Sample records for repeat analysis method

  1. On summary measure analysis of linear trend repeated measures data: performance comparison with two competing methods. (United States)

    Vossoughi, Mehrdad; Ayatollahi, S M T; Towhidi, Mina; Ketabchi, Farzaneh


    The summary measure approach (SMA) is sometimes the only applicable tool for the analysis of repeated measurements in medical research, especially when the number of measurements is relatively large. This study aimed to describe techniques based on summary measures for the analysis of linear trend repeated measures data and then to compare performances of SMA, linear mixed model (LMM), and unstructured multivariate approach (UMA). Practical guidelines based on the least squares regression slope and mean of response over time for each subject were provided to test time, group, and interaction effects. Through Monte Carlo simulation studies, the efficacy of SMA vs. LMM and traditional UMA, under different types of covariance structures, was illustrated. All the methods were also employed to analyze two real data examples. Based on the simulation and example results, it was found that the SMA completely dominated the traditional UMA and performed convincingly close to the best-fitting LMM in testing all the effects. However, the LMM was not often robust and led to non-sensible results when the covariance structure for errors was misspecified. The results emphasized discarding the UMA which often yielded extremely conservative inferences as to such data. It was shown that summary measure is a simple, safe and powerful approach in which the loss of efficiency compared to the best-fitting LMM was generally negligible. The SMA is recommended as the first choice to reliably analyze the linear trend data with a moderate to large number of measurements and/or small to moderate sample sizes.

  2. A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes. (United States)

    Hauck, Yolande; Soler, Charles; Gérôme, Patrick; Vong, Rithy; Macnab, Christine; Appere, Géraldine; Vergnaud, Gilles; Pourcel, Christine


    Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS6110 Insertions and Tandem Repeat Analysis

    Directory of Open Access Journals (Sweden)

    Eriko Maeda-Mitani


    Full Text Available QUB11a is used as a locus for variable number of tandem repeats (VNTR analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp investigated contained IS6110 insertions and varied in the number of repeats (18 patterns and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.

  4. Image analysis as a non-destructive method to assess regrowth of weeds after repeated flame weeding

    DEFF Research Database (Denmark)

    Rask, Anne Merete; Kristoffersen, Palle; Andreasen, Christian


    picture of the long-term effect of repeated treatments. Image analysis was most useful for assessing the effect of repeated treatments when weed cover was relatively low (below 40%) and when plots contained relatively much withered plant material. However, when weed cover is close to 100%, dry weight......, and therefore it may influence the long-term effect of repeated treatments. Visual assessment of weed cover or image analysis do not affect the remaining parts of the weed plants after treatment, but the methods may have other disadvantages. In order to evaluate and compare three methods we measured changes...... in vegetation cover of perennial ryegrass after flaming by (1) a simple image analysis programme counting green pixels, (2) visual assessment of images and (3) by taking biomass samples. Plants were flame treated with eight different dosages (0, 20, 30, 35, 45, 60, 90 and 180 kg propane ha-1) and with various...

  5. Determinants and Experiences of Repeat Pregnancy among HIV-Positive Kenyan Women--A Mixed-Methods Analysis.

    Directory of Open Access Journals (Sweden)

    Victor Akelo

    Full Text Available To identify factors associated with repeat pregnancy subsequent to an index pregnancy among women living with HIV (WLWH in western Kenya who were enrolled in a 24-month phase-II clinical trial of triple-ART prophylaxis for prevention of mother-to-child transmission, and to contextualize social and cultural influences on WLWH's reproductive decision making.A mixed-methods approach was used to examine repeat pregnancy within a 24 month period after birth. Counselor-administered questionnaires were collected from 500 WLWH. Forty women (22 with a repeat pregnancy; 18 with no repeat pregnancy were purposively selected for a qualitative interview (QI. Simple and multiple logistic regression analyses were performed for quantitative data. Thematic coding and saliency analysis were undertaken for qualitative data.Eighty-eight (17.6% women had a repeat pregnancy. Median maternal age was 23 years (range 15-43 years and median gestational age at enrollment was 34 weeks. In multiple logistic regression analyses, living in the same compound with a husband (adjusted odds ratio (AOR: 2.33; 95% confidence interval (CI: 1.14, 4.75 was associated with increased odds of repeat pregnancy (p ≤ 0.05. Being in the 30-43 age group (AOR: 0.25; 95% CI: 0.07, 0.87, having talked to a partner about family planning (FP use (AOR: 0.53; 95% CI: 0.29, 0.98, and prior usage of FP (AOR: 0.45; 95% CI: 0.25, 0.82 were associated with a decrease in odds of repeat pregnancy. QI findings centered on concerns about modern contraception methods (side effects and views that they 'ruined the womb' and a desire to have the right number of children. Religious leaders, family, and the broader community were viewed as reinforcing cultural expectations for married women to have children. Repeat pregnancy was commonly attributed to contraception failure or to lack of knowledge about post-delivery fertility.In addition to cultural context, reproductive health programs for WLWH may need to

