genotypes in hepatitis C patients.

    Science.gov (United States)

    Sreevatsan, S; Bookout, J B; Ringpis, F M; Pottathil, M R; Marshall, D J; De Arruda, M; Murvine, C; Fors, L; Pottathil, R M; Barathur, R R

    1998-07-01

    This study was designed to analyze the feasibility and validity of using Cleavase Fragment Length Polymorphism (CFLP) analysis as an alternative to DNA sequencing for high-throughput screening of hepatitis C virus (HCV) genotypes in a high-volume molecular pathology laboratory setting. By using a 244-bp amplicon from the 5' untranslated region of the HCV genome, 61 clinical samples received for HCV reverse transcription-PCR (RT-PCR) were genotyped by this method. The genotype frequencies assigned by the CFLP method were 44.3% for type 1a, 26.2% for 1b, 13.1% for type 2b, and 5% type 3a. The results obtained by nucleotide sequence analysis provided 100% concordance with those obtained by CFLP analysis at the major genotype level, with resolvable differences as to subtype designations for five samples. CFLP analysis-derived HCV genotype frequencies also concurred with the national estimates (N. N. Zein et al., Ann. Intern. Med. 125:634-639, 1996). Reanalysis of 42 of these samples in parallel in a different research laboratory reproduced the CFLP fingerprints for 100% of the samples. Similarly, the major subtype designations for 19 samples subjected to different incubation temperature-time conditions were also 100% reproducible. Comparative cost analysis for genotyping of HCV by line probe assay, CFLP analysis, and automated DNA sequencing indicated that the average cost per amplicon was lowest for CFLP analysis, at $20 (direct costs). On the basis of these findings we propose that CFLP analysis is a robust, sensitive, specific, and an economical method for large-scale screening of HCV-infected patients for alpha interferon-resistant HCV genotypes. The paper describes an algorithm that uses as a reflex test the RT-PCR-based qualitative screening of samples for HCV detection and also addresses genotypes that are ambiguous.

  10. Association of estrogen receptor-alpha and vitamin D receptor genotypes with therapeutic response to calcium in postmenopausal Chinese women

    Institute of Scientific and Technical Information of China (English)

    Zhen-lin ZHANG; Yue-juan QIN; Qi-ren HUANG; Jin-wei HE; Miao LI; Qi ZHOU; Yun-qiu HU; Yu-juan LIU

    2004-01-01

    AIM: To investigate the correlation between calcium treatment in postmenopausal women and estrogen receptoralpha (ER-alpha) Xba Ⅰ and Pvu Ⅱ genotype and vitamin D receptor (VDR) Apa Ⅰ genotype. METHODS: One hundred fifteen postmenopausal Chinese women of Han population were enrolled and treated with calcichew-D3(1000 mg calcium and 400 U vitamin D3) daily for 1 year. At entry and after 1 year treatment, the bone mineral density (BMD), serum and urinary bone turnover biochemical markers were evaluated. ER-alpha and VDR genotype were analyzed using PCR-restriction fragment length polymorphism. RESULTS: After 1 year of calcium supplementation, a significant increase of BMD and a marked reduction in serum ALP and PTH levels, and a significant increase of serum 25-(OH) vitamin D level were observed (P<0.01 or P<0.05). At entry and after 1 year of treatment, no significant association was found between Xba Ⅰ, Pvu Ⅱ, and Apa Ⅰ genotypes and BMD in L1-4,Neck, and Troch, and all bone turnover marker levels. However, the percentage of change (median, QR) in Neck BMD was significantly different in homozygous XX [-4.14 (from -6.54 to -1.34)] in comparison with Xx [1.72(from -1.12 to 3.20)] (P<0.001) or xx [1.22 (from -1.74 to 3.06)] Xba Ⅰ ER-alpha genotype (P=0.001).CONCLUSION: Women with ER-α Xba Ⅰ genotype XX may have a higher risk of relatively fast bone mass loss in femoral neck after menopause and that they may have a poor responsiveness to calcium supplementation. The changes in BMD are not associated with ER-alpha Pvu Ⅱ genotype and VDR Apa Ⅰ genotype after 1 year of calcium supplementation.

  11. The Control Level of Bronchial Asthma in Dependence of Genotype by BCL1 Polymorphism of Glucocorticoids Receptor Gene and Body Mass Index

    Directory of Open Access Journals (Sweden)

    Vladyslava V. Kmyta

    2014-09-01

    Full Text Available The frequency of allelic genotypes by BclI polymorphism glucocorticoids receptor gene (GR had been studied in dependence of the control level of bronchial asthma (BA and body mass index (BMI, and also- connection between those indicators. 188 patient with BA and 95 almost healthy humans were investigated. Determination of single nucleotide BclI polymorphism GR gene performed by the method of polymerase chain reaction with following analyze of the length of restriction fragments. Our studies demonstrated connection between BA control, BclI polymorphism GR gene and BMI. Proved, that distribution C/C, C/G and G/G genotypes by BclI polymorphism in patients with BA showed reliable difference between patients with different BMI and connection G/G genotype with obesity. The reliable difference in distributing of genotype in dependence of BA control level has been proved: with controlled BA reliably often met C/C genotype, without control – G/G genotype. Therefore, proved, that frequency G/G genotype by BclI polymorphism GR gene in patients with BA with obesity and absence of control for the flowing of disease is reliably higher, that confirmed the role of this genotype, likewise, in obesity occurrence, so in absence of the control of disease.

