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Sample records for genotype mixtures

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

    Science.gov (United States)

    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.

  2. Inter-varietal interactions among plants in genotypically diverse mixtures tend to decrease herbivore performance.

    Science.gov (United States)

    Grettenberger, Ian M; Tooker, John F

    2016-09-01

    Much research has explored the effects of plant species diversity on herbivore populations, but far less has considered effects of plant genotypic diversity, or how abiotic stressors, like drought, can modify effects. Mechanisms by which plant genotypic diversity affects herbivore populations remain largely unresolved. We used greenhouse studies with a model system of wheat (Triticum aestivum L.) and bird cherry-oat aphid (Rhopalosiphum padi L.) to determine whether the genotypic diversity of a plant's neighborhood influences performance and fitness of herbivores on a focal plant and if drought changes the influence of neighborhood diversity. Taken across all varieties we tested, plant-plant interactions in diverse neighborhoods reduced aphid performance and generated associational resistance, although effects on aphids depended on variety identity. In diverse mixtures, drought stress greatly diminished the genotypic diversity-driven reduction in aphid performance. Neighborhood diversity influenced mother aphid size, and appeared to partially explain how plant-plant interactions reduced the number of offspring produced in mixtures. Plant size did not mediate effects on aphid performance, although neighborhood diversity reduced plant mass across varieties and watering treatments. Our results suggest inter-varietal interactions in genotypic mixtures can affect herbivore performance in the absence of herbivore movement and that abiotic stress may diminish any effects. Accounting for how neighborhood diversity influences resistance of an individual plant to herbivores will help aid development of mixtures of varieties for managing insect pests and clarify the role of plant genotypic diversity in ecosystems.

  3. Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

    NARCIS (Netherlands)

    Johnson, David L.; Jansen, Ritsert C.; Arendonk, Johan A.M. van

    1999-01-01

    A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood estimation of model parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by

  4. Reliable single chip genotyping with semi-parametric log-concave mixtures.

    Directory of Open Access Journals (Sweden)

    Ralph C A Rippe

    Full Text Available The common approach to SNP genotyping is to use (model-based clustering per individual SNP, on a set of arrays. Genotyping all SNPs on a single array is much more attractive, in terms of flexibility, stability and applicability, when developing new chips. A new semi-parametric method, named SCALA, is proposed. It is based on a mixture model using semi-parametric log-concave densities. Instead of using the raw data, the mixture is fitted on a two-dimensional histogram, thereby making computation time almost independent of the number of SNPs. Furthermore, the algorithm is effective in low-MAF situations.Comparisons between SCALA and CRLMM on HapMap genotypes show very reliable calling of single arrays. Some heterozygous genotypes from HapMap are called homozygous by SCALA and to lesser extent by CRLMM too. Furthermore, HapMap's NoCalls (NN could be genotyped by SCALA, mostly with high probability. The software is available as R scripts from the website www.math.leidenuniv.nl/~rrippe.

  5. Variability of the anthracnose fungus Colletotrichum graminicola in sorghum genotype mixtures

    OpenAIRE

    VALERIO, H. M.; CASELA, C. R.; M. A. Resende; SANTOS, F.G.

    2004-01-01

    This paper reports partial results obtained on the variability of Colletotrichum graminicola developed in response to the host diversity generated by three-line combination of sorghum (Sorghum bicolor) genotypes. Nine sorghum lines were used in this study: CMSXS210B, CMSXS112B, CMSXS215B, CMSXS221B, CMSXS169R, CMSXS180R, CMSXS182R, CMSXS227R, and CMSXS116R. A total of 39 treatments on mixtures and pure stands of the component lines were evaluated in the field for the development of anthracnos...

  6. Mixtures of Complete and pif1- and pif2-Deficient Genotypes Are Required for Increased Potency of an Insect Nucleopolyhedrovirus▿

    Science.gov (United States)

    Clavijo, Gabriel; Williams, Trevor; Simón, Oihane; Muñoz, Delia; Cerutti, Martine; López-Ferber, Miguel; Caballero, Primitivo

    2009-01-01

    The insecticidal potency of a nucleopolyhedrovirus population (SfNIC) that infects Spodoptera frugiperda (Lepidoptera) is greater than the potency of any of the component genotypes alone. Occlusion bodies (OBs) produced in mixed infections comprising the complete genotype and a deletion genotype are as pathogenic as the natural population of genotypes from the field. To test whether this increased potency was due to the deletion or to some other characteristic of the deletion variant genome, we used the SfNIC-B genome to construct a recombinant virus (SfNIC-BΔ16K) with the same 16.4-kb deletion as that observed in SfNIC-C and another recombinant (SfNIC-BΔpifs) with a deletion encompassing two adjacent genes (pif1 and pif2) that are essential for transmission per os. Mixtures comprising SfNIC-B and SfNIC-BΔ16K in OB ratios that varied between 10:90 and 90:10 were injected into insects, and the progeny OBs were fed to larvae in an insecticidal potency assay. A densitometric analysis of PCR products indicated that SfNIC-B was generally more abundant than expected in mixtures based on the proportions of OBs used to produce the inocula. Mixtures derived from OB ratios of 10, 25, or 50% of SfNIC-BΔ16K and the corresponding SfNIC-B proportions showed a significant increase in potency compared to SfNIC-B alone. The results of potency assays with mixtures comprising various proportions of SfNIC-B plus SfNIC-BΔpifs were almost identical to the results observed with SfNIC-BΔ16K, indicating that deletion of the pif gene region was responsible for the increased potency observed in mixtures of SfNIC-B and each deletion recombinant virus. Subsequently, mixtures produced from OB ratios involving 10 or 90% of SfNIC-BΔ16K with the corresponding proportions of SfNIC-B were subjected to four rounds of per os transmission in larvae. The composition of each experimental mixture rapidly converged to a common equilibrium with a genotypic composition of ∼85% SfNIC-B plus ∼15% Sf

  7. Reliable Single Chip Genotyping with Semi-Parametric Log-Concave Mixtures

    NARCIS (Netherlands)

    R.C.A. Rippe (Ralph); J.J. Meulman (Jacqueline); P.H.C. Eilers (Paul)

    2012-01-01

    textabstractThe common approach to SNP genotyping is to use (model-based) clustering per individual SNP, on a set of arrays. Genotyping all SNPs on a single array is much more attractive, in terms of flexibility, stability and applicability, when developing new chips. A new semi-parametric method, n

  8. Mixture

    Directory of Open Access Journals (Sweden)

    Silva-Aguilar Martín

    2011-01-01

    Full Text Available Metals are ubiquitous pollutants present as mixtures. In particular, mixture of arsenic-cadmium-lead is among the leading toxic agents detected in the environment. These metals have carcinogenic and cell-transforming potential. In this study, we used a two step cell transformation model, to determine the role of oxidative stress in transformation induced by a mixture of arsenic-cadmium-lead. Oxidative damage and antioxidant response were determined. Metal mixture treatment induces the increase of damage markers and the antioxidant response. Loss of cell viability and increased transforming potential were observed during the promotion phase. This finding correlated significantly with generation of reactive oxygen species. Cotreatment with N-acetyl-cysteine induces effect on the transforming capacity; while a diminution was found in initiation, in promotion phase a total block of the transforming capacity was observed. Our results suggest that oxidative stress generated by metal mixture plays an important role only in promotion phase promoting transforming capacity.

  9. Determinant Factors in the Production of a Co-Occluded Binary Mixture of Helicoverpa armigera Alphabaculovirus (HearNPV) Genotypes with Desirable Insecticidal Characteristics

    Science.gov (United States)

    Arrizubieta, Maite; Simón, Oihane; Williams, Trevor; Caballero, Primitivo

    2016-01-01

    A co-occluded binary mixture of Helicoverpa armigera nucleopolyhedrovirus genotypes HearSP1B and HearLB6 at a 1:1 ratio (HearSP1B+HearLB6) was selected for the development of a virus-based biological insecticide, which requires an efficient large-scale production system. In vivo production systems require optimization studies in each host-virus pathosystem. In the present study, the effects of larval instar, rearing density, timing of inoculation, inoculum concentration and temperature on the production of HearSP1B+HearLB6 in its homologous host were evaluated. The high prevalence of cannibalism in infected larvae (40–87%) indicated that insects require individual rearing to avoid major losses in OB production. The OB production of recently molted fifth instars (7.0 x 109 OBs/larva), combined with a high prevalence of mortality (85.7%), resulted in the highest overall OB yield (6.0 x 1011 OBs/100 inoculated larvae), compared to those of third or fourth instars. However, as inoculum concentration did not influence final OB yield, the lowest concentration, LC80 (5.5 x 106 OBs/ml), was selected. Incubation temperature did not significantly influence OB yield, although larvae maintained at 30°C died 13 and 34 hours earlier than those incubated at 26°C and 23°C, respectively. We conclude that the efficient production of HearSP1B+HearLB6 OBs involves inoculation of recently molted fifth instars with a LC80 concentration of OBs followed by individual rearing at 30°C. PMID:27732657

  10. Effects of Hepatitis C Mixture on RNA Expression of Different Genotypic HCV Replicons%丙肝合剂对不同基因型丙型肝炎病毒复制子基因表达的影响

    Institute of Scientific and Technical Information of China (English)

    李京涛; 魏海梁; 席奇; 刘亚珠; 闫曙光; 惠毅; 宋春荣; 李日向; 常占杰

    2015-01-01

    Objective To investigate the inhibition mechanism of Hepatitis C Mixture for RNA expression of different genotypic HCV replicons in vitro.MethodsDifferent genotypic HCV replicon cell models were established. According to the disparity of genotypes, they were divided into three groups which named HCV 1b, HCV 2a and J6/JFH1. The Huh7.5.1 cell colonies which contain HCV replicon RNA were treated with various concentrations of Hepatitis C Mixture for 48 h. Then the luciferase activity and cytotoxicity of cell colonieswere detected. MTT method was used to detect cytotoxicity. IFN-2α and DMSO were selected as positive and negative control for eliminating the experiment errors.ResultsLuciferase activities of three groups showed a dose dependent decrease. Luciferase activities of three groups were significant different (P<0.05). Multiple comparisons were performed and showed the luciferase activity of HCV 2a group was lower than those in HCV 1b and J6/JFH1 groups (P<0.05). The results of MTT showed that when cells were treated with 0.2 g/mL of Hepatitis C Mixture, cellular survival rate was higher over 99%. ConclusionHepatitis C Mixture could partly inhibit the RNA expression of different genotypic HCV replicons in vitro, especially the HCV 2a replicon. The optimal inhibitory concentrations of Hepatitis C Mixture is 0.1 g/mL.%目的 通过体外实验探讨丙肝合剂抑制不同基因型丙型肝炎病毒(HCV)复制子基因表达的机制.方法建立不同基因型HCV复制子细胞模型,按基因型不同分为HCV 1b组、HCV 2a组和J6/JFH1组,不同浓度丙肝合剂干预负载复制子的Huh7.5.1细胞48 h后,收集细胞裂解液,进行荧光素酶活性测定,MTT法检测细胞毒性.选择IFN-2α和DMSO分别作为阳性对照和阴性对照以排除实验误差.结果 3组荧光素酶活性呈剂量依赖性下降,3组比较差异有统计学意义(P<0.05).多重比较显示,HCV 2a组荧光素酶活性显著低于HCV 1b组和J6/JFH1组(P<0.05).MTT实验结

  11. Biological Characteristics of Experimental Genotype Mixtures of Cydia Pomonella Granulovirus (CpGV): Ability to Control Susceptible and Resistant Pest Populations.

    Science.gov (United States)

    Graillot, Benoit; Bayle, Sandrine; Blachere-Lopez, Christine; Besse, Samantha; Siegwart, Myriam; Lopez-Ferber, Miguel

    2016-05-21

    The detection of resistance in codling moth (Cydia pomonella) populations against the Mexican isolate of its granulovirus (CpGV-M), raised questions on the sustainability of the use of this biological insecticide. In resistant host cells, CpGV-M is not able to complete its replication cycle because replication is blocked at an early step. Virus isolates able to overcome this resistance have been characterized-among them, the CpGV-R5 isolate. In mixed infections on resistant insects, both CpGV-M and CpGV-R5 viruses replicate, while CpGV-M alone does not induce mortality. Genetically heterogeneous virus populations, containing 50% of each CpGV-M and CpGV-R5 appear to control resistant host populations as well as CpGV-R5 alone at the same final concentration, even if the concentration of CpGV-R5 is only half in the former. The use of mixed genotype virus preparations instead of genotypically homogeneous populations may constitute a better approach than traditional methods for the development of baculovirus-based biological insecticides.

  12. Mixture Experiments

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, Gregory F.

    2007-12-01

    A mixture experiment involves combining two or more components in various proportions or amounts and then measuring one or more responses for the resulting end products. Other factors that affect the response(s), such as process variables and/or the total amount of the mixture, may also be studied in the experiment. A mixture experiment design specifies the combinations of mixture components and other experimental factors (if any) to be studied and the response variable(s) to be measured. Mixture experiment data analyses are then used to achieve the desired goals, which may include (i) understanding the effects of components and other factors on the response(s), (ii) identifying components and other factors with significant and nonsignificant effects on the response(s), (iii) developing models for predicting the response(s) as functions of the mixture components and any other factors, and (iv) developing end-products with desired values and uncertainties of the response(s). Given a mixture experiment problem, a practitioner must consider the possible approaches for designing the experiment and analyzing the data, and then select the approach best suited to the problem. Eight possible approaches include 1) component proportions, 2) mathematically independent variables, 3) slack variable, 4) mixture amount, 5) component amounts, 6) mixture process variable, 7) mixture of mixtures, and 8) multi-factor mixture. The article provides an overview of the mixture experiment designs, models, and data analyses for these approaches.

  13. Fitting mixture distributions to phenylthiocarbamide (PTC) sensitivity.

    OpenAIRE

    Jones, P N; G.J. McLachlan

    1991-01-01

    A technique for fitting mixture distributions to phenylthiocarbamide (PTC) sensitivity is described. Under the assumptions of Hardy-Weinberg equilibrium, a mixture of three normal components is postulated for the observed distribution, with the mixing parameters corresponding to the proportions of the three genotypes associated with two alleles A and a acting at a single locus. The corresponding genotypes AA, Aa, and aa are then considered to have separate means and variances. This paper is c...

  14. Desmanthus GENOTYPES

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    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.

  15. Seletividade de cultivares de soja RR® submetidos a misturas em tanque de glyphosate + chlorimuron-ethyl associadas a óleo mineral e inseticidas selectivity of soybean RR® genotypes submitted to glyphosate + chlorimuron-ethyl tank mixtures associated to mineral oil and insecticides

    Directory of Open Access Journals (Sweden)

    C.D.G. Maciel

    2009-01-01

    mixtures combined with insecticides and adjuvants. Aiming to evaluate the selectivity of soybean RR® genotypes submitted to tank mixtures of the glyphosate formulations (Polaris®, Roundup Ready® and Roundup WG® with chlorimuron-ethyl (Classic®, and their associations with mineral oil (Joint Oil® and novaluron insecticides (Gallaxy 100 EC®, permethrin (Piredan® and methomyl (Lannate BR®, an experiment was conducted under field conditions at Maracai -São Paulo, during the 2006/2007 growing year. The experiment was arranged in a randomized complete block design with four replications, in a factorial scheme 16 x 4, with 16 representing the tank mixture associations of glyphosate formulations, mineral oil and insecticide, and the four genotypes Monsoy 7210RR®, Monsoy 7979RR®, BRS245RR® and CD 214RR®. Visual symptoms of initial intoxication in the genotypes studied were characterized by chlorosis and wrinkle in the leaves for all tank mixtures of glyphosate + chlorimuron-ethyl, associated or not with mineral oil, and novaluron, permethrin and methomyl insecticides .None of the tank mixtures promoted significant yield reductions for Monsoy 7210RR®, Monsoy 7979RR® and BRS245RR® genotypes, and controlled Ipomoea spp with satisfactory effectiveness, starting from 21 DAA (days after application.

  16. Visible Genotype Sensor Array

    Directory of Open Access Journals (Sweden)

    Takashi Imai

    2008-04-01

    Full Text Available A visible sensor array system for simultaneous multiple SNP genotyping has been developed using a new plastic base with specific surface chemistry. Discrimination of SNP alleles is carried out by an allele-specific extension reaction using immobilized oligonucleotide primers. The 3’-ends of oligonucleotide primers are modified with a locked nucleic acid to enhance their efficiency in allelic discrimination. Biotin-dUTPs included in the reaction mixture are selectively incorporated into extending primer sequences and are utilized as tags for alkaline phosphatase-mediated precipitation of colored chemical substrates onto the surface of the plastic base. The visible precipitates allow immediate inspection of typing results by the naked eye and easy recording by a digital camera equipped on a commercial mobile phone. Up to four individuals can be analyzed on a single sensor array and multiple sensor arrays can be handled in a single operation. All of the reactions can be performed within one hour using conventional laboratory instruments. This visible genotype sensor array is suitable for “focused genomics” that follows “comprehensive genomics”.

  17. Distribution of Hepatitis B Virus Genotypes and Its Clinical Significance in Hubei Province, China

    Institute of Scientific and Technical Information of China (English)

    TONG Qiaoxia; WU Yanyan; LUO Duande

    2007-01-01

    The distribution of hepatitis B virus genotype in Hubei province and its clinical significance were investigated. HBV genotypes of 276 patients were detected by PCR-microplate sandwich hybrization-ELISA technique. The level of HBV DNA was detected by using PCR-fluorescence quantification test. Among 276 patients, there were 78 cases of HBV asymptomatic carriers, 110 cases of chronic hepatitis B (CHB), 62 cases of severe hepatitis (SH) or liver cirrhosis (LC) and 26 cases of hepatocellular carcinoma (HCC). The genotypes of HBV included C, B, mixtures (B+C, B+D, C+D) and D, accounting for 55.8%, 25.4%, 16.7% and 2.1% respectively. The average level of HBV DNA in genotypes C, B, mixtures and D was 1.20×106, 7.81×104, 3.26×105 and 5.01×104 copies/mL respectively. The ratio of SH, LC and HCC in genotype B, C and mixtures was 20%, 30% and 48% respectively. Statistical analysis revealed the percentage of genotype mixtures infection was significantly higher than that of genotype B infection. There was no significant difference in the percentage between genotype B and genotype C or between genotype C and mixtures. The distribution of genotype B, C and mixtures in SH, LC and HCC was significantly different. The frequency of HCC was zero in patients with co-infection. Genotype D was only related with SH and LC. The increased ALT could be converted to categorical grades of severity. From mild, moderate to severity,the prevalence of genotype C showed an opposite trend, although no statistically significant difference was observed. The HBeAg positive rate was higher in patients with genotype C infection than in those with genotype B, especially in the patients whose ages were from 31 to 40 years old. Compared with genotype B, genotype C showed a higher HBeAg positive rate in patients with SH and LC. The percentage of SH, LC and HCC was higher in patients with genotype C and mixtures infection. On the contrary, the percentage of genotype B was lower. The HBeAg positive rate

  18. 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.

  19. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Directory of Open Access Journals (Sweden)

    Ping Qiu

    Full Text Available 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.

  20. Mixture Density Mercer Kernels

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a method of generating Mercer Kernels from an ensemble of probabilistic mixture models, where each mixture model is generated from a Bayesian mixture...

  1. Genotype adaptability and stability

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    Dimitrijević Miodrag

    2000-01-01

    Full Text Available One of the primary concerns in breeding programs is a small genotype reaction to environmental factor variation for better usage of yield genetic potential. Particularly if one takes in consideration that yield could van greatly because of more and more variable meteorological conditions. Studies conducted to observe genotype and environmental relations relay on numerous mathematical models, but genotype behavior in various ecological conditions is not, still, precisely defined Major sources of variation influencing genotype behavior in different environments are genotype/environment interaction, genetic background and environmental conditions. These factors could play an important role in establishing growth regions for maximal realization of genotype genetic potential, as well as in selection of genotypes having better response to complex requirements of particular growth region. Stability, the genotype ability to perform high, uniform yield no meter of different environmental conditions, and adaptability, genotype ability to give uniform yield in a different environmental conditions, are two common terms used to define genotype reaction in a consequence of environmental changes. Most of the models dealing with stability and adaptability are based on variation sources appearing under the influence of treatment, multivariate effects and residue. No meter which statistical model is used for GE interaction estimation, there is an opinion that no solid proof for the existence of stable genotypes obtained in breeding programs, which make some space for further investigations. There are still questions to answer dealing with definitions, sources of variation, usage value of existent models and interpretation of the results. .

  2. Paternity testing that involves a DNA mixture.

    Science.gov (United States)

    Mortera, Julia; Vecchiotti, Carla; Zoppis, Silvia; Merigioli, Sara

    2016-07-01

    Here we analyse a complex disputed paternity case, where the DNA of the putative father was extracted from his corpse that had been inhumed for over 20 years. This DNA was contaminated and appears to be a mixture of at least two individuals. Furthermore, the mother's DNA was not available. The DNA mixture was analysed so as to predict the most probable genotypes of each contributor. The major contributor's profile was then used to compute the likelihood ratio for paternity. We also show how to take into account a dropout allele and the possibility of mutation in paternity testing.

  3. Optimal mixture experiments

    CERN Document Server

    Sinha, B K; Pal, Manisha; Das, P

    2014-01-01

    The book dwells mainly on the optimality aspects of mixture designs. As mixture models are a special case of regression models, a general discussion on regression designs has been presented, which includes topics like continuous designs, de la Garza phenomenon, Loewner order domination, Equivalence theorems for different optimality criteria and standard optimality results for single variable polynomial regression and multivariate linear and quadratic regression models. This is followed by a review of the available literature on estimation of parameters in mixture models. Based on recent research findings, the volume also introduces optimal mixture designs for estimation of optimum mixing proportions in different mixture models, which include Scheffé’s quadratic model, Darroch-Waller model, log- contrast model, mixture-amount models, random coefficient models and multi-response model.  Robust mixture designs and mixture designs in blocks have been also reviewed. Moreover, some applications of mixture desig...

  4. Low temperature asphalt mixtures

    OpenAIRE

    Modrijan, Damjan

    2006-01-01

    This thesis presents the problem of manufacturing and building in the asphalt mixtures produced by the classical hot procedure and the possibility of manufacturing low temperature asphalt mixtures.We will see the main advantages of low temperature asphalt mixtures prepared with bitumen with organic addition Sasobit and compare it to the classical asphalt mixtures. The advantages and disadvantages of that are valued in the practical example in the conclusion.

  5. Deletion Genotypes Reduce Occlusion Body Potency but Increase Occlusion Body Production in a Colombian Spodoptera frugiperda Nucleopolyhedrovirus Population

    Science.gov (United States)

    Barrera, Gloria; Williams, Trevor; Villamizar, Laura; Caballero, Primitivo; Simón, Oihane

    2013-01-01

    A Colombian field isolate (SfCOL-wt) of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) is a mixture of different genotypes. To evaluate the insecticidal properties of the different genotypic variants, 83 plaque purified virus were characterized. Ten distinct genotypes were identified (named A through J). SfCOL-A was the most prevalent (71±2%; mean ± SE) showing a PstI restriction profile indistinguishable to that of SfCOL-wt. The remaining nine genotypes presented genomic deletions of 3.8 - 21.8 Kb located mainly between nucleotides 11,436 and 33,883 in the reference genome SfMNPV-B, affecting the region between open reading frames (ORFs) sf20 and sf33. The insecticidal activity of each genotype from SfCOL-wt and several mixtures of genotypes was compared to that of SfCOL-wt. The potency of SfCOL-A occlusion bodies (OBs) was 4.4-fold higher than SfCOL-wt OBs, whereas the speed of kill of SfCOL-A was similar to that of SfCOL-wt. Deletion genotype OBs were similarly or less potent than SfCOL-wt but six deletion genotypes were faster killing than SfCOL-wt. The potency of genotype mixtures co-occluded within OBs were consistently reduced in two-genotype mixtures involving equal proportions of SfCOL-A and one of three deletion genotypes (SfCOL-C, -D or -F). Speed of kill and OB production were improved only when the certain genotype mixtures were co-occluded, although OB production was higher in the SfCOL-wt isolate than in any of the component genotypes, or mixtures thereof. Deleted genotypes reduced OB potency but increased OB production of the SfCOL-wt population, which is structured to maximize the production of OBs in each infected host. PMID:24116220

  6. Mixed genotype transmission bodies and virions contribute to the maintenance of diversity in an insect virus

    Science.gov (United States)

    Clavijo, Gabriel; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo; López-Ferber, Miguel

    2010-01-01

    An insect nucleopolyhedrovirus naturally survives as a mixture of at least nine genotypes. Infection by multiple genotypes results in the production of virus occlusion bodies (OBs) with greater pathogenicity than those of any genotype alone. We tested the hypothesis that each OB contains a genotypically diverse population of virions. Few insects died following inoculation with an experimental two-genotype mixture at a dose of one OB per insect, but a high proportion of multiple infections were observed (50%), which differed significantly from the frequencies predicted by a non-associated transmission model in which genotypes are segregated into distinct OBs. By contrast, insects that consumed multiple OBs experienced higher mortality and infection frequencies did not differ significantly from those of the non-associated model. Inoculation with genotypically complex wild-type OBs indicated that genotypes tend to be transmitted in association, rather than as independent entities, irrespective of dose. To examine the hypothesis that virions may themselves be genotypically heterogeneous, cell culture plaques derived from individual virions were analysed to reveal that one-third of virions was of mixed genotype, irrespective of the genotypic composition of the OBs. We conclude that co-occlusion of genotypically distinct virions in each OB is an adaptive mechanism that favours the maintenance of virus diversity during insect-to-insect transmission. PMID:19939845

  7. Liquids and liquid mixtures

    CERN Document Server

    Rowlinson, J S; Baldwin, J E; Buckingham, A D; Danishefsky, S

    2013-01-01

    Liquids and Liquid Mixtures, Third Edition explores the equilibrium properties of liquids and liquid mixtures and relates them to the properties of the constituent molecules using the methods of statistical thermodynamics. Topics covered include the critical state, fluid mixtures at high pressures, and the statistical thermodynamics of fluids and mixtures. This book consists of eight chapters and begins with an overview of the liquid state and the thermodynamic properties of liquids and liquid mixtures, including vapor pressure and heat capacities. The discussion then turns to the thermodynami

  8. 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 ...

  9. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B

    2009-01-01

    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....... 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......, 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...

  10. 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

  11. Perception of trigeminal mixtures.

    Science.gov (United States)

    Filiou, Renée-Pier; Lepore, Franco; Bryant, Bruce; Lundström, Johan N; Frasnelli, Johannes

    2015-01-01

    The trigeminal system is a chemical sense allowing for the perception of chemosensory information in our environment. However, contrary to smell and taste, we lack a thorough understanding of the trigeminal processing of mixtures. We, therefore, investigated trigeminal perception using mixtures of 3 relatively receptor-specific agonists together with one control odor in different proportions to determine basic perceptual dimensions of trigeminal perception. We found that 4 main dimensions were linked to trigeminal perception: sensations of intensity, warmth, coldness, and pain. We subsequently investigated perception of binary mixtures of trigeminal stimuli by means of these 4 perceptual dimensions using different concentrations of a cooling stimulus (eucalyptol) mixed with a stimulus that evokes warmth perception (cinnamaldehyde). To determine if sensory interactions are mainly of central or peripheral origin, we presented stimuli in a physical "mixture" or as a "combination" presented separately to individual nostrils. Results showed that mixtures generally yielded higher ratings than combinations on the trigeminal dimensions "intensity," "warm," and "painful," whereas combinations yielded higher ratings than mixtures on the trigeminal dimension "cold." These results suggest dimension-specific interactions in the perception of trigeminal mixtures, which may be explained by particular interactions that may take place on peripheral or central levels.

  12. 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...

  13. (Brassica napus L.) genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... The genetic diversity and relationships among rapeseed genotypes were ... dent of environment and plant growth stage, unlimited ..... interactions that lead to the expression of particular traits .... thesis, Faculty of Agriculture, University of Novi Sad. ... in the U.S. hard red winter wheat cultivars as reveled by.

  14. A sealing mixture

    Energy Technology Data Exchange (ETDEWEB)

    Khayrullin, S.R.; Firsov, I.A.; Ongoyev, V.M.; Shekhtman, E.N.; Taskarin, B.T.

    1983-01-01

    A plugging mixture is proposed which contains triethanolamine, caustic soda, water and an additive. It is distinguished by the fact that in order to reduce the cost of the mixture while preserving its operational qualities, it additionally contains clay powder and as the additive, ground limestone with the following component ratio in percent by mass: ground limestone, 50 to 60; triethanolamine, 0.1 to 0.15; caustic soda, 2 to 3; clay powder, 8 to 10 and water the remainder. The mixture is distinguished by the fact that the ground limestone has a specific surface of 2,000 to 3,000 square centimeters per gram.

  15. Hepatitis C Virus Genotypes

    Directory of Open Access Journals (Sweden)

    Kayhan Azadmanesh

    2005-09-01

    the ultimate source of the virus's genetic diversity. HCV circulates as a heterogeneous population of genetically different but closely related genomes known as the quasispecies(15.As only 30-35% of nucleotides actually differ, there is obviously considerable heterogeneity in evolutionary rates among nucleotide sites in the genome. This heterogeneity is the result of variable evolutionary constraints. The 5'-UTR contains extensive secondary RNA structure and is correspondingly the slowest evolving genomic region(16. The next slowest region is the C (Core gene, which evolves three times faster than the 5'- UTR. The envelope genes E1 and E2 constitute the most diverse genome region and evolve about nine times faster than the 5'-UTR(16, probably as a result of their presumed role in evading the host immune response. Genomic Heterogeneity and ClassificationSystemsShortly after its discovery in 1989, it became clear that HCV had substantial nucleotide sequence diversity, with only 66 to 80% overall sequencesimilarity among strains belonging to different genotypes or subtypes(17. HCV isolates show four levels of genomic variations: types, subtypes, isolates, andquasispecies. The overall sequence similarities over complete genomic sequences are at least 91% within quasispecies, approximately 79% (range, 77 to 80% between subtypes, and about 68% (range, 66 to 69% between different types. This quasispecies is composed of a group of heterogeneous RNA sequences centered around a dominant nucleotide sequence that changes, throughout the course of the infection, under the selective pressure of the host immune system(18. More than one genotype can be found in the circulations of some HCV-infected patients, particularly in individuals who have received multiple transfusions and intravenous drug users. These are referred to as mixed-genotype infections(19, 20.The lack of a routinely available cell culture system and an easily available animal model has rendered classification of HCV

  16. SNP genotyping technologies

    DEFF Research Database (Denmark)

    Studer, Bruno; Kölliker, Roland

    2013-01-01

    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.......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...

  17. 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....

  18. A Chrysodeixis chalcites single-nucleocapsid nucleopolyhedrovirus population from the Canary Islands is genotypically structured to maximize survival.

    Science.gov (United States)

    Bernal, Alexandra; Simón, Oihane; Williams, Trevor; Muñoz, Delia; Caballero, Primitivo

    2013-12-01

    A Chrysodeixis chalcites single-nucleocapsid nucleopolyhedrovirus wild-type isolate from the Canary Islands, Spain, named ChchSNPV-TF1 (ChchTF1-wt), appears to have great potential as the basis for a biological insecticide for control of the pest. An improved understanding of the genotypic structure of this wild-type strain population should facilitate the selection of genotypes for inclusion in a bioinsecticidal product. Eight genetically distinct genotypes were cloned in vitro: ChchTF1-A to ChchTF1-H. Quantitative real-time PCR (qPCR) analysis confirmed that ChchTF1-A accounted for 36% of the genotypes in the wild-type population. In bioassays, ChchTF1-wt occlusion bodies (OBs) were significantly more pathogenic than any of the component single-genotype OBs, indicating that genotype interactions were likely responsible for the pathogenicity phenotype of wild-type OBs. However, the wild-type population was slower killing and produced higher OB yields than any of the single genotypes alone. These results strongly suggested that the ChchTF1-wt population is structured to maximize its transmission efficiency. Experimental OB mixtures and cooccluded genotype mixtures containing the most abundant and the rarest genotypes, at frequencies similar to those at which they were isolated, revealed a mutualistic interaction that restored the pathogenicity of OBs. In OB and cooccluded mixtures containing only the most abundant genotypes, ChchTF1-ABC, OB pathogenicity was even greater than that of wild-type OBs. The ChchTF1-ABC cooccluded mixture killed larvae 33 h faster than the wild-type population and remained genotypically and biologically stable throughout five successive passages in vivo. In conclusion, the ChchTF1-ABC mixture shows great potential as the active ingredient of a bioinsecticide to control C. chalcites in the Canary Islands.

  19. Functional Importance of Deletion Mutant Genotypes in an Insect Nucleopolyhedrovirus Population

    Science.gov (United States)

    Simón, Oihane; Williams, Trevor; López-Ferber, Miguel; Caballero, Primitivo

    2005-01-01

    A Nicaraguan isolate of a nucleopolyhedrovirus (SfNIC) that attacks the fall armyworm, Spodoptera frugiperda, survives as a mixture of nine genotypes (SfNIC A to I) that all present genomic deletions, except variant B (complete genotype). Sequencing of cloned restriction fragments revealed that genotypic variants lack between 5 and 16 of the open reading frames present in a contiguous sequence of 18 kb of the SfNIC genome. The absence of oral infectivity of SfNIC-C and -D variants is related to the deletion of the pif and/or pif-2 gene, while that of SfNIC-G remains unexplained. The presence of open reading frame 10, homolog of Se030, also appeared to influence pathogenicity in certain variants. Previous studies demonstrated a significant positive interaction between genotypes B and C. We compared the median lethal concentration of single genotypes (A, B, C, D, and F) and co-occluded genotype mixtures (B+A, B+D, B+F, A+C, and F+C in a 3:1 ratio). Mixtures B+A and B+D showed increased pathogenicity, although only B+D restored the activity of the mixture to that of the natural population. Mixtures of two deletion variants (A+C and F+C) did not show interactions in pathogenicity. We conclude that minority genotypes have an important influence on the overall pathogenicity of the population. These results clearly demonstrate the value of retaining genotypic diversity in virus-based bioinsecticides. PMID:16085811

  20. Multilevel Mixture Kalman Filter

    Directory of Open Access Journals (Sweden)

    Xiaodong Wang

    2004-11-01

    Full Text Available The mixture Kalman filter is a general sequential Monte Carlo technique for conditional linear dynamic systems. It generates samples of some indicator variables recursively based on sequential importance sampling (SIS and integrates out the linear and Gaussian state variables conditioned on these indicators. Due to the marginalization process, the complexity of the mixture Kalman filter is quite high if the dimension of the indicator sampling space is high. In this paper, we address this difficulty by developing a new Monte Carlo sampling scheme, namely, the multilevel mixture Kalman filter. The basic idea is to make use of the multilevel or hierarchical structure of the space from which the indicator variables take values. That is, we draw samples in a multilevel fashion, beginning with sampling from the highest-level sampling space and then draw samples from the associate subspace of the newly drawn samples in a lower-level sampling space, until reaching the desired sampling space. Such a multilevel sampling scheme can be used in conjunction with the delayed estimation method, such as the delayed-sample method, resulting in delayed multilevel mixture Kalman filter. Examples in wireless communication, specifically the coherent and noncoherent 16-QAM over flat-fading channels, are provided to demonstrate the performance of the proposed multilevel mixture Kalman filter.

  1. Temporal dynamics and subpopulation analysis of Theileria orientalis genotypes in cattle.

    Science.gov (United States)

    Jenkins, C; Micallef, M; Alex, S M; Collins, D; Djordjevic, S P; Bogema, D R

    2015-06-01

    In Australia, outbreaks of clinical theileriosis caused by Theileria orientalis have been largely associated with the Ikeda genotype which can occur as a sole infection, or more commonly, as a mixture of genotypes. The most prevalent genotype, Chitose, frequently co-occurs with type Ikeda, however the role of this genotype in clinical disease has not been clearly established. Furthermore, the dynamics of individual genotypes in field infection of cattle have not been examined. In this study we developed quantitative PCR (qPCR) and genotyping methods to examine the role of the Chitose genotype in clinical disease and to investigate the temporal dynamics of T. orientalis Ikeda, Chitose and Buffeli genotypes in naïve animals introduced to a T. orientalis-endemic area. Analysis of the major piroplasm surface protein (MPSP) genes of Chitose isolates revealed the presence of two distinct phylogenetic clusters, Chitose A and Chitose B. A genotyping assay aimed at determining Chitose A/B allele frequency revealed that the Chitose A phylogenetic cluster is strongly associated with clinical disease but nearly always co-occurs with the Ikeda genotype. qPCR revealed that the Chitose genotype (particularly Chitose A), undergoes temporal switching in conjunction with the Ikeda genotype and contributes substantially to the overall parasite burden. The benign Buffeli genotype can also undergo temporal switching but levels of this genotype appear to remain low relative to the Ikeda and Chitose types. Interplay between vector and host immunological factors is presumed to be critical to the population dynamics observed in this study. Genotypic switching likely contributes to the persistence of T. orientalis in the host.

  2. 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.

  3. Entry into Midgut Epithelial Cells is a Key Step in the Selection of Genotypes in a Nucleopolyhedrovirus

    Institute of Scientific and Technical Information of China (English)

    Gabriel Clavijo; Trevor Williams; Delia Mu(n)oz; Miguel L(o)pez-Ferber; Primitivo Caballero

    2009-01-01

    An isolate of the Spodoptera frugiperda multiple nucleopolyhedrovirus comprises a stable proportion of deletion genotypes (e.g., SfNIC-C), that lack pif1 and pif2 rendering them noninfectious per os, and that survive by complementation with a complete genotype (SfNIC-B) in coinfected cells. To determine whether selection for particular ratios of complete and deletion genotypes occurs mainly during the establishment of the primary infection in insect midgut cells or during subsequent systemic infection, we examined genotype frequencies in insects that fed on OBs comprising different co-occluded mixtures of genotypes. Dramatic changes in genotype frequencies were observed between the OB inoculum and budded virus (BV) samples taken from larvae inoculated with OBs comprising 10% SfNIC-B + 90% SfNIC-C indicating that a marked reduction of SfNIC-C genotype had occurred in the insect midgut due to the immediate elimination of all OBs that originated from cells that had been infected only by SfNIC-C. In contrast, immediate changes were not observed in OBs comprising mixtures of 50% SfNIC-B + 50% SfNIC-C or those comprising 10% SfNIC-B + 90% SfNIC-C as most of the OBs in these mixtures originated from cells that had been infected by both genotypes. Subsequent changes in genotypic frequencies during five days of systemic infection were fairly small in magnitude for all genotypic mixtures. We conclude that the prevalence of defective genotypes in the SfNIC population is likely determined by a balance between host selection against OBs produced in cells infected by SfNIC-C alone and within-host selection for fast-replicating deletion genotypes. The strength of intra-host selection is likely modulated by changes in MOI during the infection period.

  4. Mixtures Estimation and Applications

    CERN Document Server

    Mengersen, Kerrie; Titterington, Mike

    2011-01-01

    This book uses the EM (expectation maximization) algorithm to simultaneously estimate the missing data and unknown parameter(s) associated with a data set. The parameters describe the component distributions of the mixture; the distributions may be continuous or discrete. The editors provide a complete account of the applications, mathematical structure and statistical analysis of finite mixture distributions along with MCMC computational methods, together with a range of detailed discussions covering the applications of the methods and features chapters from the leading experts on the subject

  5. Mixtures and interactions

    NARCIS (Netherlands)

    Groten, J.P.

    2000-01-01

    Drinking water can be considered as a complex mixture that consists of tens, hundreds or thousands of chemicals of which the composition is qualitatively and quantitatively not fully known. From a public health point of view it is most relevant to answer the question of whether chemicals in drinking

  6. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    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

  7. 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.

  8. Pointer Sentinel Mixture Models

    OpenAIRE

    Merity, Stephen; Xiong, Caiming; Bradbury, James; Socher, Richard

    2016-01-01

    Recent neural network sequence models with softmax classifiers have achieved their best language modeling performance only with very large hidden states and large vocabularies. Even then they struggle to predict rare or unseen words even if the context makes the prediction unambiguous. We introduce the pointer sentinel mixture architecture for neural sequence models which has the ability to either reproduce a word from the recent context or produce a word from a standard softmax classifier. O...

  9. 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.

  10. 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. PMID:25742179

  11. Essays on Finite Mixture Models

    NARCIS (Netherlands)

    A. van Dijk (Bram)

    2009-01-01

    textabstractFinite mixture distributions are a weighted average of a ¯nite number of distributions. The latter are usually called the mixture components. The weights are usually described by a multinomial distribution and are sometimes called mixing proportions. The mixture components may be the

  12. Essays on Finite Mixture Models

    NARCIS (Netherlands)

    A. van Dijk (Bram)

    2009-01-01

    textabstractFinite mixture distributions are a weighted average of a ¯nite number of distributions. The latter are usually called the mixture components. The weights are usually described by a multinomial distribution and are sometimes called mixing proportions. The mixture components may be the sam

  13. Mixtures of truncated basis functions

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

    2012-01-01

    In this paper we propose a framework, called mixtures of truncated basis functions (MoTBFs), for representing general hybrid Bayesian networks. The proposed framework generalizes both the mixture of truncated exponentials (MTEs) framework and the mixture of polynomials (MoPs) framework. Similar...

  14. Separating Underdetermined Convolutive Speech Mixtures

    DEFF Research Database (Denmark)

    Pedersen, Michael Syskind; Wang, DeLiang; Larsen, Jan

    2006-01-01

    a method for underdetermined blind source separation of convolutive mixtures. The proposed framework is applicable for separation of instantaneous as well as convolutive speech mixtures. It is possible to iteratively extract each speech signal from the mixture by combining blind source separation...

  15. Toxicological evaluation of chemical mixtures

    NARCIS (Netherlands)

    Feron, V.J.; Groten, J.P.

    2002-01-01

    This paper addresses major developments in the safety evaluation of chemical mixtures during the past 15 years, reviews today's state of the art of mixture toxicology, and discusses challenges ahead. Well-thought-out tailor-made mechanistic and empirical designs for studying the toxicity of mixtures

  16. Oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus

    Institute of Scientific and Technical Information of China (English)

    Yong-Zhong Wang; Guo-Xiang Wu; Li-Bo Luo; Min Chen; Li-Hua Ruan

    2007-01-01

    AIM: To compare the oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus in Chinese patients with chronic hepatitis B.METHODS: Mixture of samples with different genotypes and clinical serum samples from 126 chronic hepatitis B patients was tested for hepatitis B virus genotypes by oligonucleotide chip, real-time PCR and sequencing of PCR products, respectively. Clinical performances, time required and costs of the three assays were evaluated.RESULTS: Oligonucleotide chips and real-time PCR detected 1% and 0.1% genotypes, respectively, in mixed samples. Of the 126 clinical samples from patients with chronic hepatitis B, genotype B was detected in 41(33%), 41 (33%) and 45 (36%) samples, and genotype C in 76 (60%), 76 (60%) and 81 (64%) samples, by oligonucleotide chip, real-time PCR and sequencing,respectively. Oligonucleotide chip and real-time PCR detected mixed genotypes B and C in 9 samples. Realtime PCR was the rapidest and cheapest among the three assays.CONCLUSION: Oligonucleotide chip and real-time PCR are able to detect mixed genotypes, while sequencing only detects the dominant genotype in clinical samples.

  17. Mixture Based Outlier Filtration

    Directory of Open Access Journals (Sweden)

    P. Pecherková

    2006-01-01

    Full Text Available Success/failure of adaptive control algorithms – especially those designed using the Linear Quadratic Gaussian criterion – depends on the quality of the process data used for model identification. One of the most harmful types of process data corruptions are outliers, i.e. ‘wrong data’ lying far away from the range of real data. The presence of outliers in the data negatively affects an estimation of the dynamics of the system. This effect is magnified when the outliers are grouped into blocks. In this paper, we propose an algorithm for outlier detection and removal. It is based on modelling the corrupted data by a two-component probabilistic mixture. The first component of the mixture models uncorrupted process data, while the second models outliers. When the outlier component is detected to be active, a prediction from the uncorrupted data component is computed and used as a reconstruction of the observed data. The resulting reconstruction filter is compared to standard methods on simulated and real data. The filter exhibits excellent properties, especially in the case of blocks of outliers. 

  18. Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis.

    Science.gov (United States)

    Cox, D G; Canzian, F

    2001-08-01

    The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.