  6. A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions. (United States)

    Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon


    Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

  7. Methods for analysing cardiovascular studies with repeated measures

    NARCIS (Netherlands)

    Cleophas, T. J.; Zwinderman, A. H.; van Ouwerkerk, B. M.


    Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects. Objective. To review methods adequate for the analysis of cardiovascular studies

  8. Development of systematic evaluation method on nonlinear behavior of the constructions using repeated finite element method analysis

    International Nuclear Information System (INIS)

    Kasahara, Naoto


    Supposing that the nuclear reactor stops on any reason, the temperature of flown out coolant from the reactor core will decrease and the temperature of elements touched with the coolant in the nuclear plant equipments also decreases on response to this. On the other hand, temperature pursuit at non-touched portions is delayed to form a thermal stress due to their temperature difference. In particular, a stress over its yield value at discontinuous portion of structure due to stress concentration generates, which could be thought of possibility to form a creep fatigue crack if repeating such thermal stress under high temperature. The Power Reactor and Nuclear Fuel Development Corporation has developed the transient thermal stress real time simulation code for calculating thermal stress formed within a construction in accompany with temperature changes of the coolant once and at high speed since 1994 FY, and after 1995 FY the development of FEM simulation technique from macroscopic region to microscopic region which set an objective regions from construction level to material texture has been promoted. In future, development of total simulation technique connected both and optimum design technique due to its results will be planned. (G.K.)

  9. Analysis of repeated measures data

    CERN Document Server

    Islam, M Ataharul


    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  10. Objectivity of two methods of differentiating fibre types and repeatability of measurements by application of the TEMA image analysis system. (United States)

    Henckel, P; Ducro, B; Oksbjerg, N; Hassing, L


    The objectivity of two of the most widely used methods for differentiation of fibre types, i.e. 1) the myosin ATP-ase method (Brooke and Kaiser, 1970a,b) and 2) the combined method, by which the myosin ATP-ase reaction is used to differentiate between fast and slow twitch fibres and NADH-tetrazolium reductase activity is used to identify the subgroups of fast twitch fibres (Ashmore and Doerr, 1970, Peter et al., 1972), was assessed in muscle samples from horses, calves and pigs. We also assessed the objectivity of the alpha-amylase-PAS preparation for the visualisation of capillaries (Andersen, 1975) in these species. For the purpose of reducing the time costs of histochemical analysis of muscle samples, we have developed an interactive image analysis system which is described. All analyses are performed on this system. In accordance with several other investigations, differences between the two methods of differentiating fibre types were found only for the relative distribution of the fast-twitch fibre subgroups (p 87%), the impact of differences in pre-requisites (varied degrees of overlap between the fibre types) for performing the differentiation by the combined method raises a question of the reliability of this method. Apparently, no general rules for comparison of results of distribution of the two subgroups of fast twitch fibres by the two methods are applicable. The alpha-amylase-PAS method was found to be a fairly objective method to identify capillaries in muscles from horses, calves and pigs. However, as capillarity described in combination with other traits to give an indication of diffusion characteristics is significantly influenced by person, it is recommended that the same person perform all the analysis of a project. In addition to the methodological results in this study, we have shown that by application of the TEMA image analysis system, which is more rapid compared with the time-consuming traditional method for evaluation of histochemical

  11. The method of purging applied to repeated cross-sectional data: Practical applications using logistic and linear regression analysis

    NARCIS (Netherlands)

    Grotenhuis, H.F. te; Eisinga, R.N.; Scheepers, P.L.H.