  12. Age-related Infection with Cryptosporidium Species and Genotype in Pigs in China

    Institute of Scientific and Technical Information of China (English)

    YIN Jian Hai; YUAN Zhong Ying; CAI Hui Xia; SHEN Yu Juan; JIANG Yan Yan; ZHANG Jing; WANG Yan Juan; CAO Jian Ping

    2013-01-01

    Objective Pigs, as hosts of zoonotic Cryptosporidium species/genotypes, are domestic animals with public health significance. The present study was to characterize the infection rate and species/genotype of Cryptosporidium in pre-weaned and post-weaned pigs from Shanghai and Shaoxing, China. Methods A total of 208 fecal samples (42 from pre-weaned piglets, and 166 from post-weaned pigs) were examined by nested PCR of the 18S rRNA gene and analyzed by phylogenetic DNA fragment sequencing of secondary PCR products. Results Infection was detected in 79 samples (19/42 pre-weaned piglets, and 60/166 post-weaned pigs). C. suis (14/79) and Cryptosporidium pig genotype II (65/79) were identified; piglets were more susceptible to the former (13/14) and post-weaned pigs to the latter (59/65). Conclusion Infection of Cryptosporidium spp. in pigs was age-specific;piglets were more susceptible to C. suis while pigs were more susceptible to Cryptosporidium pig genotype II. These findings combined with the isolation of the two Cryptosporidium from water suggest that pigs may be a source of zoonotic Cryptosporidium water pollution. Improvements in pig feeding practices, sewage discharge, feces disposal and field worker protection are therefore important to prevent potential public health problems.

  13. Hepatitis E Virus Genotype 3 in Colombia: Survey in Patients with Clinical Diagnosis of Viral Hepatitis

    Science.gov (United States)

    Rendon, Julio; Hoyos, Maria Cristina; di Filippo, Diana; Cortes-Mancera, Fabian; Mantilla, Carolina; Velasquez, Maria Mercedes; Sepulveda, Maria Elsy; Restrepo, Juan Carlos; Jaramillo, Sergio; Arbelaez, Maria Patricia; Correa, Gonzalo; Navas, Maria-Cristina

    2016-01-01

    Background Hepatitis E virus is a major cause of outbreaks as well as sporadic hepatitis cases worldwide. The epidemiology of this enterically transmitted infection differs between developing and developed countries. The aims of this study were to describe HEV infection in Colombian patients and to characterize the genotype. Methods A prospective study was carried out on 40 patients aged over 15 with a clinical diagnosis of viral hepatitis, recruited from five primary health units in the city of Medellin, Colombia. Fecal samples obtained from the 40 consecutives cases were analyzed for HEV RNA using nested reverse transcription PCR for both ORF1 and ORF2-3. The amplicons were sequenced for phylogenetic analyses. Results Nine (22.5%) cases of HEV infection were identified in the study population. Three HEV strains obtained from patients were classified as genotype 3. No significant association was found between cases of Hepatitis E and the variables water drinking source, garbage collection system and contact with pigs. Conclusions This is the first prospective study of hepatitis E in Colombian patients. The circulation of the genotype 3 in this population is predictable considering the reports of the region and the identification of this genotype from pigs in the state of Antioquia, of which Medellin is the capital. Further studies are necessary to establish whether zoonotic transmission of HEV is important in Colombia. PMID:26886728

  14. Hepatitis E Virus Genotype 3 in Colombia: Survey in Patients with Clinical Diagnosis of Viral Hepatitis.

    Directory of Open Access Journals (Sweden)

    Julio Rendon

    Full Text Available Hepatitis E virus is a major cause of outbreaks as well as sporadic hepatitis cases worldwide. The epidemiology of this enterically transmitted infection differs between developing and developed countries. The aims of this study were to describe HEV infection in Colombian patients and to characterize the genotype.A prospective study was carried out on 40 patients aged over 15 with a clinical diagnosis of viral hepatitis, recruited from five primary health units in the city of Medellin, Colombia. Fecal samples obtained from the 40 consecutives cases were analyzed for HEV RNA using nested reverse transcription PCR for both ORF1 and ORF2-3. The amplicons were sequenced for phylogenetic analyses.Nine (22.5% cases of HEV infection were identified in the study population. Three HEV strains obtained from patients were classified as genotype 3. No significant association was found between cases of Hepatitis E and the variables water drinking source, garbage collection system and contact with pigs.This is the first prospective study of hepatitis E in Colombian patients. The circulation of the genotype 3 in this population is predictable considering the reports of the region and the identification of this genotype from pigs in the state of Antioquia, of which Medellin is the capital. Further studies are necessary to establish whether zoonotic transmission of HEV is important in Colombia.

  15. Genotype and ancestry modulate brain's DAT availability in healthy humans

    Energy Technology Data Exchange (ETDEWEB)

    Shumay, E.; Shumay, E.; Chen, J.; Fowler, J.S.; Volkow, N.D.

    2011-08-01

    The dopamine transporter (DAT) is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3) is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET) with [{sup 11}C] cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms - 3-UTR- and intron 8- VNTRs. The main findings are the following: (1) both polymorphisms analyzed as single genetic markers and in combination (haplotype) modulate DAT density in midbrain; (2) ethnic background and age influence the strength of these associations; and (3) age-related changes in DAT availability differ in the 3-UTR and intron8 - genotype groups.