  19. Concomitant variables in finite mixture models

    NARCIS (Netherlands)

    Wedel, M

    The standard mixture model, the concomitant variable mixture model, the mixture regression model and the concomitant variable mixture regression model all enable simultaneous identification and description of groups of observations. This study reviews the different ways in which dependencies among

  20. HBV genotypes prevalence, precore and basal core mutants in Morocco.

    Science.gov (United States)

    Baha, Warda; Ennaji, My Mustapha; Lazar, Fatiha; Melloul, Marouane; El Fahime, Elmostafa; El Malki, Abdelouahad; Bennani, Abdelouaheb

    2012-08-01

    The study of hepatitis B virus (HBV) genomic heterogeneity has become a major issue in investigations aimed at understanding the relationship between HBV mutants and the wide spectrum of clinical and pathological conditions associated with HBV infection. The objective of the current study was to find out the pattern of HBV genotypes circulating in Morocco and to investigate the precore (PC) and basal core promoter (BCP) mutants' status in Moroccan chronic hepatitis B patients. Viral genotypes were determined in 221 chronic carriers using INNO-LiPA HBV assay and hemi-nested PCR. Phylogenetic analysis was performed in 70 samples, and multiplex PCR method was used to confirm some genotyping results. PC and CP mutants were determined using Inno-Lipa. All isolates were successfully genotyped. The genotype distribution was D in 90.45% of cases, A (5.9%), E (1 case), and mixed genotypes (5 A/D and 2 D/F) in 3.17% patients. HBV carried in the HBV/D samples could be assigned to D7 (63.3%), D1 (32.7%) and 2% of strains to each D4 and D5, all HBV/A belonged to A2 subgenotype and HBV/E strain could not be sub-genotyped. In 70 studied strains, HBV mutants were detected in 88.6% of cases; PC mutants were detected in (40%) of patients and 21.5% present a mixture of wild type and G1896A mutation. BCP mutants were observed in 65.7% of cases, 22.9% were found to have the T1762/1764A double mutation, 18.6% had A1762/1764T mutation and 22.9% of patients showed the A1762T/G1764A double mutation with either A1762T/G1764T mutation. Co-infection by PC and BCP mutants was detected in 52.9% of cases. Movement from place to place most likely shapes the observed genotype distribution and consequent prevalence of genotypes other than A2 or D7 in this population. High circulation of PC and BCP mutants is common in chronic hepatitis B infection in Morocco.

  1. Virulence correlates with fitness in vivo for two M group genotypes of Infectious hematopoietic necrosis virus (IHNV).

    Science.gov (United States)

    Wargo, Andrew R; Garver, Kyle A; Kurath, Gael

    2010-08-15

    The nature of the association between viral fitness and virulence remains elusive in vertebrate virus systems, partly due to a lack of in vivo experiments using statistically sufficient numbers of replicate hosts. We examined the relationship between virulence and fitness in Infectious hematopoietic necrosis virus (IHNV), in vivo, in intact living rainbow trout. Trout were infected with a high or low virulence genotype of M genogroup IHNV, or a mixture of the two genotypes, so as to calculate relative fitness and the effect of a competition environment on fitness. Fitness was measured as total viral load in the host at time of peak viral density, quantified by genotype-specific quantitative RT-PCR (qRT-PCR). The more virulent IHNV genotype reached higher densities in both single and mixed infections. There was no effect of competition on the performance of either genotype. Our results suggest a positive link between IHNV genotype fitness and virulence.

  2. Protein mixtures: interactions and gelation

    OpenAIRE

    Ersch, C.

    2015-01-01

    Gelation is a ubiquitous process in the preparation of foods. As most foods are multi constituent mixtures, understanding gelation in mixtures is an important goal in food science. Here we presented a systematic investigation on the influence of molecular interactions on the gelation in protein mixtures. Gelatin gels with added globular protein and globular protein gels with added gelatin were analyzed for their gel microstructure and rheological properties. Mixed gels with altered microstruc...

  3. 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.

  4. Influence of host diversity on development of epidemics: An evaluation and elaboration of mixture theory

    NARCIS (Netherlands)

    Skelsey, P.; Rossing, W.A.H.; Kessel, G.J.T.; Powell, J.; Werf, van der W.

    2005-01-01

    A spatiotemporal/integro-difference equation model was developed and utilized to study the progress of epidemics in spatially heterogeneous mixtures of susceptible and resistant host plants. The effects of different scales and patterns of host genotypes on the development of focal and general epidem

  5. Neurotoxicity of Metal Mixtures.

    Science.gov (United States)

    Andrade, V M; Aschner, M; Marreilha Dos Santos, A P

    2017-01-01

    Metals are the oldest toxins known to humans. Metals differ from other toxic substances in that they are neither created nor destroyed by humans (Casarett and Doull's, Toxicology: the basic science of poisons, 8th edn. McGraw-Hill, London, 2013). Metals are of great importance in our daily life and their frequent use makes their omnipresence and a constant source of human exposure. Metals such as arsenic [As], lead [Pb], mercury [Hg], aluminum [Al] and cadmium [Cd] do not have any specific role in an organism and can be toxic even at low levels. The Substance Priority List of Agency for Toxic Substances and Disease Registry (ATSDR) ranked substances based on a combination of their frequency, toxicity, and potential for human exposure. In this list, As, Pb, Hg, and Cd occupy the first, second, third, and seventh positions, respectively (ATSDR, Priority list of hazardous substances. U.S. Department of Health and Human Services, Public Health Service, Atlanta, 2016). Besides existing individually, these metals are also (or mainly) found as mixtures in various parts of the ecosystem (Cobbina SJ, Chen Y, Zhou Z, Wub X, Feng W, Wang W, Mao G, Xu H, Zhang Z, Wua X, Yang L, Chemosphere 132:79-86, 2015). Interactions among components of a mixture may change toxicokinetics and toxicodynamics (Spurgeon DJ, Jones OAH, Dorne J-L, Svendsen C, Swain S, Stürzenbaum SR, Sci Total Environ 408:3725-3734, 2010) and may result in greater (synergistic) toxicity (Lister LJ, Svendsen C, Wright J, Hooper HL, Spurgeon DJ, Environ Int 37:663-670, 2011). This is particularly worrisome when the components of the mixture individually attack the same organs. On the other hand, metals such as manganese [Mn], iron [Fe], copper [Cu], and zinc [Zn] are essential metals, and their presence in the body below or above homeostatic levels can also lead to disease states (Annangi B, Bonassi S, Marcos R, Hernández A, Mutat Res 770(Pt A):140-161, 2016). Pb, As, Cd, and Hg can induce Fe, Cu, and Zn

  6. 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.

  7. Thermophysical Properties of Hydrocarbon Mixtures

    Science.gov (United States)

    SRD 4 NIST Thermophysical Properties of Hydrocarbon Mixtures (PC database for purchase)   Interactive computer program for predicting thermodynamic and transport properties of pure fluids and fluid mixtures containing up to 20 components. The components are selected from a database of 196 components, mostly hydrocarbons.

  8. Evaporating Drops of Alkane Mixtures

    OpenAIRE

    Guéna, Geoffroy; Poulard, Christophe; Cazabat, Anne-Marie

    2005-01-01

    22 pages 9 figures; Alkane mixtures are model systems where the influence of surface tension gradients during the spreading and the evaporation of wetting drops can be easily studied. The surface tension gradients are mainly induced by concentration gradients, mass diffusion being a stabilising process. Depending on the relative concentration of the mixture, a rich pattern of behaviours is obtained.

  9. Protein mixtures: interactions and gelation

    NARCIS (Netherlands)

    Ersch, C.

    2015-01-01

    Gelation is a ubiquitous process in the preparation of foods. As most foods are multi constituent mixtures, understanding gelation in mixtures is an important goal in food science. Here we presented a systematic investigation on the influence of molecular interactions on the gelation in protein mixt

  10. Evaporating Drops of Alkane Mixtures

    CERN Document Server

    Gu'ena, G; Poulard, C; Cazabat, Anne-Marie; Gu\\'{e}na, Geoffroy; Poulard, Christophe

    2005-01-01

    Alkane mixtures are model systems where the influence of surface tension gradients during the spreading and the evaporation of wetting drops can be easily studied. The surface tension gradients are mainly induced by concentration gradients, mass diffusion being a stabilising process. Depending on the relative concentration of the mixture, a rich pattern of behaviours is obtained.

  11. Protein mixtures: interactions and gelation

    NARCIS (Netherlands)

    Ersch, C.

    2015-01-01

    Gelation is a ubiquitous process in the preparation of foods. As most foods are multi constituent mixtures, understanding gelation in mixtures is an important goal in food science. Here we presented a systematic investigation on the influence of molecular interactions on the gelation in protein mixt

  12. Easy and flexible mixture distributions

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Mabit, Stefan L.

    2013-01-01

    We propose a method to generate flexible mixture distributions that are useful for estimating models such as the mixed logit model using simulation. The method is easy to implement, yet it can approximate essentially any mixture distribution. We test it with good results in a simulation study...

  13. Trypanosoma cruzi: gene expression surveyed by proteomic analysis reveals interaction between different genotypes in mixed in vitro cultures.

    Directory of Open Access Journals (Sweden)

    Alexandre Machin

    Full Text Available We have analyzed the comportment in in vitro culture of 2 different genotypes of Trypanosoma cruzi, the agent of Chagas disease, pertaining to 2 major genetic subdivisions (near-clades of this parasite. One of the stocks was a fast-growing one, highly virulent in mice, while the other one was slow-growing, mildly virulent in mice. The working hypothesis was that mixtures of genotypes interact, a pattern that has been observed by us in empirical experimental studies. Genotype mixtures were followed every 7 days and characterized by the DIGE technology of proteomic analysis. Proteic spots of interest were characterized by the SAMESPOT software. Patterns were compared to those of pure genotypes that were also evaluated every 7 days. One hundred and three spots exhibited changes in time by comparison with T = 0. The major part of these spots (58% exhibited an under-expression pattern by comparison with the pure genotypes. 32% of the spots were over-expressed; 10% of spots were not different from those of pure genotypes. Interestingly, interaction started a few minutes after the mixtures were performed. We have retained 43 different proteins that clearly exhibited either under- or over-expression. Proteins showing interaction were characterized by mass spectrometry (MALDI-TOF. Close to 50% of them were either tubulins or heat shock proteins. This study confirms that mixed genotypes of T. cruzi interact at the molecular level. This is of great interest because mixtures of genotypes are very frequent in Chagas natural cycles, both in insect vectors and in mammalian hosts, and may play an important role in the transmission and severity of Chagas disease. The methodology proposed here is potentially applicable to any micropathogen, including fungi, bacteria and viruses. It should be of great interest in the case of bacteria, for which the epidemiological and clinical consequences of mixed infections could be underestimated.

  14. 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.

  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. Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability.

    Directory of Open Access Journals (Sweden)

    Emily B M Drummond

    Full Text Available Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects, whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture. Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations.

  17. Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability.

    Science.gov (United States)

    Drummond, Emily B M; Vellend, Mark

    2012-01-01

    Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass) clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects), whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture). Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations.

  18. Sensitivity of Some Explosive/Brine Mixtures

    Science.gov (United States)

    1980-08-01

    concentration in brine mixtures. 3 Friction test results of brine mixtures. 10 4 Thermal test results of brine mixtures. 11 Li 71 - INTRODUCTION A...also carried out on these impact insensitive mixtures. Of the seven mixtures only the 15% M28-Comp. B sample passed the thermal test , since smoking

  19. 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...

  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. 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.

  3. A likelihood-based method for haplotype association studies of case-control data with genotyping uncertainty

    Institute of Scientific and Technical Information of China (English)

    ZHU; Wensheng; GUO; Jianhua

    2006-01-01

    This paper discusses the associations between traits and haplotypes based on Fl (fluorescent intensity) data sets, We consider a clustering algorithm based on mixtures of t distributions to obtain all possible genotypes of each individual (i.e. "GenoSpectrum"). We then propose a likelihood-based approach that incorporates the genotyping uncertainty to assessing the associations between traits and haplotypes through a haplotypebased logistic regression model, Simulation studies show that our likelihood-based method can reduce the impact induced by genotyping errors.

  4. Optimal Parameters Multicomponent Mixtures Extruding

    Directory of Open Access Journals (Sweden)

    Ramil F. Sagitov

    2013-01-01

    Full Text Available Experimental research of multicomponent mixtures extruding from production wastes are carried out, unit for production of composites from different types of waste is presented. Having analyzed dependence of multicomponent mixtures extruding energy requirements on die length and components content at three values of angular rate of screw rotation, we received the values of energy requirements at optimal length of the die, angular speed and percent of binding additives.

  5. Gaussian-mixture umbrella sampling

    OpenAIRE

    Maragakis, Paul; van der Vaart, Arjan; Karplus, Martin

    2009-01-01

    We introduce the Gaussian-mixture umbrella sampling method (GAMUS), a biased molecular dynamics technique based on adaptive umbrella sampling that efficiently escapes free energy minima in multi-dimensional problems. The prior simulation data are reweighted with a maximum likelihood formulation, and the new approximate probability density is fit to a Gaussian-mixture model, augmented by information about the unsampled areas. The method can be used to identify free energy minima in multi-dimen...

  6. Genotype × genotype interactions between the toxic cyanobacterium Microcystis and its grazer, the waterflea Daphnia

    Science.gov (United States)

    Lemaire, Veerle; Brusciotti, Silvia; van Gremberghe, Ineke; Vyverman, Wim; Vanoverbeke, Joost; De Meester, Luc

    2012-01-01

    Toxic algal blooms are an important problem worldwide. The literature on toxic cyanobacteria blooms in inland waters reports widely divergent results on whether zooplankton can control cyanobacteria blooms or cyanobacteria suppress zooplankton by their toxins. Here we test whether this may be due to genotype × genotype interactions, in which interactions between the large-bodied and efficient grazer Daphnia and the widespread cyanobacterium Microcystis are not only dependent on Microcystis strain or Daphnia genotype but are specific to genotype × genotype combinations. We show that genotype × genotype interactions are important in explaining mortality in short-time exposures of Daphnia to Microcystis. These genotype × genotype interactions may result in local coadaptation and a geographic mosaic of coevolution. Genotype × genotype interactions can explain why the literature on zooplankton–cyanobacteria interactions is seemingly inconsistent, and provide hope that zooplankton can contribute to the suppression of cyanobacteria blooms in restoration projects. PMID:25568039

  7. Responses in gas exchange and water status between drought-tolerant and-susceptible soybean genotypes with ABA application

    Institute of Scientific and Technical Information of China (English)

    Md.Mokter Hossain; Hon-Ming Lam; Jianhua Zhang

    2015-01-01

    The purpose of this study was to investigate the physiological responses of drought-tolerant and drought-susceptible soybean genotypes to exogenous abscisic acid(ABA) application during progressive soil drying at seedling stages. Five-day old soybean seedlings were transplanted into PVC tubes filled with soil mixture. Seedlings were watered daily with similar water volumes until second trifoliate leaves emerged, and thereafter soil drying with or without exogenous ABA application was imposed. Half of the seedlings of each genotype were left for regular watering as control plants. Soil water status declined significantly over seven days of withholding water supply for both genotypes. Leaf expansion rate, stomatal conductance(g_s), leaf water potential(ψ_w), and relative water content of leaves(%RWC) declined significantly under soil drying as well as soil drying with ABA application, compared to their values for well-watered soybean genotypes. However, a drought-tolerant genotype(C12) responded more rapidly than a drought-susceptible genotype(C08) after imposition of soil drying and soil drying with exogenous ABA. In addition, application of exogenous ABA to water-restricted soybeans resulted in higher %RWC and ψwin the drought-tolerant than in the drought-susceptible genotype. Compared to the drought-susceptible genotype, the drought-tolerant genotype was more responsive to exogenous ABA application, resulting in a higher root-to-shoot ratio.

  8. Analysis of asphalt mixtures on town roads

    OpenAIRE

    Glavica, Primož

    2006-01-01

    Asphalt mixtures are most commonly used composite for construction of top layers of different drive ways. By definition asphalt mixtures are composed of crushed rock, fill, bitumen and additives. Percentage of individual components wary according to the purpose asphalt mixture is to be used for. Asphalt mixtures must be capable of enduring different types of load. According to the type of load asphalt mixtures are divided into asphalt mixtures used for supporting layers and asp...

  9. 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...

  10. 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

  11. Identification of a natural intergenotypic recombinant hepatitis delta virus genotype 1 and 2 in Vietnamese HBsAg-positive patients.

    Science.gov (United States)

    Sy, B T; Nguyen, H M; Toan, N L; Song, L H; Tong, H V; Wolboldt, C; Binh, V Q; Kremsner, P G; Velavan, T P; Bock, C-T

    2015-01-01

    Hepatitis D virus (HDV) infection is acquired as a co- /superinfection of Hepatitis B virus (HBV) and can modulate the pathophysiology of chronic hepatitis B and related liver diseases including hepatocellular carcinoma. Among the eight distinct HDV genotypes reported, relatively few studies have attempted to investigate the prevalence of HDV mixed genotypes and RNA recombination of HDV. With a recorded prevalence of 10-20% HBV infection in Vietnam, this study investigated the HDV variability, HDV genotypes and HDV recombination among twenty-one HDV isolates in Vietnamese HBsAg-positive patients. HDV subgenomic and full-length genome sequences were obtained using newly established HDV-specific RT-PCR techniques. The nucleotide homology was observed from 74.6% to 99.4% among the investigated full-length genome of the HDV isolates. We observed HDV genotype 1 and HDV genotype 2 in the investigated Vietnamese patients. Although no HDV genotype mixtures were observed, we report here a newly identified recombinant of HDV genotypes (HDV 1 and HDV 2). The identified recombinant HDV isolate C03 revealed sequence homology to both HDV genotype 1 (nt1 to nt907) and HDV genotype 2 (nt908 to nt1675; HDAg coding region) with a breakpoint at nt908. Our findings demonstrate the prevalence of intergenotypic recombination between HDV genotypes 1 and 2 in a Vietnamese HBsAg-positive patient. Extended investigation on the distribution and prevalence of HDV, HDV mixed genotypes and recombinant HDV genotypes in a larger Vietnamese population offers vital insights into understanding of the micro-epidemiology of HDV and subsequent pathophysiology in chronic HBV- /HDV-related liver diseases.

  12. 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.

  13. Marangoni Convection in Binary Mixtures

    CERN Document Server

    Zhang, J; Oron, A; Behringer, Robert P.; Oron, Alexander; Zhang, Jie

    2006-01-01

    Marangoni instabilities in binary mixtures are different from those in pure liquids. In contrast to a large amount of experimental work on Marangoni convection in pure liquids, such experiments in binary mixtures are not available in the literature, to our knowledge. Using binary mixtures of sodium chloride/water, we have systematically investigated the pattern formation for a set of substrate temperatures and solute concentrations in an open system. The flow patterns evolve with time, driven by surface-tension fluctuations due to evaporation and the Soret effect, while the air-liquid interface does not deform. A shadowgraph method is used to follow the pattern formation in time. The patterns are mainly composed of polygons and rolls. The mean pattern size first decreases slightly, and then gradually increases during the evolution. Evaporation affects the pattern formation mainly at the early stage and the local evaporation rate tends to become spatially uniform at the film surface. The Soret effect becomes i...

  14. Mixtures of skewed Kalman filters

    KAUST Repository

    Kim, Hyoungmoon

    2014-01-01

    Normal state-space models are prevalent, but to increase the applicability of the Kalman filter, we propose mixtures of skewed, and extended skewed, Kalman filters. To do so, the closed skew-normal distribution is extended to a scale mixture class of closed skew-normal distributions. Some basic properties are derived and a class of closed skew. t distributions is obtained. Our suggested family of distributions is skewed and has heavy tails too, so it is appropriate for robust analysis. Our proposed special sequential Monte Carlo methods use a random mixture of the closed skew-normal distributions to approximate a target distribution. Hence it is possible to handle skewed and heavy tailed data simultaneously. These methods are illustrated with numerical experiments. © 2013 Elsevier Inc.

  15. 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.

  16. 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. .

  17. Challenges in Determining Genotypes for Pharmacogenetics in Allogeneic Hematopoietic Cell Transplant Recipients.

    Science.gov (United States)

    Langman, Loralie J; Nesher, Lior; Shah, Dimpy P; Azzi, Jacques M; Shpall, Elizabeth J; Rezvani, Katy; Black, John L; Chemaly, Roy F

    2016-09-01

    As part of a pharmacogenetic study, paired blood and oral fluid samples were tested for the IL28B polymorphism (rs12979860) before and after hematopoietic cell transplantation (HCT) to evaluate changes in the genotype and investigate the utility of genotyping in oral fluid in HCT recipients. In 54 patients with leukemia >18 years of age, samples were collected approximately 7 days before HCT and 60 days after HCT. IL28B polymorphism testing was performed using real-time PCR with allele-specific probes. Twenty-four patients had the same genotype as their donors. In 30 patients, the genotype was different from that of the donor. In the oral fluid samples, 4 retained the recipient's genotype, and 18 had a genotype that matched that of the donor. In the remaining 8 patients, the results could not be characterized and appeared to be a combination of both, suggesting mixed proportions of donor and recipient cells. The assumption was that the sloughed epithelial cells of the mouth are of recipient origin. However, oral fluid is a mixture that contains varying numbers of cells of the recipient and immunomodulatory cells from the donor. Therefore, the use of oral fluid after HCT for clinical pharmacogenetics purposes needs further investigation.

  18. 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.

  19. A Homogeneous HLA-B*27 Genotyping Assay Using Dried Reagent Mixtures

    Directory of Open Access Journals (Sweden)

    Minna Kiviniemi

    2009-01-01

    Full Text Available The presence of HLA-B*27 allele with patients suspected with ankylosing spondylitis can be used in the diagnostic process. We have developed an assay for typing for the HLA-B*27 in whole blood dried on sample collection cards using pre-dried reagent wells and homogeneous time-resolved fluorescence based PCR approach. Essentially only the sample needs to be added to the dry ready-to-use reaction well in order to start the homogenous amplification assay. The method was validated with 229 samples also typed with an existing DELFIA-based method and results of both assays were 100% concordant. The dried reagents were shown to be stable at least up to eight weeks at room temperature without any decline in their performance.

  20. Taylor dispersion analysis of mixtures.

    Science.gov (United States)

    Cottet, Hervé; Biron, Jean-Philippe; Martin, Michel

    2007-12-01

    Taylor dispersion analysis (TDA) is a fast and simple method for determining hydrodynamic radii. In the case of sample mixtures, TDA, as the other nonseparative methods, leads to an average diffusion coefficient on the different molecules constituting the mixture. We set in this work the equations giving, on a consistent basis, the average values obtained by TDA with detectors with linear response functions. These equations confronted TDA experiments of sample mixtures containing different proportions of a small molecule and a polymer standard. Very good agreement between theory and experiment was obtained. In a second part of this work, on the basis of monomodal or bimodal molar mass distributions of polymers, the different average diffusion coefficients corresponding to TDA were compared to the z-average diffusion coefficient (D(z)) obtained from dynamic light scattering (DLS) experiments and to the weight average diffusion coefficient (D(w)). This latter value is sometimes considered as the most representative of the sample mixture. From these results, it appears that, for monomodal distribution and relatively low polydispersity (I = 1.15), the average diffusion coefficient generally derived from TDA is very close to Dw. However, for highly polydisperse samples (e.g., bimodal polydisperse distributions), important differences could be obtained (up to 35% between TDA and D(w)). In all the cases, the average diffusion coefficient obtained by TDA for a mass concentration detector was closer to the Dw value than the z-average obtained by DLS.

  1. An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies

    DEFF Research Database (Denmark)

    Thompson, Wesley K.; Wang, Yunpeng; Schork, Andrew J.

    2015-01-01

    Characterizing the distribution of effects from genome-wide genotyping data is crucial for understanding important aspects of the genetic architecture of complex traits, such as number or proportion of non-null loci, average proportion of phenotypic variance explained per non-null effect, power...... for discovery, and polygenic risk prediction. To this end, previous work has used effect-size models based on various distributions, including the normal and normal mixture distributions, among others. In this paper we propose a scale mixture of two normals model for effect size distributions of genome...... of variance explained by genotyped SNPs, CD and SZ have a broadly dissimilar genetic architecture, due to differing mean effect size and proportion of non-null loci....

  2. High resolution genotyping of clinical Aspergillus flavus isolates from India using microsatellites.

    Directory of Open Access Journals (Sweden)

    Shivaprakash M Rudramurthy

    Full Text Available BACKGROUND: Worldwide, Aspergillus flavus is the second leading cause of allergic, invasive and colonizing fungal diseases in humans. However, it is the most common species causing fungal rhinosinusitis and eye infections in tropical countries. Despite the growing challenges due to A. flavus, the molecular epidemiology of this fungus has not been well studied. We evaluated the use of microsatellites for high resolution genotyping of A. flavus from India and a possible connection between clinical presentation and genotype of the involved isolate. METHODOLOGY/PRINCIPAL FINDINGS: A panel of nine microsatellite markers were selected from the genome of A. flavus NRRL 3357. These markers were used to type 162 clinical isolates of A. flavus. All nine markers proved to be polymorphic displaying up to 33 alleles per marker. Thirteen isolates proved to be a mixture of different genotypes. Among the 149 pure isolates, 124 different genotypes could be recognized. The discriminatory power (D for the individual markers ranged from 0.657 to 0.954. The D value of the panel of nine markers combined was 0.997. The multiplex multicolor approach was instrumental in rapid typing of a large number of isolates. There was no correlation between genotype and the clinical presentation of the infection. CONCLUSIONS/SIGNIFICANCE: There is a large genotypic diversity in clinical A. flavus isolates from India. The presence of more than one genotype in clinical samples illustrates the possibility that persons may be colonized by multiple genotypes and that any isolate from a clinical specimen is not necessarily the one actually causing infection. Microsatellites are excellent typing targets for discriminating between A. flavus isolates from various origins.

  3. 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.

  4. 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.

  5. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

  6. Local fluctuations in solution mixtures

    Science.gov (United States)

    Ploetz, Elizabeth A.; Smith, Paul E.

    2011-01-01

    An extension of the traditional Kirkwood-Buff (KB) theory of solutions is outlined which provides additional fluctuating quantities that can be used to characterize and probe the behavior of solution mixtures. Particle-energy and energy-energy fluctuations for local regions of any multicomponent solution are expressed in terms of experimentally obtainable quantities, thereby supplementing the usual particle-particle fluctuations provided by the established KB inversion approach. The expressions are then used to analyze experimental data for pure water over a range of temperatures and pressures, a variety of pure liquids, and three binary solution mixtures – methanol and water, benzene and methanol, and aqueous sodium chloride. In addition to providing information on local properties of solutions it is argued that the particle-energy and energy-energy fluctuations can also be used to test and refine solute and solvent force fields for use in computer simulation studies. PMID:21806137

  7. Binary mixtures of chiral gases

    CERN Document Server

    Presilla, Carlo

    2015-01-01

    A possible solution of the well known paradox of chiral molecules is based on the idea of spontaneous symmetry breaking. At low pressure the molecules are delocalized between the two minima of a given molecular potential while at higher pressure they become localized in one minimum due to the intermolecular dipole-dipole interactions. Evidence for such a phase transition is provided by measurements of the inversion spectrum of ammonia and deuterated ammonia at different pressures. In particular, at pressure greater than a critical value no inversion line is observed. These data are well accounted for by a model previously developed and recently extended to mixtures. In the present paper, we discuss the variation of the critical pressure in binary mixtures as a function of the fractions of the constituents.

  8. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

    Jiang, Yong; Wang, Hao; Kindt, James T.

    2010-01-01

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironmen...

  9. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

    Jiang, Yong; WANG, HAO; Kindt, James T.

    2010-01-01

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironmen...

  10. FRACTIONAL TRANSPORT OF SEDIMENT MIXTURES

    Institute of Scientific and Technical Information of China (English)

    Baosheng WU; Albert MOLINAS; Anping SHU

    2003-01-01

    A new method based on the Transport Capacity Fraction (TCF) concept is proposed to compute the fractional transport rates for nonuniform sediment mixtures in sand-bed channels. The TCF concept is derived from the understanding that the measurements and predictions of bed-material load are more accurate and reliable than the measurements and predictions of fractional loads. First the bed-material load is computed using an appropriate equation, then the fractional transport rates are determined by distributing the bed-material load into size groups through a transport capacity distribution function. For the computation of bed-material loads, the Aekers and White, Engelund and Hansen, and Yang equations are used in this study. Two new transport capacity distribution functions are developed for flows in sand-bed channels. The new expressions presented in this paper account for the sheltering and exposure effects that exist in mixtures. Comparisons with measured data show that the proposed method can significantly improve the predictions of fractional transport rates for nonuniform sediment mixtures.

  11. 21 CFR 82.6 - Certifiable mixtures.

    Science.gov (United States)

    2010-04-01

    ... mixture is harmless and suitable for use therein; and (3) No diluent (except resins, natural gum, pectin... mixture is for external application to shell eggs, or for use in coloring a food specified in the...

  12. A Statistical Framework for the Interpretation of mtDNA Mixtures: Forensic and Medical Applications

    Science.gov (United States)

    Egeland, Thore; Salas, Antonio

    2011-01-01

    Background Mitochondrial DNA (mtDNA) variation is commonly analyzed in a wide range of different biomedical applications. Cases where more than one individual contribute to a stain genotyped from some biological material give rise to a mixture. Most forensic mixture cases are analyzed using autosomal markers. In rape cases, Y-chromosome markers typically add useful information. However, there are important cases where autosomal and Y-chromosome markers fail to provide useful profiles. In some instances, usually involving small amounts or degraded DNA, mtDNA may be the only useful genetic evidence available. Mitochondrial DNA mixtures also arise in studies dealing with the role of mtDNA variation in tumorigenesis. Such mixtures may be generated by the tumor, but they could also originate in vitro due to inadvertent contamination or a sample mix-up. Methods/Principal Findings We present the statistical methods needed for mixture interpretation and emphasize the modifications required for the more well-known methods based on conventional markers to generalize to mtDNA mixtures. Two scenarios are considered. Firstly, only categorical mtDNA data is assumed available, that is, the variants contributing to the mixture. Secondly, quantitative data (peak heights or areas) on the allelic variants are also accessible. In cases where quantitative information is available in addition to allele designation, it is possible to extract more precise information by using regression models. More precisely, using quantitative information may lead to a unique solution in cases where the qualitative approach points to several possibilities. Importantly, these methods also apply to clinical cases where contamination is a potential alternative explanation for the data. Conclusions/Significance We argue that clinical and forensic scientists should give greater consideration to mtDNA for mixture interpretation. The results and examples show that the analysis of mtDNA mixtures contributes

  13. Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

    Directory of Open Access Journals (Sweden)

    Jian Ye

    2015-01-01

    Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

  14. Psychophysical studies of mixtures of tastants

    NARCIS (Netherlands)

    Graaf, de C.

    1988-01-01

    The human perception of mixtures of tastante was studied with reference to three central issues, i.e., 1) the paradigma of equiratio taste substance mixtures. as an instrument to manipulate the physical composition of tastant mixtures. This paradiama also enables the construction of psychophysical

  15. 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.

  16. 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.

  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

    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...... of identical genotypes between sample x and sample y by chance. Based on this we calculate a mix-up confidence score with penalization for introducing mismatches in the proposed new label and adjustment for independency among the genotypes. This confidence score is used to identify probable mix-ups.......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. 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.

  19. 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

  20. Supercritical Water Mixture (SCWM) Experiment

    Science.gov (United States)

    Hicks, Michael C.; Hegde, Uday G.

    2012-01-01

    The subject presentation, entitled, Supercritical Water Mixture (SCWM) Experiment, was presented at the International Space Station (ISS) Increment 33/34 Science Symposium. This presentation provides an overview of an international collaboration between NASA and CNES to study the behavior of a dilute aqueous solution of Na2SO4 (5% w) at near-critical conditions. The Supercritical Water Mixture (SCWM) investigation, serves as important precursor work for subsequent Supercritical Water Oxidation (SCWO) experiments. The SCWM investigation will be performed in DECLICs High Temperature Insert (HTI) for the purpose of studying critical fluid phenomena at high temperatures and pressures. The HTI includes a completely sealed and integrated test cell (i.e., Sample Cell Unit SCU) that will contain approximately 0.3 ml of the aqueous test solution. During the sequence of tests, scheduled to be performed in FY13, temperatures and pressures will be elevated to critical conditions (i.e., Tc = 374C and Pc = 22 MPa) in order to observe salt precipitation, precipitate agglomeration and precipitate transport in the presence of a temperature gradient without the influences of gravitational forces. This presentation provides an overview of the motivation for this work, a description of the DECLIC HTI hardware, the proposed test sequences, and a brief discussion of the scientific research objectives.

  1. Atomistic simulations of bicelle mixtures.

    Science.gov (United States)

    Jiang, Yong; Wang, Hao; Kindt, James T

    2010-06-16

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets.

  2. The Kinetics of Enzyme Mixtures

    Directory of Open Access Journals (Sweden)

    Simon Brown

    2014-03-01

    Full Text Available Even purified enzyme preparations are often heterogeneous. For example, preparations of aspartate aminotransferase or cytochrome oxidase can consist of several different forms of the enzyme. For this reason we consider how different the kinetics of the reactions catalysed by a mixture of forms of an enzyme must be to provide some indication of the characteristics of the species present. Based on the standard Michaelis-Menten model, we show that if the Michaelis constants (Km of two isoforms differ by a factor of at least 20 the steady-state kinetics can be used to characterise the mixture. However, even if heterogeneity is reflected in the kinetic data, the proportions of the different forms of the enzyme cannot be estimated from the kinetic data alone. Consequently, the heterogeneity of enzyme preparations is rarely reflected in measurements of their steady-state kinetics unless the species present have significantly different kinetic properties. This has two implications: (1 it is difficult, but not impossible, to detect molecular heterogeneity using kinetic data and (2 even when it is possible, a considerable quantity of high quality data is required.

  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. Effect of Mixture Pressure and Equivalence Ratio on Detonation Cell Size for Hydrogen-Air Mixtures

    Science.gov (United States)

    2015-06-01

    EFFECT OF MIXTURE PRESSURE AND EQUIVALENCE RATIO ON DETONATION CELL SIZE FOR HYDROGEN -AIR MIXTURES...protection in the United States. AFIT-ENY-MS-15-J-045 EFFECT OF MIXTURE PRESSURE AND EQUIVALENCE RATIO ON DETONATION CELL SIZE FOR HYDROGEN -AIR...DISTRIBUTION UNLIMITED. AFIT-ENY-MS-15-J-045 EFFECT OF MIXTURE PRESSURE AND EQUIVALENCE RATIO ON DETONATION CELL SIZE FOR HYDROGEN -AIR MIXTURES

  6. TrueAllele casework on Virginia DNA mixture evidence: computer and manual interpretation in 72 reported criminal cases.

    Science.gov (United States)

    Perlin, Mark W; Dormer, Kiersten; Hornyak, Jennifer; Schiermeier-Wood, Lisa; Greenspoon, Susan

    2014-01-01

    Mixtures are a commonly encountered form of biological evidence that contain DNA from two or more contributors. Laboratory analysis of mixtures produces data signals that usually cannot be separated into distinct contributor genotypes. Computer modeling can resolve the genotypes up to probability, reflecting the uncertainty inherent in the data. Human analysts address the problem by simplifying the quantitative data in a threshold process that discards considerable identification information. Elevated stochastic threshold levels potentially discard more information. This study examines three different mixture interpretation methods. In 72 criminal cases, 111 genotype comparisons were made between 92 mixture items and relevant reference samples. TrueAllele computer modeling was done on all the evidence samples, and documented in DNA match reports that were provided as evidence for each case. Threshold-based Combined Probability of Inclusion (CPI) and stochastically modified CPI (mCPI) analyses were performed as well. TrueAllele's identification information in 101 positive matches was used to assess the reliability of its modeling approach. Comparison was made with 81 CPI and 53 mCPI DNA match statistics that were manually derived from the same data. There were statistically significant differences between the DNA interpretation methods. TrueAllele gave an average match statistic of 113 billion, CPI averaged 6.68 million, and mCPI averaged 140. The computer was highly specific, with a false positive rate under 0.005%. The modeling approach was precise, having a factor of two within-group standard deviation. TrueAllele accuracy was indicated by having uniformly distributed match statistics over the data set. The computer could make genotype comparisons that were impossible or impractical using manual methods. TrueAllele computer interpretation of DNA mixture evidence is sensitive, specific, precise, accurate and more informative than manual interpretation alternatives

  7. TrueAllele casework on Virginia DNA mixture evidence: computer and manual interpretation in 72 reported criminal cases.

    Directory of Open Access Journals (Sweden)

    Mark W Perlin

    Full Text Available Mixtures are a commonly encountered form of biological evidence that contain DNA from two or more contributors. Laboratory analysis of mixtures produces data signals that usually cannot be separated into distinct contributor genotypes. Computer modeling can resolve the genotypes up to probability, reflecting the uncertainty inherent in the data. Human analysts address the problem by simplifying the quantitative data in a threshold process that discards considerable identification information. Elevated stochastic threshold levels potentially discard more information. This study examines three different mixture interpretation methods. In 72 criminal cases, 111 genotype comparisons were made between 92 mixture items and relevant reference samples. TrueAllele computer modeling was done on all the evidence samples, and documented in DNA match reports that were provided as evidence for each case. Threshold-based Combined Probability of Inclusion (CPI and stochastically modified CPI (mCPI analyses were performed as well. TrueAllele's identification information in 101 positive matches was used to assess the reliability of its modeling approach. Comparison was made with 81 CPI and 53 mCPI DNA match statistics that were manually derived from the same data. There were statistically significant differences between the DNA interpretation methods. TrueAllele gave an average match statistic of 113 billion, CPI averaged 6.68 million, and mCPI averaged 140. The computer was highly specific, with a false positive rate under 0.005%. The modeling approach was precise, having a factor of two within-group standard deviation. TrueAllele accuracy was indicated by having uniformly distributed match statistics over the data set. The computer could make genotype comparisons that were impossible or impractical using manual methods. TrueAllele computer interpretation of DNA mixture evidence is sensitive, specific, precise, accurate and more informative than manual

  8. High-resolution melting analysis for detection of a single-nucleotide polymorphism and the genotype of the myostatin gene in warmblood horses.

    Science.gov (United States)

    Serpa, Priscila B S; Garbade, Petra; Natalini, Cláudio C; Pires, Ananda R; Tisotti, Tainor M

    2017-01-01

    OBJECTIVE To develop a high-resolution melting (HRM) assay to detect the g.66493737C>T polymorphism in the myostatin gene (MSTN) and determine the frequency of 3 previously defined g.66493737 genotypes (T/T, T/C, and C/C) in warmblood horses. SAMPLES Blood samples from 23 horses. PROCEDURES From each blood sample, DNA was extracted and analyzed by standard PCR methods and an HRM assay to determine the MSTN genotype. Three protocols (standard protocol, protocol in which a high-salt solution was added to the reaction mixture before the first melting cycle, and protocol in which an unlabeled probe was added to the reaction mixture before analysis) for the HRM assay were designed and compared. Genotype results determined by the HRM protocol that generated the most consistent melting curves were compared with those determined by sequencing. RESULTS The HRM protocol in which an unlabeled probe was added to the reaction mixture generated the most consistent melting curves. The genotypes of the g.66493737C>T polymorphism were determined for 22 horses (16 by HRM analysis and 20 by sequencing); 14, 7, and 1 had the T/T, T/C, and C/C genotypes, respectively. The genotype determined by HRM analysis agreed with that determined by sequencing for 14 of 16 horses. The frequency of alleles T and C was 79.5% and 20.5%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that HRM analysis may be a faster and more economical alternative than PCR methods for genotyping. Genotyping results might be useful as predictors of athletic performance for horses.

  9. 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.

  10. 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.

  11. 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

  12. Afrikaner spirituality: A complex mixture

    Directory of Open Access Journals (Sweden)

    Erna Olivier

    2006-10-01

    Full Text Available The article argues that the perception that Afrikaner spirituality is and has always been founded mainly or only upon the Calvinistic tradition is a misconception. Nineteenth century Afrikaner spiritualism consisted of a mixture of theology, philosophy and a way of adapting to extreme living conditions. These factors, although with different contents, are also the determinant issues that made 21st century Afrikaner spirituality such a complex phenomenon. The article postulates that the Afrikaner nation’s current identity crisis can be resolved by closely looking at the different influences on the spirituality of the nation and by carefully guiding the people through the complex set of multiple choices to a fresh relation with Christ in a new found Christian identity to confirm our Christian foundation.

  13. 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.

  14. 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...

  15. 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....

  16. 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

  17. 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 ...

  18. 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...

  19. 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.

  20. AFLP analysis among Ethiopian arabica coffee genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... sequence information, produces a large number of infor- mative polymorphic markers per primer, requires a small amount of ..... and 53 were monomorphic across all coffee genotypes collected from .... molecular markers.

  1. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)

    adel

    2014-01-08

    Jan 8, 2014 ... germinated on filter papers imbibed in distilled water or in sodium .... Wards minimum variance method as a clustering algorithm. ... Mean values of plumule: radicle ratio of M. truncatula genotypes under different salt stress ...

  2. 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,...

  3. A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

    Directory of Open Access Journals (Sweden)

    Ghalia Boubaker

    Full Text Available Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10 and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3, E. equinus (G4, E. ortleppi (G5, and E. canadensis (G6-G10. The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR allowing three levels of discrimination: (i Echinococcus genus, (ii E. granulosus complex in common, and (iii the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20 and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13. The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%. Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.

  4. A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

    Science.gov (United States)

    Boubaker, Ghalia; Macchiaroli, Natalia; Prada, Laura; Cucher, Marcela A; Rosenzvit, Mara C; Ziadinov, Iskender; Deplazes, Peter; Saarma, Urmas; Babba, Hamouda; Gottstein, Bruno; Spiliotis, Markus

    2013-01-01

    Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6-G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (Echinococcus genus.

  5. Methods on Identification and Screening of Rice Genotypes with High Nitrogen Efficiency

    Institute of Scientific and Technical Information of China (English)

    CHENG Jian-feng; JIANG Han-yan; LIU Yi-bai; DAI Ting-bo; CAO Wei-xing

    2011-01-01

    In order to establish methods for indentification and screening of rice genotypes with high nitrogen (N) efficiency,N absorption efficiency (NAE),N utilization efficiency (NUE) and N harvest index (NHI) in ten rice genotypes were investgated at the elongation,booting,heading and maturity stages under six N levels in a pot experiment with soil-sand mixtures at various ratios.NAE in various rice genotypes firstly increased,peaked under a medium nitrogen rate of 0.177 g/kg and then decreased,but NUE and NHI always decreased with increasing nitrogen levels.NAE in various rice genotypes ever increased with growing process and NUE indicated a descending tendency of elongation stage>heading stage>maturity stage>booting stage.N level influenced rice NAE,NUE and NHI most,followed by genotype,and the both effects were significant at 0.01 level.In addition,the interaction effects of genotype and nitrogen level on rice NAE and NUE were significant at 0.01 level,but not significant on rice NHI.Because the maximum differences of NAE and NUE were found at the elongation stage,it was thought to be the most suitable stage for identification and screening these two paremeters.Therefore,the optimum conditions for identification and screening of rice NAE,NUE and NHI in a pot experiment were the nitrogen rate of 0.157 g/kg at the elongation stage,low nitrogen at the elongation stage,and the nitrogen rate of 0.277 g/kg at the maturity stage,respectively.

  6. Study on Hepatitis B Virus Genotypes in Groups of the Zhuang Nationality in Western Guangxi%桂西壮族人群乙肝病毒基因型研究

    Institute of Scientific and Technical Information of China (English)

    黄重敏; 覃亚勤; 覃后继; 卢东; 何延专; 覃雪英

    2004-01-01

    To study the distribution characteristics of Hepatitis B virus (HBV) genotypes in groups of the Zhuang nationality of Baishe in Guangxi, the PCR sandwich hybridization-ELISA technique was used to determine the genotypes in 30 patinets of Zhuang nationality with hepatitis B. Geontype B, C, D and non A-F were found in this group, in which 56.6% of them were type D,46.6% type C,33.3% typeA-F, 20% type B, Most patients were found with types C+D, D+B or C+B. It is suggested that there are genotypes D, C, B and non A-F in this area, and the major one was genotype D. There are mixture of genotypes C+D, B+C, D+B in this region, so the HBV genotype might be associated with area and nationality.

  7. Bayesian mixture models for spectral density estimation

    OpenAIRE

    Cadonna, Annalisa

    2017-01-01

    We introduce a novel Bayesian modeling approach to spectral density estimation for multiple time series. Considering first the case of non-stationary timeseries, the log-periodogram of each series is modeled as a mixture of Gaussiandistributions with frequency-dependent weights and mean functions. The implied model for the log-spectral density is a mixture of linear mean functionswith frequency-dependent weights. The mixture weights are built throughsuccessive differences of a logit-normal di...

  8. Thermodynamic Calculations for Complex Chemical Mixtures

    Science.gov (United States)

    Mcbride, B. J.

    1986-01-01

    General computer program, CECTRP, developed for calculation of thermodynamic properties of complex mixtures with option to calculate transport properties of these mixtures. Free-energy minimization technique used in equilibrium calculation. Rigorous equations used in transport calculations. Program calculates equilibrium compositions and corresponding thermodynamic and transport properties of mixtures. CECTRP accommodates up to 24 reactants, 20 elements, and 600 products, 400 of which are condensed. Written in FORTRAN IV for any large computer system.

  9. 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.

  10. Shear viscosity of liquid mixtures Mass dependence

    CERN Document Server

    Kaushal, R

    2002-01-01

    Expressions for zeroth, second, and fourth sum rules of transverse stress autocorrelation function of two component fluid have been derived. These sum rules and Mori's memory function formalism have been used to study shear viscosity of Ar-Kr and isotopic mixtures. It has been found that theoretical result is in good agreement with the computer simulation result for the Ar-Kr mixture. The mass dependence of shear viscosity for different mole fraction shows that deviation from ideal linear model comes even from mass difference in two species of fluid mixture. At higher mass ratio shear viscosity of mixture is not explained by any of the emperical model.