    In cross-sectional survey research, it is quite common to estimate the(standardized) effect of independent variable(s) on a dependent variable. However, if repeated cross-sectional data are available, much is to be gained if the consequences of these effects on longitudinal social change are

  12. Digital repeat analysis; setup and operation. (United States)

    Nol, J; Isouard, G; Mirecki, J


    Since the emergence of digital imaging, there have been questions about the necessity of continuing reject analysis programs in imaging departments to evaluate performance and quality. As a marketing strategy, most suppliers of digital technology focus on the supremacy of the technology and its ability to reduce the number of repeats, resulting in less radiation doses given to patients and increased productivity in the department. On the other hand, quality assurance radiographers and radiologists believe that repeats are mainly related to positioning skills, and repeat analysis is the main tool to plan training needs to up-skill radiographers. A comparative study between conventional and digital imaging was undertaken to compare outcomes and evaluate the need for reject analysis. However, digital technology still being at its early development stages, setting a credible reject analysis program became the major task of the study. It took the department, with the help of the suppliers of the computed radiography reader and the picture archiving and communication system, over 2 years of software enhancement to build a reliable digital repeat analysis system. The results were supportive of both philosophies; the number of repeats as a result of exposure factors was reduced dramatically; however, the percentage of repeats as a result of positioning skills was slightly on the increase for the simple reason that some rejects in the conventional system qualifying for both exposure and positioning errors were classified as exposure error. The ability of digitally adjusting dark or light images reclassified some of those images as positioning errors.

  13. Repeatability study of replicate crash tests: A signal analysis approach. (United States)

    Seppi, Jeremy; Toczyski, Jacek; Crandall, Jeff R; Kerrigan, Jason


    To provide an objective basis on which to evaluate the repeatability of vehicle crash test methods, a recently developed signal analysis method was used to evaluate correlation of sensor time history data between replicate vehicle crash tests. The goal of this study was to evaluate the repeatability of rollover crash tests performed with the Dynamic Rollover Test System (DRoTS) relative to other vehicle crash test methods. Test data from DRoTS tests, deceleration rollover sled (DRS) tests, frontal crash tests, frontal offset crash tests, small overlap crash tests, small overlap impact (SOI) crash tests, and oblique crash tests were obtained from the literature and publicly available databases (the NHTSA vehicle database and the Insurance Institute for Highway Safety TechData) to examine crash test repeatability. Signal analysis of the DRoTS tests showed that force and deformation time histories had good to excellent repeatability, whereas vehicle kinematics showed only fair repeatability due to the vehicle mounting method for one pair of tests and slightly dissimilar mass properties (2.2%) in a second pair of tests. Relative to the DRS, the DRoTS tests showed very similar or higher levels of repeatability in nearly all vehicle kinematic data signals with the exception of global X' (road direction of travel) velocity and displacement due to the functionality of the DRoTS fixture. Based on the average overall scoring metric of the dominant acceleration, DRoTS was found to be as repeatable as all other crash tests analyzed. Vertical force measures showed good repeatability and were on par with frontal crash barrier forces. Dynamic deformation measures showed good to excellent repeatability as opposed to poor repeatability seen in SOI and oblique deformation measures. Using the signal analysis method as outlined in this article, the DRoTS was shown to have the same or better repeatability of crash test methods used in government regulatory and consumer evaluation test

  14. Quantitative method for analysis of six anticoagulant rodenticides in faeces, applied in a case with repeated samples from a dog. (United States)

    Seljetun, Kristin Opdal; Eliassen, Elin; Karinen, Ritva; Moe, Lars; Vindenes, Vigdis