  16. Rotavirus genotype distribution during the pre-vaccine period in Bolivia: 2007–2008

    Science.gov (United States)

    Rivera, Rosario; Forney, Kristen; Castro, Maria René; Rebolledo, Paulina A.; Mamani, Nataniel; Patzi, Maritza; Halkyer, Percy; Leon, Juan S.; Iñiguez, Volga

    2013-01-01

    Summary Objectives Rotavirus is the most important etiology of severe diarrhea in Bolivia. The monovalent attenuated human oral rotavirus vaccine Rotarix® was introduced in Bolivia in 2008. We describe the molecular epidemiology of circulating rotavirus strains before vaccine introduction. Methods Two thousand one hundred thirty-five diarrheal samples were collected from hospitals in four Bolivian cities during 2007–2008. Forty-three percent (445 of 1030 rotavirus-positive samples) were analyzed for G and P genotypes. Among those, 331 were electropherotyped by polyacrylamide gel electrophoresis. Disease severity was quantified using a modified Vesikari scale. Results Among the 445 samples, five genotypes were found to be prevalent: G9P[8] (33%), G1P[6] (17%), G2P[4] (13%), G9P[6] (12%), and G1P[8] (4%). Co-infections with two or more strains accounted for 14% of samples. The most prevalent strain, G9, showed greater electropherotype diversity compared to other serogroups. Strain G1P[6] generally infected younger children and peaked later in the year than other strains. No particular genotype was associated with a higher severity score, though there was a significant difference in the duration of diarrhea between genotypes. Conclusions During the 2-year pre-vaccine period, substantial diversity of rotavirus co-circulating strains was observed. These data constitute a baseline against which changes in circulating strains post-vaccine introduction can be monitored. PMID:23688547

  17. HIV-1 genotypic resistance profile of patients failing antiretroviral therapy in Paraná, Brazil

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    Paula Virginia Michelon Toledo

    2010-08-01

    Full Text Available Antiretroviral therapy (ART has reduced morbidity and mortality related to human immunodeficiency virus (HIV infection, but in spite of this advance, HIV mutations decrease antiretroviral susceptibility, thus contributing to treatment failure in patients. Genotyping HIV-1 allows the selection of new drugs after initial drug failure. This study evaluated the genotypic profile of HIV-1 isolates from treated (drug-experienced patients in Paraná, Brazil. The prevalence of mutations in reverse transcriptase (RT and protease (PR genes were assessed. We analyzed 467 genotypes of patients with HIV-1 viral loads above 1,000 copies/mL. Mutations at HIV-1 RT and PR genes and previously used ART regimens were recorded. The most prevalent RT mutations were: 184V (68.31%, 215YF (51.6%, 103NS (46%, 41L (39.4%, 67N (38.54%, 210W (23.5%, 190ASE (23.2%, and 181C (17.4%. PR mutations were 90M (33.33%, 82ATFS (29%, 46I (26.8% and 54V (22.2%. The prevalence of mutations was in line with previous national and international reports, except to nonnucleoside analogue reverse transcriptase inhibitors related mutations, which were more prevalent in this study. Previous exposure to antiretroviral drugs was associated with genotypic resistance to specific drugs, leading to treatment failure in HIV patients.

  18. A High-throughput Genomic Tool: Diversity Array Technology Complementary for Rice Genotyping

    Institute of Scientific and Technical Information of China (English)

    Yong Xie; Kenneth McNally; Cheng-Yun Li; Hei Leung; You-Yong Zhu

    2006-01-01

    Diversity array technology (DArTTM) was a genotyping tool characterized gel-independent and high throughput.The main purpose of present study is to validate DArT for rice (Oryza sativa L.)genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a generalpurpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc (Numerical taxonomy system for cluster and ordination analysis, v. 2.02j) software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple Sequence repeats genotyping outline and varieties' pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.

  19. ADORA2A genotype modulates interoceptive and exteroceptive processing in a fronto-insular network.

    Science.gov (United States)

    Geiger, Maximilian J; Domschke, Katharina; Homola, György A; Schulz, Stefan M; Nowak, Johannes; Akhrif, Atae; Pauli, Paul; Deckert, Jürgen; Neufang, Susanne

    2016-08-01

    Facilitated processing of interoceptive and exteroceptive information in the salience network is suggested to promote the development of anxiety and anxiety disorders. Here, it was investigated whether the adenosine 2 A receptor gene (ADORA2A) 1976T/C (rs5751876) variant - previously associated with anxiety disorders and anxiety-related phenotypes as well as general attentional efficiency -was involved in the regulation of this network. In detail, fMRI recordings of 65 healthy participants (female=35) were analyzed regarding ADORA2A genotype effects on brain connectivity related to (1) interoceptive processing in terms of functional connectivity resting-state fMRI, and (2) exteroceptive processing using dynamic causal modeling in task-based fMRI. In a subsample, cardiac interoceptive accuracy was furthermore measured via the Mental Tracking Task. ADORA2A genotype was found to modulate a fronto-insular network at rest (interoceptive processing) and while performing an executive control task (exteroceptive processing). Across both modalities, the ADORA2A TT risk genotype was associated with increased connectivity between the insula and the prefrontal cortex. The strength in connectivity correlated with interoceptive accuracy. It is concluded that alterations in fronto-insular connectivity are modulated by both the adenosinergic system and interoceptive accuracy. Thus, fronto-insular connectivity in synopsis with ADORA2A genotypic information could serve as combined biomarkers for personalized treatment approaches in anxiety disorders targeting exteroceptive and interoceptive dysfunction.

  20. Hepatitis E virus genotypes 1 and 3 in wastewater samples in Tunisia.

    Science.gov (United States)

    Béji-Hamza, A; Hassine-Zaafrane, M; Khélifi-Gharbi, H; Della Libera, S; Iaconelli, M; Muscillo, M; Petricca, S; Ciccaglione, A R; Bruni, R; Taffon, S; Aouni, M; La Rosa, G

    2015-01-01

    Hepatitis E represents an important public-health concern throughout the world. It is one of the leading causes of hepatitis in North Africa, Asia and the Middle East. In Tunisia, the true burden of HEV infection is still unknown. The objectives of the present study were to assess the occurrence of hepatitis E virus in Tunisia through the monitoring of urban sewage and to characterize the strains identified using molecular assays. A total of 150 sewage samples (raw and treated) were collected from three wastewater treatment plants located in the regions of Monastir and Mahdia and analyzed by nested RT-PCR using a qualitative assay targeting the methyltransferase gene in ORF1. Of these, only three samples (2 %) were found to be positive for HEV, one belonging to genotype 1 and two to genotype 3. The results of the present study indicate a low level of virus excretion among the Tunisian population. Both genotypes 1 and 3 are circulating in this country, however, possibly causing sporadic infections. The presence of the zoonotic genotype 3, known to be transmitted to humans mainly by swine and demonstrated in Tunisia for the first time in this work, raises the question of possible reservoir species, since pork products are not consumed in this country, pigs are not bred, and wild boar is not endemic. Further studies will be needed to gather information on the occurrence and diversity of HEV strains circulating among humans and animals in Tunisia, and on possible animal reservoirs.