  11. Empirical profile mixture models for phylogenetic reconstruction

    National Research Council Canada - National Science Library

    Si Quang, Le; Gascuel, Olivier; Lartillot, Nicolas

    2008-01-01

    Motivation: Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving...

  12. A Mixture Model Approach to the Mapping of Quantitative Trait Loci in Complex Populations With an Apllication to Multiple Cattle Families

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Johnson, David L.; Arendonk, Johan A.M. van

    1998-01-01

    A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maxi

  13. A mixture model approach to the mapping of quantitative trait loci in complex populations with an application to multiple cattle families.

    NARCIS (Netherlands)

    Jansen, R.C.; Johnson, D.L.; Arendonk, van J.A.M.

    1998-01-01

    A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maxi

  14. A Mixture Model Approach to the Mapping of Quantitative Trait Loci in Complex Populations With an Application to Multiple Cattle Families

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Johnson, David L.; Arendonk, Johan A.M. van

    1998-01-01

    A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maxi

  15. 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

  16. Blood Group ABO Genotyping in Paternity Testing

    Science.gov (United States)

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

    2012-01-01

    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 A1, A2, 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 future

  17. Simulation of mixture microstructures via particle packing models and their direct comparison with real mixtures

    Science.gov (United States)

    Gulliver, Eric A.

    The objective of this thesis to identify and develop techniques providing direct comparison between simulated and real packed particle mixture microstructures containing submicron-sized particles. This entailed devising techniques for simulating powder mixtures, producing real mixtures with known powder characteristics, sectioning real mixtures, interrogating mixture cross-sections, evaluating and quantifying the mixture interrogation process and for comparing interrogation results between mixtures. A drop and roll-type particle-packing model was used to generate simulations of random mixtures. The simulated mixtures were then evaluated to establish that they were not segregated and free from gross defects. A powder processing protocol was established to provide real mixtures for direct comparison and for use in evaluating the simulation. The powder processing protocol was designed to minimize differences between measured particle size distributions and the particle size distributions in the mixture. A sectioning technique was developed that was capable of producing distortion free cross-sections of fine scale particulate mixtures. Tessellation analysis was used to interrogate mixture cross sections and statistical quality control charts were used to evaluate different types of tessellation analysis and to establish the importance of differences between simulated and real mixtures. The particle-packing program generated crescent shaped pores below large particles but realistic looking mixture microstructures otherwise. Focused ion beam milling was the only technique capable of sectioning particle compacts in a manner suitable for stereological analysis. Johnson-Mehl and Voronoi tessellation of the same cross-sections produced tessellation tiles with different the-area populations. Control charts analysis showed Johnson-Mehl tessellation measurements are superior to Voronoi tessellation measurements for detecting variations in mixture microstructure, such as altered

  18. Thermodynamics of mixtures containing amines

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Juan Antonio [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain)], E-mail: jagl@termo.uva.es; Mozo, Ismael; Garcia de la Fuente, Isaias; Cobos, Jose Carlos [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain); Riesco, Nicolas [Department of Chemical Engineering, Loughborough University, Loughborough, LE113TU Leicestershire (United Kingdom)

    2008-01-30

    Mixtures with dimethyl or trimethylpyridines and alkane, aromatic compound or 1-alkanol have been examined using different theories: DISQUAC, Flory, the concentration-concentration structure factor, S{sub CC}(0), or the Kirkwood-Buff formalism. DISQUAC represents fairly well the available experimental data, and improves theoretical calculations from Dortmund UNIFAC. Two important effects have been investigated: (i) the effect of increasing the number of methyl groups attached to the aromatic ring of the amine; (ii) the effect of modifying the position of the methyl groups in this ring. The molar excess enthalpy, H{sup E}, and the molar excess volume, V{sup E}, decrease in systems with alkane or methanol as follows: pyridine > 3-methylpyridine > 3,5-dimethylpyridine and pyridine > 2-methylpyridine > 2,4-dimethylpyridine > 2,4,6-trimethylpyridine, which has been attributed to a weakening of the amine-amine interactions in the same sequences. This is in agreement with the relative variation of the effective dipole moment, {mu}-bar, and of the differences between the boiling temperature of a pyridine base and that of the homomorphic alkane. For heptane solutions, the observed H{sup E} variation, H{sup E} (3,5-dimethylpyridine) > H{sup E} (2,4-dimethylpyridine) > H{sup E} (2,6-dimethylpyridine), is explained similarly. Calculations on the basis of the Flory model confirm that orientational effects become weaker in systems with alkane in the order: pyridine > methylpyridine > dimethylpyridine > trimethylpyridine. S{sub CC}(0) calculations show that steric effects increase with the number of CH{sub 3}- groups in the pyridine base, and that the steric effects exerted by methyl groups in positions 2 and 6 are higher than when they are placed in positions 3 and 5. The hydrogen bond energy in methanol mixtures is independent of the pyridine base, and it is estimated to be -35.2 kJ mol{sup -1}. Heterocoordination in these solutions is due in part to size effects. Their

  19. 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

  20. Pooled deep sequencing of Plasmodium falciparum isolates: an efficient and scalable tool to quantify prevailing malaria drug-resistance genotypes.

    Science.gov (United States)

    Taylor, Steve M; Parobek, Christian M; Aragam, Nash; Ngasala, Billy E; Mårtensson, Andreas; Meshnick, Steven R; Juliano, Jonathan J

    2013-12-15

    Molecular surveillance for drug-resistant malaria parasites requires reliable, timely, and scalable methods. These data may be efficiently produced by genotyping parasite populations using second-generation sequencing (SGS). We designed and validated a SGS protocol to quantify mutant allele frequencies in the Plasmodium falciparum genes dhfr and dhps in mixed isolates. We applied this new protocol to field isolates from children and compared it to standard genotyping using Sanger sequencing. The SGS protocol accurately quantified dhfr and dhps allele frequencies in a mixture of parasite strains. Using SGS of DNA that was extracted and then pooled from individual isolates, we estimated mutant allele frequencies that were closely correlated to those estimated by Sanger sequencing (correlations, >0.98). The SGS protocol obviated most molecular steps in conventional methods and is cost saving for parasite populations >50. This SGS genotyping method efficiently and reproducibly estimates parasite allele frequencies within populations of P. falciparum for molecular epidemiologic studies.

  1. Time-dependence in mixture toxicity prediction.

    Science.gov (United States)

    Dawson, Douglas A; Allen, Erin M G; Allen, Joshua L; Baumann, Hannah J; Bensinger, Heather M; Genco, Nicole; Guinn, Daphne; Hull, Michael W; Il'Giovine, Zachary J; Kaminski, Chelsea M; Peyton, Jennifer R; Schultz, T Wayne; Pöch, Gerald

    2014-12-04

    The value of time-dependent toxicity (TDT) data in predicting mixture toxicity was examined. Single chemical (A and B) and mixture (A+B) toxicity tests using Microtox(®) were conducted with inhibition of bioluminescence (Vibrio fischeri) being quantified after 15, 30 and 45-min of exposure. Single chemical and mixture tests for 25 sham (A1:A2) and 125 true (A:B) combinations had a minimum of seven duplicated concentrations with a duplicated control treatment for each test. Concentration/response (x/y) data were fitted to sigmoid curves using the five-parameter logistic minus one parameter (5PL-1P) function, from which slope, EC25, EC50, EC75, asymmetry, maximum effect, and r(2) values were obtained for each chemical and mixture at each exposure duration. Toxicity data were used to calculate percentage-based TDT values for each individual chemical and mixture of each combination. Predicted TDT values for each mixture were calculated by averaging the TDT values of the individual components and regressed against the observed TDT values obtained in testing, resulting in strong correlations for both sham (r(2)=0.989, n=25) and true mixtures (r(2)=0.944, n=125). Additionally, regression analyses confirmed that observed mixture TDT values calculated for the 50% effect level were somewhat better correlated with predicted mixture TDT values than at the 25 and 75% effect levels. Single chemical and mixture TDT values were classified into five levels in order to discern trends. The results suggested that the ability to predict mixture TDT by averaging the TDT of the single agents was modestly reduced when one agent of the combination had a positive TDT value and the other had a minimal or negative TDT value. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  2. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  3. Mixture Modeling: Applications in Educational Psychology

    Science.gov (United States)

    Harring, Jeffrey R.; Hodis, Flaviu A.

    2016-01-01

    Model-based clustering methods, commonly referred to as finite mixture modeling, have been applied to a wide variety of cross-sectional and longitudinal data to account for heterogeneity in population characteristics. In this article, we elucidate 2 such approaches: growth mixture modeling and latent profile analysis. Both techniques are…

  4. Two-microphone Separation of Speech Mixtures

    DEFF Research Database (Denmark)

    2006-01-01

    Matlab source code for underdetermined separation of instaneous speech mixtures. The algorithm is described in [1] Michael Syskind Pedersen, DeLiang Wang, Jan Larsen and Ulrik Kjems: ''Two-microphone Separation of Speech Mixtures,'' 2006, submitted for journal publoication. See also, [2] Michael...

  5. Fibril assembly in whey protein mixtures

    NARCIS (Netherlands)

    Bolder, S.G.

    2007-01-01

    The objective of this thesis was to study fibril assembly in mixtures of whey proteins. The effect of the composition of the protein mixture on the structures and the resulting phase behaviour was investigated. The current work has shown that beta-lactoglobulin is responsible for the fibril assembly

  6. 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.

  7. Supercritical separation process for complex organic mixtures

    Science.gov (United States)

    Chum, Helena L.; Filardo, Giuseppe

    1990-01-01

    A process is disclosed for separating low molecular weight components from complex aqueous organic mixtures. The process includes preparing a separation solution of supercritical carbon dioxide with an effective amount of an entrainer to modify the solvation power of the supercritical carbon dioxide and extract preselected low molecular weight components. The separation solution is maintained at a temperature of at least about 70.degree. C. and a pressure of at least about 1,500 psi. The separation solution is then contacted with the organic mixtures while maintaining the temperature and pressure as above until the mixtures and solution reach equilibrium to extract the preselected low molecular weight components from the organic mixtures. Finally, the entrainer/extracted components portion of the equilibrium mixture is isolated from the separation solution.

  8. 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.

  9. Identification of Some Walnut Genotypes in Lorestan Province of Iran and Selection of 54 Superior Genotypes

    Directory of Open Access Journals (Sweden)

    A. Mohammadi

    2015-06-01

    Full Text Available Identification and selection of superior genotypes is the first step in walnut breeding programs. For identifying superior genotypes in Lorestan province, Iran, 35000 seedling genotypes were evaluated during 2008-2009. 29 Phenological traits were evaluated using IPGIRI descriptors in 288 selected seedling genotypes. Finally 54 promising genotypes with 10 major phenological traits were evaluated and classified to five groups. Based on the results, The first group included B17 alone as a late leafing genotype. The second group included A11, J14, K20, H19, M13, J1, B14, E14, E6, G17, M7, O9, B7, L6, L10, F12, D6, J15, J16, N5 and N15 genotypes with high kernel percentage, very bright kernel colors, less shell thickness and medium basal fruit pore. M9 with the highest kernel percent among all of the genotypes and 80% of lateral bearing, closed basal fruit pore, less shell thickness and high fruit and kernel weight was classified in another groupe. A7, C5, N3, N18, A17, D1, N14, D4, I4, J6, K17, N4, N19, C10, E13, N13 and N16 genotypes with medium to high fruit diameter, less shell thickness, medium fruit and kernel weight and kernel percentage were classified in the next group. The fifth group included 10 promising genotypes consisting A1, A2, C12, D10, D11, D13, F3, D17, A3, N7, I13, J7, K9 and N11 with quite late leafing and lateral fruit bearing of more than 90% .

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. On the mixture model for multiphase flow

    Energy Technology Data Exchange (ETDEWEB)

    Manninen, M.; Taivassalo, V. [VTT Energy, Espoo (Finland). Nuclear Energy; Kallio, S. [Aabo Akademi, Turku (Finland)

    1996-12-31

    Numerical flow simulation utilising a full multiphase model is impractical for a suspension possessing wide distributions in the particle size or density. Various approximations are usually made to simplify the computational task. In the simplest approach, the suspension is represented by a homogeneous single-phase system and the influence of the particles is taken into account in the values of the physical properties. This study concentrates on the derivation and closing of the model equations. The validity of the mixture model is also carefully analysed. Starting from the continuity and momentum equations written for each phase in a multiphase system, the field equations for the mixture are derived. The mixture equations largely resemble those for a single-phase flow but are represented in terms of the mixture density and velocity. The volume fraction for each dispersed phase is solved from a phase continuity equation. Various approaches applied in closing the mixture model equations are reviewed. An algebraic equation is derived for the velocity of a dispersed phase relative to the continuous phase. Simplifications made in calculating the relative velocity restrict the applicability of the mixture model to cases in which the particles reach the terminal velocity in a short time period compared to the characteristic time scale of the flow of the mixture. (75 refs.)

  15. Foaming of mixtures of pure hydrocarbons

    Science.gov (United States)

    Robinson, J. V.; Woods, W. W.

    1950-01-01

    Mixtures of pure liquid hydrocarbons are capable of foaming. Nine hydrocarbons were mixed in pairs, in all possible combinations, and four proportions of each combination. These mixtures were sealed in glass tubes, and the foaming was tested by shaking. Mixtures of aliphatic with other aliphatic hydrocarbons, or of alkyl benzenes with other alkyl benzenes, did not foam. Mixtures of aliphatic hydrocarbons with alkyl benzenes did foam. The proportions of the mixtures greatly affected the foaming, the maximum foaming of 12 of 20 pairs being at the composition 20 percent aliphatic hydrocarbon, 80 percent alkyl benzene. Six seconds was the maximum foam lifetime of any of these mixtures. Aeroshell 120 lubricating oil was fractionated into 52 fractions and a residue by extraction with acetone in a fractionating extractor. The index of refraction, foam lifetime, color, and viscosity of these fractions were measured. Low viscosity and high index fractions were extracted first. The viscosity of the fractions extracted rose and the index decreased as fractionation proceeded. Foam lifetimes and color were lowest in the middle fractions. Significance is attached to the observation that none of the foam lifetimes of the fractions or residue is as high as the foam lifetime of the original Aeroshell, indicating that the foaming is not due to a particular foaming constituent, but rather to the entire mixture.

  16. Coking technology using packed coal mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Kuznichenko, V.M.; Shteinberg, Eh.A.; Tolstoi, A.P. (Khar' kovskii Nauchno-Issledovatel' skii Uglekhimicheskii Institut, Kharkov (Ukrainian SSR))

    1991-08-01

    Discusses coking of packed coal charges in the FRG, USSR, France, India, Poland and Czechoslovakia. The following aspects are evaluated: types of weakly caking coals that are used as components of packed mixtures, energy consumption of packing, effects of coal mixture packing on coke oven design, number of coke ovens in a battery, heating temperature, coking time, coke properties, investment and operating cost. Statistical data that characterize the Saarberg packing process used in the FRG are analyzed. Packing coal mixtures for coking improves coke quality and reduces environmental pollution. 4 refs.

  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. 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.

  19. 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

  20. Phenotyping peanut genotypes for drought tolerance

    Science.gov (United States)

    Drought and heat stress can result in aflatoxin contamination of peanuts especially when this occurs during the last three to six weeks of the growing season. Identifying drought-tolerant genotypes may aid in development of peanuts that are less susceptible to aflatoxin contamination. This study w...

  1. High prevalence of the B2+C2 subgenotype mixture in patients with chronic hepatitis B in Eastern China

    Institute of Scientific and Technical Information of China (English)

    Jun ZHONG; Yue-qiu GAO; Xue-hua SUN; Xiao-jun ZHU; Man LI

    2012-01-01

    Aim:To investigate the prevalence of hepatitis B virus (HBV) genotype mixtures among patients with chronic hepatitis B (CHB) in Eastern China.Methods:A total of 4908 chronic HBV patients from Eastern China were enrolled.HBV genotypes and subgenotypes were determined using a multiplex PCR technique.Serum viral loads and hepatitis B e antigen (HBeAg) levels detected using real-time fluorescent quantitative PCR and ELISA assay,respectively.The presence of precore/basic core promoter (PC/BCP) mutations was examined with PCR and direct sequencing of the amplified products.Results:HBV genotypes B,C,D,B+C,and B+D were found in 19.21%,64.75%,1.49%,13.63%,and 0.92% of the patients,respectively.In 669 patients with the genotype mixture B+C,the subgenotypes B2+C2 and B2+C1 accounted for 68.13% and 31.87%,respectively,no other subgenotypes were identified.HBV B+C was more frequent in the patients with moderate CHB than in patients with mild CHB.In patients with moderate CHB,the subgenotype mixture B2+C2 was lower than B2+C1 (51.97% vs 63.38%),while the opposite situation was found in patients with severe CHB (22.15% vs 15.49%).The highest average viral load was found in patients with the genotype B+C mixture.The prevalence of HBV B2+C2 increased in patients from 50 to 59 years of age and was significantly different from the proportion of patients in the same age group with genotype B (23.2% vs 15.2%).A double mutation (G1896A) in the PC was significantly more common in subgenotype B2+C2 than in subgenotype B2+C1.Conclusion:The HBV B2+C2 subgenotype was prevalent in CH patients with a high HBV replication status and correlated with a more severe course of the disease.

  2. 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.

  3. Quantiles for Finite Mixtures of Normal Distributions

    Science.gov (United States)

    Rahman, Mezbahur; Rahman, Rumanur; Pearson, Larry M.

    2006-01-01

    Quantiles for finite mixtures of normal distributions are computed. The difference between a linear combination of independent normal random variables and a linear combination of independent normal densities is emphasized. (Contains 3 tables and 1 figure.)

  4. A mixture theory for geophysical fluids

    Directory of Open Access Journals (Sweden)

    A. C. Eringen

    2004-01-01

    Full Text Available A continuum theory is developed for a geophysical fluid consisting of two species. Balance laws are given for the individual components of the mixture, modeled as micropolar viscous fluids. The continua allow independent rotational degrees of freedom, so that the fluids can exhibit couple stresses and a non-symmetric stress tensor. The second law of thermodynamics is used to develop constitutive equations. Linear constitutive equations are constituted for a heat conducting mixture, each species possessing separate viscosities. Field equations are obtained and boundary and initial conditions are stated. This theory is relevant to an atmospheric mixture consisting of any two species from rain, snow and/or sand. Also, this is a continuum theory for oceanic mixtures, such as water and silt, or water and oil spills, etc.

  5. The disentangling number for phylogenetic mixtures

    CERN Document Server

    Sullivant, Seth

    2011-01-01

    We provide a logarithmic upper bound for the disentangling number on unordered lists of leaf labeled trees. This results is useful for analyzing phylogenetic mixture models. The proof depends on interpreting multisets of trees as high dimensional contingency tables.

  6. Mapping the jamming transition of bidisperse mixtures

    Science.gov (United States)

    Koeze, D. J.; Vågberg, D.; Tjoa, B. B. T.; Tighe, B. P.

    2016-03-01

    We systematically map out the jamming transition of all 2D bidisperse mixtures of frictionless disks in the hard-particle limit. The critical volume fraction, mean coordination number, number of rattlers, structural order parameters, and bulk modulus each show a rich variation with mixture composition and particle size ratio, and can therefore be tuned by choosing certain mixtures. We identify two local minima in the critical volume fraction, both of which have low structural order; one minimum is close to the widely studied 50 : 50 mixture of particles with a ratio of radii of 1 : 1.4. We also identify a region at low size ratios characterized by increased structural order and high rattler fractions, with a corresponding enhancement in the stiffness.

  7. Ultrafiltration of a polymer-electrolyte mixture

    NARCIS (Netherlands)

    Vonk, P; Noordman, T.R; Schippers, D; Tilstra, B; Wesselingh, J.A

    1997-01-01

    We present a mathematical model to describe the ultrafiltration behaviour of polymer-electrolyte mixtures. The model combines the proper thermodynamic forces (pressure, chemical potential and electrical potential differences) with multicomponent diffusion theory. The model is verified with experimen

  8. Model structure selection in convolutive mixtures

    DEFF Research Database (Denmark)

    Dyrholm, Mads; Makeig, Scott; Hansen, Lars Kai

    2006-01-01

    The CICAAR algorithm (convolutive independent component analysis with an auto-regressive inverse model) allows separation of white (i.i.d) source signals from convolutive mixtures. We introduce a source color model as a simple extension to the CICAAR which allows for a more parsimoneous represent......The CICAAR algorithm (convolutive independent component analysis with an auto-regressive inverse model) allows separation of white (i.i.d) source signals from convolutive mixtures. We introduce a source color model as a simple extension to the CICAAR which allows for a more parsimoneous...... representation in many practical mixtures. The new filter-CICAAR allows Bayesian model selection and can help answer questions like: 'Are we actually dealing with a convolutive mixture?'. We try to answer this question for EEG data....

  9. Model structure selection in convolutive mixtures

    DEFF Research Database (Denmark)

    Dyrholm, Mads; Makeig, S.; Hansen, Lars Kai

    2006-01-01

    The CICAAR algorithm (convolutive independent component analysis with an auto-regressive inverse model) allows separation of white (i.i.d) source signals from convolutive mixtures. We introduce a source color model as a simple extension to the CICAAR which allows for a more parsimonious represent......The CICAAR algorithm (convolutive independent component analysis with an auto-regressive inverse model) allows separation of white (i.i.d) source signals from convolutive mixtures. We introduce a source color model as a simple extension to the CICAAR which allows for a more parsimonious...... representation in many practical mixtures. The new filter-CICAAR allows Bayesian model selection and can help answer questions like: ’Are we actually dealing with a convolutive mixture?’. We try to answer this question for EEG data....

  10. Multivariate Analysis of Genotype-Phenotype Association.

    Science.gov (United States)

    Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

    2016-04-01

    With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

  11. Laboratory performance of asphalt rubber mixtures

    OpenAIRE

    Fontes, Liseane; Trichês, Glicério; Pais, Jorge; Pereira, Paulo; Minhoto, Manuel

    2009-01-01

    Asphalt rubber mixtures are one of the most promising techniques to extend the service life of asphalt pavement overlays. Asphalt rubber binder is composed of crumb rubber from reclaimed tires and conventional asphalt. The asphalt rubber binder can be obtained through wet process in two different systems: tire rubber modified asphalt binder (produced at industrial plants) and continuous blending (produced in asphalt plants). This study presents a laboratory evaluation of asphalt rubber mixtur...

  12. Assessing sanitary mixtures in East African cities

    OpenAIRE

    Letema, S.C.

    2012-01-01

    The urbanisation of poverty and informality in East African cities poses a threat to environmental health, perpetuates social exclusion and inequalities, and creates service gaps (UN-Habitat, 2008). This makes conventional sanitation provision untenable citywide, giving rise to the emergence of sanitation mixtures. Sanitation mixtures have different scales, institutional arrangements, user groups, and rationalities for their establishment, location, and management. For assessing the performan...

  13. Using Big Data Analytics to Address Mixtures Exposure

    Science.gov (United States)

    The assessment of chemical mixtures is a complex issue for regulators and health scientists. We propose that assessing chemical co-occurrence patterns and prevalence rates is a relatively simple yet powerful approach in characterizing environmental mixtures and mixtures exposure...

  14. Catalyst mixture for aromatic hydrocarbon synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Minderhoud, J.K.; Huizinga, T.; Sie, S.T.

    1989-06-06

    The present invention is concerned with catalyst mixtures consisting of two catalysts, characterized in that one, which is based on zinc, is capable of catalysing the conversion of a H/sub 2//CO mixture into oxygen-containing organic compounds, and the other is a crystalline iron/boron silicate which, after one hour's calcination in air at 500/sup 0/C, has the following properties: a certain X-ray powder diffraction pattern and, in the formula that represents the composition of the silicate, expressed in moles of the oxides, a SiO/sub 2//Fe/sub 2/O/sub 3 molar ratio that is 20-2000, a SiO/sub 2//B/sub 2/O/sub 3/ molar ratio 50-5000, and a Fe/sub 2/O/sub 3//B/sub 2/O/sub 3/ molar ratio higher than 1.0. Said catalyst mixtures show higher aromatics selectivity in the preparation of hydrocarbon mixtures from H/sub 2//CO mixtures than such a mixture comprising an iron silicate instead of the above iron/boron silicates. 3 tabs.

  15. Homogeneous cooling of mixtures of particle shapes

    Science.gov (United States)

    Hidalgo, R. C.; Serero, D.; Pöschel, T.

    2016-07-01

    In this work, we examine theoretically the cooling dynamics of binary mixtures of spheres and rods. To this end, we introduce a generalized mean field analytical theory, which describes the free cooling behavior of the mixture. The relevant characteristic time scale for the cooling process is derived, depending on the mixture composition and the aspect ratio of the rods. We simulate mixtures of spherocylinders and spheres using a molecular dynamics algorithm implemented on graphics processing unit (GPU) architecture. We systematically study mixtures composed of spheres and rods with several aspect ratios and varying the mixture composition. A homogeneous cooling state, where the time dependence of the system's intensive variables occurs only through a global granular temperature, is identified. We find cooling dynamics in excellent agreement with Haff's law, when using an adequate time scale. Using the scaling properties of the homogeneous cooling dynamics, we estimated numerically the efficiency of the energy interchange between rotational and translational degrees of freedom for collisions between spheres and rods.

  16. 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...

  17. When mixtures of hard-sphere-like colloids do not behave as mixtures of hard spheres.

    Science.gov (United States)

    Germain, Ph; Malherbe, J G; Amokrane, S

    2004-10-01

    The validity of the concept of "hard-sphere-like" particles for mixtures of colloids is questioned from a theoretical point of view. This concerns the class of pseudobinary mixtures in which the nonsteric interactions between the colloids are "residual" (with very small range and moderate strength). It is shown that contrary to common expectation, such interactions may have unexpected consequences on the theoretical phase diagram. The distinction between this situation and true solute-solvent mixtures is emphasized.

  18. 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....

  19. Agronomical and phytochemical evaluation of Stevia rebaudiana genotypes

    National Research Council Canada - National Science Library

    Vouillamoz, José F; Wolfram-Schilling, Evelyn; Carron, Claude-Alain; Baroffio, Catherine A

    2016-01-01

    The agronomical potential and the phytochemical variability of 18 genotypes of the Paraguayan plant Stevia rebaudiana have been investigated in Switzerland in order identify the best genotype for local cultivation...

  20. Resistance of corn genotypes to fall armyworm Spodoptera ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-08-31

    Aug 31, 2016 ... The objective of this study was to evaluate resistance mechanisms in 12 corn genotypes (transgenic hybrids: ..... FAW that fed on GM corn genotypes exhibited lower ... preference for other food types, particularly given the.

  1. Comparison and suitability of genotype by environment analysis ...

    African Journals Online (AJOL)

    ACSS

    showed that genotype by environment interactions were significant at p<0.05 for grain .... Genotype by environment analysis methods for yield-related traits of pearl millet ...... PhD Thesis, Louisiana State ... set of sweet potato clones evaluated.

  2. Genotype W environment interaction effects on some physiological ...

    African Journals Online (AJOL)

    Genotype W environment interaction effects on some physiological yield ... Ghana Journal of Agricultural Science ... study the yield basis and environmental effects on 31cowpea genotypes of early, medium and late maturities. ... Article Metrics.

  3. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  4. Angiotensin converting enzyme genotype in cardiovascular disease

    Energy Technology Data Exchange (ETDEWEB)

    Summers, K.M.; Huggard, P.R.; West, M.J. [Univ. of Queensland, Brisbane (Australia)] [and others

    1994-09-01

    Angiotensin converting enzyme (ACE) catalyses formation of angiotensin II and degradation of bradykinin, vasoactive peptides with opposing properties. The result of ACE action is to promote vasoconstriction and cell growth. PCR is used to detect a common polymorphism due to the insertion of an Alu repeat element of 287 bp into intron 16. ACE genotype has been implicated in risk for myocardial infarction (MI) and hypertension in humans. We have studied a group of 640 patients (61% male aged 64 {plus_minus} 11 years) with myocardial ischaemic syndromes, followed for 12 months after initial hospital admission. In this group, the frequency of the insertion (I) allele was 0.47 (N=1170 chromosomes), not significantly higher than the frequency of 0.46 in 112 local blood donors (50% male aged 59 {plus_minus}5 years). In the 300 patients with diagnosed MI, I allele frequency was 0.48. This is significantly higher ({chi}{sup 2}=5.78, P=0.015) than the frequency of 0.42 reported in a multi-centre study of ACE genotype in 600 male European patients with MI . There was a non-significant increase in the frequency of a cardiac event within 6 months of hospital admission in those of II genotype (N=464, 47 events to date). These results suggest that in our population, the I allele and/or II genotype may be associated with risk of MI. This contrasts with the study cited above, where the D (deletion) allele and DD genotype frequency were raised in patients compared with controls. Hypertension is associated with the ACE D allele, and does not explain the heart disease risk, which may be associated with the I allele, in this group of survivors of myocardial ischaemic disease. The difference between our results and the previous study may be due to ascertainment or ethnic differences or to problems amplifying the I allele in some heterozygotes. Clearly, the role of ACE genotype in these diseases is complex.

  5. [Hepatitis B virus genotypes and the response to lamivudine therapy].

    Science.gov (United States)

    Zalewska, Małgorzata; Domagała, Małgorzata; Simon, Krzysztof; Gładysz, Andrzej

    2005-12-01

    Hepatitis B virus (HBV) can be classified into eight major genotypes (A-H) that have mainly a geographic distribution. The HBV genotype may influence disease progression, HBeAg seroconversion rates, response to antiviral treatment. The aim of study was to analyze the distribution and frequency of genotypes in patients with chronic hepatitis B. Response to lamivudine 100 mg daily therapy was examined in respect to genotype. Sixty six patients (45 (68,2%) male, 21 (31,8%) female) with chronic hepatits B were enrolled. HBV genotypes were assigned before treatment with INNO-LiPA HBV Genotyping, Innogenetics, N. V., Ghent assay, which is a line probe test based on the reverse hybridization principle. In baseline and after 12 months of treatment serological markers of HBV infection, alanine aminotransferase (ALT) activities and HBV DNA serum levels were tested. Patients with chronic hepatitis B were infected predominantly with genotype A. HBV genotype distribution was: 78,8% for genotype A, 13,6% for genotype D, 1,5% for mixed infection with genotypes A and D. Distribution of genotypes A and D was asymmetrically regardless of sex, HBeAg status, ALT and HBV DNA levels. Four (6,1%) specimens had indeterminate A results by LiPA. There were no significant differences between patients with genotypes A and D regarding age and sex. There were also no significant differences between these two groups regarding rates of HBeAg and anti-HBe positivity, ALT activity and viral load. Twenty months of lamivudine (100 mg daily) therapy resulted in significant decreases in serum HBV DNA and ALT activities in patients with genotype A as well as with genotype D. After 12 months of treatment there were no statistical differences in HBeAg seroconversion rates, ALT activities, viral loads, frequency of HBeAg and anti-HBe between genotypes A and D.

  6. 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

  7. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias.

    Science.gov (United States)

    Didion, John P; Yang, Hyuna; Sheppard, Keith; Fu, Chen-Ping; McMillan, Leonard; de Villena, Fernando Pardo-Manuel; Churchill, Gary A

    2012-01-19

    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. 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. The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as

  8. 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.

  9. A genotype probability index for multiple alleles and haplotypes.

    Science.gov (United States)

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  10. 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...

  11. 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.

  12. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...... significantly different from the Val/Met (13.2%) group (p = 0.001). The Val/Val COMT group was also associated with significantly more gambling disorder diagnostic criteria being met, greater frequency of gambling behavior, and significantly worse cognitive performance on the Cambridge Gamble Task (risk...... adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble...

  13. Huntington's Disease: Relationship Between Phenotype and Genotype.

    Science.gov (United States)

    Sun, Yi-Min; Zhang, Yan-Bin; Wu, Zhi-Ying

    2017-01-01

    Huntington's disease (HD) is an autosomal dominant inherited neurodegenerative disease with the typical manifestations of involuntary movements, psychiatric and behavior disorders, and cognitive impairment. It is caused by the dynamic mutation in CAG triplet repeat number in exon 1 of huntingtin (HTT) gene. The symptoms of HD especially the age at onset are related to the genetic characteristics, both the CAG triplet repeat and the modified factors. Here, we reviewed the recent advancement on the genotype-phenotype relationship of HD, mainly focus on the characteristics of different expanded CAG repeat number, genetic modifiers, and CCG repeat number in the 3' end of CAG triplet repeat and their effects on the phenotype. We also reviewed the special forms of HD (juvenile HD, atypical onset HD, and homozygous HD) and their phenotype-genotype correlations. The review will aid clinicians to predict the onset age and disease course of HD, give the genetic counseling, and accelerate research into the HD mechanism.

  14. Indexing Finite Language Representation of Population Genotypes

    CERN Document Server

    Sirén, Jouni; Mäkinen, Veli

    2010-01-01

    We propose a way to index population genotype information together with the complete genome sequence so that one can use the index to efficiently align a given sequence to the genome with all plausible genotype recombinations taken into account. This is achieved through converting the multiple alignment of individual genomes into a finite automaton recognizing the language of all substrings read from the alignment by switching the row at any time. The finite automaton is then indexed with an extension of Burrows-Wheeler transform to allow pattern search inside the plausible recombinant sequences generated in this way. The size of the finite automaton and the index created from it stay limited because of the high similarity of the individual genomes in the multiple alignment. In our experiments, the index took even less space than previous ones designed for indexing just the individual genomes. On a short-read alignment experiment, we found about 1% of matches to novel recombinants.

  15. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)

    2017-06-15

    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  16. Human papillomaviruses genotyping in plantar warts.

    Science.gov (United States)

    de Planell-Mas, Elena; Martínez-Garriga, Blanca; Zalacain, Antonio Jesús; Vinuesa, Teresa; Viñas, Miguel

    2017-05-01

    Plantar warts are caused by human papillomaviruses (HPVs) and have been associated with several HPV genotypes. However, there are few studies focused exclusively on plantar warts. In this work, we aim to identify the HPV genotypes of plantar warts and explore their relation to demographic and clinical characteristics of patients. A total of 72 patients diagnosed with plantar warts were recruited at the Laser unit at Podiatric Hospital, University of Barcelona, Spain. Inner hyperkeratosis laminar sections of warts were collected and DNA of samples were extracted. Amplification of a conserved region of the HPV L1 gene was performed with the SK-Polymerase chain reaction method. DNA amplicons were sequenced and HPV types identified. The most prevalent genotypes detected among the 105 analyzed plantar warts were HPV-57 (37.1%), HPV-27 (23.8%), HPV-1a (20.9%), HPV-2 (15.2%), and HPV-65 (2.8%). The majority of patients (78%) presented one single plantar wart, whereas multiple warts were detected in 22.2% of patients. One patient with multiple warts presented HPV types from two different genera, suggesting the spread of warts by self-inoculation as well as by de novo infection. No significant differences between the number of warts in toes, midfoot and heel were found. The most prevalent HPV types detected in all areas belonged to the alpha genus. This work provides new insight on plantar warts and their associated HPV genotypes, and evidences the usefulness and reliability of both the sample collection procedure and the PCR method used for HPV detection and typing. J. Med. Virol. 89:902-907, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. 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.

  18. Identifiability of large phylogenetic mixture models.

    Science.gov (United States)

    Rhodes, John A; Sullivant, Seth

    2012-01-01

    Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. Such models are of increasing interest for data analysis, as they can capture the variety of evolutionary processes that may be occurring across long sequences of DNA or proteins. The fundamental question of whether parameters of such a model are identifiable is difficult to address, due to the complexity of the parameterization. Identifiability is, however, essential to their use for statistical inference.We analyze mixture models on large trees, with many mixture components, showing that both numerical and tree parameters are indeed identifiable in these models when all trees are the same. This provides a theoretical justification for some current empirical studies, and indicates that extensions to even more mixture components should be theoretically well behaved. We also extend our results to certain mixtures on different trees, using the same algebraic techniques.

  19. Relativistic mixtures of charged and uncharged particles

    Energy Technology Data Exchange (ETDEWEB)

    Kremer, Gilberto M. [Departamento de Física, Universidade Federal do Paraná, Curitiba (Brazil)

    2014-01-14

    Mixtures of relativistic gases within the framework of Boltzmann equation are analyzed. Three systems are considered. The first one refers to a mixture of uncharged particles by using Grad’s moment method, where the relativistic mixture is characterized by the moments of the distribution functions: particle four-flows, energy-momentum tensors, and third-order moment tensors. In the second Fick’s law for a mixture of relativistic gases of non-disparate rest masses in a Schwarzschild metric are derived from an extension of Marle and McCormack model equations applied to a relativistic truncated Grad’s distribution function, where it is shown the dependence of the diffusion coefficient on the gravitational potential. The third one consists in the derivation of the relativistic laws of Ohm and Fourier for a binary mixtures of electrons with protons and electrons with photons subjected to external electromagnetic fields and in presence of gravitational fields by using the Anderson and Witting model of the Boltzmann equation.

  20. Microsiemens or Milligrams: Measures of Ionic Mixtures ...

    Science.gov (United States)

    In December of 2016, EPA released the Draft Field-Based Methods for Developing Aquatic Life Criteria for Specific Conductivity for public comment. Once final, states and authorized tribes may use these methods to derive field-based ecoregional ambient Aquatic Life Ambient Water Quality Criteria (AWQC) for specific conductivity (SC) in flowing waters. The methods provide flexible approaches for developing science-based SC criteria that reflect ecoregional or state specific factors. The concentration of a dissolved salt mixture can be measured in a number of ways including measurement of total dissolved solids, freezing point depression, refractive index, density, or the sum of the concentrations of individually measured ions. For the draft method, SC was selected as the measure because SC is a measure of all ions in the mixture; the measurement technology is fast, inexpensive, and accurate, and it measures only dissolved ions. When developing water quality criteria for major ions, some stakeholders may prefer to identify the ionic constituents as a measure of exposure instead of SC. A field-based method was used to derive example chronic and acute water quality criteria for SC and two anions a common mixture of ions (bicarbonate plus sulfate, [HCO3−] + [SO42−] in mg/L) that represent common mixtures in streams. These two anions are sufficient to model the ion mixture and SC (R2 = 0.94). Using [HCO3−] + [SO42−] does not imply that these two anions are the

  1. ASPECTS OF THERMODYNAMICS OF POLYMER MIXTURES

    Institute of Scientific and Technical Information of China (English)

    CHAI Zhikuan

    1987-01-01

    In this brief review article some aspects of the thermodynamics of polymer mixtures are discussed,mainly based on the author's research. The studies of poly (methyl methacrylate)/chlorinated polyethylene (CPE), poly (butyl acrylate)/CPE and CPE/CPE (different chlorine content) mixture verify the "dissimilarity" and "similarity" principles for predicting miscibility of polymer mixtures. The sign of heat of mixing of oligomeric analogues is not sufficient in predicting the miscibility. The Flory equation of state theory has been applied to simulate the phase boundaries of polymer mixtures. The empirical entropy parameter Q12 plays an important role in the calculation, this reduces the usefulness of the theory. With energy parameter X12 ≠ 0 and Q12 ≠ 0 the spinodals so calculated are reasonable compared to experiments.A hole model was suggested for the statistics of polymer mixtures. The new hole theory combines the features of both the Flory equation of state theory and the Sanchez lattice fluid theory and can be reduced to them under some conditions.

  2. A constitutive theory of reacting electrolyte mixtures

    Science.gov (United States)

    Costa Reis, Martina; Wang, Yongqi; Bono Maurizio Sacchi Bassi, Adalberto

    2013-11-01

    A constitutive theory of reacting electrolyte mixtures is formulated. The intermolecular interactions among the constituents of the mixture are accounted for through additional freedom degrees to each constituent of the mixture. Balance equations for polar reacting continuum mixtures are accordingly formulated and a proper set of constitutive equations is derived with basis in the Müller-Liu formulation of the second law of thermodynamics. Moreover, the non-equilibrium and equilibrium responses of the reacting mixture are investigated in detail by emphasizing the inner and reactive structures of the medium. From the balance laws and constitutive relations, the effects of molecular structure of constituents upon the fluid flow are studied. It is also demonstrated that the local thermodynamic equilibrium state can be reached without imposing that the set of independent constitutive variables is time independent, neither spatially homogeneous nor null. The resulting constitutive relations presented throughout this work are of relevance to many practical applications, such as swelling of clays, developing of bio and polymeric membranes, and use of electrorheological fluids in industrial processes. The first author acknowledges financial support from National Counsel of Technological and Scientific Development (CNPq) and German Academic Exchange Service (DAAD).

  3. Asbestos Tailings as Aggregates for Asphalt Mixture

    Institute of Scientific and Technical Information of China (English)

    LIU Xinoming; XU Linrong

    2011-01-01

    To use many asbestos tailings collected in Ya-Lu highway, and to explore the feasibility of using asbestos tailings as aggregates in common asphalt mixtures, and properties of some asphalt mixtures were evaluated as well. X-ray diffraction (XRD), X-ray fluorescent (XRF), and atomic absorption spectrophotometry (AAS) were employed to determine the solid waste content of copper, zinc, lead, and cadmium. Volume properties and pavement performances of AC-25 asphalt mixture with asbestos tailings were also evaluated compared with those with basalt as aggregates.XRD and XRF measurement results infer that asbestos tailing is an excellent road material. Volume properties of AC-25 asphalt mixture with asbestos tailings satisfied the related specifications. No heavy metals and toxic pollution were detected in AAS test and the value of pH test is 8.23, which is help to the adhesion with asphalt in the asphalt concrete. When compared with basalt, high temperature property and the resistance to low temperature cracking of AC-25 asphalt mixture was improved by using asbestos tailings as aggregates. In-service AC-25 asphalt pavement with asbestos tailings also presented excellent performance and British Pendulum Number (BPN) coefficient of surface.

  4. 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.

  5. 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.

  6. A cold energy mixture theory for the equation of state in solid and porous metal mixtures

    Science.gov (United States)

    Zhang, X. F.; Qiao, L.; Shi, A. S.; Zhang, J.; Guan, Z. W.

    2011-07-01

    Porous or solid multi-component mixtures are ubiquitous in nature and extensively used as industrial materials such as multifunctional energetic structural materials (MESMs), metallic and ceramic powder for shock consolidation, and porous armor materials. In order to analyze the dynamic behavior of a particular solid or porous metal mixture in any given situation, a model is developed to calculate the Hugoniot data for solid or porous mixtures using only static thermodynamic properties of the components. The model applies the cold energy mixture theory to calculate the isotherm of the components to avoid temperature effects on the mixtures. The isobaric contribution from the thermodynamic equation of state is used to describe the porous material Hugoniot. Dynamic shock responses of solid or porous powder mixtures compacted by shock waves have been analyzed based on the mixture theory and Hugoniot for porous materials. The model is tested on both single-component porous materials such as aluminum 2024, copper, and iron; and on multi-component mixtures such as W/Cu, Fe/Ni, and Al/Ni. The theoretical calculations agree well with the corresponding experimental and simulation results. The present model produces satisfactory correlation with the experimentally obtained Hugoniot data for solid porous materials over a wide pressure range.

  7. Flavanols and Flavonols in the Nuclei of Conifer Genotypes with Different Growth

    Directory of Open Access Journals (Sweden)

    Walter Feucht

    2014-09-01

    Full Text Available Flavanols and flavonols of mitotic and post-mitotic nuclei in needles of Taxus baccata L., Tsuga canadensis L., and slow growing dwarf genotypes of both genera are investigated histochemically. The flavanols of nuclear chromatins and in the vacuoles stain blue with the p-dimethylamino-cinnamaldehyde (DMACA reagent. Flavonols do not react with the reagent but owing to their UV absorbance they can be seen as bright yellow pigments. The nuclei in the photomicrographs obtained by microscopy were measured for flavanols at 640 nm. The vigorously sprouting Taxus baccata L. displays the most rapid cell cycling of the needles and the nuclei reveal clear blue and white mosaic structures. The flavanol component of Taxus baccata nuclei remains relatively stable most of the growing season. The dwarf genotypes also display fairly blue stained meristematic nuclei during the intense spring flush. However, after the spring flush and towards mid-summer the nuclear flavanols slowly decrease in parallel with a gradual increase in yellow staining nuclear flavonols. A mixture of blue stained flavanols and yellow flavonols results in greenish coloration of the nuclei. The greenish tint becomes more pronounced when the parenchyma cells mature and age. At the same time, the cytoplasm of the dwarf genotypes also begins to attain a more yellow tint. This trend continues towards mid-summer and autumn, particularly in the nana genotypes. It would appear that the yellow staining flavonols are linked to restricted growth conditions. In the present study, it becomes evident that the species-typical endogenous growth potential is related to both flavanol and flavonol allocation into the nuclei. The vigorously growing species of Taxus and Tsuga have a higher capacity for recruitment of flavanols into the nuclei than the very slow growing dwarf species.

  8. 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

  9. 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.