    Accidental poisoning with anticoagulant rodenticides is not uncommon in dogs, but few reports of the elimination kinetics and half-lives in this species have been published. Our objectives were to develop and validate a new method for the quantification of anticoagulant rodenticides in canine blood and faeces using reversed phase ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and apply the method on a case of anticoagulant rodenticide intoxication. Sample preparation was liquid-liquid extraction. Six anticoagulant rodenticides were separated using a UPLC ® BEH C 18 -column with a mobile phase consisting of 5 mM ammonium formate buffer pH 10.2 and methanol. MS/MS detection was performed with positive electrospray ionization and two multiple reaction monitoring transitions. The limits of quantification were set at the levels of the lowest calibrator (1.5-2.7 ng/mL or ng/g). The method was successfully applied to a case from a dog accidentally poisoned with anticoagulant rodenticide. Coumatetralyl and brodifacoum concentrations were determined from serial blood and faecal samples. A terminal half-life of at least 81 days for coumatetralyl in blood was estimated, which is longer than previous reported in other species. A slow elimination of brodifacoum from the faeces was found, with traces still detectable in the faeces at day 513. This study offers a new method of detection and quantification of six frequently used anticoagulant rodenticides in canine faeces. Such drugs might cause serious health effects and it is important to be able to detect these drugs, to initiate proper treatment. The very long elimination half-lives detected in our study is important to be aware of in assessment of anticoagulant rodenticide burden to the environment.

  15. Analysis of Longitudinal Studies With Repeated Outcome Measures: Adjusting for Time-Dependent Confounding Using Conventional Methods. (United States)

    Keogh, Ruth H; Daniel, Rhian M; VanderWeele, Tyler J; Vansteelandt, Stijn


    Estimation of causal effects of time-varying exposures using longitudinal data is a common problem in epidemiology. When there are time-varying confounders, which may include past outcomes, affected by prior exposure, standard regression methods can lead to bias. Methods such as inverse probability weighted estimation of marginal structural models have been developed to address this problem. However, in this paper we show how standard regression methods can be used, even in the presence of time-dependent confounding, to estimate the total effect of an exposure on a subsequent outcome by controlling appropriately for prior exposures, outcomes, and time-varying covariates. We refer to the resulting estimation approach as sequential conditional mean models (SCMMs), which can be fitted using generalized estimating equations. We outline this approach and describe how including propensity score adjustment is advantageous. We compare the causal effects being estimated using SCMMs and marginal structural models, and we compare the two approaches using simulations. SCMMs enable more precise inferences, with greater robustness against model misspecification via propensity score adjustment, and easily accommodate continuous exposures and interactions. A new test for direct effects of past exposures on a subsequent outcome is described.

  16. Development of a spatial analysis method using ground-based repeat photography to detect changes in the alpine treeline ecotone, Glacier National Park, Montana, U.S.A. (United States)

    Roush, W.; Munroe, Jeffrey S.; Fagre, D.B.


    Repeat photography is a powerful tool for detection of landscape change over decadal timescales. Here a novel method is presented that applies spatial analysis software to digital photo-pairs, allowing vegetation change to be categorized and quantified. This method is applied to 12 sites within the alpine treeline ecotone of Glacier National Park, Montana, and is used to examine vegetation changes over timescales ranging from 71 to 93 years. Tree cover at the treeline ecotone increased in 10 out of the 12 photo-pairs (mean increase of 60%). Establishment occurred at all sites, infilling occurred at 11 sites. To demonstrate the utility of this method, patterns of tree establishment at treeline are described and the possible causes of changes within the treeline ecotone are discussed. Local factors undoubtedly affect the magnitude and type of the observed changes, however the ubiquity of the increase in tree cover implies a common forcing mechanism. Mean minimum summer temperatures have increased by 1.5??C over the past century and, coupled with variations in the amount of early spring snow water equivalent, likely account for much of the increase in tree cover at the treeline ecotone. Lastly, shortcomings of this method are presented along with possible solutions and areas for future research. ?? 2007 Regents of the University of Colorado.

  17. Measurement System Analyses - Gauge Repeatability and Reproducibility Methods (United States)

    Cepova, Lenka; Kovacikova, Andrea; Cep, Robert; Klaput, Pavel; Mizera, Ondrej


    The submitted article focuses on a detailed explanation of the average and range method (Automotive Industry Action Group, Measurement System Analysis approach) and of the honest Gauge Repeatability and Reproducibility method (Evaluating the Measurement Process approach). The measured data (thickness of plastic parts) were evaluated by both methods and their results were compared on the basis of numerical evaluation. Both methods were additionally compared and their advantages and disadvantages were discussed. One difference between both methods is the calculation of variation components. The AIAG method calculates the variation components based on standard deviation (then a sum of variation components does not give 100 %) and the honest GRR study calculates the variation components based on variance, where the sum of all variation components (part to part variation, EV & AV) gives the total variation of 100 %. Acceptance of both methods among the professional society, future use, and acceptance by manufacturing industry were also discussed. Nowadays, the AIAG is the leading method in the industry.