  1. Type-specific PCR assays for Babesia bovis msa-1 genotypes in Asia: Revisiting the genetic diversity in Sri Lanka, Mongolia, and Vietnam.

    Science.gov (United States)

    Liyanagunawardena, Nilukshi; Sivakumar, Thillaiampalam; Kothalawala, Hemal; Silva, Seekkuge Susil Priyantha; Battsetseg, Badgar; Lan, Dinh Thi Bich; Inoue, Noboru; Igarashi, Ikuo; Yokoyama, Naoaki

    2016-01-01

    Babesia bovis is the most virulent Babesia organism, resulting in a high mortality rate in cattle. The genetic diversity of B. bovis merozoite surface antigens (MSAs), such as MSA-1, MSA-2b, and MSA-2c, might be linked to altered immune profiles in the host animals. The present study aimed to develop type-specific PCR assays for Asian msa-1 genotypes, thereby re-analyzing the genetic diversity of msa-1 in Sri Lanka, Mongolia, and Vietnam. Specific primers were designed for nine Asian msa-1 genotypes, which had been detected based on the phylogeny constructed using msa-1 gene sequences retrieved from the GenBank database. Specificity of the type-specific PCR assays was confirmed using plasmids containing the inserts of msa-1 gene fragments that represent Asian genotypes. Furthermore, no amplicons were observed by these PCR assays when DNA samples of Babesia bigemina, Babesia ovata, Theileria annulata, Theileria orientalis, Trypanosoma evansi, Trypanosoma theileri, Anaplasma marginale, and Anaplasma bovis, and non-infected bovine blood were analyzed. In total, 109 B. bovis-positive blood DNA samples sourced from Sri Lanka (44 cattle), Mongolia (26 cattle), and Vietnam (23 cattle and 16 water buffaloes) were then screened by the type-specific PCR assays. The sequences derived from all of the PCR amplicons were phylogenetically analyzed. Out of 109 DNA samples, 23 (20 from cattle and 3 from water buffaloes) were positive for at least one genotype. In agreement with previous studies, five and four different genotypes were detected among the DNA samples from Sri Lanka and Vietnam, respectively. In contrast, four genotypes, including three novel genotypes, were detected from Mongolia. Five DNA samples were found to be co-infected with multiple genotypes. The sequences of the PCR amplicons clustered phylogenetically within the corresponding clades. These findings indicated that the type-specific PCR assays described herein are useful for the determination of genotypic

  2. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes

    Science.gov (United States)

    The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNPs) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local popula...

  3. Classification of cassava genotypes based on qualitative and quantitative data.

    Science.gov (United States)

    Oliveira, E J; Oliveira Filho, O S; Santos, V S

    2015-02-02

    We evaluated the genetic variation of cassava accessions based on qualitative (binomial and multicategorical) and quantitative traits (continuous). We characterized 95 accessions obtained from the Cassava Germplasm Bank of Embrapa Mandioca e Fruticultura; we evaluated these accessions for 13 continuous, 10 binary, and 25 multicategorical traits. First, we analyzed the accessions based only on quantitative traits; next, we conducted joint analysis (qualitative and quantitative traits) based on the Ward-MLM method, which performs clustering in two stages. According to the pseudo-F, pseudo-t2, and maximum likelihood criteria, we identified five and four groups based on quantitative trait and joint analysis, respectively. The smaller number of groups identified based on joint analysis may be related to the nature of the data. On the other hand, quantitative data are more subject to environmental effects in the phenotype expression; this results in the absence of genetic differences, thereby contributing to greater differentiation among accessions. For most of the accessions, the maximum probability of classification was >0.90, independent of the trait analyzed, indicating a good fit of the clustering method. Differences in clustering according to the type of data implied that analysis of quantitative and qualitative traits in cassava germplasm might explore different genomic regions. On the other hand, when joint analysis was used, the means and ranges of genetic distances were high, indicating that the Ward-MLM method is very useful for clustering genotypes when there are several phenotypic traits, such as in the case of genetic resources and breeding programs.

  4. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

  5. Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

    Science.gov (United States)

    Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

    2016-11-01

    Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

  6. Efavirenz and Metabolites in Cerebrospinal Fluid: Relationship with CYP2B6 c.516G→T Genotype and Perturbed Blood-Brain Barrier Due to Tuberculous Meningitis

    Science.gov (United States)

    Chau, Tran Thi Hong; Fisher, Martin; Nelson, Mark; Winston, Alan; Else, Laura; Carr, Daniel F.; Taylor, Steven; Ustianowski, Andrew; Back, David; Pirmohamed, Munir; Solomon, Tom; Farrar, Jeremy; Törok, M. Estée; Khoo, Saye