  10. A new strategy for sperm isolation and STR typing from multi-donor sperm mixtures.

    Science.gov (United States)

    Han, Jun-Ping; Yang, Fan; Xu, Cheng; Wei, Yi-Liang; Zhao, Xing-Chun; Hu, Lan; Ye, Jian; Li, Cai-Xia

    2014-11-01

    Mixed semen stains from multiple contributors are challenging samples in sexual assault casework, and it is crucial to obtain the DNA profiles of different donors to allow the evidence to play an important role in investigations and judicial proceedings. Current standard procedures, including preferential lysis, are incapable of separating single-source sperm from multiple male donors. Mixed profiles are often obtained and may not directly exclude or identify suspects. In this case, computational methods for mixture interpretation are often used, which rely on different types of calculation models. Here, we explored a new strategy for sperm cell isolation and detection from mixtures. It is a direct way to obtain genotypes of different sperm donors compared to computation-based mixture interpretation. Laser capture microdissection (LCM) and low volume-PCR (LV-PCR) were used for single sperm isolation and detection. The platform was sensitive; profiling of a single sperm cell generated a minimum of 13-16 loci in 73.1% of Y short tandem repeat (Y-STR) assays. A new Y-STR and autosomal STR multiplex system (YA-STR) were optimized by the combination of the Y-STR locus and 10 autosomal STR (auto STR) loci. The Y-STR locus acted as a tag to discriminate profile groups from different donors. Subsequently, consensus auto STR profiles of various persons could be received. The accuracy and availability of this method were evaluated on a three-donor semen mixture and found to be effective for the resolution of a multi-donor sperm mixture.

  11. Adaptive Mixture Methods Based on Bregman Divergences

    CERN Document Server

    Donmez, Mehmet A; Kozat, Suleyman S

    2012-01-01

    We investigate adaptive mixture methods that linearly combine outputs of $m$ constituent filters running in parallel to model a desired signal. We use "Bregman divergences" and obtain certain multiplicative updates to train the linear combination weights under an affine constraint or without any constraints. We use unnormalized relative entropy and relative entropy to define two different Bregman divergences that produce an unnormalized exponentiated gradient update and a normalized exponentiated gradient update on the mixture weights, respectively. We then carry out the mean and the mean-square transient analysis of these adaptive algorithms when they are used to combine outputs of $m$ constituent filters. We illustrate the accuracy of our results and demonstrate the effectiveness of these updates for sparse mixture systems.

  12. Computer simulation of rod-sphere mixtures

    CERN Document Server

    Antypov, D

    2003-01-01

    Results are presented from a series of simulations undertaken to investigate the effect of adding small spherical particles to a fluid of rods which would otherwise represent a liquid crystalline (LC) substance. Firstly, a bulk mixture of Hard Gaussian Overlap particles with an aspect ratio of 3:1 and hard spheres with diameters equal to the breadth of the rods is simulated at various sphere concentrations. Both mixing-demixing and isotropic-nematic transition are studied using Monte Carlo techniques. Secondly, the effect of adding Lennard-Jones particles to an LC system modelled using the well established Gay-Berne potential is investigated. These rod-sphere mixtures are simulated using both the original set of interaction parameters and a modified version of the rod-sphere potential proposed in this work. The subject of interest is the internal structure of the binary mixture and its dependence on density, temperature, concentration and various parameters characterising the intermolecular interactions. Both...

  13. Quasi-chemical approximation for polyatomic mixtures

    CERN Document Server

    Dávila, M V; Matoz-Fernandez, D A; Ramirez-Pastor, A J

    2016-01-01

    The statistical thermodynamics of binary mixtures of polyatomic species was developed on a generalization in the spirit of the lattice-gas model and the quasi-chemical approximation (QCA). The new theoretical framework is obtained by combining: (i) the exact analytical expression for the partition function of non-interacting mixtures of linear $k$-mers and $l$-mers (species occupying $k$ sites and $l$ sites, respectively) adsorbed in one dimension, and its extension to higher dimensions; and (ii) a generalization of the classical QCA for multicomponent adsorbates and multisite-occupancy adsorption. The process is analyzed through the partial adsorption isotherms corresponding to both species of the mixture. Comparisons with analytical data from Bragg-Williams approximation (BWA) and Monte Carlo simulations are performed in order to test the validity of the theoretical model. Even though a good fitting is obtained from BWA, it is found that QCA provides a more accurate description of the phenomenon of adsorpti...

  14. Efficient radiative transfer in dust grain mixtures

    CERN Document Server

    Wolf, S

    2003-01-01

    The influence of a dust grain mixture consisting of spherical dust grains with different radii and/or chemical composition on the resulting temperature structure and spectral energy distribution of a circumstellar shell is investigated. The comparison with the results based on an approximation of dust grain parameters representing the mean optical properties of the corresponding dust grain mixture reveal that (1) the temperature dispersion of a real dust grain mixture decreases substantially with increasing optical depth, converging towards the temperature distribution resulting from the approximation of mean dust grain parameters, and (2) the resulting spectral energy distributions do not differ by more than 10% if >= 2^5 grain sizes are considered which justifies the mean parameter approximation and the many results obtained under its assumption so far. Nevertheless, the dust grain temperature dispersion at the inner boundary of a dust shell may amount to >>100K and has therefore to be considered in the cor...

  15. Two-Microphone Separation of Speech Mixtures

    DEFF Research Database (Denmark)

    Pedersen, Michael Syskind; Wang, DeLiang; Larsen, Jan

    2008-01-01

    Separation of speech mixtures, often referred to as the cocktail party problem, has been studied for decades. In many source separation tasks, the separation method is limited by the assumption of at least as many sensors as sources. Further, many methods require that the number of signals within...... the recorded mixtures be known in advance. In many real-world applications, these limitations are too restrictive. We propose a novel method for underdetermined blind source separation using an instantaneous mixing model which assumes closely spaced microphones. Two source separation techniques have been...... similar signals. Using two microphones, we can separate, in principle, an arbitrary number of mixed speech signals. We show separation results for mixtures with as many as seven speech signals under instantaneous conditions. We also show that the proposed method is applicable to segregate speech signals...

  16. 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

  17. Modeling methods for mixture-of-mixtures experiments applied to a tablet formulation problem.

    Science.gov (United States)

    Piepel, G F

    1999-01-01

    During the past few years, statistical methods for the experimental design, modeling, and optimization of mixture experiments have been widely applied to drug formulation problems. Different methods are required for mixture-of-mixtures (MoM) experiments in which a formulation is a mixture of two or more "major" components, each of which is a mixture of one or more "minor" components. Two types of MoM experiments are briefly described. A tablet formulation optimization example from a 1997 article in this journal is used to illustrate one type of MoM experiment and corresponding empirical modeling methods. Literature references that discuss other methods for MoM experiments are also provided.

  18. Avian nephritis virus (ANV) on Brazilian chickens farms: circulating genotypes and intra-genotypic diversity.

    Science.gov (United States)

    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.

  19. Mutation spectra of complex environmental mixtures

    Energy Technology Data Exchange (ETDEWEB)

    DeMarini, D.M. [EPA, Research Triangle Park, NC (United States)

    1997-10-01

    Bioassay-directed chemical analysis of complex environmental mixtures has indicated that much of the genotoxic activity of mixtures is due to the presence of one or a few classes or chemicals within the mixture. We have extended this observation to the molecular level by using colony probe hybridization and PCR/DNA sequence analysis to determine the mutation spectra of {approximately}8,000 revertants induced by a variety of complex mixtures and their chemical fractions in TA100 and TA98 of Salmonella. For urban air, >80% of mutagenic activity was due to a base/neutral fraction that contained primarily PAHs. The mutation spectrum induced by unfractionated urban air was not significantly different from that produced by a model PAH, B(a)P. The mutation spectrum induced by organic extracts of chlorinated drinking water were similar to those produced by the chlorinated furanone MX, which accounted for {approximately}20% of the mutagenic activity of the samples. The base/neutral fraction of municipal waste incinerator emissions accounted for the primary class of mutations induced by the emissions, and a polar neutral fraction accounted for the secondary class of mutations induced by the emissions. The primary class of mutations induced by cigarette smoke condensate in TA100 (GC {yields} TA) is also the primary class of mutations in the p53 gene of lung tumors of cigarette smokers. These results confirm at the molecular level that the mutations induced by a complex mixture reflect the dominance of one or a few classes of chemicals within the mixture.

  20. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

    Directory of Open Access Journals (Sweden)

    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.

  1. Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups

    Science.gov (United States)

    Harper, S. J.

    2013-01-01

    Amongst the Closteroviridae, Citrus tristeza virus (CTV) is almost unique in possessing a number of distinct and characterized strains, isolates of which produce a wide range of phenotype combinations among its different hosts. There is little understanding to connect genotypes to phenotypes, and to complicate matters more, these genotypes are found throughout the world as members of mixed populations within a single host plant. There is essentially no understanding of how combinations of genotypes affect symptom expression and disease severity. We know little about the evolution of the genotypes that have been characterized to date, little about the biological role of their diversity and particularly, about the effects of recombination. Additionally, genotype grouping has not been standardized. In this study we utilized an extensive array of CTV genomic information to classify the major genotypes, and to determine the major evolutionary processes that led to their formation and subsequent retention. Our analyses suggest that three major processes act on these genotypes: (1) ancestral diversification of the major CTV lineages, followed by (2) conservation and co-evolution of the major functional domains within, though not between CTV genotypes, and (3) extensive recombination between lineages that have given rise to new genotypes that have subsequently been retained within the global population. The effects of genotype diversity and host-interaction are discussed, as is a proposal for standardizing the classification of existing and novel CTV genotypes. PMID:23630519

  2. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  3. Epidemiology and Treatment of Hepatitis C Genotypes 5 and 6

    Directory of Open Access Journals (Sweden)

    Khalid Al Naamani

    2013-01-01

    Full Text Available Chronic hepatitis C infection is a major global health problem. The WHO estimates the number of infected people worldwide to be approximately 170 million. The estimated number of hepatitis C virus (HCV-infected people in Canada is approximately 250,000, with approximately 5000 Canadians newly infected each year. Based on the identification of genomic differences, HCV has been classified into six genotypes; genotype may influence the outcome of antiviral therapy. HCV genotypes 1, 2 and 3 are widely distributed throughout the world and have been the focus of the majority of epidemiological, natural course and treatment studies. Although HCV genotypes 5 and 6 are prevalent in certain geographical areas, they are studied less extensively. HCV genotypes 5 and 6 are uncommon in Canada and account for less than 5% of HCV-infected Canadians. However, immigration and travel can alter the epidemiology of these uncommon genotypes. The present article reviews and summarizes the available data regarding the epidemiology and treatment of HCV genotypes 5 and 6. Genotype 5 is endemic in the northern part of South Africa while genotype 6 is reported primarily in Asia. Available data show that 48 weeks of treatment with a combination of pegylated interferon and ribavirin lead to a higher sustained virological response compared with HCV genotypes 1 and 4. None of the approved direct-acting antiviral agents is currently recommended for the treatment of HCV genotypes 5 or 6.

  4. Thermophysical Properties of Fluids and Fluid Mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Sengers, Jan V.; Anisimov, Mikhail A.

    2004-05-03

    The major goal of the project was to study the effect of critical fluctuations on the thermophysical properties and phase behavior of fluids and fluid mixtures. Long-range fluctuations appear because of the presence of critical phase transitions. A global theory of critical fluctuations was developed and applied to represent thermodynamic properties and transport properties of molecular fluids and fluid mixtures. In the second phase of the project, the theory was extended to deal with critical fluctuations in complex fluids such as polymer solutions and electrolyte solutions. The theoretical predictions have been confirmed by computer simulations and by light-scattering experiments. Fluctuations in fluids in nonequilibrium states have also been investigated.

  5. Mixture Distribution Approach In Financial Risk Analysis

    OpenAIRE

    Kocak, Keziban; Calis, Nazif; Unal, Deniz

    2014-01-01

    In recent years, major changes occurred in the prices of stock exchange appeared the necessity of measuring the financial risk. Nowadays, Value-atRisk (VaR) is often used to calculate the financial risk. Parametric methods which need normality are mostly used in the calculation of VaR.If the financial data does not fit the normal distribution, mixture of normal distribution models can be fitted to this data. In this study, the financial risk is calculated by using normal mixture distribution ...

  6. Boiler derating for coal-water mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Horney, F.A.; Nolte, F.S.

    1983-11-01

    The authors demonstrated a method for approximating the derating required when converting an oil or natural gas fired unit to a coal-water mixture. If the results show that a retrofit to coal-water mixture appears economically reasonable, then a more detailed analysis should be made by the boiler manufacturer whose methods are more precise than the methods of this paper. The expense of having the boiler manufacturer make a precise analysis can be avoided if the results of the analysis of this paper show conversion not to be viable.

  7. Conditional Density Approximations with Mixtures of Polynomials

    DEFF Research Database (Denmark)

    Varando, Gherardo; López-Cruz, Pedro L.; Nielsen, Thomas Dyhre

    2015-01-01

    Mixtures of polynomials (MoPs) are a non-parametric density estimation technique especially designed for hybrid Bayesian networks with continuous and discrete variables. Algorithms to learn one- and multi-dimensional (marginal) MoPs from data have recently been proposed. In this paper we introduce...... is found. We illustrate and study the methods using data sampled from known parametric distributions, and we demonstrate their applicability by learning models based on real neuroscience data. Finally, we compare the performance of the proposed methods with an approach for learning mixtures of truncated...

  8. Flows and chemical reactions in homogeneous mixtures

    CERN Document Server

    Prud'homme, Roger

    2013-01-01

    Flows with chemical reactions can occur in various fields such as combustion, process engineering, aeronautics, the atmospheric environment and aquatics. The examples of application chosen in this book mainly concern homogeneous reactive mixtures that can occur in propellers within the fields of process engineering and combustion: - propagation of sound and monodimensional flows in nozzles, which may include disequilibria of the internal modes of the energy of molecules; - ideal chemical reactors, stabilization of their steady operation points in the homogeneous case of a perfect mixture and c

  9. Mixture for removing tar and paraffin deposits

    Energy Technology Data Exchange (ETDEWEB)

    kamenshchikov, F.A.; Frolov, M.A.; Golovin, I.N.; Khusainov, Z.M.; Smirnov, Ya.L.; Suchkov, B.M.

    1981-05-23

    Mixture is claimed for removing tar and paraffin deposits (TPD) on the basis of the butyl-benzene fraction (BBF), which is intended to more efficiently remove TPD from the surface of refinery equipment, additionally has piperylene, isoprene and isoamine with the following ratio of the components: piperylene, 19-31%; isoprene, 8-12%; isoamines, 8-12%, while BBF, the rest. The efficiency of the given compositions was assessed by the rate at which the plates were cleaned of TPD and pure commercial paraffin. It has been shown that BBF dissolves 4-6 times faster in the given mixture than in BBF and pyperylene.

  10. Viscosity of oil and water mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Corlett, A.E.; Hall, A.R.W. [National Engineering Laboratory, Glasgow (United Kingdom)

    1999-07-01

    A study was performed to investigate the apparent viscosity of oil and water mixtures using the pressure loss along a horizontal pipe. Water fractions between 100% to 5% were examined at three flow velocities and three temperatures. Four combinations of crude oil and saline solution were used. Tests found that the mixture viscosity exhibited a peak at the position of phase inversion. The value of this maximum viscosity depended upon the temperature and fluid combination used, but not the velocity. Physical properties of the fluids were important factors in the viscosity/water fraction behaviour. (author)

  11. Bacterial histo-blood group antigens contributing to genotype-dependent removal of human noroviruses with a microfiltration membrane.

    Science.gov (United States)

    Amarasiri, Mohan; Hashiba, Satoshi; Miura, Takayuki; Nakagomi, Toyoko; Nakagomi, Osamu; Ishii, Satoshi; Okabe, Satoshi; Sano, Daisuke

    2016-05-15

    We demonstrated the genotype-dependent removal of human norovirus particles with a microfiltration (MF) membrane in the presence of bacteria bearing histo-blood group antigens (HBGAs). Three genotypes (GII.3, GII.4, and GII.6) of norovirus-like particles (NoVLPs) were mixed with three bacterial strains (Enterobacter sp. SENG-6, Escherichia coli O86:K61:B7, and Staphylococcus epidermidis), respectively, and the mixture was filtered with an MF membrane having a nominal pore size of 0.45 μm. All NoVLP genotypes were rejected by the MF membrane in the presence of Enterobacter sp. SENG-6, which excreted HBGAs as extracellular polymeric substances (EPS). This MF membrane removal of NoVLPs was not significant when EPS was removed from cells of Enterobacter sp. SENG-6. GII.6 NoVLP was not rejected with the MF membrane in the presence of E. coli O86:K61:B7, but the removal of EPS of E. coli O86:K61:B7 increased the removal efficiency due to the interaction of NoVLPs with the exposed B-antigen in lipopolysaccharide (LPS) of E. coli O86:K61:B7. No MF membrane removal of all three genotypes was observed when S. epidermidis, an HBGA-negative strain, was mixed with NoVLPs. These results demonstrate that the location of HBGAs on bacterial cells is an important factor in determining the genotype-dependent removal efficiency of norovirus particles with the MF membrane. The presence of HBGAs in mixed liquor suspended solids from a membrane bioreactor (MBR) pilot plant was confirmed by immune-transmission electron microscopy, which implies that bacterial HBGAs can contribute to the genotype-dependent removal of human noroviruses with MBR using MF membrane.

  12. A comparison of Mg/Ca ratios in Globigerinoides ruber (white): sensu stricto versus a mixture of genotypes

    Digital Repository Service at National Institute of Oceanography (India)

    Naik, S.S.

    stream_size 14072 stream_content_type text/plain stream_name J_Geol_Soc_india_87_323a.pdf.txt stream_source_info J_Geol_Soc_india_87_323a.pdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 Author...., 2005; Govil and Naidu, 2010, Naik and Naidu, 2014). Conventionally, studies have selected planktonic foraminifera G. ruber without differentiation into morphotypes. In the case of G. ruber, two morphotypes can be differentiated based on taxonomic...

  13. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    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

  14. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Directory of Open Access Journals (Sweden)

    Shu-Chuan Chen

    Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  15. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Science.gov (United States)

    Chen, Shu-Chuan; Ogata, Aaron

    2015-01-01

    The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  16. 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

  17. A Skew-Normal Mixture Regression Model

    Science.gov (United States)

    Liu, Min; Lin, Tsung-I

    2014-01-01

    A challenge associated with traditional mixture regression models (MRMs), which rest on the assumption of normally distributed errors, is determining the number of unobserved groups. Specifically, even slight deviations from normality can lead to the detection of spurious classes. The current work aims to (a) examine how sensitive the commonly…

  18. Uniform design of experiments with mixtures

    Institute of Scientific and Technical Information of China (English)

    王元; 方开泰

    1996-01-01

    Consider a design of experiments with mixtures:0≤ai

  19. Modeling text with generalizable Gaussian mixtures

    DEFF Research Database (Denmark)

    Hansen, Lars Kai; Sigurdsson, Sigurdur; Kolenda, Thomas

    2000-01-01

    We apply and discuss generalizable Gaussian mixture (GGM) models for text mining. The model automatically adapts model complexity for a given text representation. We show that the generalizability of these models depends on the dimensionality of the representation and the sample size. We discuss...

  20. The Coffee-Milk Mixture Problem Revisited

    Science.gov (United States)

    Marion, Charles F.

    2015-01-01

    This analysis of a problem that is frequently posed at professional development workshops, in print, and on the Web--the coffee-milk mixture riddle--illustrates the timeless advice of George Pólya's masterpiece on problem solving in mathematics, "How to Solve It." In his book, Pólya recommends that problems previously solved and put…

  1. Quantification of complex mixtures by NMR

    NARCIS (Netherlands)

    Duynhoven, van J.P.M.; Velzen, van E.; Jacobs, D.M.

    2013-01-01

    NMR has firmly established itself as an analytical tool that can quantify analyte concentrations in complex mixtures in a rapid, cost-effective, accurate and precise manner. Here, the technological advances with respect to instrumentation, sample preparation, data acquisition and data processing ove

  2. Toxicology of chemical mixtures: International perspective

    NARCIS (Netherlands)

    Feron, V.J.; Cassee, F.R.; Groten, J.P.

    1998-01-01

    This paper reviews major activities outside the United States on human health issues related to chemical mixtures. In Europe an international study group on combination effects has been formed and has started by defining synergism and antagonism. Successful research programs in Europe include the de

  3. Mixture toxicity of PBT-like chemicals

    DEFF Research Database (Denmark)

    Syberg, Kristian; Dai, Lina; Ramskov, Tina

    beyond that of the individual components. Firstly, the effects of three chemicals with PBT-like properties (acetyl cedrene, pyrene and triclosan) was examined on the freshwater snail, Potamopyrgus antipodarum. Secondly, mixture bioaccumulation of the same three chemicals were assessed experimentally...

  4. Concrete mixture characterization. Cementitious barriers partnership

    Energy Technology Data Exchange (ETDEWEB)

    Langton, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Protiere, Yannick [SIMCO Technologies, Inc., Quebec (Canada)

    2014-12-01

    This report summarizes the characterization study performed on two concrete mixtures used for radioactive waste storage. Both mixtures were prepared with approximately 425 kg of binder. The testing protocol mostly focused on determining the transport properties of the mixtures; volume of permeable voids (porosity), diffusion coefficients, and water permeability were evaluated. Tests were performed after different curing durations. In order to obtain data on the statistical distribution of transport properties, the measurements after 2 years of curing were performed on 10+ samples. Overall, both mixtures exhibited very low tortuosities and permeabilities, a direct consequence of their low water-to-binder ratio and the use of supplementary cementitious materials. The data generated on 2-year old samples showed that porosity, tortuosity and permeability follow a normal distribution. Chloride ponding tests were also performed on test samples. They showed limited chloride ingress, in line with measured transport properties. These test results also showed that both materials react differently with chloride, a consequence of the differences in the binder chemical compositions.

  5. Predicting diffusivities in dense fluid mixtures

    Directory of Open Access Journals (Sweden)

    C. DARIVA

    1999-09-01

    Full Text Available In this work the Enskog solution of the Boltzmann equation, as corrected by Speedy, together with the Weeks-Chandler-Andersen (WCA perturbation theory of liquids is employed in correlating and predicting self-diffusivities of dense fluids. Afterwards this theory is used to estimate mutual diffusion coefficients of solutes at infinite dilution in sub and supercritical solvents. We have also investigated the behavior of Fick diffusion coefficients in the proximity of a binary vapor-liquid critical point since this subject is of great interest for extraction purposes. The approach presented here, which makes use of a density and temperature dependent hard-sphere diameter, is shown to be excellent for predicting diffusivities in dense pure fluids and fluid mixtures. The calculations involved highly nonideal mixtures as well as systems with high molecular asymmetry. The predicted diffusivities are in good agreement with the experimental data for the pure and binary systems. The methodology proposed here makes only use of pure component information and density of mixtures. The simple algebraic relations are proposed without any binary adjustable parameters and can be readily used for estimating diffusivities in multicomponent mixtures.

  6. Self-assembly models for lipid mixtures

    Science.gov (United States)

    Singh, Divya; Porcar, Lionel; Butler, Paul; Perez-Salas, Ursula

    2006-03-01

    Solutions of mixed long and short (detergent-like) phospholipids referred to as ``bicelle'' mixtures in the literature, are known to form a variety of different morphologies based on their total lipid composition and temperature in a complex phase diagram. Some of these morphologies have been found to orient in a magnetic field, and consequently bicelle mixtures are widely used to study the structure of soluble as well as membrane embedded proteins using NMR. In this work, we report on the low temperature phase of the DMPC and DHPC bicelle mixture, where there is agreement on the discoid structures but where molecular packing models are still being contested. The most widely accepted packing arrangement, first proposed by Vold and Prosser had the lipids completely segregated in the disk: DHPC in the rim and DMPC in the disk. Using data from small angle neutron scattering (SANS) experiments, we show how radius of the planar domain of the disks is governed by the effective molar ratio qeff of lipids in aggregate and not the molar ratio q (q = [DMPC]/[DHPC] ) as has been understood previously. We propose a new quantitative (packing) model and show that in this self assembly scheme, qeff is the real determinant of disk sizes. Based on qeff , a master equation can then scale the radii of disks from mixtures with varying q and total lipid concentration.

  7. Flexible Rasch Mixture Models with Package psychomix

    Directory of Open Access Journals (Sweden)

    Hannah Frick

    2012-05-01

    Full Text Available Measurement invariance is an important assumption in the Rasch model and mixture models constitute a flexible way of checking for a violation of this assumption by detecting unobserved heterogeneity in item response data. Here, a general class of Rasch mixture models is established and implemented in R, using conditional maximum likelihood estimation of the item parameters (given the raw scores along with flexible specification of two model building blocks: (1 Mixture weights for the unobserved classes can be treated as model parameters or based on covariates in a concomitant variable model. (2 The distribution of raw score probabilities can be parametrized in two possible ways, either using a saturated model or a specification through mean and variance. The function raschmix( in the R package psychomix provides these models, leveraging the general infrastructure for fitting mixture models in the flexmix package. Usage of the function and its associated methods is illustrated on artificial data as well as empirical data from a study of verbally aggressive behavior.

  8. Spinodal decomposition of chemically reactive binary mixtures

    Science.gov (United States)

    Lamorgese, A.; Mauri, R.

    2016-08-01

    We simulate the influence of a reversible isomerization reaction on the phase segregation process occurring after spinodal decomposition of a deeply quenched regular binary mixture, restricting attention to systems wherein material transport occurs solely by diffusion. Our theoretical approach follows a diffuse-interface model of partially miscible binary mixtures wherein the coupling between reaction and diffusion is addressed within the frame of nonequilibrium thermodynamics, leading to a linear dependence of the reaction rate on the chemical affinity. Ultimately, the rate for an elementary reaction depends on the local part of the chemical potential difference since reaction is an inherently local phenomenon. Based on two-dimensional simulation results, we express the competition between segregation and reaction as a function of the Damköhler number. For a phase-separating mixture with components having different physical properties, a skewed phase diagram leads, at large times, to a system converging to a single-phase equilibrium state, corresponding to the absolute minimum of the Gibbs free energy. This conclusion continues to hold for the critical phase separation of an ideally perfectly symmetric binary mixture, where the choice of final equilibrium state at large times depends on the initial mean concentration being slightly larger or less than the critical concentration.

  9. Toxicity of metal mixtures to chick embryos

    Energy Technology Data Exchange (ETDEWEB)

    Birge, W.J.; Roberts, O.W.; Black, J.A.

    1976-09-01

    The toxic effects of mercury/selenium and certain other metal mixtures on the chick embryo are examined to determine whether antagonistic, additive or synergistic interactions occur. White Plymouth Rock chicken eggs were treated by yolk injection with cadmium chloride, mercuric chloride, zinc chloride and sodium selenate. Test aliquots were injected prior to incubation using the needle track procedure. Using a sample size of 200, percent survival was determined as hatchability of experimental eggs/controls. Metal mixtures used included mercury/cadmium, mercury/selenium, mercury/zinc, cadmium/selenium, and cadmium/zinc. Except for mercury/selenium, all other metal mixtures gave actual values that were within 5% of those for additive toxic effects. Actual hatchability frequencies for test concentrations of mercury/selenium indicated a moderate degree of synergism. Results indicate that the strong mercury/selenium synergism which affects embryonic development in the carp does not apply for the chick embryo; that most two-way combinations of cadmium, mercury, selenium and zinc exert purely additive effects on chick hatchability; and that these metal mixtures give no discernible antagonistic interactions which affect survival of chick embryos. (MFB)

  10. Using Regression Mixture Analysis in Educational Research

    Directory of Open Access Journals (Sweden)

    Cody S. Ding

    2006-11-01

    Full Text Available Conventional regression analysis is typically used in educational research. Usually such an analysis implicitly assumes that a common set of regression parameter estimates captures the population characteristics represented in the sample. In some situations, however, this implicit assumption may not be realistic, and the sample may contain several subpopulations such as high math achievers and low math achievers. In these cases, conventional regression models may provide biased estimates since the parameter estimates are constrained to be the same across subpopulations. This paper advocates the applications of regression mixture models, also known as latent class regression analysis, in educational research. Regression mixture analysis is more flexible than conventional regression analysis in that latent classes in the data can be identified and regression parameter estimates can vary within each latent class. An illustration of regression mixture analysis is provided based on a dataset of authentic data. The strengths and limitations of the regression mixture models are discussed in the context of educational research.

  11. Two-microphone Separation of Speech Mixtures

    DEFF Research Database (Denmark)

    2006-01-01

    of Speech Mixtures," 2006, submited for journal publication. See also, [2] Michael Syskind Pedersen, DeLiang Wang, Jan Larsen and Ulrik Kjems: "Overcomplete Blind Source Separation by Combining ICA and Binary Time-Frequency Masking," in proceedings of IEEE International workshop on Machine Learning...

  12. Structure of cholesterol/ceramide monolayer mixtures

    DEFF Research Database (Denmark)

    Scheffer, L.; Solomonov, I.; Weygand, M.J.

    2005-01-01

    The structure of monolayers of cholesterol/ ceramide mixtures was investigated using grazing incidence x-ray diffraction, immunofluorescence, and atomic force microscopy techniques. Grazing incidence x-ray diffraction measurements showed the existence of a crystalline mixed phase of the two...

  13. Mixture model analysis of complex samples

    NARCIS (Netherlands)

    Wedel, M; ter Hofstede, F; Steenkamp, JBEM

    1998-01-01

    We investigate the effects of a complex sampling design on the estimation of mixture models. An approximate or pseudo likelihood approach is proposed to obtain consistent estimates of class-specific parameters when the sample arises from such a complex design. The effects of ignoring the sample desi

  14. Numerical Solution of Hard-Core Mixtures

    OpenAIRE

    Buhot, Arnaud; Krauth, Werner

    1997-01-01

    We study the equilibrium phase diagram of binary mixtures of hard spheres as well as of parallel hard cubes. A superior cluster algorithm allows us to establish and to access the demixed phase for both systems and to investigate the subtle interplay between short-range depletion and long-range demixing.

  15. Pool Boiling of Hydrocarbon Mixtures on Water

    Energy Technology Data Exchange (ETDEWEB)

    Boee, R.

    1996-09-01

    In maritime transport of liquefied natural gas (LNG) there is a risk of spilling cryogenic liquid onto water. The present doctoral thesis discusses transient boiling experiments in which liquid hydrocarbons were poured onto water and left to boil off. Composition changes during boiling are believed to be connected with the initiation of rapid phase transition in LNG spilled on water. 64 experimental runs were carried out, 14 using pure liquid methane, 36 using methane-ethane, and 14 using methane-propane binary mixtures of different composition. The water surface was open to the atmosphere and covered an area of 200 cm{sup 2} at 25 - 40{sup o}C. The heat flux was obtained by monitoring the change of mass vs time. The void fraction in the boiling layer was measured with a gamma densitometer, and a method for adapting this measurement concept to the case of a boiling cryogenic liquid mixture is suggested. Significant differences in the boil-off characteristics between pure methane and binary mixtures revealed by previous studies are confirmed. Pure methane is in film boiling, whereas the mixtures appear to enter the transitional boiling regime with only small amounts of the second component added. The results indicate that the common assumption that LNG will be in film boiling on water because of the high temperature difference, may be questioned. Comparison with previous work shows that at this small scale the results are influenced by the experimental apparatus and procedures. 66 refs., 76 figs., 28 tabs.

  16. Mixtures of Ultracold Fermions with Unequal Masses

    Science.gov (United States)

    de Melo, Carlos A. R. Sa

    2008-05-01

    The quantum phases of ultracold fermions with unequal masses are discussed in continuum and lattice models for a wide variety of mixtures which exhibit Feshbach resonances, e.g., mixtures of ^6Li and ^40K. The evolution of superfluidity from the Bardeen-Cooper-Schrieffer (BCS) to the Bose-Einstein condensation (BEC) regime in the continuum is analyzed as a function of scattering parameter, population imbalance and mass anisotropy. In the continuum case, regions corresponding to normal, phase-separated or coexisting uniform-superfluid/excess-fermion phases are identified and the possibility of topological phase transitions is discussed [1]. For optical lattices, the phase diagrams as a function of interaction strength, population imbalance, filling fraction and tunneling parameters are presented [2]. In addition to the characteristic phases of the continuum, a series of insulating phases emerge in the phase diagrams of optical lattices, including a Bose-Mott insulator (BMI), a Fermi-Pauli insulator (FPI), a phase-separated BMI/FPI mixture, and a Bose-Fermi checkerboard (BFC) phase. Lastly, the effects of harmonic traps and the emergence of unusual shell structures are discussed for mixtures of fermions with unequal masses. [1] M. Iskin, and C. A. R. S' a de Melo, Phys. Rev. Lett 97, 100404 (2006); [2] M. Iskin, and C. A. R. S' a de Melo, Phys. Rev. Lett. 99, 080403 (2007).

  17. Cementitious barriers partnership concrete mixture characterization

    Energy Technology Data Exchange (ETDEWEB)

    Langton, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Protiere, Yannick [SIMCO Technologies, Inc., Quebec (Canada)

    2014-12-01

    This report summarizes the characterization study performed on two concrete mixtures used for radioactive waste storage. Both mixtures were prepared with approximately 425 kg of binder. The testing protocol mostly focused on determining the transport properties of the mixtures; volume of permeable voids (porosity), diffusion coefficients, and water permeability were evaluated. Tests were performed after different curing durations. In order to obtain data on the statistical distribution of transport properties, the measurements after 2 years of curing were performed on 10+ samples. Overall, both mixtures exhibited very low tortuosities and permeabilities, a direct consequence of their low water-to-binder ratio and the use of supplementary cementitious materials. The data generated on 2-year old samples showed that porosity, tortuosity and permeability follow a normal distribution. Chloride ponding tests were also performed on test samples. They showed limited chloride ingress, in line with measured transport properties. These test results also showed that both materials react differently with chloride, a consequence of the differences in the binder chemical compositions.

  18. Some aspects of symmetric Gamma process mixtures

    OpenAIRE

    Naulet, Zacharie; Barat, Eric

    2015-01-01

    In this article, we present some specific aspects of symmetric Gamma process mixtures for use in regression models. We propose a new Gibbs sampler for simulating the posterior and we establish adaptive posterior rates of convergence related to the Gaussian mean regression problem.

  19. The Coffee-Milk Mixture Problem Revisited

    Science.gov (United States)

    Marion, Charles F.

    2015-01-01

    This analysis of a problem that is frequently posed at professional development workshops, in print, and on the Web--the coffee-milk mixture riddle--illustrates the timeless advice of George Pólya's masterpiece on problem solving in mathematics, "How to Solve It." In his book, Pólya recommends that problems previously solved and put…

  20. Theory of dynamic arrest in colloidal mixtures.

    Science.gov (United States)

    Juárez-Maldonado, R; Medina-Noyola, M

    2008-05-01

    We present a first-principles theory of dynamic arrest in colloidal mixtures based on the multicomponent self-consistent generalized Langevin equation theory of colloid dynamics [M. A. Chávez-Rojo and M. Medina-Noyola, Phys. Rev. E 72, 031107 (2005); M. A. Chávez-Rojo and M. Medina-Noyola, Phys. Rev. E76, 039902 (2007)]. We illustrate its application with a description of dynamic arrest in two simple model colloidal mixtures: namely, hard-sphere and repulsive Yukawa binary mixtures. Our results include observation of the two patterns of dynamic arrest, one in which both species become simultaneously arrested and the other involving the sequential arrest of the two species. The latter case gives rise to mixed states in which one species is arrested while the other species remains mobile. We also derive the ("bifurcation" or fixed-point") equations for the nonergodic parameters of the system, which takes the surprisingly simple form of a system of coupled equations for the localization length of the particles of each species. The solution of this system of equations indicates unambiguously which species is arrested (finite localization length) and which species remains ergodic (infinite localization length). As a result, we are able to draw the entire ergodic-nonergodic phase diagram of the binary hard-sphere mixture.

  1. Toxicology of chemical mixtures: International perspective

    NARCIS (Netherlands)

    Feron, V.J.; Cassee, F.R.; Groten, J.P.

    1998-01-01

    This paper reviews major activities outside the United States on human health issues related to chemical mixtures. In Europe an international study group on combination effects has been formed and has started by defining synergism and antagonism. Successful research programs in Europe include the

  2. 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.

  3. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    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

  4. 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).

  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

    Directory of Open Access Journals (Sweden)

    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. Celer: an Efficient Program for Genotype Elimination

    CERN Document Server

    De Francesco, Nicoletta; Martini, Luca; 10.4204/EPTCS.33.4

    2010-01-01

    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.

  8. The influence and possible recombination of genotypes on the production of microspore embryoids in anther cultures of Solanum tuberosum and dihaploid hybrids.

    Science.gov (United States)

    Jacobsen, E; Sopory, S K

    1978-05-01

    In addition to physical and chemical factors, genotype appears to be a very important factor influencing success in anther culture. Recombination by making crosses with selected responding clones has been introduced as a possible helpful method to positively influence the success and response type via the factor genotype. From the progeny of such a cross, one genotype could be selected, producing in 30 to 40 percent of the cultured anthers, fully developed embryoids and plantlets, which are a mixture of polyploids, dihaploids and monohaploids.Further, a pleiotropic marker 'embryo spot' visible as a 'nodal band' in the plant stage, has been used to confirm the microsporic origin of dihaploids and polyploids and to prove their homozygous nature. This marker also shows potential use in confirming the origin of calli from individual microspores.

  9. Computer simulation of rod-sphere mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Antypov, Dmytro

    2003-07-01

    Results are presented from a series of simulations undertaken to investigate the effect of adding small spherical particles to a fluid of rods which would otherwise represent a liquid crystalline (LC) substance. Firstly, a bulk mixture of Hard Gaussian Overlap particles with an aspect ratio of 3:1 and hard spheres with diameters equal to the breadth of the rods is simulated at various sphere concentrations. Both mixing-demixing and isotropic-nematic transition are studied using Monte Carlo techniques. Secondly, the effect of adding Lennard-Jones particles to an LC system modelled using the well established Gay-Berne potential is investigated. These rod-sphere mixtures are simulated using both the original set of interaction parameters and a modified version of the rod-sphere potential proposed in this work. The subject of interest is the internal structure of the binary mixture and its dependence on density, temperature, concentration and various parameters characterising the intermolecular interactions. Both the mixing-demixing behaviour and the transitions between the isotropic and any LC phases have been studied for four systems which differ in the interaction potential between unlike particles. A range of contrasting microphase separated structures including bicontinuous, cubic, and micelle-like arrangement have been observed in bulk. Thirdly, the four types of mixtures previously studied in bulk are subjected to a static magnetic field. A variety of novel phases are observed for the cases of positive and negative anisotropy in the magnetic susceptibility. These include a lamellar structure, in which layers of rods are separated by layers of spheres, and a configuration with a self-assembling hexagonal array of spheres. Finally, two new models are presented to study liquid crystal mixtures in the presence of curved substrates. These are implemented for the cases of convex and concave spherical surfaces. The simulation results obtained in these geometries

  10. Experiments with Mixtures Designs, Models, and the Analysis of Mixture Data

    CERN Document Server

    Cornell, John A

    2011-01-01

    The most comprehensive, single-volume guide to conducting experiments with mixtures"If one is involved, or heavily interested, in experiments on mixtures of ingredients, one must obtain this book. It is, as was the first edition, the definitive work."-Short Book Reviews (Publication of the International Statistical Institute)"The text contains many examples with worked solutions and with its extensive coverage of the subject matter will prove invaluable to those in the industrial and educational sectors whose work involves the design and analysis of mixture experiments."-Journal of the Royal S

  11. 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.

  12. 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.

  13. 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.

  14. Identification of Cryptosporidium species and genotypes in Scottish raw and drinking waters during a one-year monitoring period.

    Science.gov (United States)

    Nichols, R A B; Connelly, L; Sullivan, C B; Smith, H V

    2010-09-01

    We analyzed 1,042 Cryptosporidium oocyst-positive slides (456 from raw waters and 586 from drinking waters) of which 55.7% contained 1 or 2 oocysts, to determine species/genotypes present in Scottish waters. Two nested PCR-restriction fragment length polymorphism (RFLP) assays targeting different loci (1 and 2) of the hypervariable region of the 18S rRNA gene were used for species identification, and 62.4% of samples were amplified with at least one of the PCR assays. More samples (577 slides; 48.7% from raw water and 51.3% from drinking water) were amplified at locus 1 than at locus 2 (419 slides; 50.1% from raw water and 49.9% from drinking water). PCR at loci 1 and 2 amplified 45.4% and 31.7% of samples containing 1 or 2 oocysts, respectively. We detected both human-infectious and non-human-infectious species/genotype oocysts in Scottish raw and drinking waters. Cryptosporidium andersoni, Cryptosporidium parvum, and the Cryptosporidium cervine genotype (now Cryptosporidium ubiquitum) were most commonly detected in both raw and drinking waters, with C. ubiquitum being most common in drinking waters (12.5%) followed by C. parvum (4.2%) and C. andersoni (4.0%). Numerous samples (16.6% total; 18.9% from drinking water) contained mixtures of two or more species/genotypes, and we describe strategies for unraveling their identity. Repetitive analysis for discriminating mixtures proved useful, but both template concentration and PCR assay influenced outcomes. Five novel Cryptosporidium spp. (SW1 to SW5) were identified by RFLP/sequencing, and Cryptosporidium sp. SW1 was the fourth most common contaminant of Scottish drinking water (3%).

  15. Validation of a DNA mixture statistics tool incorporating allelic drop-out and drop-in.

    Science.gov (United States)

    Mitchell, Adele A; Tamariz, Jeannie; O'Connell, Kathleen; Ducasse, Nubia; Budimlija, Zoran; Prinz, Mechthild; Caragine, Theresa

    2012-12-01

    DNA mixture analysis is a current topic of discussion in the forensics literature. Of particular interest is how to approach mixtures where allelic drop-out and/or drop-in may have occurred. The Office of Chief Medical Examiner (OCME) of The City of New York has developed and validated the Forensic Statistical Tool (FST), a software tool for likelihood ratio analysis of forensic DNA samples, allowing for allelic drop-out and drop-in. FST can be used for single source samples and for mixtures of DNA from two or three contributors, with or without known contributors. Drop-out and drop-in probabilities were estimated empirically through analysis of over 2000 amplifications of more than 700 mixtures and single source samples. Drop-out rates used by FST are a function of the Identifiler(®) locus, the quantity of template DNA amplified, the number of amplification cycles, the number of contributors to the sample, and the approximate mixture ratio (either unequal or approximately equal). Drop-out rates were estimated separately for heterozygous and homozygous genotypes. Drop-in rates used by FST are a function of number of amplification cycles only. FST was validated using 454 mock evidence samples generated from DNA mixtures and from items handled by one to four persons. For each sample, likelihood ratios (LRs) were computed for each true contributor and for each profile in a database of over 1200 non-contributors. A wide range of LRs for true contributors was obtained, as true contributors' alleles may be labeled at some or all of the tested loci. However, the LRs were consistent with OCME's qualitative assessments of the results. The second set of data was used to evaluate FST LR results when the test sample in the prosecution hypothesis of the LR is not a contributor to the mixture. With this validation, we demonstrate that LRs generated using FST are consistent with, but more informative than, OCME's qualitative sample assessments and that LRs for non

  16. 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...

  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

    for WClMV to provoke differential selection on T. repens genotypes, which may lead to negative frequency-dependent selection in host populations. †Conclusions The apparent G × E interaction and evident repercussions for relative fitness reported in this study stress the importance of viruses...

  18. Properties of Direct Coal Liquefaction Residue Modified Asphalt Mixture

    Directory of Open Access Journals (Sweden)

    Jie Ji

    2017-01-01

    Full Text Available The objectives of this paper are to use Direct Coal Liquefaction Residue (DLCR to modify the asphalt binders and mixtures and to evaluate the performance of modified asphalt mixtures. The dynamic modulus and phase angle of DCLR and DCLR-composite modified asphalt mixture were analyzed, and the viscoelastic properties of these modified asphalt mixtures were compared to the base asphalt binder SK-90 and Styrene-Butadiene-Styrene (SBS modified asphalt mixtures. The master curves of the asphalt mixtures were shown, and dynamic and viscoelastic behaviors of asphalt mixtures were described using the Christensen-Anderson-Marasteanu (CAM model. The test results show that the dynamic moduli of DCLR and DCLR-composite asphalt mixtures are higher than those of the SK-90 and SBS modified asphalt mixtures. Based on the viscoelastic parameters of CAM models of the asphalt mixtures, the high- and low-temperature performance of DLCR and DCLR-composite modified asphalt mixtures are obviously better than the SK-90 and SBS modified asphalt mixtures. In addition, the DCLR and DCLR-composite modified asphalt mixtures are more insensitive to the frequency compared to SK-90 and SBS modified asphalt mixtures.

  19. Thermodiffusion in binary and ternary nonpolar hydrocarbon + alcohol mixtures

    Science.gov (United States)

    Eslamian, Morteza; Saghir, M. Ziad

    2012-12-01

    Thermodiffusion in complex mixtures, such as associating, molten metal, and polymer mixtures is difficult to model usually owing to the occurrence of a sign change in the thermodiffusion coefficient when the mixture concentration and temperature change. A mixture comprised of a nonpolar hydrocarbon and an alcohol is a complex and highly non-ideal mixture. In this paper an existing binary non-equilibrium thermodynamics model (Eslamian and Saghir, Physical Review E 80, 061201, 2009) developed for aqueous mixtures of alcohols is examined against the experimental data of binary nonpolar hydrocarbon and alcohol mixtures. For ternary mixtures, non-equilibrium thermodynamic expressions developed by the authors for aqueous mixtures of alcohols (Eslamian and Saghir, Canadian Journal of Chemical Engineering, DOI 10.1002/cjce.20581) is used to predict thermodiffusion coefficients of ternary nonpolar hydrocarbon and alcohol mixtures. The rationale behind the sign change is elucidated and attributed to an anomalous change in the molecular structure and therefore viscosity of such mixtures. Model predictions of thermodiffusion coefficients of binary mixtures predict a sign change consistent with the experimental data although the model is still too primitive to capture all structural complexities. For instance, in the methanol-benzene mixture where the model predictions are poorest, the viscosity data show that when concentration varies, the mixture's molecular structure experiences a severe change twice, the first major change leading to a maximum in the thermodiffusion coefficient, whereas the second change causes a sign change.