  18. Longitudinal survey of Staphylococcus aureus in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method


    Vergnaud Gilles; Moissenet Didier; Corvol Harriet; Fauroux Brigitte; Corbineau Gaëlle; Hormigos Katia; Vu-Thien Hoang; Pourcel Christine


    Abstract Background Staphylococcus aureus infection in patients with cystic fibrosis (CF) is frequent and may be due to colonization by a few pathogenic lineages. Systematic genotyping of all isolates, methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) is necessary to identify such lineages and follow their evolution in patients. Multiple-locus variable-number tandem repeat analysis (MLVA/VNTR) was used to survey S. aureus clinical isolates in a French ...

  19. Short tandem repeat analysis in Japanese population. (United States)

    Hashiyada, M


    Short tandem repeats (STRs), known as microsatellites, are one of the most informative genetic markers for characterizing biological materials. Because of the relatively small size of STR alleles (generally 100-350 nucleotides), amplification by polymerase chain reaction (PCR) is relatively easy, affording a high sensitivity of detection. In addition, STR loci can be amplified simultaneously in a multiplex PCR. Thus, substantial information can be obtained in a single analysis with the benefits of using less template DNA, reducing labor, and reducing the contamination. We investigated 14 STR loci in a Japanese population living in Sendai by three multiplex PCR kits, GenePrint PowerPlex 1.1 and 2.2. Fluorescent STR System (Promega, Madison, WI, USA) and AmpF/STR Profiler (Perkin-Elmer, Norwalk, CT, USA). Genomic DNA was extracted using sodium dodecyl sulfate (SDS) proteinase K or Chelex 100 treatment followed by the phenol/chloroform extraction. PCR was performed according to the manufacturer's protocols. Electrophoresis was carried out on an ABI 377 sequencer and the alleles were determined by GeneScan 2.0.2 software (Perkin-Elmer). In 14 STRs loci, statistical parameters indicated a relatively high rate, and no significant deviation from Hardy-Weinberg equilibrium was detected. We apply this STR system to paternity testing and forensic casework, e.g., personal identification in rape cases. This system is an effective tool in the forensic sciences to obtain information on individual identification.

  20. Insertion device and method for accurate and repeatable target insertion (United States)

    Gubeli, III, Joseph F.; Shinn, Michelle D.; Bevins, Michael E.; Dillon-Townes, Lawrence; Neil, George R.


    The present invention discloses a device and a method for inserting and positioning a target within a free electron laser, particle accelerator, or other such device that generates or utilizes a beam of energy or particles. The system includes a three-point registration mechanism that insures angular and translational accuracy and repeatability of positioning upon multiple insertions within the same structure.

  1. Reject/repeat analysis and the effect prior film viewing has on a department's reject/repeat rate

    International Nuclear Information System (INIS)

    Clark, P.A.; Hogg, P.


    Purpose: Achieving cost-effectiveness within the NHS is an old initiative but one that has again been highlighted by recent government policies (The New NHS-Modern and Dependable, Stationary Office, London, 1997). It has been reiterated that it is the responsibility of individual Trusts to devise means to provide such a service. Reject/repeat analyses have long been the primary tool used to assess the cost-effectiveness of radiography departments (Quality Assurance in Diagnostic Radiology, WHO, Geneva, 1982). This research paper examines an in-house initiative (viewing patients' previous films) commonly employed in other Health Trusts in order to reduce departmental repeat/reject rates. Method: Three hundred orthopaedic patients with hip, knee and ankle prostheses were included in a reject/repeat analysis. The aim was to investigate whether or not viewing patient's previous relevant radiographs would be advantageous to the practicing radiographer. This was done through an audit cycle consisting of two audit periods each lasting for 3 months. The primary audit period recorded the baseline repeat/reject rate, with the secondary audit period recording the repeat/reject rate under an experimental condition of viewing the relevant radiographs. Results: The baseline audit revealed repeat rates of 33% in orthopaedic patients with hip, knee and ankle prostheses. The availability of prior film viewing to the radiographer reduced this repeat rate to 10.6%. Conclusion: Prior film viewing dramatically reduced the department's repeat/reject rate by 22.4%. This provides scope for significant patient dose reductions as well as reducing departmental film expenses. This is an underestimated initiative and should be used appropriately in routine clinical practice