    2016-01-01

    Efavirenz (EFZ) has been associated with neuropsychiatric side effects. Recently, the 8-hydroxy-EFZ (8OH-EFZ) metabolite has been shown to be a potent neurotoxin in vitro, inducing neuronal damage at concentrations of 3.3 ng/ml. EFZ induced similar neuronal damage at concentrations of 31.6 ng/ml. We investigated the effect of genotype and blood-brain barrier integrity on EFZ metabolite concentrations in cerebrospinal fluid (CSF). We measured CSF drug concentrations in subjects from two separate study populations: 47 subjects with tuberculous meningitis (TBM) coinfection in Vietnam receiving 800 mg EFZ with standard antituberculous treatment and 25 subjects from the PARTITION study in the United Kingdom without central nervous system infection receiving 600 mg EFZ. EFZ and metabolite concentrations in CSF and plasma were measured and compared with estimates of effectiveness and neurotoxicity from available published in vitro and in vivo data. The effect of the CYP2B6 c.516G→T genotype (GG genotype, fast EFV metabolizer status; GT genotype, intermediate EFV metabolizer status; TT genotype, slow EFV metabolizer status) was examined. The mean CSF concentrations of EFZ and 8OH-EFZ in the TBM group were 60.3 and 39.3 ng/ml, respectively, and those in the no-TBM group were 15.0 and 5.9 ng/ml, respectively. Plasma EFZ and 8OH-EFZ concentrations were similar between the two groups. CSF EFZ concentrations were above the in vitro toxic concentration in 76% of samples (GG genotype, 61%; GT genotype, 90%; TT genotype, 100%) in the TBM group and 13% of samples (GG genotype, 0%; GT genotype, 18%; TT genotype, 50%) in the no-TBM group. CSF 8OH-EFZ concentrations were above the in vitro toxic concentration in 98% of the TBM group and 87% of the no-TBM group; levels were independent of genotype but correlated with the CSF/plasma albumin ratio. Potentially neurotoxic concentrations of 8OH-EFZ are frequently observed in CSF independently of the CYP2B6 genotype, particularly in those

  7. Evaluation of genotype and environment effects on taste and aroma flavor components of Spanish fresh tomato varieties.

    Science.gov (United States)

    Cebolla-Cornejo, Jaime; Roselló, Salvador; Valcárcel, Mercedes; Serrano, Elena; Beltrán, Joaquim; Nuez, Fernando

    2011-03-23

    Taste and aroma related compounds have been analyzed in a collection of four traditional varieties and two tomato hybrids, representing a wide variability in fruit shape and color, grown in different environments: screenhouse and open field. Protected cultivation tended to show lower sugar concentration (fructose and glucose) but similar acid contents (citric, malic, and glutamic acids). The decreased levels of sucrose equivalents and the similar ratios of sucrose equivalents to citric or glutamic acid contents indicated that protected cultivation, despite being useful to reduce the incidence of pests and viral diseases, reduces the organoleptic quality. Additionally, it doubles the interaccession variability and increased the level of intra-accession variability. In the case of aroma, the genotypic effect was considerably higher than the environmental component on the 12 main volatiles analyzed. Only hexanal and methyl salicylate were significantly affected by environment, while 10 out of 12 volatiles were affected by the genotype. Biplot analysis showed that, even in considerably different environments, it is possible to identify genotype-dependent main aroma profiles. In the case of 13 background volatiles, the environment showed no significant effects and the genotypic effect was lower, though it is possible to identify genotypic trends in background notes.

  8. Resistance of soybean genotypes to Bemisia tabaci (Genn.) Biotype B (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Vieira, S S; Bueno, A F; Boff, M I C; Bueno, R C O F; Hoffman-Campo, C B

    2011-01-01

    The silverleaf whitefly Bemisia tabaci (Genn.) biotype B has become a serious problem for soybean cultivation because it can significantly reduce soybean productivity. The use of soybean cultivars resistant to whitefly attack is an important strategy in an integrated pest management (IPM) program. This study evaluated the preference for oviposition and colonization by B. tabaci biotype B on different soybean genotypes. In the free-choice test, the genotypes studied were 'IAC 17' and 'IAC 19' as the standards for resistance and 'IAC Holambra Stwart' as the standard for susceptibility, as well as BABR01-0492, BABR01-0173, BABR01-1259, BABR01-1576, BABR99-4021HC, BABR99-4021HP, 'Barreiras', 'Conquista', 'Corisco', 'BRS Gralha', PI274454, PI227687, and PI171451. In the no-choice test, the four best genotypes selected in the free-choice test, in addition to the susceptible and resistant standards were evaluated. Our data indicated 'Barreiras' as the most resistant genotype against B. tabaci biotype B. 'BRS Gralha', which was the least attractive to whitefly adults in the free-choice test, did not show resistance to insect attack when they were confined in cages in the no-choice test. Despite the high number of eggs observed, BABR01-1576 and BABR99-4021HC showed a reduced number of nymphs, indicating antibiosis. The genotypes with a high level of resistance can be used as a tool against B. tabaci in IPM or as a source of resistance in plant-breeding programs.

  9. Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes

    NARCIS (Netherlands)

    Babaei, A.; Tabaei-Aghdaei, S.R.; Khosh-Khui, M.; Omidbaigi, R.; Naghavi, M.R.; Esselink, G.D.; Smulders, M.J.M.

    2007-01-01

    Background - Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 a

  10. Effect of flour polymeric proteins on dough thermal properties and breadmaking characteristics for hard red spring wheat genotypes

    Science.gov (United States)

    The aim of this research was to investigate the effect of variation of flour polymeric proteins on rheological properties of dough under continuous mixing and thermal treatment for hard red spring (HRS) wheat genotypes grown in North Dakota, USA. Flour polymeric proteins were analyzed by size exclus...

  11. Genotypic and environmental effects on cottonseed oil, nitrogen, and gossypol contents in eighteen years Regional High Quality tests

    Science.gov (United States)

    Determination of environmental influence on seed traits is critical for genetic improvement of seed quality in Upland cotton (Gossypium hirsutum L.). The objective of this study was to analyze the relative contribution of environment and genotype (G) for seed oil, nitrogen (N), and gossypol content...