  20. 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.

  1. 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

  2. Complex mixtures, complex responses: Assessing pharmaceutical mixtures using field and laboratory approaches

    Science.gov (United States)

    Schoenfuss, Heiko L.; Furlong, Edward T.; Phillips, Patrick J.; Scott, Tia-Marie; Kolpin, Dana W.; Cetkovic-Cvrlje, Marina; Lesteberg, Kelsey E.; Rearick, Daniel C.

    2016-01-01

    Pharmaceuticals are present in low concentrations (tramadol), a muscle relaxant (methocarbamol), a simple antidepressant mixture (fluoxetine, paroxetine, venlafaxine), a sleep aid (temazepam), or a complex mixture of all compounds. Larval minnow response to effluent exposure was not consistent. The 2010 exposures resulted in shorter exposed minnow larvae, whereas the larvae exposed in 2012 exhibited altered escape behavior. Mature minnows exhibited altered hepatosomatic indices, with the strongest effects in females and in mixture exposures. In addition, laboratory-exposed, mature male minnows exposed to all pharmaceuticals (except the selective serotonin reuptake inhibitor mixture) defended nest sites less rigorously than fish in the control group. Tramadol or antidepressant mixture exposure resulted in increased splenic T lymphocytes. Only male minnows exposed to whole effluent responded with increased plasma vitellogenin concentrations. Female minnows exposed to pharmaceuticals (except the opioid mixture) had larger livers, likely as a compensatory result of greater prominence of vacuoles in liver hepatocytes. The observed alteration of apical endpoints central to sustaining fish populations confirms that effluents containing waste streams from pharmaceutical formulation facilities can adversely impact fish populations but that the effects may not be temporally consistent. The present study highlights the importance of including diverse biological endpoints spanning levels of biological organization and life stages when assessing contaminant interactions.

  3. 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.

  4. 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.

  5. Phase structure of liposome in lipid mixtures.

    Science.gov (United States)

    Zhang, Tianxi; Li, Yuzhuo; Mueller, Anja

    2011-11-01

    Gas microbubbles present in ultrasound imaging contrast agents are stabilized by lipid aggregates that typically contain a mixture of lipids. In this study, the phase structure of the lipid mixtures that contained two or three lipids was investigated using three different methods: dynamic light scattering, (1)H NMR, and microfluidity measurements with fluorescence probes. Three lipids that are commonly present in imaging agents (DPPC, DPPE-PEG, and DPPA) were used. Two types of systems, two-lipid model systems and simulated imaging systems were investigated. The results show that liposomes were the dominant aggregates in all the samples studied. The polar PEG side chains from the PEGylated lipid lead to the formation of micelles and micellar aggregates in small sizes. In the ternary lipid systems, almost all the lipids were present in bilayers with micelles absent and free lipids at very low concentration. These results suggest that liposomes, not micelles, contribute to the stabilization of microbubbles in an ultrasound imaging contrast agent.

  6. Molecular thermodiffusion (thermophoresis) in liquid mixtures.

    Science.gov (United States)

    Semenov, Semen N; Schimpf, Martin E

    2005-10-01

    Thermodiffusion (thermophoresis) in liquid mixtures is theoretically examined using a hydrodynamic approach. Thermodiffusion is related to the local temperature-induced pressure gradient in the liquid layer surrounding the selected molecule and to the secondary macroscopic pressure gradient established in the system. The local pressure gradient is produced by excess pressure due to the asymmetry of interactions with surrounding molecules in a nonuniform temperature field. The secondary pressure gradient is considered an independent parameter related to the concentration gradient formed by volume forces, calculated from the generalized equations for mass transfer. Values of Soret coefficients for mixtures of toluene and -hexane are calculated using parameters in the literature. When the molecules are assumed to be similar in shape, the calculated Soret coefficients are lower than the empirical values found in the literature. However, by introducing an asymmetry parameter, which is calculated from independent measurements of component diffusion in the literature, very good agreement is obtained.

  7. Quantum state smoothing for classical mixtures

    CERN Document Server

    Tan, D; Mølmer, K; Murch, K W

    2016-01-01

    In quantum mechanics, wave functions and density matrices represent our knowledge about a quantum system and give probabilities for the outcomes of measurements. If the combined dynamics and measurements on a system lead to a density matrix $\\rho(t)$ with only diagonal elements in a given basis $\\{|n\\rangle\\}$, it may be treated as a classical mixture, i.e., a system which randomly occupies the basis states $|n\\rangle$ with probabilities $\\rho_{nn}(t)$. Fully equivalent to so-called smoothing in classical probability theory, subsequent probing of the occupation of the states $|n\\rangle$ improves our ability to retrodict what was the outcome of a projective state measurement at time $t$. Here, we show with experiments on a superconducting qubit that the smoothed probabilities do not, in the same way as the diagonal elements of $\\rho$, permit a classical mixture interpretation of the state of the system at the past time $t$.

  8. Excess compressibility in binary liquid mixtures.

    Science.gov (United States)

    Aliotta, F; Gapiński, J; Pochylski, M; Ponterio, R C; Saija, F; Salvato, G

    2007-06-14

    Brillouin scattering experiments have been carried out on some mixtures of molecular liquids. From the measurement of the hypersonic velocities we have evaluated the adiabatic compressibility as a function of the volume fraction. We show how the quadratic form of the excess compressibility dependence on the solute volume fraction can be derived by simple statistical effects and does not imply any interaction among the components of the system other than excluded volume effects. This idea is supported by the comparison of the experimental results with a well-established prototype model, consisting of a binary mixture of hard spheres with a nonadditive interaction potential. This naive model turns out to be able to produce a very wide spectrum of structural and thermodynamic features depending on values of its parameters. An attempt has made to understand what kind of structural information can be gained through the analysis of the volume fraction dependence of the compressibility.

  9. The Supervised Learning Gaussian Mixture Model

    Institute of Scientific and Technical Information of China (English)

    马继涌; 高文

    1998-01-01

    The traditional Gaussian Mixture Model(GMM)for pattern recognition is an unsupervised learning method.The parameters in the model are derived only by the training samples in one class without taking into account the effect of sample distributions of other classes,hence,its recognition accuracy is not ideal sometimes.This paper introduces an approach for estimating the parameters in GMM in a supervising way.The Supervised Learning Gaussian Mixture Model(SLGMM)improves the recognition accuracy of the GMM.An experimental example has shown its effectiveness.The experimental results have shown that the recognition accuracy derived by the approach is higher than those obtained by the Vector Quantization(VQ)approach,the Radial Basis Function (RBF) network model,the Learning Vector Quantization (LVQ) approach and the GMM.In addition,the training time of the approach is less than that of Multilayer Perceptrom(MLP).

  10. Sum of Bernoulli Mixtures: Beyond Conditional Independence

    Directory of Open Access Journals (Sweden)

    Taehan Bae

    2014-01-01

    Full Text Available We consider the distribution of the sum of Bernoulli mixtures under a general dependence structure. The level of dependence is measured in terms of a limiting conditional correlation between two of the Bernoulli random variables. The conditioning event is that the mixing random variable is larger than a threshold and the limit is with respect to the threshold tending to one. The large-sample distribution of the empirical frequency and its use in approximating the risk measures, value at risk and conditional tail expectation, are presented for a new class of models which we call double mixtures. Several illustrative examples with a Beta mixing distribution, are given. As well, some data from the area of credit risk are fit with the models, and comparisons are made between the new models and also the classical Beta-binomial model.

  11. Robust classification using mixtures of dependency networks

    DEFF Research Database (Denmark)

    Gámez, José A.; Mateo, Juan L.; Nielsen, Thomas Dyhre

    2008-01-01

    Dependency networks have previously been proposed as alternatives to e.g. Bayesian networks by supporting fast algorithms for automatic learning. Recently dependency networks have also been proposed as classification models, but as with e.g. general probabilistic inference, the reported speed......-ups are often obtained at the expense of accuracy. In this paper we try to address this issue through the use of mixtures of dependency networks. To reduce learning time and improve robustness when dealing with data sparse classes, we outline methods for reusing calculations across mixture components. Finally......, the proposed model is empirically compared to other state-of-the-art classifiers, both in terms of accuracy and learning time....

  12. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    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.

  13. 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)...

  14. 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.

  15. Variability of acorn anatomical characteristics in Quercus robur L. genotypes

    Directory of Open Access Journals (Sweden)

    Nikolić Nataša P.

    2010-01-01

    Full Text Available The aim of this study was to examine variability of acorn anatomical characteristics in seventeen Quercus robur L. genotypes. Acorns were collected in clonal seed orchard Banov Brod (Srem, Vojvodina, Serbia. Microscopic measurements were done for pericarp (total thickness, thickness of exocarp and mesocarp, seed coat (total thickness, thickness of outer epidermis, parenchyma, and inner epidermis, and embryo axis (diameter, thickness of cortical region, and diameter of stellar zone. Obtained results revealed certain divergence between genotypes. The thickness of pericarp varied from 418 to 559 mm (genotypes 20 and 22, respectively. On average, the participation of exocarp in the total thickness of pericarp was 36.3%, of mesocarp 61.0%, while of endocarp 2.6%. The thickness of seed coat for individual genotypes ranged from 71 mm (genotype 28 to 157 mm (genotype 38. In addition, anatomic parameters of embryo axis varied among studied genotypes. The lowest cortical zone thickness and stellar zone diameter were measured in genotype 40, while the highest values in genotype 33.

  16. Using a Genetic mixture model to study Phenotypic traits: Differential fecundity among Yukon river Chinook Salmon

    Science.gov (United States)

    Bromaghin, J.F.; Evenson, D.F.; McLain, T.H.; Flannery, B.G.

    2011-01-01

    Fecundity is a vital population characteristic that is directly linked to the productivity of fish populations. Historic data from Yukon River (Alaska) Chinook salmon Oncorhynchus tshawytscha suggest that length-adjusted fecundity differs among populations within the drainage and either is temporally variable or has declined. Yukon River Chinook salmon have been harvested in large-mesh gill-net fisheries for decades, and a decline in fecundity was considered a potential evolutionary response to size-selective exploitation. The implications for fishery conservation and management led us to further investigate the fecundity of Yukon River Chinook salmon populations. Matched observations of fecundity, length, and genotype were collected from a sample of adult females captured from the multipopulation spawning migration near the mouth of the Yukon River in 2008. These data were modeled by using a new mixture model, which was developed by extending the conditional maximum likelihood mixture model that is commonly used to estimate the composition of multipopulation mixtures based on genetic data. The new model facilitates maximum likelihood estimation of stock-specific fecundity parameters without first using individual assignment to a putative population of origin, thus avoiding potential biases caused by assignment error.The hypothesis that fecundity of Chinook salmon has declined was not supported; this result implies that fecundity exhibits high interannual variability. However, length-adjusted fecundity estimates decreased as migratory distance increased, and fecundity was more strongly dependent on fish size for populations spawning in the middle and upper portions of the drainage. These findings provide insights into potential constraints on reproductive investment imposed by long migrations and warrant consideration in fisheries management and conservation. The new mixture model extends the utility of genetic markers to new applications and can be easily adapted

  17. Lattice Model for water-solute mixtures

    OpenAIRE

    Furlan, A. P.; Almarza, N. G.; M. C. Barbosa

    2016-01-01

    A lattice model for the study of mixtures of associating liquids is proposed. Solvent and solute are modeled by adapting the associating lattice gas (ALG) model. The nature of interaction solute/solvent is controlled by tuning the energy interactions between the patches of ALG model. We have studied three set of parameters, resulting on, hydrophilic, inert and hydrophobic interactions. Extensive Monte Carlo simulations were carried out and the behavior of pure components and the excess proper...

  18. Fluorous Mixture Synthesis of Asymmetric Dendrimers

    Science.gov (United States)

    Jiang, Zhong-Xing; Yu, Yihua Bruce

    2010-01-01

    A divergent fluorous mixture synthesis (FMS) of asymmetric fluorinated dendrimers has been developed. Four generations of fluorinated dendrimers with the same fluorinated moiety were prepared with high efficiency, yield and purity. Comparison of the physicochemical properties of these dendrimers provided valuable information for their application and future optimization. This strategy has not only provided a practical method for the synthesis and purification of dendrimers, but also established the possibility of utilizing the same fluorinated moiety for FMS. PMID:20170088

  19. Nitrocarburising in ammonia-hydrocarbon gas mixtures

    DEFF Research Database (Denmark)

    Pedersen, Hanne; Christiansen, Thomas; Somers, Marcel A. J.

    2010-01-01

    The present work investigates the possibility of nitrocarburising in ammonia-acetylene-hydrogen and ammoniapropene- hydrogen gas mixtures, where unsaturated hydrocarbon gas is the carbon source during nitrocarburising. Consequently, nitrocarburising is carried out in a reducing atmosphere...... microscopy and X-ray diffraction analysis. It is shown that the use of unsaturated hydrocarbon gas in nitrocarburising processes is a viable alternative to traditional nitrocarburising methods....

  20. Nitrocarburizing in ammonia-hydrocarbon gas mixtures

    DEFF Research Database (Denmark)

    Pedersen, Hanne; Christiansen, Thomas; Somers, Marcel A. J.

    2011-01-01

    The present work investigates the possibility of nitrocarburising in ammonia-acetylene-hydrogen and ammonia-propene-hydrogen gas mixtures, where unsaturated hydrocarbon gas is the carbon source during nitrocarburising. Consequently, nitrocarburising is carried out in a reducing atmosphere...... microscopy and X-ray diffraction analysis. It is shown that the use of unsaturated hydrocarbon gas in nitrocarburising processes is a viable alternative to traditional nitrocarburising methods....

  1. Endocrine activity of mycotoxins and mycotoxin mixtures.

    Science.gov (United States)

    Demaegdt, Heidi; Daminet, Britt; Evrard, Annick; Scippo, Marie-Louise; Muller, Marc; Pussemier, Luc; Callebaut, Alfons; Vandermeiren, Karine

    2016-10-01

    Reporter gene assays incorporating nuclear receptors (estrogen, androgen, thyroid β and PPARγ2) have been implemented to assess the endocrine activity of 13 mycotoxins and their mixtures. As expected, zearalenone and its metabolites α-zearalenol and β- zearalenol turned out to have the strongest estrogenic potency (EC50 8,7 10-10 ± 0,8; 3,1 10-11 ± 0,5 and 1,3 10-8 ± 0,3 M respectively). The metabolite of deoxynivalenol, 3-acetyl-deoxynivalenol also had estrogenic activity (EC50 3,8 10-7 ± 1,1 M). Furthermore, most of the mycotoxins (and their mixtures) showed anti-androgenic effects (15-acetyldeoxynivalenol, 3-acetyl-deoxynivalenol and α-zearalenol with potencies within one order of magnitude of that of the reference compound flutamide). In particular, deoxynivalenol and 15-acetyl-deoxynivalenol acted as antagonists for the PPARy2 receptor. When testing mixtures of mycotoxins on the same cell systems, we showed that most of the mixtures reacted as predicted by the concentration addition (CA) theory. Generally, the CA was within the 95% confidence interval of the observed ones, only minor deviations were detected. Although these reporter gene tests cannot be directly extrapolated in vivo, they can be the basis for further research. Especially the additive effects of ZEN and its metabolites are of importance and could have repercussions in vivo.

  2. Method for Predicting Hypergolic Mixture Flammability Limits

    Science.gov (United States)

    2017-02-01

    AFRL-AFOSR-UK-TR-2017-0003 Method for Predicting Hypergolic Mixture Flammability Limits Laurent Catoire Ecole Nat Sup De Techniques Avancees Final...TASK NUMBER 5f.  WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Ecole Nat Sup De Techniques Avancees 828, Boulevard Des Marechaux...provides a mitigation strategy to reduce the risk of failure for the insertion of IL fuel technology into the small satellite market as AFRL/RQRP

  3. Population mixture model for nonlinear telomere dynamics

    Science.gov (United States)

    Itzkovitz, Shalev; Shlush, Liran I.; Gluck, Dan; Skorecki, Karl

    2008-12-01

    Telomeres are DNA repeats protecting chromosomal ends which shorten with each cell division, eventually leading to cessation of cell growth. We present a population mixture model that predicts an exponential decrease in telomere length with time. We analytically solve the dynamics of the telomere length distribution. The model provides an excellent fit to available telomere data and accounts for the previously unexplained observation of telomere elongation following stress and bone marrow transplantation, thereby providing insight into the nature of the telomere clock.

  4. Hierarchical mixture models for assessing fingerprint individuality

    OpenAIRE

    Dass, Sarat C.; Li, Mingfei

    2009-01-01

    The study of fingerprint individuality aims to determine to what extent a fingerprint uniquely identifies an individual. Recent court cases have highlighted the need for measures of fingerprint individuality when a person is identified based on fingerprint evidence. The main challenge in studies of fingerprint individuality is to adequately capture the variability of fingerprint features in a population. In this paper hierarchical mixture models are introduced to infer the extent of individua...

  5. Statistical mechanical theory of fluid mixtures

    Science.gov (United States)

    Zhao, Yueqiang; Wu, Zhengming; Liu, Weiwei

    2014-01-01

    A general statistical mechanical theory of fluid mixtures (liquid mixtures and gas mixtures) is developed based on the statistical mechanical expression of chemical potential of components in the grand canonical ensemble, which gives some new relationships between thermodynamic quantities (equilibrium ratio Ki, separation factor α and activity coefficient γi) and ensemble average potential energy u for one molecule. The statistical mechanical expressions of separation factor α and activity coefficient γi derived in this work make the fluid phase equilibrium calculations can be performed by molecular simulation simply and efficiently, or by the statistical thermodynamic approach (based on the saturated-vapor pressure of pure substance) that does not need microscopic intermolecular pair potential functions. The physical meaning of activity coefficient γi in the liquid phase is discussed in detail from a viewpoint of molecular thermodynamics. The calculated Vapor-Liquid Equilibrium (VLE) properties of argon-methane, methanol-water and n-hexane-benzene systems by this model fit well with experimental data in references, which indicates that this model is accurate and reliable in the prediction of VLE properties for small, large and strongly associating molecules; furthermore the statistical mechanical expressions of separation factor α and activity coefficient γi have good compatibility with classical thermodynamic equations and quantum mechanical COSMO-SAC approach.

  6. Familial searching on DNA mixtures with dropout.

    Science.gov (United States)

    Slooten, K

    2016-05-01

    Familial searching, the act of searching a database for a relative of an unknown individual whose DNA profile has been obtained, is usually restricted to cases where the DNA profile of that person has been unambiguously determined. Therefore, it is normally applied only with a good quality single source profile as starting point. In this article we investigate the performance of the method if applied to mixtures with and without allelic dropout, when likelihood ratios are computed with a semi-continuous (binary) model. We show that mixtures with dropout do not necessarily perform worse than mixtures without, especially if some separation between the donors is possible due to their different dropout probabilities. The familial searching true and false positive rates of mixed profiles on 15 loci are in some cases better than those of single source profiles on 10 loci. Thus, the information loss due to the fact that the person of interest's DNA has been mixed with that of other, and is affected by dropout, can be less than the loss of information corresponding to having 5 fewer loci available for a single source trace. Profiles typed on 10 autosomal loci are often involved in familial searching casework since many databases, including the Dutch one, in part consist of such profiles. Therefore, from this point of view, there seems to be no objection to extend familial searching to mixed or degraded profiles.

  7. Ethane-xenon mixtures under shock conditions

    Science.gov (United States)

    Flicker, Dawn; Magyar, Rudolph; Root, Seth; Cochrane, Kyle; Mattsson, Thomas

    2015-06-01

    Mixtures of light and heavy elements arise in inertial confinement fusion and planetary science. We present results on the physics of molecular scale mixing through a validation study of equation of state (EOS) properties. Density functional theory molecular dynamics (DFT/QMD) at elevated-temperature and pressure is used to obtain the properties of pure xenon, ethane, and various compressed mixture compositions along their principal Hugoniots. To validate the QMD simulations, we performed high-precision shock compression experiments using Sandia's Z-Machine. A bond tracking analysis of the simulations correlates the sharp rise in the Hugoniot curve with completion of dissociation in ethane. DFT-based simulation results compare well with experimental data and are used to provide insight into the dissociation as a function of mixture composition. Interestingly, we find that the compression ratio for complete dissociation is similar for ethane, Xe-ethane, polymethyl-pentene, and polystyrene, suggesting that a limiting compression exists for C-C bonded systems. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, Security Administration under contract DE-AC04-94AL85000.

  8. Crowding in polymer-nanoparticle mixtures.

    Science.gov (United States)

    Denton, Alan R

    2014-01-01

    The cell nucleus is a highly crowded environment, filled with a multicomponent, polydisperse mixture of biopolymers and nuclear bodies dispersed in a viscous solvent. With volume fractions approaching 20%, excluded-volume interactions play a key role in determining the structure, dynamics, and function of macromolecules in vivo. Under such constraints, the ensembles of macromolecular conformations can differ substantially from those prevailing in dilute solutions. Crowding thus can affect protein and RNA folding, conformational stability, and reaction kinetics, as well as phase stability of macromolecular mixtures. From the perspective of soft matter physics, this chapter reviews recent studies on crowding in polymer-nanoparticle mixtures, seeking to demonstrate the utility of simple physical models for addressing challenging issues in cell biology. The focus is on applications of free-volume theory and Monte Carlo simulation, based on geometrical models of polymers as fluctuating spheres or ellipsoids. Ideal polymer coils respond to hard-sphere crowding agents by compactifying, reducing their radius of gyration, and becoming more spherical. At sufficiently high concentrations, polymers and crowders phase-separate. The goal of this review is to identify universal principles governing macromolecular crowding and to establish a general framework for future explorations of more realistic models that may include nonsteric (e.g., electrostatic) interactions. © 2014 Elsevier Inc. All rights reserved.

  9. Tandem mass spectrometry: analysis of complex mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Singleton, K.E.

    1985-01-01

    Applications of tandem mass spectrometry (MS/MS) for the analysis of complex mixtures results in increased specificity and selectivity by using a variety of reagent gases in both negative and positive ion modes. Natural isotopic abundance ratios were examined in both simple and complex mixtures using parent, daughter and neutral loss scans. MS/MS was also used to discover new compounds. Daughter scans were used to identify seven new alkaloids in a cactus species. Three of these alkaloids were novel compounds, and included the first simple, fully aromatic isoquinoline alkaloids reported in Cactaceae. MS/MS was used to characterize the chemical reaction products of coal in studies designed to probe its macromolecular structure. Negative ion chemical ionization was utilized to study reaction products resulting from the oxidation of coal. Possible structural units in the precursor coal were predicted based on the reaction products identified, aliphatic and aromatic acids and their anhydrides. The MS/MS method was also used to characterize reaction products resulting from coal liquefaction and/or extraction. These studies illustrate the types of problems for which MS/MS is useful. Emphasis has been placed on characterization of complex mixtures by selecting experimental parameters which enhance the information obtained. The value of using MS/MS in conjunction with other analytical techniques as well as the chemical pretreatment is demonstrated.

  10. Confusion of concepts in mixture toxicology.

    Science.gov (United States)

    Könemann, W H; Pieters, M N

    1996-01-01

    Regulatory limit values are generally set for single compounds. However, humans are exposed both simultaneously and sequentially to a wide variety of compounds. Some concepts on mixture toxicology are discussed in this introduction to the European Conference on Combination Toxicology. Studies on mixtures are often accompanied by statements about the type of combined action, which can be, for example, additive, synergistic or antagonistic. Unfortunately, comparison of results is hardly possible for various reasons. First, the terminology for indicating combined action is far from consistent. Bearing this in mind, researchers should be explicit in the definitions of terms. Secondly, depending on the model, different conclusions may be drawn from the same results. It is therefore important to provide clear definitions of the null hypothesis. Thirdly, adequate statistical methods should be used for testing the null hypothesis. In the past, many mixtures studies either used no statistics or used statistics incorrectly. Last, but not least, the study should be designed in such a way that it should be possible to obtain clear answers. In this introduction, it is stressed that environmental toxicologists should focus on the low-dose region of the dose-effect curves. It appears that interactions are less plausible at low doses. Dose additivity, however, cannot be excluded.

  11. Mixture risk assessment: a case study of Monsanto experiences.

    Science.gov (United States)

    Nair, R S; Dudek, B R; Grothe, D R; Johannsen, F R; Lamb, I C; Martens, M A; Sherman, J H; Stevens, M W

    1996-01-01

    Monsanto employs several pragmatic approaches for evaluating the toxicity of mixtures. These approaches are similar to those recommended by many national and international agencies. When conducting hazard and risk assessments, priority is always given to using data collected directly on the mixture of concern. To provide an example of the first tier of evaluation, actual data on acute respiratory irritation studies on mixtures were evaluated to determine whether the principle of additivity was applicable to the mixture evaluated. If actual data on the mixture are unavailable, extrapolation across similar mixtures is considered. Because many formulations are quite similar in composition, the toxicity data from one mixture can be extended to a closely related mixture in a scientifically justifiable manner. An example of a family of products where such extrapolations have been made is presented to exemplify this second approach. Lastly, if data on similar mixtures are unavailable, data on component fractions are used to predict the toxicity of the mixture. In this third approach, process knowledge and scientific judgement are used to determine how the known toxicological properties of the individual fractions affect toxicity of the mixture. Three examples of plant effluents where toxicological data on fractions were used to predict the toxicity of the mixture are discussed. The results of the analysis are used to discuss the predictive value of each of the above mentioned toxicological approaches for evaluating chemical mixtures.

  12. Physical Compatibility of Propofol-Sufentanil Mixtures.

    Science.gov (United States)

    Zbytovská, Jarmila; Gallusová, Jana; Vidlářová, Lucie; Procházková, Kamila; Šimek, Jan; Štěpánek, František

    2017-03-01

    Combined infusions of propofol and sufentanil preparations are frequently used in clinical practice to induce anesthesia and analgesia. However, the stability of propofol emulsions can be affected by dilution with another preparation, sometimes leading to particle coalescence and enlargement. Such unwanted effects can lead to fat embolism syndrome after intravenous application. This study describes the physical stability of 5 commercially available propofol preparations mixed with sufentanil citrate solutions. Two common markers of emulsion stability were used in this study; namely, the zeta potential and size distribution of the emulsion droplets. Both were measured using dynamic light scattering. The data for the pure propofol preparations and their mixtures with sufentanil citrate solution were compared. The absolute value of zeta potential decreased in 4 of the 5 propofol preparations after they had been mixed with sufentanil citrate. This effect indicates a lowering of repulsive interactions between the emulsion droplets. Although this phenomenon tends to cause agglomeration, none of the studied mixtures displayed a substantial increase in droplet size within 24 hours of blending. However, our long-term stability study revealed the instability of some of the propofol-sufentanil samples. Two of the 5 studied mixtures displayed a continual increase in particle size. The same 2 preparations showed the greatest reductions in the absolute value of zeta potential, thereby confirming the correlation of both measurement methods. The increase in particle size was more distinct in the samples stored at higher temperatures and with higher sufentanil concentrations. To ensure the microbial stability of an emulsion infusion preparation, clinical regulations require that such preparations should be applied to patients within 12 hours of opening. In this respect, we can confirm that during this period, none of the studied propofol-sufentanil mixtures displayed any physical

  13. Separation of gas mixtures by supported complexes

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, D.A.; Lilga, M.A.; Hallen, R.T.; Lyke, S.E.

    1986-08-01

    The goal of this program is to determine the feasibility of solvent-dissolved coordination complexes for the separation of gas mixtures under bench-scale conditions. In particular, mixtures such as low-Btu gas are examined for CO and H/sub 2/ separation. Two complexes, Pd/sub 2/(dpm)/sub 2/Br/sub 2/ and Ru(CO)/sub 2/(PPh/sub 3/)/sub 3/, were examined in a bench-scale apparatus for the separation of binary (CO-N/sub 2/ or H/sub 2/-N/sub 2/) and quinary (H/sub 2/, CO, CO/sub 2/, CH/sub 4/, and N/sub 2/) mixtures. The separation of CO-N/sub 2/ was enhanced by the presence of the palladium complex in the 1,1,2-trichloroethane (TCE) solvent, especially at high gas and low liquid rates. The five-component gas mixture separation with the palladium complex in TCE provided quite unexpected results based on physical solubility and chemical coordination. The complex retained CO, while the solvent retained CO/sub 2/, CH/sub 4/, and N/sub 2/ to varying degrees. This allowed the hydrogen content to be enhanced due to its low solubility in TCE and inertness to the complex. Thus, a one-step, hydrogen separation can be achieved from gas mixtures with compositions similar to that of oxygen-blown coal gas. A preliminary economic evaluation of hydrogen separation was made for a system based on the palladium complex. The palladium system has a separation cost of 50 to 60 cents/MSCF with an assumed capital investment of $1.60/MSCF of annual capacity charged at 30% per year. This assumes a 3 to 4 year life for the complex. Starting with a 90% hydrogen feed, PSA separation costs are in the range of 30 to 50 cents/MSCF. The ruthenium complex was not as successful for hydrogen or carbon monoxide separation due to unfavorable kinetics. The palladium complex was found to strip hydrogen gas from H/sub 2/S. The complex could be regenerated with mild oxidants which removed the sulfur as SO/sub 2/. 24 refs., 26 figs., 10 tabs.

  14. Mixtures as a fungicide resistance management tactic.

    Science.gov (United States)

    van den Bosch, Frank; Paveley, Neil; van den Berg, Femke; Hobbelen, Peter; Oliver, Richard

    2014-12-01

    We have reviewed the experimental and modeling evidence on the use of mixtures of fungicides of differing modes of action as a resistance management tactic. The evidence supports the following conclusions. 1. Adding a mixing partner to a fungicide that is at-risk of resistance (without lowering the dose of the at-risk fungicide) reduces the rate of selection for fungicide resistance. This holds for the use of mixing partner fungicides that have either multi-site or single-site modes of action. The resulting predicted increase in the effective life of the at-risk fungicide can be large enough to be of practical relevance. The more effective the mixing partner (due to inherent activity and/or dose), the larger the reduction in selection and the larger the increase in effective life of the at-risk fungicide. 2. Adding a mixing partner while lowering the dose of the at-risk fungicide reduces the selection for fungicide resistance, without compromising effective disease control. The very few studies existing suggest that the reduction in selection is more sensitive to lowering the dose of the at-risk fungicide than to increasing the dose of the mixing partner. 3. Although there are very few studies, the existing evidence suggests that mixing two at-risk fungicides is also a useful resistance management tactic. The aspects that have received too little attention to draw generic conclusions about the effectiveness of fungicide mixtures as resistance management strategies are as follows: (i) the relative effect of the dose of the two mixing partners on selection for fungicide resistance, (ii) the effect of mixing on the effective life of a fungicide (the time from introduction of the fungicide mode of action to the time point where the fungicide can no longer maintain effective disease control), (iii) polygenically determined resistance, (iv) mixtures of two at-risk fungicides, (v) the emergence phase of resistance evolution and the effects of mixtures during this phase

  15. A mixture detection method based on separate amplification using primer specific alleles of INDELs-a study based on two person's DNA mixture.

    Science.gov (United States)

    Liu, Jinding; Wang, Jiaqi; Zhang, Xiaojia; Li, Zeqin; Yun, Keming; Liu, Zhizhen; Zhang, Gengqian

    2017-02-01

    Samples containing unbalanced DNA mixtures from individuals often occur in forensic DNA examination and clinical detection. Because of the PCR amplification bias, the minor contributor DNA is often masked by the major contributor DNA when using traditional STR or SNP typing techniques. Here we propose a method based in allele-specific Insertion/Deletion (INDEL) genotyping to detect DNA mixtures in forensic samples. Fourteen INDELs were surveyed in the Chinese Han population of Shanxi Province. The INDELs were amplified using two separate primer-specific reactions by real-time PCR. The difference Ct value of the 2 reactions (D-value) were used for determination of the single source DNA. INDELs types and further confirmed by electrophoresis separation. The minor allele frequency (MAF) was above 0.2 in 10 INDELs. The detection limit was 0.3125 ng-1.25 ng template DNA for real-time PCR in all 14 INDEL markers. For single source 10 ng DNA, the average D-value was 0.31 ± 0.14 for LS type, 6.96 ± 1.05 for LL type and 7.20 ± 1.09 for SS type. For the series of simulated DNA mixture, the Ct value varied between the ranges of single source DNA, depending on their INDEL typing and mixture ratios. This method can detect the specific allele of the minor DNA contributor as little as 1:50 in rs397782455 and rs397696936; 1:100 in rs397832665, rs397822382 and rs397897230; the detection limit of the minor DNA contributor was as little as 1:500-1:1000 in the rest INDEL markers, a much higher sensitivity compared with traditional STR typing. The D-value variation depended on the alternation of dilution ratio and INDEL types. When the dilution was 1:1000, the maximum and minimum D-values were 8.84 ± 0.11 in rs397897230 and 4.27 ± 0.19 in rs397897239 for LL and SS type mixture, the maximum and minimum D-values were 9.32 ± 0.54 in rs397897230 and 4.38 ± 0.26 in rs 397897239 for LL(SS) and LS type mixture, separately. Any D-value between 0.86 and 5.11 in the 14

  16. Plant genotype, microbial recruitment and nutritional security.

    Science.gov (United States)

    Patel, Jai S; Singh, Akanksha; Singh, Harikesh B; Sarma, Birinchi K

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).

  17. Apolipoprotein-E genotypes and myasthenia gravis.

    Science.gov (United States)

    Suhail, Hamid; Soundararajan, Christhunesa C; Vivekanandhan, Subbiah; Singh, Sumit; Behari, Madhuri

    2010-01-01

    Autoimmune myasthenia gravis (MG) is a disorder of neuromuscular junction. Possible role of multiple genes in the development of the MG has been documented. This case-control study, studied the association of apolipoprotein E (Apo-E) alleles with MG. Anti-AChR antibody was measured using radio receptor immunoassay. Apo-E genotypes were analyzed in 120 MG patients and 120 healthy subjects. Comparison between patients with MG and controls showed no significant association with Apo-E allelic variants. However, a significant association of Apo-E4 allele with AChR-antibody positive patients was observed (P = 0.007). Also, among seropositive patients, a significant association was seen between female gender and Apo-E4 allele (P = 0.023). Our results suggest that the presence of Apo-E4 allele might influence seropositive status in patients with MG and seems an associated susceptible factor in female patients.

  18. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics......, together with an application of the latter method to a large Danish sequencing project. The rst is a probabilistic method for transcriptome assembly that is based on a novel generative model of the RNA sequencing process and provides condence estimates on the assembled transcripts. We show...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  19. Investigation of rheological properties of mixtures of soft ice cream

    Directory of Open Access Journals (Sweden)

    L. V. Golubeva

    2012-01-01

    Full Text Available The paper presents the study of the rheological properties of multicomponent mixtures for soft ice cream enriched with various stabilizers to facilitate evaluation and selection of the optimal mixture.

  20. Methods for Assessing Curvature and Interaction in Mixture Experiments

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, Gregory F.(BATTELLE (PACIFIC NW LAB)); Hicks, Ruel D.(ASSOC WESTERN UNIVERSITY); Szychowski, Jeffrey M.(ASSOC WESTERN UNIVERSITY); Loeppky, Jason L.(ASSOC WESTERN UNIVERSITY)

    2002-05-01

    The terms curvature and interaction traditionally are not defined or used in the context of mixture experiments because curvature and interaction effects are partially confounded due to the mixture constrain that the component proportions sum to 1.

  1. Mixture Density Mercer Kernels: A Method to Learn Kernels

    Data.gov (United States)

    National Aeronautics and Space Administration — This paper presents a method of generating Mercer Kernels from an ensemble of probabilistic mixture models, where each mixture model is generated from a Bayesian...

  2. Optimal (Solvent) Mixture Design through a Decomposition Based CAMD methodology

    DEFF Research Database (Denmark)

    Achenie, L.; Karunanithi, Arunprakash T.; Gani, Rafiqul

    2004-01-01

    Computer Aided Molecular/Mixture design (CAMD) is one of the most promising techniques for solvent design and selection. A decomposition based CAMD methodology has been formulated where the mixture design problem is solved as a series of molecular and mixture design sub-problems. This approach is...... is able to overcome most of the difficulties associated with the solution of mixture design problems. The new methodology has been illustrated with the help of a case study involving the design of solvent-anti solvent binary mixtures for crystallization of Ibuprofen.......Computer Aided Molecular/Mixture design (CAMD) is one of the most promising techniques for solvent design and selection. A decomposition based CAMD methodology has been formulated where the mixture design problem is solved as a series of molecular and mixture design sub-problems. This approach...

  3. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  4. An assessment of the information content of likelihood ratios derived from complex mixtures.

    Science.gov (United States)

    Marsden, Clare D; Rudin, Norah; Inman, Keith; Lohmueller, Kirk E

    2016-05-01

    With the increasing sensitivity of DNA typing methodologies, as well as increasing awareness by law enforcement of the perceived capabilities of DNA typing, complex mixtures consisting of DNA from two or more contributors are increasingly being encountered. However, insufficient research has been conducted to characterize the ability to distinguish a true contributor (TC) from a known non-contributor (KNC) in these complex samples, and under what specific conditions. In order to investigate this question, sets of six 15-locus Caucasian genotype profiles were simulated and used to create mixtures containing 2-5 contributors. Likelihood ratios were computed for various situations, including varying numbers of contributors and unknowns in the evidence profile, as well as comparisons of the evidence profile to TCs and KNCs. This work was intended to illustrate the best-case scenario, in which all alleles from the TC were detected in the simulated evidence samples. Therefore the possibility of drop-out was not modeled in this study. The computer program DNAMIX was then used to compute LRs comparing the evidence profile to TCs and KNCs. This resulted in 140,000 LRs for each of the two scenarios. These complex mixture simulations show that, even when all alleles are detected (i.e. no drop-out), TCs can generate LRs less than 1 across a 15-locus profile. However, this outcome was rare, 7 of 140,000 replicates (0.005%), and associated only with mixtures comprising 5 contributors in which the numerator hypothesis includes one or more unknown contributors. For KNCs, LRs were found to be greater than 1 in a small number of replicates (75 of 140,000 replicates, or 0.05%). These replicates were limited to 4 and 5 person mixtures with 1 or more unknowns in the numerator. Only 5 of these 75 replicates (0.004%) yielded an LR greater than 1,000. Thus, overall, these results imply that the weight of evidence that can be derived from complex mixtures containing up to 5 contributors

  5. Comparative study of the biological properties of Trypanosoma cruzi I genotypes in a murine experimental model.

    Science.gov (United States)

    Cruz, Lissa; Vivas, Angie; Montilla, Marleny; Hernández, Carolina; Flórez, Carolina; Parra, Edgar; Ramírez, Juan David

    2015-01-01

    Chagas disease is an endemic zoonosis in Latin America and caused by the parasite Trypanosoma cruzi. This kinetoplastid displays remarkable genetic variability, allowing its classification into six Discrete Typing Units (DTUs) from TcI to TcVI. T. cruzi I presents the broadest geographical distribution in the continent and has been associated to severe forms of cardiomyopathies. Recently, a particular genotype associated to human infections has been reported and named as TcIDOM (previously named TcIa-b). This genotype shows to be clonal and adapted to the domestic cycle but so far no studies have determined the biological properties of domestic (TcIDOM) and sylvatic TcI strains (previously named TcIc-e). Hence, the aim of this study was to untangle the biological features of these genotypes in murine models. We infected ICR-CD1 mice with five TcI strains (two domestic, two sylvatic and one natural mixture) and determined the course of infection during 91 days (acute and chronic phase of the disease) in terms of parasitemia, tissue tropism, immune response (IgG titers) and tissue invasion by means of histopathology studies. Statistically significant differences were observed in terms of parasitemia curves and prepatent period between domestic (TcIDOM) and sylvatic strains. There were no differences in terms of IgG antibodies response across the mice infected with the five strains. Regarding the histopathology, our results indicate that domestic strains present higher parasitemias and low levels of histopathological damage. In contrast, sylvatic strains showed lower parasitemias and high levels of histopathological damage. These results highlight the sympatric and behavioral differences of domestic and sylvatic TcI strains; the clinical and epidemiological implications are herein discussed.

  6. Investigation of a Gamma model for mixture STR samples

    DEFF Research Database (Denmark)

    Christensen, Susanne; Bøttcher, Susanne Gammelgaard; Lauritzen, Steffen L.

    The behaviour of PCR Amplification Kit, when used for mixture STR samples, is investigated. A model based on the Gamma distribution is fitted to the amplifier output for constructed mixtures, and the assumptions of the model is evaluated via residual analysis.......The behaviour of PCR Amplification Kit, when used for mixture STR samples, is investigated. A model based on the Gamma distribution is fitted to the amplifier output for constructed mixtures, and the assumptions of the model is evaluated via residual analysis....

  7. Quantum phases of Fermi-Fermi mixtures in optical lattices

    OpenAIRE

    Iskin, M.; de Melo, C. A. R. Sa

    2007-01-01

    The ground state phase diagram of Fermi-Fermi mixtures in optical lattices is analyzed as a function of interaction strength, population imbalance, filling fraction and tunneling parameters. It is shown that population imbalanced Fermi-Fermi mixtures reduce to strongly interacting Bose-Fermi mixtures in the molecular limit, in sharp contrast to homogeneous or harmonically trapped systems where the resulting Bose-Fermi mixture is weakly interacting. Furthermore, insulating phases are found in ...

  8. A distinct Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodidae) genotype cluster is associated with the epidemic of severe cassava mosaic virus disease in Uganda.

    Science.gov (United States)

    Legg, J P; French, R; Rogan, D; Okao-Okuja, G; Brown, J K

    2002-07-01

    During the 1990s, an epidemic of cassava mosaic virus disease caused major losses to cassava production in Uganda. Two factors associated with the epidemic were the occurrence of a novel recombinant begomovirus, EACMV-Ug, and unusually high populations of the whitefly vector, Bemisia tabaci. Here we present molecular evidence for the occurrence of two cassava-colonizing B. tabaci genotype clusters, Ug1 and Ug2, one of which, Ug2, can be consistently associated with the CMD epidemic in Uganda at the time of collection in 1997. By contrast, a second genotype cluster, Ug1, only occurred 'at' or 'ahead of' the epidemic 'front', sometimes in mixtures with Ug2. Comparison of mitochondrial cytochrome oxidase I gene sequences for Ug1 and Ug2 and well-studied B. tabaci reference populations indicated that the two Ugandan populations exhibited approximately 8% divergence, suggesting they represent distinct sub-Saharan African lineages. Neither Ugandan genotype cluster was identified as the widely distributed, polyphagous, and highly fecund B biotype of Old World origin, with which they both diverged by approximately 8%. Within genotype cluster divergence of Ug1 at 0.61 +/- 0.1% was twice that of Ug2 at 0.35 +/- 0.1%. Mismatch analysis suggested that Ug2 has undergone a recent population expansion and may be of nonUgandan origin, whereas Ug1 has diverged more slowly, and is likely to be an indigenous genotype cluster.

  9. Hepatitis C virus genotypes in Cordoba, Argentina unexpected high prevalence of genotype 2

    Directory of Open Access Journals (Sweden)

    V. Re

    2003-06-01

    Full Text Available To determine hepatitis C virus (HCV genotypes circulating in the central region of Argentina, 96 consecutive anti-HCV positive subjects were studied. The presence of HCV RNA was detected in 60 samples by RT-nested PCR of the 5' noncoding region (5' NCR. Genotyping was performed by restriction fragment length polymorphism analysis of 5' NCR region combined with PCR using type-specific primers of the core region. The groups of individuals in this study included hemophilia and hemodialysis patients, injecting drug users, screened blood donors, and patients with acute or chronic liver disease, all from Córdoba, Argentina. Overall, genotype 2 was the most prevalent (55.0%, followed by genotypes 1 (38.3 %, and 3 (5.0%. Within genotype 1, subtype 1b was the most prevalent. An unexpected high prevalence of genotype 2 (61.9% was found among patients with acute or chronic HCV infection (without known risk factors. These figures differ from other cohorts from East-Argentina where genotype 1 has been found as the most prevalent. This indicates that regional differences of genotype distribution might exist between Central and East Argentina.A fin de determinar los genotipos del virus de la hepatitis C (HCV circulantes en la región central de Argentina, se estudiaron 96 individuos anti-HCV positivos. La presencia del ARN de HCV se detectó en 60 muestras mediante RT-nested PCR de la región 5' no codificante (5' NCR. La genotipificación se realizó mediante restricción enzimática y el análisis del polimorfismo de los fragmentos largos de la región 5' NCR combinada con PCR usando primers tipo específico de la región del core. El grupo de individuos estudiados incluyó pacientes hemofílicos y hemodializados, drogadictos intravenosos, donantes de sangre y pacientes con enfermedad hepática aguda y crónica, todos provenientes de Córdoba, Argentina. El genotipo 2 fue el más prevalente (55.0%, seguido por los genotipos 1 (38.3 %, con mayor prevalencia

  10. Continuous mixtures with bathtub-shaped failure rates

    OpenAIRE

    Block, Henry W.; LI, YULIN; Savits, Thomas H.; Wang, Jie

    2008-01-01

    The failure rate of a mixture of even the most standard distributions used in reliability can have a complicated shape. However, failure rates of mixtures of two carefully selected distributions will have the well-known bathtub shape. Here we show that mixtures of whole families of distribtions can have a bathtub-shaped failure rate.