  12. HMR Log Analyzer: Analyze Web Application Logs Over Hadoop MapReduce

    Directory of Open Access Journals (Sweden)

    Sayalee Narkhede

    2013-07-01

    Full Text Available In today’s Internet world, log file analysis is becoming a necessary task for analyzing the customer’sbehavior in order to improve advertising and sales as well as for datasets like environment, medical,banking system it is important to analyze the log data to get required knowledge from it. Web mining is theprocess of discovering the knowledge from the web data. Log files are getting generated very fast at therate of 1-10 Mb/s per machine, a single data center can generate tens of terabytes of log data in a day.These datasets are huge. In order to analyze such large datasets we need parallel processing system andreliable data storage mechanism. Virtual database system is an effective solution for integrating the databut it becomes inefficient for large datasets. The Hadoop framework provides reliable data storage byHadoop Distributed File System and MapReduce programming model which is a parallel processingsystem for large datasets. Hadoop distributed file system breaks up input data and sends fractions of theoriginal data to several machines in hadoop cluster to hold blocks of data. This mechanism helps toprocess log data in parallel using all the machines in the hadoop cluster and computes result efficiently.The dominant approach provided by hadoop to “Store first query later”, loads the data to the HadoopDistributed File System and then executes queries written in Pig Latin. This approach reduces the responsetime as well as the load on to the end system. This paper proposes a log analysis system using HadoopMapReduce which will provide accurate results in minimum response time.

  13. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

  14. Stress, genotype and norepinephrine in the prediction of mouse behavior using reinforcement learning.

    Science.gov (United States)

    Luksys, Gediminas; Gerstner, Wulfram; Sandi, Carmen

    2009-09-01

    Individual behavioral performance during learning is known to be affected by modulatory factors, such as stress and motivation, and by genetic predispositions that influence sensitivity to these factors. Despite numerous studies, no integrative framework is available that could predict how a given animal would perform a certain learning task in a realistic situation. We found that a simple reinforcement learning model can predict mouse behavior in a hole-box conditioning task if model metaparameters are dynamically controlled on the basis of the mouse's genotype and phenotype, stress conditions, recent performance feedback and pharmacological manipulations of adrenergic alpha-2 receptors. We find that stress and motivation affect behavioral performance by altering the exploration-exploitation balance in a genotype-dependent manner. Our results also provide computational insights into how an inverted U-shape relation between stress/arousal/norepinephrine levels and behavioral performance could be explained through changes in task performance accuracy and future reward discounting.

  15. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  16. Phenotypic characteristics of isolates of Aspergillus section Fumigati from different geographic origins and their relationships with genotypic characteristics

    Directory of Open Access Journals (Sweden)

    del Rocío Reyes-Montes María

    2011-05-01

    Full Text Available Abstract Background Epidemiological studies worldwide have shown that A. fumigatus exhibits important phenotypic and genotypic diversity, and these findings have been of great importance in improving the diagnosis and treatment of diseases caused by this fungus. However, few studies have been carried out related to the epidemiology of this fungus in Latin America. This study´s aim is to report on the epidemiology of the fungus by analyzing the phenotypic variability of Aspergillus section Fumigati isolates from different Latin American countries and the relationship between this variability, the geographical origin and genotypic characteristics. Methods We analyzed the phenotypic characteristics (macro- and micromorphology, conidial size, vesicles size, antifungal susceptibility and thermotolerance at 28, 37 and 48°C of A. section Fumigati isolates from Mexico (MX, Argentina (AR, Peru (PE and France (FR. The results were analyzed using analysis of variance (ANOVA and Tukey's multiple comparison test to detect significant differences. Two dendrograms among isolates were obtained with UPGMA using the Euclidean distance index. One was drawn for phenotypic data, and the other for phenotypic and genotypic data. A PCoA was done for shown isolates in a space of reduced dimensionality. In order to determine the degree of association between the phenotypic and genotypic characteristics AFLP, we calculated the correlation between parwise Euclidean distance matrices of both data sets with the nonparametric Mantel test. Results No variability was found in the macromorphology of the studied isolates; however, the micromorphology and growth rate showed that the PE isolates grew at a faster rate and exhibited the widest vesicles in comparison to the isolates from MX, AR and FR. The dendrogram constructed with phenotypic data showed three distinct groups. The group I and II were formed with isolates from PE and FR, respectively, while group III was formed

  17. Chlorophyll a fluorescence to phenotype wheat genotypes for heat tolerance

    DEFF Research Database (Denmark)

    Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto

    In prospects of global climate change, heat stress is a rising constraint for the productivity of wheat (Triticum aestivum L.). It is a heat-susceptible crop beyond 17-23oC temperature throughout its phenological stages, flowering phase being the most sensitive stage. Chlorophyll a fluorescence...... for 72h was appropriate to induce genotype dependent variation in Fv/Fm. This standardized protocol was used to phenotype wheat genotypes until the variation in the genotypes was consistently high with increased heritability for the trait, Fv/Fm. Mass screening of 1273 wheat genotypes in a milder stress...

  18. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

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    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  19. Trichothecene genotypes of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, Dinorah; Calero, Natalia; Mionetto, Ana; Bettucci, Lina

    2013-03-01

    Gibberella zeae (Schwein.) Petch (anamorph F. graminearum Schwabe) is the primary causal agent of FHB of wheat in Uruguay. In the last decade, F. graminearum has produced destructive epidemics on wheat in Uruguay, causing yield losses and price discounts due to reduced seed quality. Strains of F. graminearum clade usually express one of three strain-specific profiles of trichothecene metabolites: nivalenol and its acetylated derivatives (NIV chemotype), deoxynivalenol and 3-acetyldeoxynivalenol (3-AcDON chemotype), or deoxynivalenol and 15-acetyldeoxynivalenol (15-AcDON chemotype). A multiplex PCR assay of Tri3, Tri5, and Tri7 was used to determine the trichothecene genotype of 111 strains of F. graminearum collected during 2003 and 2009 growing seasons from fields located in the major wheat production area of Uruguay. The result showed that all except one of the isolates were of DON genotype, with the remainder of NIV genotype in years 2003 and 2009. All strains with the DON genotype were also of the 15-AcDON genotype in 2003 and nearly all (45/50) in 2009. No DON/3-AcDON genotypes were found in either growing season. No potential shifts in the populations were found in the trichothecene genotypes between 2003 and the 2009 epidemic FHB harvest seasons. This study provides the first data on trichothecene genotypes of F. graminearum strains isolated from wheat in Uruguay and add to the current regional knowledge of trichothecene genotypes.