  11. Lessons learned in managing alfalfa-grass mixtures

    Science.gov (United States)

    Grass-alfalfa mixtures have a number of benefits that make them attractive to producers. However, they can be problematic to establish and maintain. Research programs have made progress in understanding the benefits and challenges of alfalfa-grass mixtures. Mixtures may have greater winter survival ...

  12. 40 CFR 721.5769 - Mixture of nitrated alkylated phenols.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Mixture of nitrated alkylated phenols... Substances § 721.5769 Mixture of nitrated alkylated phenols. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as a mixture of nitrated alkylated...

  13. 21 CFR 864.8625 - Hematology quality control mixture.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Hematology quality control mixture. 864.8625 Section 864.8625 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... quality control mixture. (a) Identification. A hematology quality control mixture is a device used...

  14. TEMPERATURE INFLUENCE ON PHASE STABILITY OF ETHANOL-GASOLINE MIXTURES

    Directory of Open Access Journals (Sweden)

    Valerian Cerempei

    2011-06-01

    Full Text Available The article investigates phase stability of ethanol-gasoline mixtures depending on their composition, water concentration in ethanol and ethanol-gasoline mixture and temperature. There have been determined the perfect functioning conditions of spark ignition engines fueled with ethanol-gasoline mixtures.

  15. 46 CFR 154.1735 - Methyl acetylene-propadiene mixture.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Methyl acetylene-propadiene mixture. 154.1735 Section... Operating Requirements § 154.1735 Methyl acetylene-propadiene mixture. (a) The composition of the methyl acetylene-propadiene mixture at loading must be within the following limits or specially approved by...

  16. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia.

    Directory of Open Access Journals (Sweden)

    I-Ching Sam

    Full Text Available BACKGROUND: Mosquito-borne Chikungunya virus (CHIKV has recently re-emerged globally. The epidemic East/Central/South African (ECSA strains have spread for the first time to Asia, which previously only had endemic Asian strains. In Malaysia, the ECSA strain caused an extensive nationwide outbreak in 2008, while the Asian strains only caused limited outbreaks prior to this. To gain insight into these observed epidemiological differences, we compared genotypic and phenotypic characteristics of CHIKV of Asian and ECSA genotypes isolated in Malaysia. METHODS AND FINDINGS: CHIKV of Asian and ECSA genotypes were isolated from patients during outbreaks in Bagan Panchor in 2006, and Johor in 2008. Sequencing of the CHIKV strains revealed 96.8% amino acid similarity, including an unusual 7 residue deletion in the nsP3 protein of the Asian strain. CHIKV replication in cells and Aedes mosquitoes was measured by virus titration. There were no differences in mammalian cell lines. The ECSA strain reached significantly higher titres in Ae. albopictus cells (C6/36. Both CHIKV strains infected Ae. albopictus mosquitoes at a higher rate than Ae. aegypti, but when compared to each other, the ECSA strain had much higher midgut infection and replication, and salivary gland dissemination, while the Asian strain infected Ae. aegypti at higher rates. CONCLUSIONS: The greater ability of the ECSA strain to replicate in Ae. albopictus may explain why it spread far more quickly and extensively in humans in Malaysia than the Asian strain ever did, particularly in rural areas where Ae. albopictus predominates. Intergenotypic genetic differences were found at E1, E2, and nsP3 sites previously reported to be determinants of host adaptability in alphaviruses. Transmission of CHIKV in humans is influenced by virus strain and vector species, which has implications for regions with more than one circulating CHIKV genotype and Aedes species.

  17. Genotypic character relationship and phenotypic path coefficient analysis in chili pepper genotypes grown under tropical condition.

    Science.gov (United States)

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Oladosu, Yusuff; Kashiani, Pedram

    2017-03-01

    Studies on genotypic and phenotypic correlations among characters of crop plants are useful in planning, evaluating and setting selection criteria for the desired characters in a breeding program. The present study aimed to estimate the phenotypic correlation coefficients among yield and yield attributed characters and to work out the direct and indirect effects of yield-related characters on yield per plant using path coefficient analysis. Twenty-six genotypes of chili pepper were laid out in a randomized complete block design with three replications. Yield per plant showed positive and highly significant (P ≤ 0.01) correlations with most of the characters studied at both the phenotypic and genotypic levels. By contrast, disease incidence and days to flowering showed a significant negative association with yield. Fruit weight and number of fruits exerted positive direct effect on yield and also had a positive and significant (P ≤ 0.01) correlation with yield per plant. However, fruit length showed a low negative direct effect with a strong and positive indirect effect through fruit weight on yield and had a positive and significant association with yield. Longer fruits, heavy fruits and a high number of fruits are variables that are related to higher yields of chili pepper under tropical conditions and hence could be used as a reliable indicator in indirect selection for yield. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  18. 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.

  19. The influence of temperature on photosynthesis of different tomato genotypes

    NARCIS (Netherlands)

    Gosiewski, W.; Nilwik, H.J.M.; Bierhuizen, J.F.

    1982-01-01

    Net photosynthesis and dark respiration from whole plants of various tomato genotypes were measured in a closed system. At low irradiance (27 W m−2) and low external CO2 concentration (550 mg m−3), net photosynthesis of 10 genotypes was found to vary between 0.122 and 0.209 mg CO2 m−2 s−1. Correlati

  20. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  1. Reaction of Drought Tolerant Soybean Genotypes to Macrophomina phaseolina

    Science.gov (United States)

    Charcoal rot caused by Macrophomina phaseolina is a common disease of soybean, and resistant genotypes are not available. Level of soybean genotype resistance and susceptibility to M. phaseolina is most frequently measured by determining colony forming units of M. phaseolina/g root, but using this ...

  2. Paternity testing and delivering trait-predictive genotypic data

    Science.gov (United States)

    In the RosBREED project, the Genotyping Team (Team Leader: Nahla Bassil) leads the effort to obtain DNA data needed to enable marker-assisted breeding for critical fruit quality traits. These data are obtained from reference genotypes of apple, peach, cherry and strawberry carefully chosen to repres...

  3. 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....

  4. Clusters of incompatible genotypes evolve with limited dispersal

    Science.gov (United States)

    Erin L. Landguth; Norman A. Johnson; Samuel A. Cushman

    2015-01-01

    Theoretical and empirical studies have shown heterogeneous selection to be the primary driver for the evolution of reproductively isolated genotypes in the absence of geographic barriers. Here, we ask whether limited dispersal alone can lead to the evolution of reproductively isolated genotypes despite the absence of any geographic barriers or heterogeneous...

  5. Protein profiles and immunoreactivities of Acanthamoeba morphological groups and genotypes.

    Science.gov (United States)

    Pumidonming, Wilawan; Koehsler, Martina; Leitsch, David; Walochnik, Julia

    2014-11-01

    Acanthamoeba is a free-living protozoan found in a wide variety of habitats. A classification of Acanthamoeba into currently eighteen genotypes (T1-T18) has been established, however, data on differences between genotypes on the protein level are scarce. The aim of this study was to compare protein and immunoreactivity profiles of Acanthamoeba genotypes. Thirteen strains, both clinical and non-clinical, from genotypes T4, T5, T6, T7, T9, T11 and T12, representing three morphological groups, were investigated for their protein profiles and IgG, IgM and IgA immunoreactivities. It was shown that protein and immunoreactivity profiles of Acanthamoeba genotypes T4, T5, T6, T7, T9, T11 and T12 are clearly distinct from each other, but the banding patterns correlate to the morphological groups. Normal human sera revealed anti-Acanthamoeba antibodies against isolates of all investigated genotypes, interestingly, however only very weak IgM and virtually no IgA immunoreactivity with T7 and T9, both representing morphological group I. The strongest IgG, IgM and IgA immunoreactivities were observed for genotypes T4, T5 and T6. Differences of both, protein and immunological patterns, between cytopathic and non-cytopathic strains, particularly within genotype T4, were not at the level of banding patterns, but rather in expression levels.

  6. compensatory and susceptive responses of cowpea genotypes to ...

    African Journals Online (AJOL)

    User

    ABSTRACT. The aim of the study was to estimate yield loss to10 selected genotypes of cowpea as a result of ... Aphid's infestation period for studies in susceptive response in medium to .... The dry grain and biomass loss/gain due to ... Mean Grain weight (±SE) and Dry biomass (±SE) of cowpea genotypes on no infesta-.

  7. Characterization of cassava starch attributes of different genotypes

    NARCIS (Netherlands)

    Anggraini, V.; Sudarmonowati, E.; Hartati, N.Sri.; Suurs, L.C.J.M.; Visser, R.G.F.

    2009-01-01

    The genetic variation of starch of Indonesian cassava genotypes with various morphological characteristics of roots and eco-geographical origin was characterized and compared. The morphological characteristics of the roots of 71 collected cassava genotypes were classified into yellow and white for

  8. Breeding of a Tomato Genotype Readily Accessible to Genetic Manipulation

    NARCIS (Netherlands)

    Koornneef, Maarten; Hanhart, Corrie; Jongsma, Maarten; Toma, Ingrid; Weide, Rob; Zabel, Pim; Hille, Jacques

    1986-01-01

    A tomato genotype, superior in regenerating plants from cell cultures, was obtained by transferring regeneration capacity from Lycopersicon peruvianum into L. esculentum by classical breeding. This genotype, MsK93, greatly facilitates genetic manipulation of tomato, as was demonstrated by successful

  9. Caffeoylquinic Acids in Storage Roots of Sixteen Sweetpotato Genotypes

    Science.gov (United States)

    The contents of chlorogenic acid and the 3,4-, 3,5- and 4,5- isomers of dicaffeoylquinic acid (DCQA) in the storage root tissues of sixteen sweetpotato genotypes were determined. Averaged over genotypes, the contents of the four compounds were highest in the cortex, intermediate in the stele and lo...

  10. MLVA genotyping of human Brucella isolates from Peru

    NARCIS (Netherlands)

    H.L. Smits; B. Espinosa; R. Castillo; E. Hall; A. Guillen; M. Zevaleta; R.H. Gilman; P. Melendez; C. Guerra; A. Draeger; A. Broglia; K. Nöckler

    2009-01-01

    Recent human Brucella melitensis isolates from Peru were genotyped by multiple locus variable number repeat analysis. All 24 isolates originated from hospitalized patients living in the central part of Peru and consisted of six genomic groups comprising two to four isolates and nine unique genotypes

  11. Regional selection of hybrid Nacional cacao genotypes in Coastal Ecuador

    Science.gov (United States)

    Recent international demand for “nacional” flavour cacao has increased the need for local cacao producers in Ecuador to use high-yielding “nacional” hybrid genotypes. The relative potential of cacao genotypes over various environments needs to be assessed prior to final selection of potential candid...

  12. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke

    DEFF Research Database (Denmark)

    Khan, Tauseef A; Shah, Tina; Prieto, David;

    2013-01-01

    At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less...

  13. 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

  14. The Association of Il28b Genotype with the Histological Features of Chronic Hepatitis C Is HCV Genotype Dependent

    Directory of Open Access Journals (Sweden)

    Roberta D'Ambrosio

    2014-04-01

    Full Text Available The interleukin 28B (IL28B rs12979860 polymorphism is associated with treatment outcome in hepatitis C virus (HCV genotype 1 and 4 patients. Its association with the histological features of chronic hepatitis C and disease severity needs further clarifications. To assess the correlation between IL28B genotype, HCV genotype and liver biopsy findings in untreated patients. Materials and Methods: Pre-treatment liver biopsies from 335 HCV Caucasian patients (59% males, age 50 years enrolled in the MIST study were staged for fibrosis and inflammation according to the METAVIR and the Ishak scoring systems; steatosis was dichotomized as <5% or ≥5%. IL28B was typed by Taqman Single Nucleotide Polymorphism (SNP genotyping assay. HCV genotype was 1 in 151 (45%, 2 in 99 (30%, 3 in 50 (15% and 4 in 35 (10% patients. IL28B genotype was CC in 117 (34%, CT in 166 (49% and TT in 52 (15%. At univariate analysis, the IL28B CC genotype was associated with severe portal inflammation in HCV-1 patients (CC vs. CT/TT: 86% vs. 63%, p = 0.005, severe lobular inflammation in HCV-2 patients (CC vs. CT/TT: 44% vs. 23%, p = 0.03, and less fatty infiltration in HCV-1 patients (CC vs. CT/TT: 72% vs. 51%, p = 0.02. Despite the lack of any association between IL28B and fibrosis stage, in HCV-3 patients IL28B CC correlated with METAVIR F3-F4 (CC vs. CT/TT: 74% vs. 26%, p = 0.05. At multivariate analysis, the genotype CC remained associated with severe portal inflammation in HCV-1, only (Odds Ratio (OR: 95% Confidence Interval (CI: 3.24 (1.23–8.51. IL28B genotype is associated with the histological features of chronic hepatitis C in a HCV genotype dependent manner, with CC genotype being independently associated with severe portal inflammation.

  15. Distribution study of Chlamydia trachomatis genotypes in symptomatic patients in Buenos Aires, Argentina: association between genotype E and neonatal conjunctivitis

    Directory of Open Access Journals (Sweden)

    Corominas Ana I

    2010-02-01

    Full Text Available Abstract Background Chlamydia trachomatis infections are the most prevalent sexually transmitted bacterial infections in the world. There is scarce data available referring to the distribution of C. trachomatis genotypes in Argentina. The aim of this study was to identify the genotypes of C. trachomatis circulating in the metropolitan area of Buenos Aires (Argentina associated with ophthalmia neonatorum and genital infections. Findings From 2001 to 2006, 199 positive samples for C. trachomatis infection from symptomatic adult patients and neonates with ophthalmia neonatorum from two public hospitals were studied. C. trachomatis genotypes were determined by PCR-RFLP of an ompA fragment. Genotype E was the most prevalent regardless of the sample origin (46.3% 57/123 in adults and 72.4% 55/76 in neonates, followed by genotype D (19.5% 24/123 and F (14.6% 18/123 in adults, and G (9.2% 7/76 and D (7.9% 6/76 in neonates. We detected a significantly higher frequency of genotype E (p ophthalmia neonatorum than in genital specimens. Genotype D was associated with genital localization (p Conclusion We found a particularly increased frequency of C. trachomatis genotype E in neonatal conjunctivitis, which may indicate an epidemiological association between this genotype and the newborn population. The present study also contributed to increase the knowledge on genotype distribution of Chlamydia trachomatis in symptomatic adult patients in Buenos Aires, Argentina, in which genotypes E, D and F were the predominant ones.

  16. Silhouette scores for assessment of SNP genotype clusters

    Directory of Open Access Journals (Sweden)

    Jonsson Mats

    2005-03-01

    Full Text Available Abstract Background High-throughput genotyping of single nucleotide polymorphisms (SNPs generates large amounts of data. In many SNP genotyping assays, the genotype assignment is based on scatter plots of signals corresponding to the two SNP alleles. In a robust assay the three clusters that define the genotypes are well separated and the distances between the data points within a cluster are short. "Silhouettes" is a graphical aid for interpretation and validation of data clusters that provides a measure of how well a data point was classified when it was assigned to a cluster. Thus "Silhouettes" can potentially be used as a quality measure for SNP genotyping results and for objective comparison of the performance of SNP assays at different circumstances. Results We created a program (ClusterA for calculating "Silhouette scores", and applied it to assess the quality of SNP genotype clusters obtained by single nucleotide primer extension ("minisequencing" in the Tag-microarray format. A Silhouette score condenses the quality of the genotype assignment for each SNP assay into a single numeric value, which ranges from 1.0, when the genotype assignment is unequivocal, down to -1.0, when the genotype assignment has been arbitrary. In the present study we applied Silhouette scores to compare the performance of four DNA polymerases in our minisequencing system by analyzing 26 SNPs in both DNA polarities in 16 DNA samples. We found Silhouettes to provide a relevant measure for the quality of SNP assays at different reaction conditions, illustrated by the four DNA polymerases here. According to our result, the genotypes can be unequivocally assigned without manual inspection when the Silhouette score for a SNP assay is > 0.65. All four DNA polymerases performed satisfactorily in our Tag-array minisequencing system. Conclusion "Silhouette scores" for assessing the quality of SNP genotyping clusters is convenient for evaluating the quality of SNP genotype

  17. SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

    Directory of Open Access Journals (Sweden)

    Stephen W. Erickson

    2016-07-01

    Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

  18. Effect of genotype on sugar beet yield and quality

    Directory of Open Access Journals (Sweden)

    Nenadić N.

    2003-01-01

    Full Text Available The effect of a considerable number of both domestic and foreign sugar beet genotypes on root yield and quality was investigated. The data demonstrated the most favorable results of some genotypes for root yield and sugar content. Trials were conducted on rhizomania infested soil, thus tolerant genotypes were used. Susceptible cultivars represented the control. In the trial root yield was high and sugar content low. On average, in the genotypes tested, root yield varied from 73.98 to 93.30 t/ha and sugar content from 11.90 to 13.36%, depending on weather conditions. Root yield of the genotypes investigated varied from 30.61 to 112.64 t/ha and sugar content from 10.60 to 14.20%. The Swedish cultivar Dorotea (tolerant to both rhizomania and cercospora was the most yielding. The least yielding (susceptible to both rhizomania and cercospora was the domestic cultivar Dana.

  19. Genetic relationships among some hawthorn (Crataegus spp.) species and genotypes.

    Science.gov (United States)

    Yilmaz, Kadir Ugurtan; Yanar, Makbule; Ercisli, Sezai; Sahiner, Hatice; Taskin, Tuncer; Zengin, Yasar

    2010-10-01

    The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus x bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard's index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

  20. HCV prevalence and predominant genotype in IV drug users

    Directory of Open Access Journals (Sweden)

    Asad Andalibalshohada

    2014-07-01

    Full Text Available Hepatitis C virus (HCV causes 308000 deaths due to liver cancer and 758000 deaths due to cirrhosis every year. Almost 170 million people have HCV infection around the world. Information regarding this virus helps us to determine the prevalence of other hepatitis C genotypes in population, especially in intravenous drug users. It is assumed that some genotypes are more common in certain areas or groups of people. A recent study strongly confirms the central role of injecting network traits, not only as a transmission factor but also as a predictor of HCV genotype and phylogenetic determination in different communities. Hepatitis C genotypes and subtypes have different prevalence considering the country. Risk factors such as transfusion, hemodialysis, root of acquisition and etc, are detected in intravenous drug users. Several conducted studies have investigated the prevalence, risk factors, and predominance of HCV genotypes infection in different parts of Iran.

  1. Micropropagation of six Paulownia genotypes through tissue culture

    Directory of Open Access Journals (Sweden)

    Lydia Shtereva

    2014-12-01

    Full Text Available We investigated the effect of genotype and culture medium on the in vitro germination and development of plantlets from seeds of 6 different Paulownia genotypes (P. tomentosa, hybrid lines P. tomentosa P. fortunei (Mega, Ganter and Caroline, P. elongata and hybrid line P. elongata P. fortunei. Nodal and shoot tip explants were used for micropropagation of Paulownia genotypes by manipulating plant growth regulators. The highest germination percentage for all genotypes was obtained for seeds inoculated on medium supplemented with 50 mg*L GA3 (MSG2. On Thidiazuron containing media, the explants of hybrid line P. elongata P. fortunei exhibited the highest frequency of axillary shoot proliferation following by P. tomentosa P. fortunei. The results are discussed with the perspective of applying an improved protocol for in vitro seed germination and plantlet formation in several economically valuable Paulownia genotypes.

  2. [Comparison of two spectral mixture analysis models].

    Science.gov (United States)

    Wang, Qin-Jun; Lin, Qi-Zhong; Li, Ming-Xiao; Wang, Li-Ming

    2009-10-01

    A spectral mixture analysis experiment was designed to compare the spectral unmixing effects of linear spectral mixture analysis (LSMA) and constraint linear spectral mixture analysis (CLSMA). In the experiment, red, green, blue and yellow colors were printed on a coarse album as four end members. Thirty nine mixed samples were made according to each end member's different percent in one pixel. Then, field spectrometer was located on the top of the mixed samples' center to measure spectrum one by one. Inversion percent of each end member in the pixel was extracted using LSMA and CLSMA models. Finally, normalized mean squared error was calculated between inversion and real percent to compare the two models' effects on spectral unmixing. Results from experiment showed that the total error of LSMA was 0.30087 and that of CLSMA was 0.37552 when using all bands in the spectrum. Therefore, LSMA was 0.075 less than that of CLSMA when the whole bands of four end members' spectra were used. On the other hand, the total error of LSMA was 0.28095 and that of CLSMA was 0.29805 after band selection. So, LSMA was 0.017 less than that of CLSMA when bands selection was performed. Therefore, whether all or selected bands were used, the accuracy of LSMA was better than that of CLSMA because during the process of spectrum measurement, errors caused by instrument or human were introduced into the model, leading to that the measured data could not mean the strict requirement of CLSMA and therefore reduced its accuracy: Furthermore, the total error of LSMA using selected bands was 0.02 less than that using the whole bands. The total error of CLSMA using selected bands was 0.077 less than that using the whole bands. So, in the same model, spectral unmixing using selected bands to reduce the correlation of end members' spectra was superior to that using the whole bands.

  3. Flows and chemical reactions in heterogeneous mixtures

    CERN Document Server

    Prud'homme, Roger

    2014-01-01

    This book - a sequel of previous publications 'Flows and Chemical Reactions' and 'Chemical Reactions in Flows and Homogeneous Mixtures' - is devoted to flows with chemical reactions in heterogeneous environments.  Heterogeneous media in this volume include interfaces and lines. They may be the site of radiation. Each type of flow is the subject of a chapter in this volume. We consider first, in Chapter 1, the question of the generation of environments biphasic individuals: dusty gas, mist, bubble flow.  Chapter 2 is devoted to the study at the mesoscopic scale: particle-fluid exchange of mom

  4. Temperature relaxation in dense plasma mixtures

    Science.gov (United States)

    Faussurier, Gérald; Blancard, Christophe

    2016-09-01

    We present a model to calculate temperature-relaxation rates in dense plasma mixtures. The electron-ion relaxation rates are calculated using an average-atom model and the ion-ion relaxation rates by the Landau-Spitzer approach. This method allows the study of the temperature relaxation in many-temperature electron-ion and ion-ion systems such as those encountered in inertial confinement fusion simulations. It is of interest for general nonequilibrium thermodynamics dealing with energy flows between various systems and should find broad use in present high energy density experiments.

  5. Gaussian mixture model of heart rate variability.

    Directory of Open Access Journals (Sweden)

    Tommaso Costa

    Full Text Available Heart rate variability (HRV is an important measure of sympathetic and parasympathetic functions of the autonomic nervous system and a key indicator of cardiovascular condition. This paper proposes a novel method to investigate HRV, namely by modelling it as a linear combination of Gaussians. Results show that three Gaussians are enough to describe the stationary statistics of heart variability and to provide a straightforward interpretation of the HRV power spectrum. Comparisons have been made also with synthetic data generated from different physiologically based models showing the plausibility of the Gaussian mixture parameters.

  6. Spectrometric mixture analysis: An unexpected wrinkle

    Indian Academy of Sciences (India)

    Robert De Levie

    2009-09-01

    The spectrometric analysis of a mixture of two chemically and spectroscopically similar compounds is illustrated for the simultaneous spectrometric determination of caffeine and theobromine, the primary stimulants in coffee and tea, based on their ultraviolet absorbances. Their analysis indicates that such measurements may need an unexpectedly high precision to yield accurate answers, because of an artifact of inverse cancellation, in which a small noise or drift signal is misinterpreted in terms of a concentration difference. The computed sum of the concentrations is not affected.

  7. Bayesian mixture models for partially verified data

    DEFF Research Database (Denmark)

    Kostoulas, Polychronis; Browne, William J.; Nielsen, Søren Saxmose;

    2013-01-01

    for some individuals, in order to minimize this loss in the discriminatory power. The distribution of the continuous antibody response against MAP has been obtained for healthy, MAP-infected and MAP-infectious cows of different age groups. The overall power of the milk-ELISA to discriminate between healthy......Bayesian mixture models can be used to discriminate between the distributions of continuous test responses for different infection stages. These models are particularly useful in case of chronic infections with a long latent period, like Mycobacterium avium subsp. paratuberculosis (MAP) infection...

  8. Two-microphone Separation of Speech Mixtures

    DEFF Research Database (Denmark)

    2006-01-01

    of Speech Mixtures," 2006, submited for journal publication. See also, [2] Michael Syskind Pedersen, DeLiang Wang, Jan Larsen and Ulrik Kjems: "Overcomplete Blind Source Separation by Combining ICA and Binary Time-Frequency Masking," in proceedings of IEEE International workshop on Machine Learning......In this demonstration we show the separation of 3-7 mixed speech sources based on information from two microphones. Separation with background noise is demonstrated too. The algorithms are described in 1] Michael Syskind Pedersen, DeLiang Wang, Jan Larsen and Ulrik Kjems: "Two-microphone Separation...

  9. Video compressive sensing using Gaussian mixture models.

    Science.gov (United States)

    Yang, Jianbo; Yuan, Xin; Liao, Xuejun; Llull, Patrick; Brady, David J; Sapiro, Guillermo; Carin, Lawrence

    2014-11-01

    A Gaussian mixture model (GMM)-based algorithm is proposed for video reconstruction from temporally compressed video measurements. The GMM is used to model spatio-temporal video patches, and the reconstruction can be efficiently computed based on analytic expressions. The GMM-based inversion method benefits from online adaptive learning and parallel computation. We demonstrate the efficacy of the proposed inversion method with videos reconstructed from simulated compressive video measurements, and from a real compressive video camera. We also use the GMM as a tool to investigate adaptive video compressive sensing, i.e., adaptive rate of temporal compression.

  10. Molecular weight scaling in critical polymer mixtures

    DEFF Research Database (Denmark)

    Gehlsen, M.D.; Rosedale, J.R.; Bates, F.S.

    1992-01-01

    , DELTA-X(D), and molecular weight by small-angle neutron scattering. The critical point for demixing was determined to scale as chi(eff,c) is similar to N(-delta) with delta = 1.01 +/- 0.05, where N is the degree of polymerization. This result confirms the mean-field prediction of Flory and Huggins.......Symmetric binary mixtures of partially deuterated polymers were prepared at the critical composition. The segment-segment interaction energy parameter chi(eff) was varied by adjusting the difference in deuterium content DELTA-X(D) between species. Chi(eff) was measured as a function of temperature...

  11. Comparison of methods for analysis of selective genotyping survival data

    Directory of Open Access Journals (Sweden)

    Dekkers Jack CM

    2006-11-01

    Full Text Available Abstract Survival traits and selective genotyping datasets are typically not normally distributed, thus common models used to identify QTL may not be statistically appropriate for their analysis. The objective of the present study was to compare models for identification of QTL associated with survival traits, in particular when combined with selective genotyping. Data were simulated to model the survival distribution of a population of chickens challenged with Marek disease virus. Cox proportional hazards (CPH, linear regression (LR, and Weibull models were compared for their appropriateness to analyze the data, ability to identify associations of marker alleles with survival, and estimation of effects when all individuals were genotyped (full genotyping and when selective genotyping was used. Little difference in power was found between the CPH and the LR model for low censoring cases for both full and selective genotyping. The simulated data were not transformed to follow a Weibull distribution and, as a result, the Weibull model generally resulted in less power than the other two models and overestimated effects. Effect estimates from LR and CPH were unbiased when all individuals were genotyped, but overestimated when selective genotyping was used. Thus, LR is preferred for analyzing survival data when the amount of censoring is low because of ease of implementation and interpretation. Including phenotypic data of non-genotyped individuals in selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate, and therefore the CPH model is preferred for this scenario, although transformation of the data may also make the Weibull model appropriate for this case. The results from the research presented herein are directly applicable to interval mapping analyses.

  12. An equiratio mixture model for non-additive components : a case study for aspartame/acesulfame-K mixtures

    NARCIS (Netherlands)

    Schifferstein, H.N.J.

    1996-01-01

    The Equiratio Mixture Model predicts the psychophysical function for an equiratio mixture type on the basis of the psychophysical functions for the unmixed components. The model reliably estimates the sweetness of mixtures of sugars and sugar-alchohols, but is unable to predict intensity for asparta

  13. Prediction of saturated liquid enthalpy of refrigerant mixtures

    Institute of Scientific and Technical Information of China (English)

    CHEN ZeShao; CHEN JianXin; HU Peng

    2007-01-01

    New corresponding temperature and corresponding enthalpy of refrigerant mixtures were defined. The relationship between saturated liquid corresponding enthalpy and corresponding temperature of refrigerant mixtures accorded with that of pure components. The characteristic parameters of saturated liquid enthalpy difference of refrigerant mixtures were calculated by three methods according to the different application conditions. The generalized equation of saturated liquid enthalpy of refrigerant mixtures was presented. The calculated values were compared with the values in literature for five ternary and binary refrigerant mixtures, namely R404A, R407A, R407B, R32/R134a, and R410A. The overall average absolute deviation was less than 1.0%.

  14. Uniform designs for mixture-amount experiments and for mixture experiments under order restrictions

    Institute of Scientific and Technical Information of China (English)

    田国梁; 方开泰

    1999-01-01

    With order statistics of the uniform distribution on [0, 1], exponential and beta distributions, a stochastic representation is obtained for the uniform distribution over various domains, where A-type domains are closely associated with reliability growth analysis, order restricted statistical inference and isotonic regression theory, V-type domains are connected with the mixture-amount experiments, and T-type domains are well related to mixture experiments. With these stochastic representations, the corresponding uniform distribution and number-theoretic nets can be generated. This approach seems to be new and is called order statistics method. Some examples on reliability growth analysis and experimental design are presented.

  15. Genetic diversity of the genotype VII Newcastle disease virus: identification of a novel VIIj sub-genotype.

    Science.gov (United States)

    Xue, Cong; Cong, Yanlong; Yin, Renfu; Sun, Yixue; Ding, Chan; Yu, Shengqing; Liu, Xiufan; Hu, Shunlin; Qian, Jing; Yuan, Qianliang; Yang, Mingxi; Wang, Chunfeng; Ding, Zhuang

    2017-02-01

    Newcastle disease (ND) is a highly contagious disease of poultry caused by Newcastle disease virus (NDV). Multiple genotypes of NDV have been circulating worldwide and NDV is continuously evolving, resulting into more diversity. Of multiple viral genotypes, VII is particularly important given that it had been associated with most recent ND outbreaks worldwide. In this study, an epidemiological investigation performed in northeastern China during 2014-2015 showed that 11 genotype VII isolates amounted to 55 percent in a total number of NDV isolates. Therefore, to evaluate the genetic diversity worldwide and epidemiological distribution in China of genotype VII NDV, a phylogenetic analysis based on the 1255 complete F gene sequences showed that VII is the most predominant genotype worldwide. A further detailed characterization on genotype VII was conducted based on the 477 complete F gene sequences from 11 isolates and 466 reference viruses available in GenBank. The results demonstrated that VII can be further divided into 8 sub-genotypes (VIIb, VIId-VIIj), indicating its complex genetic diversity. It is worthy of note that the isolation rate of VIIj is increasing recently. It emphasizes the necessity to pay close attention to the epidemiological dynamic of genotype VII NDV and highlights the importance of vaccination program.

  16. Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification

    Science.gov (United States)

    Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study in 2006-2007 demonstrated a predominant EU genotype ...

  17. Changing genotypes of cholera toxin (CT) of Vibrio cholerae O139 in Bangladesh and description of three new CT genotypes.

    Science.gov (United States)

    Bhuiyan, Nurul A; Nusrin, Suraia; Alam, Munirul; Morita, Masatomo; Watanabe, Haruo; Ramamurthy, Thandavarayan; Cravioto, Alejandro; Nair, Gopinath Balakrish

    2009-11-01

    We determined the genotype of cholera toxin by amplifying and sequencing the B-subunit in a sequential collection of 90 strains of Vibrio cholerae O139 isolated over the past 13 years since its first description in 1992. Representative strains isolated during 1993-1997 harboured ctxB of El Tor type (genotype 3). Twenty-six strains isolated during 1999, 2001, 2005 and three strains isolated in 1998, 2000 and 2002 were identified to belong to new ctxB genotypes 4 and 5, respectively. Genotype 5 was similar to genotype 1 except at position 28 (D-->A). The genotype 6 was similar to genotype 4 except at position 34 (H-->P). The implication of switch in terms of function of the toxin and its impact on human disease is unclear. How this change has influenced their prevalence relative to that of V. cholerae O1 in human infection is also not clear. The other common virulence gene clusters including the Vibrio pathogenicity island-1, Vibrio seventh pandemic island (VSP)-I and VSP-II of V. cholerae O139 did not show any remarkable difference from that of the O1 El Tor strains. Overall, the majority of the O139 strains tested in this study were similar to the El Tor strains but had altered ctxB genotype. This change and the impact that it causes to the epidemiology of cholera caused by O139 should be closely monitored.

  18. Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data

    Directory of Open Access Journals (Sweden)

    Nettelblad Carl

    2012-10-01

    Full Text Available Abstract Background In many contexts, pedigrees for individuals are known even though not all individuals have been fully genotyped. In one extreme case, the genotypes for a set of full siblings are known, with no knowledge of parental genotypes. We propose a method for inferring phased haplotypes and genotypes for all individuals, even those with missing data, in such pedigrees, allowing a multitude of classic and recent methods for linkage and genome analysis to be used more efficiently. Results By artificially removing the founder generation genotype data from a well-studied simulated dataset, the quality of reconstructed genotypes in that generation can be verified. For the full structure of repeated matings with 15 offspring per mating, 10 dams per sire, 99.89%of all founder markers were phased correctly, given only the unphased genotypes for offspring. The accuracy was reduced only slightly, to 99.51%, when introducing a 2% error rate in offspring genotypes. When reduced to only 5 full-sib offspring in a single sire-dam mating, the corresponding percentage is 92.62%, which compares favorably with 89.28%from the leading Merlin package. Furthermore, Merlin is unable to handle more than approximately 10 sibs, as the number of states tracked rises exponentially with family size, while our approach has no such limit and handles 150 half-sibs with ease in our experiments. Conclusions Our method is able to reconstruct genotypes for parents when genotype data is only available for offspring individuals, as well as haplotypes for all individuals. Compared to the Merlin package, we can handle larger pedigrees and produce superior results, mainly due to the fact that Merlin uses the Viterbi algorithm on the state space to infer the genotype sequence. Tracking of haplotype and allele origin can be used in any application where the marker set does not directly influence genotype variation influencing traits. Inference of genotypes can also reduce the

  19. 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...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family....... The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL...

  20. Investigation of Adding Proportion of RAP in Recycled Asphalt Mixture

    Directory of Open Access Journals (Sweden)

    Cao He

    2016-01-01

    Full Text Available According to the relationship between gradation and proportion of Reclaimed Asphalt Pavement (RAP and design gradation of recycled mixture, the authors discussed the influence of proportion of RAP on gradation adjustment of recycled mixture. And then, recycled mixture with 0%, 30%, 50%, 70% of RAP were made, and Influence of proportion of RAP on high and low temperature performance, water stability and anti-aging performance of recycled mixture were discussed. The results and analysis indicate that gradation of recycled mixture would not be adjusted to aiming gradation if proportion of RAP was too big. With the increase of proportion of RAP, high temperature performance and anti-aging performance of recycled mixture enhanced, but low temperature performance and water stability decayed sharply. In practical application, reasonable proportion of RAP should be determined according to gradation, performance demand and economy of recycled mixture.

  1. Systems and methods for removing components of a gas mixture

    Science.gov (United States)

    None

    2016-09-06

    A system for removing components of a gaseous mixture is provided comprising: a reactor fluid containing vessel having conduits extending therefrom, aqueous fluid within the reactor, the fluid containing a ligand and a metal, and at least one reactive surface within the vessel coupled to a power source. A method for removing a component from a gaseous mixture is provided comprising exposing the gaseous mixture to a fluid containing a ligand and a reactive metal, the exposing chemically binding the component of the gaseous mixture to the ligand. A method of capturing a component of a gaseous mixture is provided comprising: exposing the gaseous mixture to a fluid containing a ligand and a reactive metal, the exposing chemically binding the component of the gaseous mixture to the ligand, altering the oxidation state of the metal, the altering unbinding the component from the ligand, and capturing the component.

  2. Health and environmental effects of complex chemical mixtures: proceedings

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    The Office of Health and Environmental Research (OHER) of the Department of Energy supports a broad long-term research program on human health and environmental effects from potential exposure to energy-related complex chemical mixtures. The program seeks basic mechanistic data on the effects of complex mixtures at the cellular, molecular, and whole animal levels to aid in predicting human health effects and seeks ecological data on biological and physical transformations in the mixtures, concentrations of the mixtures in various compartments of the environment, and potential routes for human exposure to these mixtures (e.g., food chain). On June 17-18, 1985, OHER held its First Annual Technical Meeting on the Complex Chemical Mixtures Program in Chicago, IL. The primary purpose of the meeting was to enable principal investigators to report the research status and accomplishments of ongoing complex chemical mixture studies supported by OHER. To help focus future research directions round table discussions were conducted.

  3. Comparison of two PCR-based human papillomavirus genotyping methods.

    Science.gov (United States)

    Castle, Philip E; Porras, Carolina; Quint, Wim G; Rodriguez, Ana Cecilia; Schiffman, Mark; Gravitt, Patti E; González, Paula; Katki, Hormuzd A; Silva, Sandra; Freer, Enrique; Van Doorn, Leen-Jan; Jiménez, Silvia; Herrero, Rolando; Hildesheim, Allan

    2008-10-01

    We compared two consensus primer PCR human papillomavirus (HPV) genotyping methods for the detection of individual HPV genotypes and carcinogenic HPV genotypes as a group, using a stratified sample of enrollment cervical specimens from sexually active women participating in the NCI/Costa Rica HPV16/18 Vaccine Efficacy Trial. For the SPF(10) method, DNA was extracted from 0.1% of the cervical specimen by using a MagNA Pure LC instrument, a 65-bp region of the HPV L1 gene was targeted for PCR amplification by using SPF(10) primers, and 25 genotypes were detected by reverse-line blot hybridization of the amplicons. For the Linear Array (LA) method, DNA was extracted from 0.5% of the cervical specimen by using an MDx robot, a 450-bp region of the HPV L1 gene was targeted for PCR amplification by using PGMY09/11 L1 primers, and 37 genotypes were detected by reverse-line blot hybridization of the amplicons. Specimens (n = 1,427) for testing by the LA method were randomly selected from strata defined on the basis of enrollment test results from the SPF(10) method, cytology, and Hybrid Capture 2. LA results were extrapolated to the trial cohort (n = 5,659). The LA and SPF(10) methods detected 21 genotypes in common; HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, and -73 were considered the carcinogenic HPV genotypes. There was no difference in the overall results for grouped detection of carcinogenic HPV by the SPF(10) and LA methods (35.3% versus 35.9%, respectively; P = 0.5), with a 91.8% overall agreement and a kappa value of 0.82. In comparisons of individual HPV genotypes, the LA method detected significantly more HPV16, HPV18, HPV39, HPV58, HPV59, HPV66, and HPV68/73 and less HPV31 and HPV52 than the SPF(10) method; inclusion of genotype-specific testing for HPV16 and HPV18 for those specimens testing positive for HPV by the SPF(10) method but for which no individual HPV genotype was detected abrogated any differences between the LA and SPF

  4. Effect of Co-Inoculation with Mycorrhiza and Rhizobia on the Nodule Trehalose Content of Different Bean Genotypes

    Science.gov (United States)

    Ballesteros-Almanza, L; Altamirano-Hernandez, J; Peña-Cabriales, J.J; Santoyo, G; Sanchez-Yañez, J.M; Valencia-Cantero, E; Macias-Rodriguez, L; Lopez-Bucio, J; Cardenas-Navarro, R; Farias-Rodriguez, R

    2010-01-01

    Studies on Rhizobium-legume symbiosis show that trehalose content in nodules under drought stress correlates positively with an increase in plant tolerance to this stress. Fewer reports describe trehalose accumulation in mycorrhiza where, in contrast with rhizobia, there is no flux of carbohydrates from the microsymbiont to the plant. However, the trehalose dynamics in the Mycorrhiza-Rhizobium-Legume tripartite symbiosis is unknown. The present study explores the role of this tripartite symbiosis in the trehalose content of nodules grown under contrasting moisture conditions. Three wild genotypes (P. filiformis, P. acutifolis and P. vulgaris) and two commercial genotypes of Phaseolus vulgaris (Pinto villa and Flor de Mayo) were used. Co-inoculation treatments were conducted with Glomus intraradices and a mixture of seven native rhizobial strains, and trehalose content was determined by GC/MS. The results showed a negative effect of mycorrhizal inoculation on nodule development, as mycorrhized plants showed fewer nodules and lower nodule dry weight compared to plants inoculated only with Rhizobium. Mycorrhizal colonization was also higher in plants inoculated only with Glomus as compared to plants co-inoculated with both microsymbionts. In regard to trehalose, co-inoculation negatively affects its accumulation in the nodules of each genotype tested. However, the correlation analysis showed a significantly positive correlation between mycorrhizal colonization and nodule trehalose content. PMID:21253462

  5. A simple mixture to enhance muscle transmittance

    Science.gov (United States)

    Oliveira, Luís; Lage, Armindo; Clemente, Manuel Pais; Tuchin, Valery V.

    2008-06-01

    Skeletal muscle is a fibrous tissue composed by muscle fibers and interstitial fluid. Due to this constitution, the muscle presents a non uniform refractive index profile that origins strong light scattering. One way to improve tissue transmittance is to reduce this refractive index mismatch by immersing the muscle in an optical clearing agent. As a consequence of such immersion tissue also suffers dehydration. The study of the optical clearing effect created by a simple mixture composed by ethanol, glycerol and distilled water has proven its effectiveness according to the variations observed in the parameters under study. The effect was characterized in terms of its magnitude, time duration and histological variations. The applied treatment has created a small reduction of the global sample refractive index that is justified by the long time rehydration caused by water in the immersing solution. From the reduction in sample pH we could also identify the dehydration process created in the sample. The immersion treatment has originated fiber bundle contraction and a spread distribution of the muscle fiber bundles inside. New studies with the mixture used, or with other combinations of its constituents might be interesting to perform with the objective to develop new clinical procedures.

  6. Non-equilibrium properties of hadronic mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Prakasch, Madappa (State Univ. of New York, Stony Brook, NY (United States). Physics Dept.); Prakasch, Manju (State Univ. of New York, Stony Brook, NY (United States). Physics Dept.); Venugopalan, R. (State Univ. of New York, Stony Brook, NY (United States). Physics Dept.); Welke, G. (Michigan State Univ., East Lansing, MI (United States). National Superconducting Cyclotron Lab.)

    1993-05-01

    The equilibration of hot hadronic matter is studied in the framework of relativistic kinetic theory. Various non-equilibrium properties of a mixture comprised of pions, kaons and nucleons are calculated in the dilute limit for small deviations from local thermal equilibrium. Interactions between these constituents are specified through the empirical phase shifts. The properties calculated include the relaxation/collision times, momentum and energy persistence ratios in elastic collisions, and transport properties such as the viscosity, the thermal conductivity, and the diffusion and thermal diffusion coefficients. The Chapman-Enskog formalism is extended to extract relaxation times associated with shear and heat flows, and drag and diffusion flows in a mixture. The equilibrium number concentration of the constituents is chosen to mimic those expected in the mid-rapidity interval of CERN and RHIC experiments. In this case, kaons and nucleons are found to equilibrate significantly more slowly than pions. These results shed new light on the influence of collective flow effects on the transverse momentum distributions of kaons and nucleons versus those of pions in ultra-relativistic nuclear collisions. (orig.)

  7. Spinodal Decomposition in Mixtures Containing Surfactants

    Science.gov (United States)

    Melenekvitz, J.

    1998-03-01

    Spinodal decomposition in mixtures containing two immiscible liquids (A and B) plus surfactant was investigated using a recently developed (J. Melenkevitz and S. H. Javadpour, J. Chem. Phys., 107, 623 (1997).) 3-component Ginzburg-Landau model. The time dependent Ginzburg-Landau (TDGL) equations governing the evolution of structure were numerically integrated in 2-dimensions. We found the growth rate of the average domain size, R(t), decreased with increasing surfactant concentration over a wide range of relative amounts of A and B. This can be attributed to the surfactant accumulating at the growing interface between the immiscible liquids, which leads to a reduction in the surface tension. At late times, the growth rate was noticeably altered when thermal fluctuations were added to the numerical simulations. In this case, power law behavior was observed for R(t) at late times, R(t) ~ t^α, with the exponent α decreasing as the amount of surfactant increased. The dynamics at early times were determined by linearizing the TDGL equations about a uniformly mixed state. The growth rate at ealry times was found to be strongly dependent on the model parameters describing the surfactant miscibility in A and B and the surfactant strength. Comparison with recent measurements on SBR / PB mixtures with added PB-SBR diblock copolymer will also be presented.