  20. Genotype X environment interactions. II. Some genetical considerations.

    Science.gov (United States)

    Mather, K

    1975-08-01

    An algebraic formulation, alternative to that of Mather and Jones (1958) and hierarchial rather than factorial in nauture, is presented for describing the differences among the phenotypes produced by a number of genotypes each grown in each of a number of environments. This formuationdoes not include terms representing statistical interactions between genotypes and environments: it depends instead on comparisons between the different genotypes in their variation over the relevant ranges of environemnts. The two-line case is considered ant eht condition established for linearity of the regress ion of genotype X enviroment interaction (g in Mather and Jones' formulation) on overall effect of the envirronment (e in Mather and Jones' formulation)...

  1. Usage of data mining for analyzing customer mindset

    Directory of Open Access Journals (Sweden)

    Priti Sadaria

    2012-09-01

    Full Text Available As this is the era of Information Technology, no filed remains untouched by computer science. The technology has become an integral part of the business process. By implementing different data mining techniques and algorithms on the feedback collected from the customer, we can analyzed the data. With help of this analyzed information we have clear idea about the customer’s mind set and can take meaning full decision for production and marketing of particular product. To study about customer mindset differentmodels like classification and association models are used in data mining.

  2. Portable Programmable Multifunction Body Fluids Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Liquid Logic proposes to develop a very capable analyzer based on its digital microfluidic technology. Such an analyzer would be:  Capable of both...

  3. Resistant starch content among several sorghum (Sorghum bicolor) genotypes and the effect of heat treatment on resistant starch retention in two genotypes.

    Science.gov (United States)

    Teixeira, Natália de Carvalho; Queiroz, Valéria Aparecida Vieira; Rocha, Maria Clara; Amorim, Aline Cristina Pinheiro; Soares, Thayana Oliveira; Monteiro, Marlene Azevedo Magalhães; de Menezes, Cícero Beserra; Schaffert, Robert Eugene; Garcia, Maria Aparecida Vieira Teixeira; Junqueira, Roberto Gonçalves

    2016-04-15

    The resistant starch (RS) contents in 49 sorghum genotypes and the effects of heat treatment using dry and wet heat on the grain and flour from two sorghum genotypes were investigated. The results showed a wide variation in the RS contents of the genotypes analyzed. The RS mean values were grouped into six distinct groups and ranged from 0.31±0.33 g/100 g to 65.66±5.46 g/100 g sorghum flour on dry basis. Dry heat causes minor losses in the RS content with retentions of up to 97.19±1.92% of this compound, whereas wet heat retained at most 6.98±0.43% of the RS. The SC 59 and (SSN76)FC6608 RED KAFIR BAZINE (ASA N23) cultivars, which have an average RS content of 65.51 g/100 g, were appropriate for human consumption, and the use of dry heat is presented as a better alternative for the preservation of RS in heat-treated grains.

  4. Immigrant Integration: Acculturation and Social Integration

    Directory of Open Access Journals (Sweden)

    Astrid HAMBERGER

    2009-11-01

    Full Text Available This article tackles the concept of “immigrant integration” as it is analyzed by different authors in the international migration field. In this article, I will use the terms “refugee” and “immigrant” as equivalent to each other due to the interchangeable character of these concepts throughout the integration literature. First, the article brings into discussion the definitional and conceptual battle around the concept of immigrant “integration”, and second, it will describe and analyze cultural and social integration with their presupposing processes.

  5. Understanding and utilization of genotype-by-environment interaction in maize breeding

    Directory of Open Access Journals (Sweden)

    Babić Vojka

    2010-01-01

    Full Text Available Due to the interaction and noise in the experiments, yield trails for studying varieties are carried out in numerous locations and in the course of several years. Data of such trials have three principle tasks: to evaluate precisely and to predict the yield on the basis of limited experimental data; to determine stability and explain variability in the response of genotypes across locations; and to be a good guide for the selection of the best genotype for sowing under new agroecological conditions. The yield prediction without the inclusion of the interaction with the environments is incomplete and imprecise. Therefore, a great deal of breeding and agronomic studies are devoted to observing of the interaction via multilocation trials with replicates with the aim to use the interaction to obtain the maximum yield in any environment. Fifteen maize hybrids were analyzed in 24 environments. As the interaction participates in the total sum of squares with 6%, and genotypes with 2%, the interaction deserves observations more detailed than the classical analysis of variance (ANOVA provides it. With a view to observe the interaction effect in detail in order to prove better understanding of genotypes, environments and their interactions AMMI (Additive Main Effect and Multiplicative Interaction and the cluster analysis were applied. The partition of the interaction into the principal components by the PCA analysis (Principal Components Analysis revealed a part of systematic variations in the interaction. These variations are attributed to the length of the growing season in genotypes and to the precipitation sum during the growing season in environments. Results of grouping by the cluster analysis are in high accordance with grouping observed in the biplot of the AMMI1 model.

  6. Pseudomonas aeruginosa in Dairy Goats: Genotypic and Phenotypic Comparison of Intramammary and Environmental Isolates

    Science.gov (United States)

    Scaccabarozzi, Licia; Leoni, Livia; Ballarini, Annalisa; Barberio, Antonio; Locatelli, Clara; Casula, Antonio; Bronzo, Valerio; Pisoni, Giuliano; Jousson, Olivier; Morandi, Stefano; Rapetti, Luca; García-Fernández, Aurora; Moroni, Paolo

    2015-01-01

    Following the identification of a case of severe clinical mastitis in a Saanen dairy goat (goat A), an average of 26 lactating goats in the herd was monitored over a period of 11 months. Milk microbiological analysis revealed the presence of Pseudomonas aeruginosa in 7 of the goats. Among these 7 does, only goat A showed clinical signs of mastitis. The 7 P. aeruginosa isolates from the goat milk and 26 P. aeruginosa isolates from environmental samples were clustered by RAPD-PCR and PFGE analyses in 3 genotypes (G1, G2, G3) and 4 clusters (A, B, C, D), respectively. PFGE clusters A and B correlated with the G1 genotype and included the 7 milk isolates. Although it was not possible to identify the infection source, these results strongly suggest a spreading of the infection from goat A. Clusters C and D overlapped with genotypes G2 and G3, respectively, and included only environmental isolates. The outcome of the antimicrobial susceptibility test performed on the isolates revealed 2 main patterns of multiple resistance to beta-lactam antibiotics and macrolides. Virulence related phenotypes were analyzed, such as swarming and swimming motility, production of biofilm and production of secreted virulence factors. The isolates had distinct phenotypic profiles, corresponding to genotypes G1, G2 and G3. Overall, correlation analysis showed a strong correlation between sampling source, RAPD genotype, PFGE clusters, and phenotypic clusters. The comparison of the levels of virulence related phenotypes did not indicate a higher pathogenic potential in the milk isolates as compared to the environmental isolates. PMID:26606430

  7. Influence of Atg5 mutation in SLE depends on functional IL-10 genotype.

    Directory of Open Access Journals (Sweden)

    Patricia López

    Full Text Available Increasing evidence supports the involvement of autophagy in the etiopathology of autoimmune diseases. Despite the identification of autophagy-related protein (Atg-5 as one of the susceptibility loci in systemic Lupus erythematosus (SLE, the consequences of the carriage of these mutations for patients remain unclear. The present work analyzed the association of Atg5 rs573775 single nucleotide polymorphism (SNP with SLE susceptibility, IFNα, TNFα and IL-10 serum levels, and clinical features, in 115 patients and 170 healthy individuals. Patients who where carriers of the rs573775 T* minor allele presented lower IFNα levels than those with the wild genotype, whereas the opposite result was detected for IL-10. Thus, since IL-10 production was regulated by rs1800896 polymorphisms, we evaluated the effect of this Atg5 mutation in genetically high and low IL-10 producers. Interestingly, we found that the rs573775 T* allele was a risk factor for SLE in carriers of the high IL-10 producer genotype, but not among genetically low producers. Moreover, IL-10 genotype influences SLE features in patients presenting the Atg5 mutated allele. Specifically, carriage of the rs573775 T* allele led to IL-10 upregulation, reduced IFNα and TNFα production and a low frequency of cytopenia in patients with the high IL-10 producer genotype, whereas patients with the same Atg5 allele that were low IL-10 producers presented reduced amounts of all these cytokines, had a lower prevalence of anti-dsDNA antibodies and the latest onset age. In conclusion, the Atg5 rs573775 T* allele seems to influence SLE susceptibility, cytokine production and disease features depending on other factors such as functional IL-10 genotype.

  8. Helicobacter pylori in Vegetables and Salads: Genotyping and Antimicrobial Resistance Properties

    Directory of Open Access Journals (Sweden)

    Emad Yahaghi

    2014-01-01

    Full Text Available From a clinical and epidemiological perspective, it is important to know which genotypes and antibiotic resistance patterns are present in H. pylori strains isolated from salads and vegetables. Therefore, the present investigation was carried out to find this purpose. Three hundred eighty washed and unwashed vegetable samples and fifty commercial and traditional salad samples were collected from Isfahan, Iran. Samples were cultured and those found positive for H. pylori were analyzed using PCR. Antimicrobial susceptibility testing was performed using disk diffusion method. Seven out of 50 (14% salad and 52 out of 380 (13.68% vegetable samples harbored H. pylori. In addition, leek, lettuce, and cabbage were the most commonly contaminated samples (30%. The most prevalent virulence genes were oipA (86.44% and cagA (57.625. VacA s1a (37.28% and iceA1 (47.45% were the most prevalent genotypes. Forty different genotypic combinations were recognized. S1a/cagA+/iceA1/oipA+ (33.89%, s1a/cagA+/iceA2/oipA (30.50%, and m1a/cagA+/iceA1/oipA+ (28.81% were the most prevalent combined genotypes. Bacterial strains had the highest levels of resistance against metronidazole (77.96%, amoxicillin (67.79%, and ampicillin (61.01%. High similarity in the genotyping pattern of H. pylori among vegetable and salad samples and human specimens suggests that vegetable and salads may be the sources of the bacteria.

  9. Sex influences on the penetrance of HLA shared-epitope genotypes for rheumatoid arthritis

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    Meyer, J.M. [Virginia Commonwealth Univ., Richmond, VA (United States)] [and others

    1996-02-01

    The association between rheumatoid arthritis (RA) and HLA DRB1 alleles may arise through linkage disequilibrium with a disease locus or the direct involvement of HLA alleles in RA. In support of the latter possibility, the shared-epitope hypothesis has been postulated, stating that conformationally similar DR{beta} chains encoded by several DRB1 alleles confer disease susceptibility. To examine these alternative hypotheses of marker-disease association and to investigate gender d