  8. A mixture approach to vagueness and ambiguity.

    Directory of Open Access Journals (Sweden)

    Steven Verheyen

    Full Text Available When asked to indicate which items from a set of candidates belong to a particular natural language category inter-individual differences occur: Individuals disagree which items should be considered category members. The premise of this paper is that these inter-individual differences in semantic categorization reflect both ambiguity and vagueness. Categorization differences are said to be due to ambiguity when individuals employ different criteria for categorization. For instance, individuals may disagree whether hiking or darts is the better example of sports because they emphasize respectively whether an activity is strenuous and whether rules apply. Categorization differences are said to be due to vagueness when individuals employ different cut-offs for separating members from non-members. For instance, the decision to include hiking in the sports category or not, may hinge on how strenuous different individuals require sports to be. This claim is supported by the application of a mixture model to categorization data for eight natural language categories. The mixture model can identify latent groups of categorizers who regard different items likely category members (i.e., ambiguity with categorizers within each of the groups differing in their propensity to provide membership responses (i.e., vagueness. The identified subgroups are shown to emphasize different sets of category attributes when making their categorization decisions.

  9. Predicting the toxicity of metal mixtures.

    Science.gov (United States)

    Balistrieri, Laurie S; Mebane, Christopher A

    2014-01-01

    The toxicity of single and multiple metal (Cd, Cu, Pb, and Zn) solutions to trout is predicted using an approach that combines calculations of: (1) solution speciation; (2) competition and accumulation of cations (H, Ca, Mg, Na, Cd, Cu, Pb, and Zn) on low abundance, high affinity and high abundance, low affinity biotic ligand sites; (3) a toxicity function that accounts for accumulation and potency of individual toxicants; and (4) biological response. The approach is evaluated by examining water composition from single metal toxicity tests of trout at 50% mortality, results of theoretical calculations of metal accumulation on fish gills and associated mortality for single, binary, ternary, and quaternary metal solutions, and predictions for a field site impacted by acid rock drainage. These evaluations indicate that toxicity of metal mixtures depends on the relative affinity and potency of toxicants for a given aquatic organism, suites of metals in the mixture, dissolved metal concentrations and ratios, and background solution composition (temperature, pH, and concentrations of major ions and dissolved organic carbon). A composite function that incorporates solution composition, affinity and competition of cations for two types of biotic ligand sites, and potencies of hydrogen and individual metals is proposed as a tool to evaluate potential toxicity of environmental solutions to trout.

  10. Transport and radiation in complex LTE mixtures

    Science.gov (United States)

    Janssen, Jesper; Peerenboom, Kim; Suijker, Jos; Gnybida, Mykhailo; van Dijk, Jan

    2014-10-01

    Complex LTE mixtures are for example encountered in re-entry, welding, spraying and lighting. These mixtures typically contain a rich chemistry in combination with large temperature gradients. LTE conditions are also interesting because they can aid in the validation of NLTE algorithms. An example is the calculation of transport properties. In this work a mercury free high intensity discharge lamp is considered. The investigation focusses on using salts like InI or SnI as a buffer species. By using these species a dominant background gas like mercury is no longer present. As a consequence the diffusion algorithms based on Fick's law are no longer applicable and the Stefan-Maxwell equations must be solved. This system of equations is modified with conservation rules to set a coldspot pressure for saturated species and enforce the mass dosage for unsaturated species. The radiative energy transport is taken into account by raytracing. Quantum mechanical simulations have been used to calculate the potential curves and the transition dipole moments for indium with iodine and tin with iodine. The results of these calculations have been used to predict the quasistatic broadening by iodine. The work was supported by the project SCHELP from the Belgium IWT (Project Number 110003) and the CATRENE SEEL Project (CA502).

  11. Foaming characteristics of refigerant/lubricant mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Goswami, D.Y.; Shah, D.O.; Jotshi, C.K.; Bhagwat, S.; Leung, M.; Gregory, A.

    1997-04-01

    The air-conditioning and refrigeration industry has moved to HFC refrigerants which have zero ozone depletion and low global warming potential due to regulations on CFC and HCFC refrigerants and concerns for the environment. The change in refrigerants has prompted the switch from mineral oil and alkylbenzene lubricants to polyolester-based lubricants. This change has also brought about a desire for lubricant, refrigerant and compressor manufacturers to understand the foaming properties of alternative refrigerant/ lubricant mixtures, as well as the mechanisms which affect these properties. The objectives of this investigation are to experimentally determine the foaming absorption and desorption rates of HFC and blended refrigerants in polyolester lubricant and to define the characteristics of the foam formed when the refrigerant leaves the refrigerant/ lubricant mixture after being exposed to a pressure drop. The refrigerants being examined include baseline refrigerants: CFC-12 (R-12) and HCFC-22 (R-22); alternative refrigerants: HFC-32 (R-32), R-125, R-134a, and R-143a; and blended refrigerants: R-404A, R-407C, and R-410A. The baseline refrigerants are tested with ISO 32 (Witco 3GS) and ISO 68 (4GS) mineral oils while the alternative and blended refrigerants are tested with two ISO 68 polyolesters (Witco SL68 and ICI RL68H).

  12. Optical properties of a heated cornstarch mixture

    Science.gov (United States)

    Vazquez-Landaverde, Pedro A.; Morales Sánchez, Eduardo; Huerta-Ruelas, Jorge A.

    2007-03-01

    In this study, the objective was to evaluate optical properties of a corn starch-water mixture as descriptors of its behavior under processing conditions. A solution of corn starch in water was prepared and heated from 25 to 85°C in a temperature-controlled optical cell. For the measurement of optical properties, a polarized laser beam modulated through a photoelastic modulator and an analyzer, was used as optical probe. It was possible to measure transmitted light, along with optical rotation. Optical measurements showed changes related to temperature dependent phenomena such as starch granule swelling and gelatinization, in the ranges 25 to 60°C, 60 to 85°C. Above 80°C transmission values were higher, due to the solution clarification caused by corn starch gelatinization. Regarding optical rotation, it was difficult to obtain reliable measurements at low temperatures due to the high turbidity of the system. However, once gel was formed at higher temperatures, optical rotation and light transmission increased. This study demonstrated that optical techniques are suitable for the study of the behavior of water-starch mixtures under processing conditions such as heating, revealing a promising future for the monitoring of such phenomena in the production line to lower costs and improve product quality.

  13. Thermodynamics of organic mixtures containing amines

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Juan Antonio [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain)]. E-mail: jagl@termo.uva.es; Mozo, Ismael [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain); Fuente, Isaias Garcia de la [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain); Cobos, Jose Carlos [G.E.T.E.F. Dpto Termodinamica y Fisica Aplicada, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47071 (Spain)

    2006-02-01

    Binary mixtures containing pyridine (PY), or 2-methylpyridine (2MPY) or 3-methylpyridine (3MPY) or 4-methylpyridine (4MPY) and an organic solvent as benzene, toluene, alkane, or 1-alkanol are investigated in the framework of DISQUAC. The corresponding interaction parameters are reported. The model describes accurately a whole set of thermodynamic properties: vapor-liquid equilibria (VLE), liquid-liquid equilibria (LLE), solid-liquid equilibria (SLE), molar excess Gibbs energies (G{sup E}), molar excess enthalpies (H{sup E}), molar excess heat capacities at constant pressure (C{sub P}{sup E}) and the concentration-concentration structure factor (S{sub CC}(0)). It is remarkable that DISQUAC correctly predicts the W-shaped curve of the C{sub P}{sup E} of the pyridine + n-hexadecane system. The model can be applied successfully to mixtures with strong positive or negative deviations from the Raoult's law. DISQUAC improves the theoretical results from UNIFAC (Dortmund version). The replacement of pyridine by a methylpyridine leads to a weakening of the amine-amine interactions, ascribed to the steric effect caused by the methyl group attached to the aromatic ring. This explains that for a given solvent (alkane, 1-alkanol) H{sup E}(pyridine)>H{sup E}(methylpyridine)

  14. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    Science.gov (United States)

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  15. Molecular characterization of the Hepatitis B virus genotypes in Colombia: a Bayesian inference on the genotype F.

    Science.gov (United States)

    Alvarado Mora, Mónica Viviana; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutierrez, Maria Fernanda; Botelho, Livia; Carrilho, Flair José; Pinho, João Renato Rebello

    2011-01-01

    Hepatitis B is a worldwide health problem affecting about 2 billion people and more than 350 million are chronic carriers of the virus. Nine HBV genotypes (A to I) have been described. The geographical distribution of HBV genotypes is not completely understood due to the limited number of samples from some parts of the world. One such example is Colombia, in which few studies have described the HBV genotypes. In this study, we characterized HBV genotypes in 143 HBsAg-positive volunteer blood donors from Colombia. A fragment of 1306 bp partially comprising HBsAg and the DNA polymerase coding regions (S/POL) was amplified and sequenced. Bayesian phylogenetic analyses were conducted using the Markov Chain Monte Carlo (MCMC) approach to obtain the maximum clade credibility (MCC) tree using BEAST v.1.5.3. Of all samples, 68 were positive and 52 were successfully sequenced. Genotype F was the most prevalent in this population (77%) - subgenotypes F3 (75%) and F1b (2%). Genotype G (7.7%) and subgenotype A2 (15.3%) were also found. Genotype G sequence analysis suggests distinct introductions of this genotype in the country. Furthermore, we estimated the time of the most recent common ancestor (TMRCA) for each HBV/F subgenotype and also for Colombian F3 sequences using two different datasets: (i) 77 sequences comprising 1306 bp of S/POL region and (ii) 283 sequences comprising 681 bp of S/POL region. We also used two other previously estimated evolutionary rates: (i) 2.60 × 10(-4)s/s/y and (ii) 1.5 × 10(-5)s/s/y. Here we report the HBV genotypes circulating in Colombia and estimated the TMRCA for the four different subgenotypes of genotype F.

  16. Plant genotype, microbial recruitment and nutritional security

    Directory of Open Access Journals (Sweden)

    Jai Singh Patel

    2015-08-01

    Full Text Available Agricultural food products with high nutritive value are always preferred over food products with low nutritive value. Efforts are being made to increase the nutritive value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritive value of food is increased under natural conditions in the food products especially in the agricultural produces. Fragmented researches have led to the conclusion that it is possible to increase nutritive value of the agricultural products naturally in agricultural fields. The rhizosphere is of vital importance in this regard for not only health and nutritional status of plants but also for the microorganisms colonising the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of plant host in discriminating its colonisers. A large amount of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome.

  17. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    The introduction of second-generation sequencing, has in recent years allowed the biological community to determine the genomes and transcriptomes of organisms and individuals at an unprecedented rate. However, almost every step in the sequencing protocol introduces uncertainties in how the resul......The introduction of second-generation sequencing, has in recent years allowed the biological community to determine the genomes and transcriptomes of organisms and individuals at an unprecedented rate. However, almost every step in the sequencing protocol introduces uncertainties in how...... the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  18. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

    Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

  19. Genotyping of Canine parvovirus in western Mexico.

    Science.gov (United States)

    Pedroza-Roldán, César; Páez-Magallan, Varinia; Charles-Niño, Claudia; Elizondo-Quiroga, Darwin; De Cervantes-Mireles, Raúl Leonel; López-Amezcua, Mario Alberto

    2015-01-01

    Canine parvovirus (CPV) is one of the most common infectious agents related to high morbidity rates in dogs. In addition, the virus is associated with severe gastroenteritis, diarrhea, and vomiting, resulting in high death rates, especially in puppies and nonvaccinated dogs. To date, there are 3 variants of the virus (CPV-2a, CPV-2b, and CPV-2c) circulating worldwide. In Mexico, reports describing the viral variants circulating in dog populations are lacking. In response to this deficiency, a total of 41 fecal samples of suspected dogs were collected from October 2013 through April 2014 in the Veterinary Hospital of the University of Guadalajara in western Mexico. From these, 24 samples resulted positive by polymerase chain reaction, and the viral variant was determined by restriction fragment length polymorphism. Five positive diagnosed samples were selected for partial sequencing of the vp2 gene and codon analysis. The results demonstrated that the current dominant viral variant in Mexico is CPV-2c. The current study describes the genotyping of CPV strains, providing valuable evidence of the dominant frequency of this virus in a dog population from western Mexico.

  20. Genotype phenotype classification of hepatocellular adenoma

    Institute of Scientific and Technical Information of China (English)

    Paulette Bioulac-Sage; Jean Frédéric Blanc; Sandra Rebouissou; Charles Balabaud; Jessica Zucman-Rossi

    2007-01-01

    Studies that compare tumor genotype with phenotype have provided the basis of a new histological/molecular classification of hepatocellular adenomas. Based on two molecular criteria (presence of a TCF1/HNF1α or β-catenin mutation), and an additional histological criterion (presence or absence of an inflammatory infiltrate), subgroups of hepatocellular adenoma can be defined and distinguished from focal nodular hyperplasia. Analysis of 96 hepatocellular adenomas performed by a French collaborative network showed that they can be divided into four broad subgroups: the first one is defined by the presence of mutations in TCF1 gene inactivating the hepatocyte nuclear factor 1 (HNF1α); the second by the presence of β-catenin activating mutations; the category without mutations of HNF1α or β-catenin is further divided into 2 subgroups depending on the presence or absence of inflammation. Therefore, the approach to the diagnosis of problematic benign hepatocytic nodules may be entering a new era directed by new molecular information. It is hoped that immunohistological tools will improve significantly diagnosis of liver biopsy in our ability to distinguish hepatocellular adenoma from focal nodular hyperplasia (FNH), and to delineate clinically meaningful entities within each group to define the best clinical management. The optimal care of patients with a liver nodule will benefit from the recent knowledge coming from molecular biology and the combined expertise of hepatologists, pathologists, radiologists, and surgeons.

  1. Object-oriented Bayesian networks for evaluating DIP-STR profiling results from unbalanced DNA mixtures.

    Science.gov (United States)

    Cereda, G; Biedermann, A; Hall, D; Taroni, F

    2014-01-01

    The genetic characterization of unbalanced mixed stains remains an important area where improvement is imperative. In fact, with current methods for DNA analysis (Polymerase Chain Reaction with the SGM Plus multiplex kit), it is generally not possible to obtain a conventional autosomal DNA profile of the minor contributor if the ratio between the two contributors in a mixture is smaller than 1:10. This is a consequence of the fact that the major contributor's profile 'masks' that of the minor contributor. Besides known remedies to this problem, such as Y-STR analysis, a new compound genetic marker that consists of a Deletion/Insertion Polymorphism (DIP), linked to a Short Tandem Repeat (STR) polymorphism, has recently been developed and proposed elsewhere in literature. The present paper reports on the derivation of an approach for the probabilistic evaluation of DIP-STR profiling results obtained from unbalanced DNA mixtures. The procedure is based on object-oriented Bayesian networks (OOBNs) and uses the likelihood ratio as an expression of the probative value. OOBNs are retained in this paper because they allow one to provide a clear description of the genotypic configuration observed for the mixed stain as well as for the various potential contributors (e.g., victim and suspect). These models also allow one to depict the assumed relevance relationships and perform the necessary probabilistic computations.

  2. Hepatitis B virus genotypes and lamivudine resistance mutations in Jordan

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    AIM: To investigate and identify prevalent hepatitis B virus (HBV) genotypes and to explore lamivudine-resistant mutations among treated and untreated patients in Jordan.METHODS: A total of 107 cases with chronic hepatitis B were recruited from different medical centers in Jordan. Serological tests were preformed for all cases using a microparticle enzyme immunoassay. HBV Genotyping was performed for 70 cases using Line probe genotyping assay, The YMDD mutations were explored for 20 cases (4 were lamivudine naive) using the INNO-LiPA HBV DR assay.RESULTS: Genotype D was the only detected genotype. A total of 6 YMDD mutations were detected in 5 treated patients (31%) while one mutation was detected in the naive patients. Seventeen percent of cases were positive for HBeAg and had statistically significant higher levels of serum aminotransferases.CONCLUSION: HBV genotype D appears to be the only circulating type in Jordanian patients. The YMDD mutations were detected in 31% of lamivudine-treated cases with similar patterns to those found in the lit-erature. We also found a relatively low prevalence of HBeAg expression among examined cases (17%). Awareness of these serologic, genotypic and resistance patterns might help in the formulation of management plans and for predicting clinical outcomes. Further larger scale studies are needed to confirm our results and to examine possible associations among clinical, serologic, and genetic patterns of HBV infections in Jordan.

  3. Preliminary report of hepatitis B virus genotype prevalence in Iran

    Institute of Scientific and Technical Information of China (English)

    Seyed-Moayed Alavian; Hossein Keyvani; Mahdi Rezai; Neda Ashayeri; Homa Mohammad Sadeghi

    2006-01-01

    AIM: To determine the prevalence of hepatitis B virus (HBV) genotypes in Iranian hepatitis B surface antigen (HBsAg) carriers, chronic hepatitis B and cirrhotic patients.METIHODS: A total of 109 HBsAg-positive patients were included in this study. HBV genotypes were determined by using INNO-LiPA methodology which is based on the reverse hybridization principle.RESULTS: The distribution of patients with different stages of liver disease was as follows: 95 (86.4%) chronic hepatitis, 11 (10%) liver cirrhosis, and 3 (2.7%)inactive carrier. Of the chronic hepatitis and liver cirrhosis patients, 26.4% were HBeAg-positive while 70% were HBeAg-negative. Genotype D was the only detected type found in all patients. CONCLUSION: Classifying HBV into genotypes has to be cost-effective and clinically relevant. Our study indicates that HBV genotype D prevails in the Mediterranean area, Near and Middle East, and South Asia. Continued efforts for understanding HBV genotype through international co-operation will reveal further virological differences of the genotypes and their clinical relevance.

  4. Antixenosis of bean genotypes to Chrysodeixis includens (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Rafaela Morando

    2015-06-01

    Full Text Available The objective of this work was to evaluate bean genotypes for resistance to soybean looper (Chrysodeixis includens. Initially, free-choice tests were carried out with 59 genotypes, divided into three groups according to leaf color intensity (dark green, light green, and medium green, in order to evaluate oviposition preference. Subsequently, 12 genotypes with high potential for resistance were selected, as well as two susceptible commercial standards. With these genotypes, new tests were performed for oviposition in a greenhouse, besides tests for attractiveness and consumption under laboratory conditions (26±2ºC, 65±10% RH, and 14 h light: 10 h dark photophase. In the no-choice test with adults, in the greenhouse, the 'IAC Jabola', Arcelina 1, 'IAC Boreal', 'Flor de Mayo', and 'IAC Formoso' genotypes were the least oviposited, showing antixenosis-type resistance for oviposition. In the free-choice test with larvae, Arcelina 4, 'BRS Horizonte', 'Pérola', H96A102-1-1-1-52, 'IAC Boreal', 'IAC Harmonia', and 'IAC Formoso' were the less consumed genotypes, which indicates antixenosis to feeding. In the no-choice test, all genotypes (except for 'IAPAR 57' expressed moderate levels of antixenosis to feeding against C. includens larvae.

  5. Salinity Responses of Grafted Grapevines: Effects of Scion and Rootstock Genotypes

    Directory of Open Access Journals (Sweden)

    Nuray SIVRITEPE

    2010-12-01

    Full Text Available Two-year-old Sultana and Mke vines (Vitis vinifera L. grafted onto Rupestris du Lot (Vitis rupestris Scheele and 110 R (Vitis berlandieri Vitis rupestris were grown in soil, sand, sphagnum peat and farmyard manure mixture (2:1:1:1 v/v irrigated with 0.3, 2.7 and 5.45 dS m-1 NaCl solutions for a period of 60 days. Biomass accumulation, relative chlorophyll content, leaf water potential, stomatal conductance and transpiration were significantly reduced by salinity in all graft combinations. The inhibiting effect of salinity on growth varied according to the characteristics of the scion genotype and the level of salinity. The results imply the predominance of the scion genotype in determining variation in the leaf-level physiological characteristics of grafted vines because stomatal conductance and transpiration were higher in Sultana than in Mke at the same leaf water potential and the level of salinity, regardless of the rootstock genotype. NaCl treatments did not affect leaf Cu concentration while inducing significant Na, K, Ca, N, P, Mg, Fe, Mn and Zn elevations in the leaves of all scion/rootstock combinations. While salinity caused an increase in N content and a decrease in K content in the roots of all graft combinations, it had no influence on Ca, P, Cu and Zn concentrations. In contrast to the Sultana grafted vines, NaCl salinity led to a decrease in Mg, Fe and Mn concentrations in the roots of Mke grafted vines. Nevertheless, ion accumulation in leaves and roots of grafted vines under saline or non-saline conditions was controlled predominantly by the genotype of the scion. In response to salinity, Sultana grafts accumulated higher amounts of ions in their leaves than in their roots. However, in Mke, higher ion concentrations were seen in the roots. Therefore, the increase in the transport of inorganic ions up to the leaves seems to be the major component of osmotic adjustment in salt-stressed Sultana vines.

  6. 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

  7. Imputation of missing genotypes: an empirical evaluation of IMPUTE

    Directory of Open Access Journals (Sweden)

    Steinberg Martin H

    2008-12-01

    Full Text Available Abstract Background Imputation of missing genotypes is becoming a very popular solution for synchronizing genotype data collected with different microarray platforms but the effect of ethnic background, subject ascertainment, and amount of missing data on the accuracy of imputation are not well understood. Results We evaluated the accuracy of the program IMPUTE to generate the genotype data of partially or fully untyped single nucleotide polymorphisms (SNPs. The program uses a model-based approach to imputation that reconstructs the genotype distribution given a set of referent haplotypes and the observed data, and uses this distribution to compute the marginal probability of each missing genotype for each individual subject that is used to impute the missing data. We assembled genome-wide data from five different studies and three different ethnic groups comprising Caucasians, African Americans and Asians. We randomly removed genotype data and then compared the observed genotypes with those generated by IMPUTE. Our analysis shows 97% median accuracy in Caucasian subjects when less than 10% of the SNPs are untyped and missing genotypes are accepted regardless of their posterior probability. The median accuracy increases to 99% when we require 0.95 minimum posterior probability for an imputed genotype to be acceptable. The accuracy decreases to 86% or 94% when subjects are African Americans or Asians. We propose a strategy to improve the accuracy by leveraging the level of admixture in African Americans. Conclusion Our analysis suggests that IMPUTE is very accurate in samples of Caucasians origin, it is slightly less accurate in samples of Asians background, but substantially less accurate in samples of admixed background such as African Americans. Sample size and ascertainment do not seem to affect the accuracy of imputation.

  8. 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.

  9. Genotype networks, innovation, and robustness in sulfur metabolism

    Science.gov (United States)

    2011-01-01

    Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes involved in sulfur metabolism

  10. Analytical processing of binary mixture information by olfactory bulb glomeruli.

    Directory of Open Access Journals (Sweden)

    Max L Fletcher

    Full Text Available Odors are rarely composed of a single compound, but rather contain a large and complex variety of chemical components. Often, these mixtures are perceived as having unique qualities that can be quite different than the combination of their components. In many cases, a majority of the components of a mixture cannot be individually identified. This synthetic processing of odor information suggests that individual component representations of the mixture must interact somewhere along the olfactory pathway. The anatomical nature of sensory neuron input into segregated glomeruli with the bulb suggests that initial input of odor information into the bulb is analytic. However, a large network of interneurons within the olfactory bulb could allow for mixture interactions via mechanisms such as lateral inhibition. Currently in mammals, it is unclear if postsynaptic mitral/tufted cell glomerular mixture responses reflect the analytical mixture input, or provide the initial basis for synthetic processing with the olfactory system. To address this, olfactory bulb glomerular binary mixture representations were compared to representations of each component using transgenic mice expressing the calcium indicator G-CaMP2 in olfactory bulb mitral/tufted cells. Overall, dorsal surface mixture representations showed little mixture interaction and often appeared as a simple combination of the component representations. Based on this, it is concluded that dorsal surface glomerular mixture representations remain largely analytical with nearly all component information preserved.

  11. Mixture Model and MDSDCA for Textual Data

    Science.gov (United States)

    Allouti, Faryel; Nadif, Mohamed; Hoai An, Le Thi; Otjacques, Benoît

    E-mailing has become an essential component of cooperation in business. Consequently, the large number of messages manually produced or automatically generated can rapidly cause information overflow for users. Many research projects have examined this issue but surprisingly few have tackled the problem of the files attached to e-mails that, in many cases, contain a substantial part of the semantics of the message. This paper considers this specific topic and focuses on the problem of clustering and visualization of attached files. Relying on the multinomial mixture model, we used the Classification EM algorithm (CEM) to cluster the set of files, and MDSDCA to visualize the obtained classes of documents. Like the Multidimensional Scaling method, the aim of the MDSDCA algorithm based on the Difference of Convex functions is to optimize the stress criterion. As MDSDCA is iterative, we propose an initialization approach to avoid starting with random values. Experiments are investigated using simulations and textual data.

  12. Bayesian Estimation of a Mixture Model

    Directory of Open Access Journals (Sweden)

    Ilhem Merah

    2015-05-01

    Full Text Available We present the properties of a bathtub curve reliability model having both a sufficient adaptability and a minimal number of parameters introduced by Idée and Pierrat (2010. This one is a mixture of a Gamma distribution G(2, (1/θ and a new distribution L(θ. We are interesting by Bayesian estimation of the parameters and survival function of this model with a squared-error loss function and non-informative prior using the approximations of Lindley (1980 and Tierney and Kadane (1986. Using a statistical sample of 60 failure data relative to a technical device, we illustrate the results derived. Based on a simulation study, comparisons are made between these two methods and the maximum likelihood method of this two parameters model.

  13. CRITICALITY CURVES FOR PLUTONIUM HYDRAULIC FLUID MIXTURES

    Energy Technology Data Exchange (ETDEWEB)

    WITTEKIND WD

    2007-10-03

    This Calculation Note performs and documents MCNP criticality calculations for plutonium (100% {sup 239}Pu) hydraulic fluid mixtures. Spherical geometry was used for these generalized criticality safety calculations and three geometries of neutron reflection are: {sm_bullet}bare, {sm_bullet}1 inch of hydraulic fluid, or {sm_bullet}12 inches of hydraulic fluid. This document shows the critical volume and critical mass for various concentrations of plutonium in hydraulic fluid. Between 1 and 2 gallons of hydraulic fluid were discovered in the bottom of HA-23S. This HA-23S hydraulic fluid was reported by engineering to be Fyrquel 220. The hydraulic fluid in GLovebox HA-23S is Fyrquel 220 which contains phosphorus. Critical spherical geometry in air is calculated with 0 in., 1 in., or 12 inches hydraulic fluid reflection.

  14. POROSITY CALCULATION OF MIXTURES OF FIBROUS PARTICLES

    Institute of Scientific and Technical Information of China (English)

    Ruping Zou; Aibing Yu

    2003-01-01

    The initial forming of fiber blend to high green density, i.e. the packing of fibrous particles, is important to the reinforcement of composite materials. It is very useful to develop a general predictive method for the optimum selection of particle mixtures for the property control of ceramic or composite products. This paper presents such a mathematical model developed on the basis of the similarity analysis between the spherical and non-spherical particle packings and assesses its applicability to the packing of fibrous particles with discrete and/or continuous length distributions. The results indicate that the model can predict this packing system well and hence provide an effective way to solve various packing problems in the composite materials processing.

  15. Continuum thermodynamics of chemically reacting fluid mixtures

    CERN Document Server

    Bothe, Dieter

    2014-01-01

    We consider viscous and heat conducting mixtures of molecularly miscible chemical species forming a fluid in which the constituents can undergo chemical reactions. Assuming a common temperature for all components, a first main aim is the derivation of a closed system of partial mass and partial momentum balances plus a common balance of internal energy. This is achieved by careful exploitation of the entropy principle which, in particular, requires appropriate definitions of absolute temperature and chemical potentials based on an adequate definition of thermal energy that excludes diffusive contributions. The latter is crucial in order to obtain a closure framework for the interaction forces between the different species. The interaction forces split into a thermo-mechanical and a chemical part, where the former turns out to be symmetric if binary interactions are assumed. In the non-reactive case, this leads to a system of Navier-Stokes type sub-systems, coupled by interspecies friction forces. For chemical...

  16. Quantum-coherent mixtures of causal relations

    CERN Document Server

    MacLean, Jean-Philippe W; Spekkens, Robert W; Resch, Kevin J

    2016-01-01

    Understanding the causal influences that hold among the parts of a system is critical both to explaining that system's natural behaviour and to controlling it through targeted interventions. In a quantum world, understanding causal relations is equally important, but the set of possibilities is far richer. The two basic ways in which a pair of time-ordered quantum systems may be causally related are by a cause-effect mechanism or by a common cause acting on both. Here, we show that it is possible to have a coherent mixture of these two possibilities. We realize such a nonclassical causal relation in a quantum optics experiment and derive a set of criteria for witnessing the coherence based on a quantum version of Berkson's paradox. The interplay of causality and quantum theory lies at the heart of challenging foundational puzzles, such as Bell's theorem and the search for quantum gravity, but could also provide a resource for novel quantum technologies.

  17. Processes assessment in binary mixture plant

    Directory of Open Access Journals (Sweden)

    N. Shankar Ganesh, T. Srinivas

    2013-01-01

    Full Text Available Binary fluid system has an efficient system of heat recovery compared to a single fluid system due to a better temperature match between hot and cold fluids. There are many applications with binary fluid system i.e. Kalina power generation, vapor absorption refrigeration, combined power and cooling etc. Due to involvement of three properties (pressure, temperature and concentration in the processes evaluation, the solution is complicated compared to a pure substance. The current work simplifies this complex nature of solution and analyzes the basic processes to understand the processes behavior in power generation as well as cooling plants. Kalina power plant consists of regenerator, heat recovery vapor generator, condenser, mixture, separator, turbine, pump and throttling device. In addition to some of these components, the cooling plant consists of absorber which is similar in operation of condenser. The amount of vapor at the separator decreases with an increase in its pressure and temperature.

  18. Derived thermodynamic properties of alcohol + cyclohexylamine mixtures

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    IVONA R. RADOVIĆ

    2010-02-01

    Full Text Available Thermal expansion coefficients, α, excess thermal expansion coefficients, αE, isothermal coefficients of pressure excess molar enthalpy, (∂HE/∂pT,x, partial molar volumes, , partial molar volumes at infinite dilution, , partial excess molar volumes, , and partial excess molar volumes at infinite dilution, , were calculated using experimental densities and excess molar volumes, , data. All calculations are performed for the binary systems of cyclohexylamine with 1-propanol or 1-butanol or 2-butanol or 2-methyl-2-propanol. The Redlich–Kister polynomial and the reduced excess molar volume approach were used in the evaluation of these properties. In addition, the aim of this investigation was to provide a set of various volumetric data in order to asses the influence of temperature, chain length and position of hydroxyl group in the alcohol molecule on the molecular interactions in the examined binary mixtures.

  19. Thermodynamic modeling of CO2 mixtures

    DEFF Research Database (Denmark)

    Bjørner, Martin Gamel

    performed satisfactorily and predicted the general behavior of the systems, but qCPA used fewer adjustable parameters to achieve similar predictions. It has been demonstrated that qCPA is a promising model which, compared to CPA, systematically improves the predictions of the experimentally determined phase......, accurate predictions of the thermodynamic properties and phase equilibria of mixtures containing CO2 are challenging with classical models such as the Soave-Redlich-Kwong (SRK) equation of state (EoS). This is believed to be due to the fact, that CO2 has a large quadrupole moment which the classical models...... do not explicitly account for. In this thesis, in an attempt to obtain a physically more consistent model, the cubicplus association (CPA) EoS is extended to include quadrupolar interactions. The new quadrupolar CPA (qCPA) can be used with the experimental value of the quadrupolemoment...

  20. Urea and deuterium mixtures at high pressures

    Energy Technology Data Exchange (ETDEWEB)

    Donnelly, M., E-mail: m.donnelly-2@sms.ed.ac.uk; Husband, R. J.; Frantzana, A. D.; Loveday, J. S. [Centre for Science at Extreme Conditions and School of Physics and Astronomy, The University of Edinburgh, Erskine Williamson Building, Peter Guthrie Tait Road, The King’s Buildings, Edinburgh EH9 3FD (United Kingdom); Bull, C. L. [ISIS, Rutherford Appleton Laboratory, Oxford Harwell, Didcot OX11 0QX (United Kingdom); Klotz, S. [IMPMC, CNRS UMR 7590, Université P and M Curie, 4 Place Jussieu, 75252 Paris (France)

    2015-03-28

    Urea, like many network forming compounds, has long been known to form inclusion (guest-host) compounds. Unlike other network formers like water, urea is not known to form such inclusion compounds with simple molecules like hydrogen. Such compounds if they existed would be of interest both for the fundamental insight they provide into molecular bonding and as potential gas storage systems. Urea has been proposed as a potential hydrogen storage material [T. A. Strobel et al., Chem. Phys. Lett. 478, 97 (2009)]. Here, we report the results of high-pressure neutron diffraction studies of urea and D{sub 2} mixtures that indicate no inclusion compound forms up to 3.7 GPa.

  1. Quantum-coherent mixtures of causal relations

    Science.gov (United States)

    MacLean, Jean-Philippe W.; Ried, Katja; Spekkens, Robert W.; Resch, Kevin J.

    2017-01-01

    Understanding the causal influences that hold among parts of a system is critical both to explaining that system's natural behaviour and to controlling it through targeted interventions. In a quantum world, understanding causal relations is equally important, but the set of possibilities is far richer. The two basic ways in which a pair of time-ordered quantum systems may be causally related are by a cause-effect mechanism or by a common-cause acting on both. Here we show a coherent mixture of these two possibilities. We realize this nonclassical causal relation in a quantum optics experiment and derive a set of criteria for witnessing the coherence based on a quantum version of Berkson's effect, whereby two independent causes can become correlated on observation of their common effect. The interplay of causality and quantum theory lies at the heart of challenging foundational puzzles, including Bell's theorem and the search for quantum gravity. PMID:28485394

  2. Bioavailability and variability of biphasic insulin mixtures

    DEFF Research Database (Denmark)

    Søeborg, Tue; Rasmussen, Christian Hove; Mosekilde, Erik

    2012-01-01

    Absorption of subcutaneously administered insulin is associated with considerable variability. Some of this variability was quantitatively explained for both soluble insulin and insulin suspensions in a recent contribution to this journal (Søeborg et al., 2009). In the present article......, the absorption kinetics for mixtures of insulins is described. This requires that the bioavailability of the different insulins is considered. A short review of insulin bioavailability and a description of the subcutaneous depot thus precede the presentation of possible mechanisms associated with subcutaneous...... insulin degradation. Soluble insulins are assumed to be degraded enzymatically in the subcutaneous tissue. Suspended insulin crystals form condensed heaps that are assumed to be degraded from their surface by invading macrophages. It is demonstrated how the shape of the heaps affects the absorption...

  3. Phasing of many thousands of genotyped samples.

    Science.gov (United States)

    Williams, Amy L; Patterson, Nick; Glessner, Joseph; Hakonarson, Hakon; Reich, David

    2012-08-10

    Haplotypes are an important resource for a large number of applications in human genetics, but computationally inferred haplotypes are subject to switch errors that decrease their utility. The accuracy of computationally inferred haplotypes increases with sample size, and although ever larger genotypic data sets are being generated, the fact that existing methods require substantial computational resources limits their applicability to data sets containing tens or hundreds of thousands of samples. Here, we present HAPI-UR (haplotype inference for unrelated samples), an algorithm that is designed to handle unrelated and/or trio and duo family data, that has accuracy comparable to or greater than existing methods, and that is computationally efficient and can be applied to 100,000 samples or more. We use HAPI-UR to phase a data set with 58,207 samples and show that it achieves practical runtime and that switch errors decrease with sample size even with the use of samples from multiple ethnicities. Using a data set with 16,353 samples, we compare HAPI-UR to Beagle, MaCH, IMPUTE2, and SHAPEIT and show that HAPI-UR runs 18× faster than all methods and has a lower switch-error rate than do other methods except for Beagle; with the use of consensus phasing, running HAPI-UR three times gives a slightly lower switch-error rate than Beagle does and is more than six times faster. We demonstrate results similar to those from Beagle on another data set with a higher marker density. Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources).

  4. PAX6 mutations: genotype-phenotype correlations

    Directory of Open Access Journals (Sweden)

    Hanson Isabel M

    2005-05-01

    Full Text Available Abstract Background The PAX6 protein is a highly conserved transcriptional regulator that is important for normal ocular and neural development. In humans, heterozygous mutations of the PAX6 gene cause aniridia (absence of the iris and related developmental eye diseases. PAX6 mutations are archived in the Human PAX6 Allelic Variant Database, which currently contains 309 records, 286 of which are mutations in patients with eye malformations. Results We examined the records in the Human PAX6 Allelic Variant Database and documented the frequency of different mutation types, the phenotypes associated with different mutation types, the contribution of CpG transitions to the PAX6 mutation spectrum, and the distribution of chain-terminating mutations in the open reading frame. Mutations that introduce a premature termination codon into the open reading frame are predominantly associated with aniridia; in contrast, non-aniridia phenotypes are typically associated with missense mutations. Four CpG dinucleotides in exons 8, 9, 10 and 11 are major mutation hotspots, and transitions at these CpG's account for over half of all nonsense mutations in the database. Truncating mutations are distributed throughout the PAX6 coding region, except for the last half of exon 12 and the coding part of exon 13, where they are completely absent. The absence of truncating mutations in the 3' part of the coding region is statistically significant and is consistent with the idea that nonsense-mediated decay acts on PAX6 mutant alleles. Conclusion The PAX6 Allelic Variant Database is a valuable resource for studying genotype-phenotype correlations. The consistent association of truncating mutations with the aniridia phenotype, and the distribution of truncating mutations in the PAX6 open reading frame, suggests that nonsense-mediated decay acts on PAX6 mutant alleles.

  5. Critical Phenomena in Liquid-Liquid Mixtures

    Science.gov (United States)

    Jacobs, D. T.

    2000-04-01

    Critical phenomena provide intriguing and essential insight into many issues in condensed matter physics because of the many length scales involved. Large density or concentration fluctuations near a system's critical point effectively mask the identity of the system and produce universal phenomena that have been well studied in simple liquid-vapor and liquid-liquid systems. Such systems have provided useful model systems to test theoretical predictions which can then be extended to more complicated systems. Along various thermodynamic paths, several quantities exhibit a simple power-law dependence close to the critical point. The critical exponents describing these relationships are universal and should depend only on a universality class determined by the order-parameter and spatial dimensionality of the system. Liquid gas, binary fluid mixtures, uniaxial ferromagnetism, polymer-solvent, and protein solutions all belong to the same (Ising model) universality class. The diversity of critical systems that can be described by universal relations indicates that experimental measurements on one system should yield the same information as on another. Our experimental investigations have tested existing theory and also extended universal behavior into new areas. By measuring the coexistence curve, heat capacity, thermal expansion and static light scattering (turbidity) in various liquid-liquid and polymer-solvent systems, we have determined critical exponents and amplitudes that have sometimes confirmed and other times challenged current theory. Recent experiments investigating the heat capacity and light scattering in a liquid-liquid mixture very close to the critical point will be discussed. This research is currently supported by The Petroleum Research Fund and by NASA grant NAG8-1433 with some student support from NSF-DMR 9619406.

  6. Clustering high-dimensional mixed data to uncover sub-phenotypes: joint analysis of phenotypic and genotypic data.

    Science.gov (United States)

    McParland, D; Phillips, C M; Brennan, L; Roche, H M; Gormley, I C

    2017-06-30

    The LIPGENE-SU.VI.MAX study, like many others, recorded high-dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the metabolic syndrome (MetS), a complex disorder that can lead to higher risk of type 2 diabetes and cardiovascular disease. Interest lies in clustering the LIPGENE-SU.VI.MAX participants into homogeneous groups or sub-phenotypes, by jointly considering their phenotypic and genotypic data, and in determining which variables are discriminatory. A novel latent variable model that elegantly accommodates high dimensional, mixed data is developed to cluster LIPGENE-SU.VI.MAX participants using a Bayesian finite mixture model. A computationally efficient variable selection algorithm is incorporated, estimation is via a Gibbs sampling algorithm and an approximate BIC-MCMC criterion is developed to select the optimal model. Two clusters or sub-phenotypes ('healthy' and 'at risk') are uncovered. A small subset of variables is deemed discriminatory, which notably includes phenotypic and genotypic variables, highlighting the need to jointly consider both factors. Further, 7 years after the LIPGENE-SU.VI.MAX data were collected, participants underwent further analysis to diagnose presence or absence of the MetS. The two uncovered sub-phenotypes strongly correspond to the 7-year follow-up disease classification, highlighting the role of phenotypic and genotypic factors in the MetS and emphasising the potential utility of the clustering approach in early screening. Additionally, the ability of the proposed approach to define the uncertainty in sub-phenotype membership at the participant level is synonymous with the concepts of precision medicine and nutrition. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  7. Reduced Uptake of Family Screening in Genotype-Negative Versus Genotype-Positive Long QT Syndrome.

    Science.gov (United States)

    Hanninen, Mikael; Klein, George J; Laksman, Zachary; Conacher, Susan S; Skanes, Allan C; Yee, Raymond; Gula, Lorne J; Leong-Sit, Peter; Manlucu, Jaimie; Krahn, Andrew D

    2015-08-01

    The acceptance and yield of family screening in genotype-negative long QT syndrome (LQTS) remains incompletely characterized. In this study of family screening for phenotype-definite Long QT Syndrome (LQTS, Schwartz score ≥3.5), probands at a regional Inherited Cardiac Arrhythmia clinic were reviewed. All LQTS patients were offered education by a qualified genetic counselor, along with materials for family screening including electronic and paper correspondence to provide to family members. Thirty-eight qualifying probands were identified and 20 of these had family members who participated in cascade screening. The acceptance of screening was found to be lower among families without a known pathogenic mutation (33 vs. 77 %, p = 0.02). A total of 52 relatives were screened; fewer relatives were screened per index case when the proband was genotype-negative (1.7 vs. 3.1, p = 0.02). The clinical yield of screening appeared to be similar irrespective of gene testing results (38 vs. 33 %, p = 0.69). Additional efforts to promote family screening among gene-negative long QT families may be warranted.

  8. Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

    Directory of Open Access Journals (Sweden)

    Katy Denise Heath

    2014-04-01

    Full Text Available Predicting how species interactions evolve requires that we understand the mechanistic basis of coevolution, and thus the functional genotype-by-genotype interactions (G × G that drive reciprocal natural selection. Theory on host-parasite coevolution provides testable hypotheses for empiricists, but depends upon models of functional G × G that remain loosely tethered to the molecular details of any particular system. In practice, reciprocal cross-infection studies are often used to partition the variation in infection or fitness in a population that is attributable to G × G (statistical G × G. Here we use simulations to demonstrate that within-population statistical G × G likely tells us little about the existence of coevolution, its strength, or the genetic basis of functional G × G. Combined with studies of multiple populations or points in time, mapping and molecular techniques can bridge the gap between natural variation and mechanistic models of coevolution, while model-based statistics can formally confront coevolutionary models with cross-infection data. Together these approaches provide a robust framework for inferring the infection genetics underlying statistical G × G, helping unravel the genetic basis of coevolution.

  9. In Vitro screening of tomato genotypes for drought resistance using ...

    African Journals Online (AJOL)

    ... crop and area under production is limited by irrigation water scarcity. ... conditions indicating there ability to fight with sever water stress situation. ... and hybrids performed better than cultivated genotypes under all levels of water stress.

  10. Identification of blast resistance expression in rice genotypes using ...

    African Journals Online (AJOL)

    USER

    2010-06-14

    Jun 14, 2010 ... genotypes were evaluated for resistance to blast disease under induced epiphytotic conditions obtained in the ..... desirable changes in the population through selection ..... that resistance sources are non-allelic for resistance.

  11. genotype by environment interaction and grain yield stability ...

    African Journals Online (AJOL)

    Preferred Customer

    ABSTRACT: Genotypes by environment (GXE) interactions are almost unanimously considered to be ... important tool in plant breeding and this has to be ..... Pakistan Journal of Biological Sci- ... mosome Engineering and Crop Improvement.

  12. Large SNP arrays for genotyping in crop plants

    Indian Academy of Sciences (India)

    Martin W Ganal; Andreas Polley; Eva-Maria Graner; Joerg Plieske; Ralf Wieseke; Hartmut Luerssen; Gregor Durstewitz

    2012-11-01

    Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

  13. Multiple centroid method to evaluate the adaptability of alfalfa genotypes

    Directory of Open Access Journals (Sweden)

    Moysés Nascimento

    2015-02-01

    Full Text Available This study aimed to evaluate the efficiency of multiple centroids to study the adaptability of alfalfa genotypes (Medicago sativa L.. In this method, the genotypes are compared with ideotypes defined by the bissegmented regression model, according to the researcher's interest. Thus, genotype classification is carried out as determined by the objective of the researcher and the proposed recommendation strategy. Despite the great potential of the method, it needs to be evaluated under the biological context (with real data. In this context, we used data on the evaluation of dry matter production of 92 alfalfa cultivars, with 20 cuttings, from an experiment in randomized blocks with two repetitions carried out from November 2004 to June 2006. The multiple centroid method proved efficient for classifying alfalfa genotypes. Moreover, it showed no unambiguous indications and provided that ideotypes were defined according to the researcher's interest, facilitating data interpretation.

  14. Genotype by Environment Interaction (G x E) and Grain Yield ...

    African Journals Online (AJOL)

    SARAH

    2014-08-31

    Aug 31, 2014 ... Genotype by Environment Interaction and Grain yield stability analysis of Ethiopian ..... common bean (Abeya et al., 2008); for durum wheat. (Alamnie et al. .... A thesis presented in accordance with the requirements for the ...

  15. Molecular methods for bacterial genotyping and analyzed gene regions

    Directory of Open Access Journals (Sweden)

    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.

  16. Superoxide Dismutase and Catalase Genotypes in Pediatric Migraine Patients.

    Science.gov (United States)

    Saygi, Semra; Erol, İlknur; Alehan, Füsun; Yalçın, Yaprak Yılmaz; Kubat, Gözde; Ataç, Fatma Belgin

    2015-10-01

    This study compared superoxide dismutase (SOD) and catalase (CAT) alleles in 97 consecutive children and adolescents with migraine to 96 healthy children and adolescents. Isolated genomic DNA was used as a template for SOD1 (35 A/C), SOD2 16 C/T, and CAT2 [(-262 C/T) and (-21 A/T)] allele genotyping. The SOD2 16 C/T genotype and C allele frequency differed significantly between controls and migraine (P = .047; P = .038). CAT -21 AA genotype and A allele frequency were significantly higher in both migraine with aura patients (P = .013; P = .004) and migraine without aura patients (P = .003; P = .001) compared to controls. To our knowledge, this is the first demonstration of differences in SOD and CAT genotypes between pediatric migraine patients and age-matched controls. Further studies on the functional implications of these genetic variants on neural antioxidant capacity and the use of antioxidant modulators for migraine treatment are warranted.

  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. Genotype versus phenotype in families with androgen insensitivity syndrome

    NARCIS (Netherlands)

    Boehmer, ALM; Bruggenwirth, H; Van Assendelft, C; Otten, BJ; Verleun-Mooijman, MCT; Niermeijer, MF; Brunner, HG; Rouwe, CW; Waelkens, JJ; Oostdijk, W; Kleijer, WJ; Van der Kwast, TH; De Vroede, MA; Drop, SLS

    2001-01-01

    Androgen insensitivity syndrome encompasses a wide range of phenotypes, which are caused by numerous different mutations in the AR gene. Detailed information on the genotype/ phenotype relationship in androgen insensitivity syndrome is important for sex assignment, treatment of androgen insensitivit

  19. relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    jen

    The nine primers produced 60 amplification products, of which 9 were monomorphic and 51 were polymorphic. The ... Key Words: Eleusine coracana, genotypic adaptation, molecular markers .... Table 2 presents detailed information about the.

  20. Characterization of cowpea genotype resistance to Callosobruchus maculatus

    Directory of Open Access Journals (Sweden)

    Maria de Jesus Passos de Castro

    2013-09-01

    Full Text Available The objective of this work was to characterize the resistance of 50 cowpea (Vigna unguiculata genotypes to Callosobruchus maculatus. A completely randomized design with five replicates per treatment (genotype was used. No-choice tests were performed using the 50 cowpea genotypes to evaluate the preference for oviposition and the development of the weevil. The genotypes IT85 F-2687, MN05-841 B-49, MNC99-508-1, MNC99-510-8, TVu 1593, Canapuzinho-1-2, and Sanzi Sambili show non-preference-type resistance (oviposition and feeding. IT81 D-1045 Ereto and IT81 D-1045 Enramador exhibit antibiosis against C. maculatus and descend from resistant genitors, which grants them potential to be used in future crossings to obtain cowpea varieties with higher levels of resistance.

  1. Forensic SNP Genotyping using Nanopore MinION Sequencing

    Science.gov (United States)

    Cornelis, Senne; Gansemans, Yannick; Deleye, Lieselot; Deforce, Dieter; Van Nieuwerburgh, Filip

    2017-01-01

    One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies’ (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies. When these problematic loci are avoided, correct forensic genotyping using nanopore sequencing is technically feasible. PMID:28155888

  2. Effect of Genotypes and Seed Production Environments on Seed ...

    African Journals Online (AJOL)

    Key words: Genotypes. plant popUlation, seed production. seed quality. sesame. ..... (68%). Greater standard gennination and EWSG occurred in seed produced in 2001 .... Table 7: Heritability (H2B) and genetic advance (GA) of seed quality ...

  3. Nuclear fuel alloys or mixtures and method of making thereof

    Science.gov (United States)

    Mariani, Robert Dominick; Porter, Douglas Lloyd

    2016-04-05

    Nuclear fuel alloys or mixtures and methods of making nuclear fuel mixtures are provided. Pseudo-binary actinide-M fuel mixtures form alloys and exhibit: body-centered cubic solid phases at low temperatures; high solidus temperatures; and/or minimal or no reaction or inter-diffusion with steel and other cladding materials. Methods described herein through metallurgical and thermodynamics advancements guide the selection of amounts of fuel mixture components by use of phase diagrams. Weight percentages for components of a metallic additive to an actinide fuel are selected in a solid phase region of an isothermal phase diagram taken at a temperature below an upper temperature limit for the resulting fuel mixture in reactor use. Fuel mixtures include uranium-molybdenum-tungsten, uranium-molybdenum-tantalum, molybdenum-titanium-zirconium, and uranium-molybdenum-titanium systems.

  4. Maximum likelihood estimation of finite mixture model for economic data

    Science.gov (United States)

    Phoong, Seuk-Yen; Ismail, Mohd Tahir

    2014-06-01

    Finite mixture model is a mixture model with finite-dimension. This models are provides a natural representation of heterogeneity in a finite number of latent classes. In addition, finite mixture models also known as latent class models or unsupervised learning models. Recently, maximum likelihood estimation fitted finite mixture models has greatly drawn statistician's attention. The main reason is because maximum likelihood estimation is a powerful statistical method which provides consistent findings as the sample sizes increases to infinity. Thus, the application of maximum likelihood estimation is used to fit finite mixture model in the present paper in order to explore the relationship between nonlinear economic data. In this paper, a two-component normal mixture model is fitted by maximum likelihood estimation in order to investigate the relationship among stock market price and rubber price for sampled countries. Results described that there is a negative effect among rubber price and stock market price for Malaysia, Thailand, Philippines and Indonesia.

  5. A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

    Directory of Open Access Journals (Sweden)

    Torring Niels

    2007-11-01

    Full Text Available Abstract Background Affymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlying events leading to cancer. Genomic copy-numbers are today routinely derived from SNP array data, but the proposed algorithms for this task most often disregard the genotype information available from germline cells in paired germline-tumour samples. Including this information may deepen our understanding of the "true" biological situation e.g. by enabling analysis of allele specific copy-numbers. Here we rely on matched germline-tumour samples and have developed a Hidden Markov Model (HMM to estimate allelic copy-number changes in tumour cells. Further with this approach we are able to estimate the proportion of normal cells in the tumour (mixture proportion. Results We show that our method is able to recover the underlying copy-number changes in simulated data sets with high accuracy (above 97.71%. Moreover, although the known copy-numbers could be well recovered in simulated cancer samples with more than 70% cancer cells (and less than 30% normal cells, we demonstrate that including the mixture proportion in the HMM increases the accuracy of the method. Finally, the method is tested on HapMap samples and on bladder and prostate cancer samples. Conclusion The HMM method developed here uses the genotype calls of germline DNA and the allelic SNP intensities from the tumour DNA to estimate allelic copy-numbers (including changes in the tumour. It differentiates between different events like uniparental disomy and allelic imbalances. Moreover, the HMM can estimate the mixture proportion, and thus inform about the purity of the tumour sample.

  6. Complex DNA mixture analysis in a forensic context: evaluating the probative value using a likelihood ratio model.

    Science.gov (United States)

    Haned, Hinda; Benschop, Corina C G; Gill, Peter D; Sijen, Titia

    2015-05-01

    The interpretation of mixed DNA profiles obtained from low template DNA samples has proven to be a particularly difficult task in forensic casework. Newly developed likelihood ratio (LR) models that account for PCR-related stochastic effects, such as allelic drop-out, drop-in and stutters, have enabled the analysis of complex cases that would otherwise have been reported as inconclusive. In such samples, there are uncertainties about the number of contributors, and the correct sets of propositions to consider. Using experimental samples, where the genotypes of the donors are known, we evaluated the feasibility and the relevance of the interpretation of high order mixtures, of three, four and five donors. The relative risks of analyzing high order mixtures of three, four, and five donors, were established by comparison of a 'gold standard' LR, to the LR that would be obtained in casework. The 'gold standard' LR is the ideal LR: since the genotypes and number of contributors are known, it follows that the parameters needed to compute the LR can be determined per contributor. The 'casework LR' was calculated as used in standard practice, where unknown donors are assumed; the parameters were estimated from the available data. Both LRs were calculated using the basic standard model, also termed the drop-out/drop-in model, implemented in the LRmix module of the R package Forensim. We show how our results furthered the understanding of the relevance of analyzing high order mixtures in a forensic context. Limitations are highlighted, and it is illustrated how our study serves as a guide to implement likelihood ratio interpretation of complex DNA profiles in forensic casework.

  7. Circulation of genotype-I hepatitis B virus in the primitive tribes of Arunachal Pradesh in early sixties and molecular evolution of genotype-I.

    Science.gov (United States)

    Haldipur, Bangari P; Walimbe, Atul M; Arankalle, Vidya A

    2014-10-01

    Retrospective serologic screening of 1077 serum samples collected from the primitive tribe from north-eastern India in 1963 revealed high prevalence of HBV (15% HBsAg carrier rate) and HCV (7% anti-HCV positivity) and co-circulation of multiple HBV genotypes-A, C, D and G. Full genome sequencing classified all the G-genotype samples as genotype-I. Comparison of genotype-I-HBV full-genome sequences representing 1963 (n=5, this study) and 2005 (reported earlier) showed identical recombination break-points of genotypes-A/G/C. Genotype-C and genotype-C-fragment of I-genotype circulating in 1963 were distinctly different. The data demonstrates that the recombination events were not recent. Molecular clock analysis predicted existence of genotype-I in this tribe during 1920s.

  8. High Diversity of vacA and cagA Helicobacter pylori Genotypes in Patients with and without Gastric Cancer

    Science.gov (United States)

    López-Vidal, Yolanda; Ponce-de-León, Sergio; Castillo-Rojas, Gonzalo; Barreto-Zúñiga, Rafael; Torre-Delgadillo, Aldo

    2008-01-01

    Background Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. The aim of this study was to assess the topographical distribution of H. pylori in the stomach as well as the vacA and cagA genotypes in patients with and without gastric cancer. Methodology/Principal Findings Three gastric biopsies, from predetermined regions, were evaluated in 16 patients with gastric cancer and 14 patients with dyspeptic symptoms. From cancer patients, additional biopsy specimens were obtained from tumor centers and margins; among these samples, the presence of H. pylori vacA and cagA genotypes was evaluated. Positive H. pylori was 38% and 26% in biopsies obtained from the gastric cancer and non-cancer groups, respectively (p = 0.008), and 36% in tumor sites. In cancer patients, we found a preferential distribution of H. pylori in the fundus and corpus, whereas, in the non-cancer group, the distribution was uniform (p = 0.003). A majority of the biopsies were simultaneously cagA gene-positive and -negative. The fundus and corpus demonstrated a higher positivity rate for the cagA gene in the non-cancer group (p = 0.036). A mixture of cagA gene sizes was also significantly more frequent in this group (p = 0.003). Ninety-two percent of all the subjects showed more than one vacA gene genotype; s1b and m1 vacA genotypes were predominantly found in the gastric cancer group. The highest vacA-genotype signal-sequence diversity was found in the corpus and 5 cm from tumor margins. Conclusion/Significance High H. pylori colonization diversity, along with the cagA gene, was found predominantly in the fundus and corpus of patients with gastric cancer. The genotype diversity observed across systematic whole-organ and tumor sampling was remarkable. We find that there is insufficient evidence to support the association of one isolate with a specific disease, due to the multistrain nature of H. pylori infection shown in this work. PMID:19050763

  9. High diversity of vacA and cagA Helicobacter pylori genotypes in patients with and without gastric cancer.

    Directory of Open Access Journals (Sweden)

    Yolanda López-Vidal

    Full Text Available BACKGROUND: Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. The aim of this study was to assess the topographical distribution of H. pylori in the stomach as well as the vacA and cagA genotypes in patients with and without gastric cancer. METHODOLOGY/PRINCIPAL FINDINGS: Three gastric biopsies, from predetermined regions, were evaluated in 16 patients with gastric cancer and 14 patients with dyspeptic symptoms. From cancer patients, additional biopsy specimens were obtained from tumor centers and margins; among these samples, the presence of H. pylori vacA and cagA genotypes was evaluated. Positive H. pylori was 38% and 26% in biopsies obtained from the gastric cancer and non-cancer groups, respectively (p = 0.008, and 36% in tumor sites. In cancer patients, we found a preferential distribution of H. pylori in the fundus and corpus, whereas, in the non-cancer group, the distribution was uniform (p = 0.003. A majority of the biopsies were simultaneously cagA gene-positive and -negative. The fundus and corpus demonstrated a higher positivity rate for the cagA gene in the non-cancer group (p = 0.036. A mixture of cagA gene sizes was also significantly more frequent in this group (p = 0.003. Ninety-two percent of all the subjects showed more than one vacA gene genotype; s1b and m1 vacA genotypes were predominantly found in the gastric cancer group. The highest vacA-genotype signal-sequence diversity was found in the corpus and 5 cm from tumor margins. CONCLUSION/SIGNIFICANCE: High H. pylori colonization diversity, along with the cagA gene, was found predominantly in the fundus and corpus of patients with gastric cancer. The genotype diversity observed across systematic whole-organ and tumor sampling was remarkable. We find that there is insufficient evidence to support the association of one isolate with a specific disease, due to the multistrain nature of H. pylori infection shown in this work.

  10. Robust SNP genotyping by multiplex PCR and arrayed primer extension

    Directory of Open Access Journals (Sweden)

    Podder Mohua

    2008-01-01

    Full Text Available Abstract Background Arrayed primer extension (APEX is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs. However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project. Results In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs. In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy. Conclusion We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.

  11. Antioxidant Defense Mechanisms of Salinity Tolerance in Rice Genotypes

    Directory of Open Access Journals (Sweden)

    Mohammad Golam Kibria

    2017-05-01

    Full Text Available In order to elucidate the role of antioxidant responses in salinity tolerance in rice genotypes under salt stress, experiments were conducted using four rice varieties, including salt-sensitive BRRI dhan 28 and three salt-tolerant varieties BRRI dhan 47, BINA dhan 8 and BINA dhan 10. Thirty-day-old rice seedlings were transplanted into pots. At the active tillering stage (35 d after transplanting, plants were exposed to different salinity levels (0, 20, 40 and 60 mmol/L NaCl. Salt stress caused a significant reduction in growth for all the rice genotypes. Growth reduction was higher in the salt-sensitive genotype than in the salt-tolerant ones, and BINA dhan 10 showed higher salt tolerance in all measured physiological parameters. The reduction in shoot and root biomass was found to be minimal in BINA dhan 10. Chlorophyll content significantly decreased under salt stress except for BINA dhan 10. Proline content significantly increased in salt-tolerant rice genotypes with increased salt concentration, and the highest proline content was obtained from BINA dhan 10 under salt stress. Catalase and ascorbate peroxidase activities significantly decreased in salt-sensitive genotype whereas significantly increased in salt-tolerant ones with increasing salt concentration. However, salt stress significantly decreased guaiacol peroxidase activity in all the rice genotypes irrespective of salt tolerance. K+/Na+ ratio also significantly decreased in shoots and roots of all the rice genotypes. The salt-tolerant genotype BINA dhan 10 maintained higher levels of chlorophyll and proline contents as well as catalase and ascorbate peroxidase activities under salt stress, thus, this might be the underlying mechanism for salt tolerance.

  12. ABO genotyping in leukemia patients reveals new ABO variant alleles

    OpenAIRE

    Novaretti,M.C.Z.; DOMINGUES, A. E.; MANHANI, R.; Pinto, E M; Dorlhiac-Llacer, P.E.; Chamone, D.A.F.

    2008-01-01

    The ABO blood group is the most important blood group system in transfusion medicine and organ transplantation. To date, more than 160 ABO alleles have been identified by molecular investigation. Almost all ABO genotyping studies have been performed in blood donors and families and for investigation of ABO subgroups detected serologically. The aim of the present study was to perform ABO genotyping in patients with leukemia. Blood samples were collected from 108 Brazilian patients with chronic...

  13. Campylobacter concisus: an evaluation of certain phenotypic and genotypic characteristics

    DEFF Research Database (Denmark)

    Engberg, J.; Bang, D. D.; Aabenhus, R.

    2005-01-01

    The clinical relevance of Campylobacter concisus in gastrointestinal disease has not been determined definitively. This study investigated the phenotypic and genotypic characteristics of 39 C. concisus isolates from Danish patients with diarrhoea, three isolates from healthy individuals and the t......The clinical relevance of Campylobacter concisus in gastrointestinal disease has not been determined definitively. This study investigated the phenotypic and genotypic characteristics of 39 C. concisus isolates from Danish patients with diarrhoea, three isolates from healthy individuals...

  14. Sex and PRNP genotype determination in preimplantation caprine embryos.

    Science.gov (United States)

    Guignot, F; Perreau, C; Cavarroc, C; Touzé, J-L; Pougnard, J-L; Dupont, F; Beckers, J-F; Rémy, B; Babilliot, J-M; Bed'Hom, B; Lamorinière, J M; Mermillod, P; Baril, G

    2011-08-01

    The objective of this study was to test the accuracy of genotype diagnosis after whole amplification of DNA extracted from biopsies obtained by trimming goat embryos and to evaluate the viability of biopsied embryos after vitrification/warming and transfer. Whole genome amplification (WGA) was performed using Multiple Displacement Amplification (MDA). Sex and prion protein (PRNP) genotypes were determined. Sex diagnosis was carried out by PCR amplification of ZFX/ZFY and Y chromosome-specific sequences. Prion protein genotype determination was performed on codons 142, 154, 211, 222 and 240. Embryos were collected at day 7 after oestrus and biopsied either immediately after collection (blastocysts and expanded blastocysts) or after 24 h of in vitro culture (compacted morulae). Biopsied embryos were frozen by vitrification. Vitrified whole embryos were kept as control. DNA of biopsies was extracted and amplified using MDA. Sex diagnosis was efficient for 97.4% of biopsies and PRNP genotyping was determined in 78.7% of biopsies. After embryo transfer, no significant difference was observed in kidding rate between biopsied and vitrified control embryos, whereas embryo survival rate was different between biopsied and whole vitrified embryos (p = 0.032). At birth, 100% of diagnosed sex and 98.2% of predetermined codons were correct. Offspring PRNP profiles were in agreement with parental genotype. Whole genome amplification with MDA kit coupled with sex diagnosis and PRNP genotype predetermination are very accurate techniques to genotype goat embryos before transfer. These novel results allow us to plan selection of scrapie-resistant genotypes and kid sex before transfer of cryopreserved embryo.

  15. 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...

  16. Evaluation of allelopathic potential of safflower genotypes (Carthamus tinctorius L.

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    Motamedi Marzieh

    2016-12-01

    Full Text Available Forty safflower genotypes were grown under normal irrigation and drought stress. In the first experiment, the allelopathic potential of shoot residues was evaluated using the sandwich method. Each genotype residue (0.4 g was placed in a sterile Petri dish and two layers of agar were poured on that. Radish seeds were placed on agar medium. The radish seeds were cultivated without safflower residues as the controls. The length of the radicle, hypocotyl, and fresh biomass weight and seed germination percentages were measured. A pot experiment was also done on two genotypes with the highest and two with the lowest allelopathic activity selected after screening genotypes in the first experiment. Before entering the reproductive phase, irrigation treatments (normal irrigation and drought stress were applied. Shoots were harvested, dried, milled and mixed with the topsoil of new pots and then radish seeds were sown. The pots with safflower genotypes were used to evaluate the effect of root residue allelopathy. The shoot length, fresh biomass weight, and germination percentage were measured. Different safflower genotypes showed varied allelopathic potential. The results of the first experiment showed that Egypt and Iran-Khorasan genotypes caused maximum inhibitory responses and Australia and Iran-Kerman genotypes resulted in minimum inhibitory responses on radish seedling growth. Fresh biomass weight had the most sensitivity to safflower residues. The results of the pot experiment were consistent with the results of in vitro experiments. Residues produced under drought stress had more inhibitory effects on the measured traits. Safflower root residue may have a higher level of allelochemicals or different allelochemicals than shoot residue.

  17. Genotype and SNP calling from next-generation sequencing data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Paul, Joshua S.; Albrechtsen, Anders

    2011-01-01

    Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated w...... with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies....

  18. DURABILITY OF ASPHALT CONCRETE MIXTURES USING DOLOMITE AGGREGATES

    Directory of Open Access Journals (Sweden)

    Imad Al-Shalout

    2015-12-01

    Full Text Available This study deals with the durability of asphalt concrete, including the effects of different gradations, compaction temperatures and immersion time on the durability potential of mixtures. The specific objectives of this study are: to investigate the effect of compaction temperature on the mechanical properties of asphalt concrete mixtures; investigate the effect of bitumen content and different aggregate gradations on the durability potential of bituminous mixtures.

  19. Antiandrogenic activity of phthalate mixtures: Validity of concentration addition

    Energy Technology Data Exchange (ETDEWEB)

    Christen, Verena [University of Applied Sciences Northwestern Switzerland, School of Life Sciences, Gründenstrasse 40, CH-4132 Muttenz (Switzerland); Crettaz, Pierre; Oberli-Schrämmli, Aurelia [Swiss Federal Office of Public Health, Division Chemical Products, 3003 Bern (Switzerland); Fent, Karl, E-mail: karl.fent@bluewin.ch [University of Applied Sciences Northwestern Switzerland, School of Life Sciences, Gründenstrasse 40, CH-4132 Muttenz (Switzerland); Swiss Federal Institute of Technology Zürich (ETH Zürich), Department of Environmental Sciences, 8092 Zürich (Switzerland)

    2012-03-01

    Phthalates and bisphenol A have very widespread use leading to significant exposure of humans. They are suspected to interfere with the endocrine system, including the androgen, estrogen and the thyroid hormone system. Here we analyzed the antiandrogenic activity of six binary, and one ternary mixture of phthalates exhibiting complete antiandrogenic dose–response curves, and binary mixtures of phthalates and bisphenol A at equi-effective concentrations of EC{sub 10}, EC{sub 25} and EC{sub 50} in MDA-kb2 cells. Mixture activity followed the concentration addition (CA) model with a tendency to synergism at high and antagonism at low concentrations. Isoboles and the toxic unit approach (TUA) confirmed the additive to synergistic activity of the binary mixtures BBP + DBP, DBP + DEP and DEP + BPA at high concentrations. Both methods indicate a tendency to antagonism for the EC{sub 10} mixtures BBP + DBP, BBP + DEP and DBP + DEP, and the EC{sub 25} mixture of DBP + BPA. A ternary mixture revealed synergism at the EC{sub 50}, and weak antagonistic activity at the EC{sub 25} level by the TUA. A mixture of five phthalates representing a human urine composition and reflecting exposure to corresponding parent compounds showed no antiandrogenic activity. Our study demonstrates that CA is an appropriate concept to account for mixture effects of antiandrogenic phthalates and bisphenol A. The interaction indicates a departure from additivity to antagonism at low concentrations, probably due to interaction with the androgen receptor and/or cofactors. This study emphasizes that a risk assessment of phthalates should account for mixture effects by applying the CA concept. -- Highlights: ► Antiandrogenic activity of mixtures of 2 and 3 phthalates are assessed in MDA-kb2 cells. ► Mixture activities followed the concentration addition model. ► A tendency to synergism at high and antagonism at low levels occurred.

  20. Determination of thermal conductivity in foundry mould mixtures

    Directory of Open Access Journals (Sweden)

    G. Solenički

    2010-01-01

    Full Text Available For a thorough understanding of the behaviour of foundry mould mixtures, a good knowledge of thermal properties of mould materials is needed. Laboratory determination of thermal conductivity of mould mixtures enables a better control over scabbing defects which are a major problem in green sand mould mixtures. A special instrument has been designed for that purpose and it is described in this work.

  1. Tails assumptions and posterior concentration rates for mixtures of Gaussians

    OpenAIRE

    Naulet, Zacharie; Rousseau, Judith

    2016-01-01

    Nowadays in density estimation, posterior rates of convergence for location and location-scale mixtures of Gaussians are only known under light-tail assumptions; with better rates achieved by location mixtures. It is conjectured, but not proved, that the situation should be reversed under heavy tails assumptions. The conjecture is based on the feeling that there is no need to achieve a good order of approximation in regions with few data (say, in the tails), favoring location-scale mixtures w...

  2. Constrained Fisher Scoring for a Mixture of Factor Analyzers

    Science.gov (United States)

    2016-09-01

    global appearance model across the entire sensor network. constrained maximum likelihood estimation, mixture of factor analyzers, Newton’s method...ARL-TR-7836• SEP 2016 US Army Research Laboratory Constrained Fisher Scoring for a Mixture of Factor Analyzers by Gene T Whipps, Emre Ertin, and...TR-7836• SEP 2016 US Army Research Laboratory Constrained Fisher Scoring for a Mixture of Factor Analyzers by Gene T Whipps Sensors and Electron

  3. Performance of genotype-MTBDR test directly on clinical specimens

    Directory of Open Access Journals (Sweden)

    Gülden Yılmaz

    2012-12-01

    Full Text Available Objectives: Most important point for the control and effective treatment of multidrug resistant tuberculosis (MDR-TBis early diagnosis and rapid determination of the resistance. The aim of this study is to assess the performance of theGenotype-MTBDR assay applied directly on sputum samples and compare the results with those obtained by DNA sequencingand phenotypic susceptibility testing.Materials and methods: Between November 2005 and February 2006, 93 smear and culture positive sputum sampleswere included in the study. Drug susceptibility results for rifampin (RIF and isoniazid (INH, obtained by proportionmethod on L-J medium, Genotype-MTBDR and DNA sequencing were compared.Results: The rate of concordance between the results of the Genotype-MTBDR and DNA sequencing was 93.5% and96.7% for RIF and INH, respectively. Moreover, Genotype-MTBDR detected all the RIF (24 and INH (18 resistant strainsobtained by sequencing (100%. Compared to the DNA sequencing method; the sensitivity, specificity, positive predictiveand negative predictive value for RIF and INH were 100%, 91.3%, 80%, 100% and 100%, 96%, 85.7%, 100% respectively.Conclusion: Genotype-MTBDR, one of molecular assays, distinctly shortens the time for diagnosis and detection of resistanceto INH and RIF, essential for management of MDR-TB. The test appears to have good sensitivity and specificitywhen also used directly on sputum specimens. J Microbiol Infect Dis 2012; 2(4: 135-141Key words: Mycobacterium tuberculosis; drug resistance; genotype-MTBDR.

  4. Genetic diversity of some chili (Capsicum annuum L. genotypes

    Directory of Open Access Journals (Sweden)

    M.J. Hasan

    2014-06-01

    Full Text Available A study on genetic diversity was conducted with 54 Chili (Capsicum annuum L. genotypes through Mohalanobis’s D2 and principal component analysis for twelve quantitative characters viz. plant height, number of secondary branch/plant, canopy breadth , days to first flowering, days to 50% flowering, fruits/plant, 5 fruits weight, fruit length, fruit diameter, seeds/fruit, 1000 seed weight and yield/plant were taken into consideration. Cluster analysis was used for grouping of 54 chili genotypes and the genotypes were fallen into seven clusters. Cluster II had maximum (13 and cluster III had the minimum number (1 of genotypes. The highest inter-cluster distance was observed between cluster I and III and the lowest between cluster II and VII. The characters yield/plant, canopy breadth, secondary branches/plant, plant height and seeds/fruit contributed most for divergence in the studied genotypes. Considering group distance, mean performance and variability the inter genotypic crosses between cluster I and cluster III, cluster III and cluster VI, cluster II and cluster III and cluster III and cluster VII may be suggested to use for future hybridization program.

  5. Genotyping panel for assessing response to cancer chemotherapy

    Directory of Open Access Journals (Sweden)

    Hampel Heather

    2008-06-01

    Full Text Available Abstract Background Variants in numerous genes are thought to affect the success or failure of cancer chemotherapy. Interindividual variability can result from genes involved in drug metabolism and transport, drug targets (receptors, enzymes, etc, and proteins relevant to cell survival (e.g., cell cycle, DNA repair, and apoptosis. The purpose of the current study is to establish a flexible, cost-effective, high-throughput genotyping platform for candidate genes involved in chemoresistance and -sensitivity, and treatment outcomes. Methods We have adopted SNPlex for genotyping 432 single nucleotide polymorphisms (SNPs in 160 candidate genes implicated in response to anticancer chemotherapy. Results The genotyping panels were applied to 39 patients with chronic lymphocytic leukemia undergoing flavopiridol chemotherapy, and 90 patients with colorectal cancer. 408 SNPs (94% produced successful genotyping results. Additional genotyping methods were established for polymorphisms undetectable by SNPlex, including multiplexed SNaPshot for CYP2D6 SNPs, and PCR amplification with fluorescently labeled primers for the UGT1A1 promoter (TAnTAA repeat polymorphism. Conclusion This genotyping panel is useful for supporting clinical anticancer drug trials to identify polymorphisms that contribute to interindividual variability in drug response. Availability of population genetic data across multiple studies has the potential to yield genetic biomarkers for optimizing anticancer therapy.

  6. Genotyping of Rotavirus by Using RT-PCR Methods

    Directory of Open Access Journals (Sweden)

    Hera Nirwati

    2015-11-01

    Full Text Available There is a great diversity of rotavirus genotypes circulating worldwide, with dominant genotypes changing from year to year. Rotavirus genotyping was performed by using reverse transcription PCR with type-specifi c-primers. Since rotavirus is a RNA virus that has high mutation rate, there was a possibility of technical diffi culty in genotyping due to mutation in the primer binding sites. During Indonesian rotavirus surveillance study 2006-2009, it was reported that 17% of samples subjected for G type and 21% of samplessubjected for P type were untypeable. The objective of this study was to identify genotypes of the samples that were untypeable previously using RT-PCR based on the method described by Das et al. (1994 and Gentsch et al. (1992. There were 30 samples subjected to G type and 61 samples subjected to P type to be re-typed using method described by Gouvea et al. (1990 and Simmond et al. (2008 for G and P typing, respectively. By using another set of primer, the genotype of all samples was identifi ed. This study highlights the importance of a constant reconsideration of primer sequences employed for the molecular typing of rotaviruses.Key words: rotavirus, G typing, P typing

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Methylenetetrahydrofolate Reductase Genotypes, Dietary Habits and Susceptibility to Stomach Cancer

    Institute of Scientific and Technical Information of China (English)

    ChangmingGao; TakezakiToshiro; JianzhongWu; JianhuoDing; YantingLiu; SupingLi; PingSu; XuHu; TianliongXu; HamajimaNobuyuki; TajimaKazuo

    2004-01-01

    OBJECTIVE To study the relation among methylenetetrahydrofolate reductase (MTHFR) C677T genotypes, dietary habits and the risk of stomach cancer (SC).METHODS A case-control study was conducted with 107 cases of SC and 200 population-based controls in Chuzhou district, Huaian, Jiangsu province, China. The epidemiological data were collected, and DNA of peripheral blood leukocytes was obtained from all of the subjects..MTHFR genotypes were detected by PCR-RFLP. RESULTS (1) The prevalence of the MTHFR C/T or T/T genotypes was found to be significantly different between controls (68.5%) and SC cases (79.4%,P=0.0416), the increased risk had an adjusted OR of 1.79 (95%C1:1.01-3.19). (2) Among subjects who had a low intake of garlic or Chinese onion, MTHFR C/T or T/T genotypes significantly increased the risk of developing SC. Among non-tea drinkers or among subjects who had a frequent intakeof meat, the carriers of the MTHFR C/T or T/T genotypes had a higher risk of SC than individuals with the C/C type MTHFR. CONCLUSION The polymorphism of MTHFR C677T was associated with increased risk of developing SC, and that individuals with differing genotypes may have different susceptibilities to SC, based on their exposure level to environmental factors.

  9. Differential activation of dendritic cells by Mycobacterium tuberculosis Beijing genotype.

    Science.gov (United States)

    Reyes-Martínez, Juana Elizabeth; Nieto-Patlán, Erik; Nieto-Patlán, Alejandro; Gonzaga-Bernachi, Job; Santos-Mendoza, Teresa; Serafín-López, Jeanet; Chávez-Blanco, Alma; Sandoval-Montes, Claudia; Flores-Romo, Leopoldo; Estrada-Parra, Sergio; Estrada-García, Iris; Chacón-Salinas, Rommel

    2014-01-01

    Mycobacterium tuberculosis (Mtb) inhibits dendritric cells (DC) function in order to delay T cell response. Furthermore, there is increasing evidence that genetic diversity of Mtb strains can affect their interaction with the immune system. Beijing genotype has attracted attention because of its high prevalence and multi-drug resistance. Although it is known that this genotype is hypervirulent and differentially activates macrophages when compared to other genotypes, little is known about its interaction with DC. In order to address this issue, murine bone marrow derived DC (BMDC) were stimulated with soluble extracts (SE) from BCG, H37Rv, Canetti and Beijing genotypes. We observed that unlike other mycobacteria strains, SE-Beijing was unable to induce maturation of DC as assessed by cell surface MHC-II expression. DC stimulated with SE-Beijing failed to produce IL-12 and TNF-α, but did secrete IL-10. Interestingly, SE-Beijing induced CCR7 and PDL-1 on BMDC, but did not induce the expression of CD86. When BMDC stimulated with SE-Beijing were used to activate CD4+ cells they were unable to induce a Th1 response when compared with less virulent genotypes. These results indicate that Beijing is able to modulate DC activation and function, which may be related to the pathogenesis induced by this genotype.

  10. Mixtures of conditional Gaussian scale mixtures applied to multiscale image representations.

    Directory of Open Access Journals (Sweden)

    Lucas Theis

    Full Text Available We present a probabilistic model for natural images that is based on mixtures of Gaussian scale mixtures and a simple multiscale representation. We show that it is able to generate images with interesting higher-order correlations when trained on natural images or samples from an occlusion-based model. More importantly, our multiscale model allows for a principled evaluation. While it is easy to generate visually appealing images, we demonstrate that our model also yields the best performance reported to date when evaluated with respect to the cross-entropy rate, a measure tightly linked to the average log-likelihood. The ability to quantitatively evaluate our model differentiates it from other multiscale models, for which evaluation of these kinds of measures is usually intractable.

  11. Use of multiline cultivars and cultivar mixtures for disease management.

    Science.gov (United States)

    Mundt, C C

    2002-01-01

    The usefulness of mixtures (multiline cultivars and cultivar mixtures) for disease management has been well demonstrated for rusts and powdery mildews of small grain crops. Such mixtures are more useful under some epidemiological conditions than under others, and experimental methodology, especially problems of scale, may be crucial in evaluating the potential efficacy of mixtures on disease. There are now examples of mixtures providing both low and high degrees of disease control for a wide range of pathosystems, including crops with large plants, and pathogens that demonstrate low host specificity, or are splash dispersed, soilborne, or insect vectored. Though most analyses of pathogen evolution in mixtures consider static costs of virulence to be the main mechanism countering selection for pathogen complexity, many other potential mechanisms need to be investigated. Agronomic and marketing considerations must be carefully evaluated when implementing mixture approaches to crop management. Practical difficulties associated with mixtures have often been overestimated, however, and mixtures will likely play an increasingly important role as we develop more sustainable agricultural systems.

  12. UTILIZATION OF WASTE PLASTIC BOTTLES IN ASPHALT MIXTURE

    Directory of Open Access Journals (Sweden)

    TAHER BAGHAEE MOGHADDAM

    2013-06-01

    Full Text Available Nowadays, large amounts of waste materials are being produced in the world. One of the waste materials is plastic bottle. Generating disposable plastic bottles is becoming a major problem in many countries. Using waste plastic as a secondary material in construction projects would be a solution to overcome the crisis of producing large amount of waste plastics in one hand and improving the structure’s characteristics such as resistance against cracking on the other hand. This study aimed to investigate the effects of adding plastic bottles in road pavement. Marshall properties as well as specific gravity of asphalt mixture containing different percentages of plastic bottles were evaluated. Besides, Optimum Asphalt Content (OAC was calculated for each percentages of plastic bottles used in the mix. The stiffness and fatigue characteristics of mixture were assessed at OAC value. Results showed that the stability and flow values of asphalt mixture increased by adding waste crushed plastic bottle into the asphalt mixture. Further, it was shown that the bulk specific gravity and stiffness of mixtures increased by adding lower amount of plastic bottles; however, adding higher amounts of plastic resulted in lower specific gravity and mix stiffness. In addition, it was concluded that the mixtures containing waste plastic bottles have lower OAC values compared to the conventional mixture, and this may reduce the amount of asphalt binder can be used in road construction projects. Besides, the mixtures containing waste plastic showed significantly greater fatigue resistance than the conventional mixture.

  13. [Construction of Three-Dimensional Isobologram for Ternary Pollutant Mixtures].

    Science.gov (United States)

    2015-12-01

    Tongji University, Shanghai 200092, China) Isobolographic analysis was widely used in the interaction assessment of binary mixtures. However, how to construct a three-dimensional (3D) isobologram for the assessment of toxicity interaction within ternary mixtures is still not reported up to date. The main purpose of this paper is to develop a 3D isobologram where the relative concentrations of three components are acted as three coordinate axes in 3D space to examine the toxicity interaction within ternary mixtures. Taking six commonly used pesticides in China, including three herbicides (2, 4-D, desmetryne and simetryn) and three insecticides ( dimethoate, imidacloprid and propoxur) as the mixture components, the uniform design ray procedure (UD-Ray) was used to rationally design the concentration composition of various components in the ternary mixtures so that effectively and comprehensively reflected the variety of actual environmental concentrations. The luminescent inhibition toxicities of single pesticides and their ternary mixtures to Vibrio fischeri at various concentration levels were determined by the microplate toxicity analysis. Selecting concentration addition (CA) as the addition reference, 3D isobolograms were constructed to study the toxicity interactions of various ternary mixtures. The results showed that the 3D isobologram could clearly and directly exhibit the toxicity interactions of ternary mixtures, and extend the use of isobolographic analysis into the ternary mixtures.

  14. Calculation and Analysis of Mean Opacity of Gold Mixtures

    Institute of Scientific and Technical Information of China (English)

    YAN An-ying; JIANG Ming; CHENG Xin-lu; YANG Xiang-dong

    2007-01-01

    A screened hydrogenic model for l splitting (SHML) is used to calculate the Rosseland mean opacities of high-Z Au, Ta, Yb, Ho, Gd, Sm, Nd, Sn, Ag plasmas and mixtures of gold and these elements at high temperature (T=200-400eV) and dense (ρ=1g/cm3).From the calculated Rosseland mean opacities of the mixtures, Au-Nd seems to be a better choice than other mixtures.Simultaneously, the reason that the mean opacities of mixture of Au-Sn decrease slightly when T=400eV is analyzed.

  15. Swelling characteristics of immersed sand-bentonite mixtures

    Institute of Scientific and Technical Information of China (English)

    丰土根; 崔红斌; 孙德安; 杜冰

    2008-01-01

    A laboratory one-dimensional consolidation apparatus was employed to research the swelling stress and volume of the sand-bentonite mixture under immersed conditions. The stress-strain characteristics of mixtures under varied mixing ratios and loading statuses were analyzed. Based on the results of tests, the mechanism of mixture swelling and collapsing was further discussed. The results show that mixtures with low sand ratios are suitable as hydraulic barrier or containment barriers of general landfills, geological repository and other hydraulic infrastructure works.

  16. Physical Stability of Freeze-Dried Isomalt Diastereomer Mixtures

    DEFF Research Database (Denmark)

    Koskinen, Anna-Kaisa; Fraser-Miller, Sara J.; Bøtker, Johan P.

    2016-01-01

    of the diastereomer compositions showed signs of physical instability when stored in the highest relative humidity condition. The four different crystalline diastereomer mixtures showed specific identifiable solid state properties. Conclusions Isomalt was shown to be a suitable excipient for freeze-drying. Preferably...... a mixture of the diastereomers should be used, as the mixture containing only one of the isomers showed physical instability. A mixture containing a 1:1 ratio of the two diastereomers showed the best physical stability in the amorphous form....

  17. Opacity Calculations for Non-Local Thermodynamic Equilibrium Mixtures

    Institute of Scientific and Technical Information of China (English)

    吴泽清; 韩国兴; 逄锦桥

    2002-01-01

    Based on the average atom model, a non-local thermodynamic equilibrium (non-LTE) model is developed to calculate opacity for mixtures. This model could be applied to high-Z problems. The mean ionization degrees of SiO2 of the present calculation are slightly higher compared with another model for mixtures. As an example, the opacity of Au and Nd mixture is calculated. The results show concrete non-LTE effects and the increase in opacity of the mixture is shown clearly.

  18. Moisture sensitivity examination of asphalt mixtures using thermodynamic, direct adhesion peel and compacted mixture mechanical tests

    OpenAIRE

    Zhang, Jizhe; AIREY, Gordon D; Grenfell, James; Apeagyei, Alex K.

    2016-01-01

    Moisture damage in asphalt mixtures is a complicated mode of pavement distress that results in the loss of stiffness and structural strength of the asphalt pavement layers. This paper evaluated the moisture sensitivity of different aggregate–bitumen combinations through three different approaches: surface energy, peel adhesion and the Saturation Ageing Tensile Stiffness (SATS) tests. In addition, the results obtained from these three tests were compared so as to characterise the relationship ...

  19. Porous concrete mixtures for pervious urban pavements

    Directory of Open Access Journals (Sweden)

    Castro, J.

    2007-08-01

    Full Text Available The present study aimed to analyze the hydraulic and mechanical behaviour of a series of roller-compacted, laboratory porous concrete mixtures. The mix design variables examined were the actual void ratio in the hardened concrete and the water/cement ratio. From these results the better dosages from the mechanical and hydraulical behaviour point of view were determined. One of the designs developed was found to exhibit excellent hydraulic capacity and 20% greater strength than the mixtures recommended in the literature. Moreover, concrete with an actual void ratio of only 14% was observed to meet permeability requirements. Maximum flexural strength of concretes with different w/c ratios was achieved with a cement paste content of 250 l/m3. Relationships were found between the void ratio and both 28-day concrete permeability and flexural strength. Finally, the doses exhibiting the best mechanical and hydraulic performance were identified.El trabajo realizado en este estudio consistió en analizar el comportamiento de diferentes dosificaciones de mezclas de hormigón poroso, fabricadas en laboratorio y compactadas con rodillo pesado para simular las condiciones de terreno. Las variables consideradas para el diseño de las mezclas fueron el porcentaje real de huecos en el hormigón endurecido y la razón agua/cemento. A partir de estos resultados se determinaron las dosificaciones que presentan mejor comportamiento desde el punto de vista mecánico e hidráulico. Los resultados muestran que existe una dosificación de hormigón poroso, distinta a las encontradas actualmente en la literatura internacional, que permite obtener resistencias hasta 20% más altas, manteniendo todavía una excelente capacidad hidráulica. Se determinó que una permeabilidad suficiente se puede obtener con un porcentaje real de huecos de 14%, y que agregar pasta de cemento en una proporción de 250 l/m3 permite maximizar la resistencia a flexotracción de hormigones que

  20. Realistic environmental mixtures of micropollutants in surface, drinking, and recycled water: herbicides dominate the mixture toxicity toward algae.

    Science.gov (United States)

    Tang, Janet Y M; Escher, Beate I

    2014-06-01

    Mixture toxicity studies with herbicides have focused on a few priority components that are most likely to cause environmental impacts, and experimental mixtures were often designed as equipotent mixtures; however, real-world mixtures are made up of chemicals with different modes of toxic action at arbitrary concentration ratios. The toxicological significance of environmentally realistic mixtures has only been scarcely studied. Few studies have simultaneously compared the mixture effect of water samples with designed reference mixtures comprised of the ratios of analytically detected concentrations in toxicity tests. In the present study, the authors address the effect of herbicides and other chemicals on inhibition of photosynthesis and algal growth rate. The authors tested water samples including secondary treated wastewater effluent, recycled water, drinking water, and storm water in the combined algae assay. The detected chemicals were mixed in the concentration ratios detected, and the biological effects of the water samples were compared with the designed mixtures of individual detected chemicals to quantify the fraction of effect caused by unknown chemicals. The results showed that herbicides dominated the algal toxicity in these environmentally realistic mixtures, and the contribution by the non-herbicides was negligible. A 2-stage model, which used concentration addition within the groups of herbicides and non-herbicides followed by the model of independent action to predict the mixture effect of the two groups, could predict the experimental mixture toxicity effectively, but the concentration addition model for herbicides was robust and sufficient for complex mixtures. Therefore, the authors used the bioanalytical equivalency concept to derive effect-based trigger values for algal toxicity for monitoring water quality in recycled and surface water. All water samples tested would be compliant with the proposed trigger values associated with the