  2. [Analysis of variance of repeated data measured by water maze with SPSS]. (United States)

    Qiu, Hong; Jin, Guo-qin; Jin, Ru-feng; Zhao, Wei-kang


    To introduce the method of analyzing repeated data measured by water maze with SPSS 11.0, and offer a reference statistical method to clinical and basic medicine researchers who take the design of repeated measures. Using repeated measures and multivariate analysis of variance (ANOVA) process of the general linear model in SPSS and giving comparison among different groups and different measure time pairwise. Firstly, Mauchly's test of sphericity should be used to judge whether there were relations among the repeatedly measured data. If any (PSPSS statistical package is available to fulfil this process.

  3. Modeling intraindividual variability with repeated measures data methods and applications

    CERN Document Server

    Hershberger, Scott L


    This book examines how individuals behave across time and to what degree that behavior changes, fluctuates, or remains stable.It features the most current methods on modeling repeated measures data as reported by a distinguished group of experts in the field. The goal is to make the latest techniques used to assess intraindividual variability accessible to a wide range of researchers. Each chapter is written in a ""user-friendly"" style such that even the ""novice"" data analyst can easily apply the techniques.Each chapter features:a minimum discussion of mathematical detail;an empirical examp

  4. Incremental Dynamic Analysis of Koyna Dam under Repeated Ground Motions (United States)

    Zainab Nik Azizan, Nik; Majid, Taksiah A.; Nazri, Fadzli Mohamed; Maity, Damodar; Abdullah, Junaidah


    This paper discovers the incremental dynamic analysis (IDA) of concrete gravity dam under single and repeated earthquake loadings to identify the limit state of the dam. Seven ground motions with horizontal and vertical direction as seismic input considered in the nonlinear dynamic analysis based on the real repeated earthquake in the worldwide. All the ground motions convert to respond spectrum and scaled according to the developed elastic respond spectrum in order to match the characteristic of the ground motion to the soil type. The scaled was depends on the fundamental period, T1 of the dam. The Koyna dam has been selected as a case study for the purpose of the analysis by assuming that no sliding and rigid foundation, has been estimated. IDA curves for Koyna dam developed for single and repeated ground motions and the performance level of the dam identifies. The IDA curve of repeated ground motion shown stiffer rather than single ground motion. The ultimate state displacement for a single event is 45.59mm and decreased to 39.33mm under repeated events which are decreased about 14%. This showed that the performance level of the dam based on seismic loadings depend on ground motion pattern.

  5. Genetic Analysis of Eight X-Chromosomal Short Tandem Repeat ...

    African Journals Online (AJOL)

    X-Chromosome short tandem repeat (STR) typing can complement existing DNA profiling protocols and can also offer useful information in cases of complex kinship analysis. This is the first population study of 8 X-linked STRs in Iraq. The purpose of this work was to provide a basic data of allele and haplotype frequency for ...

  6. Conservative Sample Size Determination for Repeated Measures Analysis of Covariance. (United States)

    Morgan, Timothy M; Case, L Douglas


    In the design of a randomized clinical trial with one pre and multiple post randomized assessments of the outcome variable, one needs to account for the repeated measures in determining the appropriate sample size. Unfortunately, one seldom has a good estimate of the variance of the outcome measure, let alone the correlations among the measurements over time. We show how sample sizes can be calculated by making conservative assumptions regarding the correlations for a variety of covariance structures. The most conservative choice for the correlation depends on the covariance structure and the number of repeated measures. In the absence of good estimates of the correlations, the sample size is often based on a two-sample t-test, making the 'ultra' conservative and unrealistic assumption that there are zero correlations between the baseline and follow-up measures while at the same time assuming there are perfect correlations between the follow-up measures. Compared to the case of taking a single measurement, substantial savings in sample size can be realized by accounting for the repeated measures, even with very conservative assumptions regarding the parameters of the assumed correlation matrix. Assuming compound symmetry, the sample size from the two-sample t-test calculation can be reduced at least 44%, 56%, and 61% for repeated measures analysis of covariance by taking 2, 3, and 4 follow-up measures, respectively. The results offer a rational basis for determining a fairly conservative, yet efficient, sample size for clinical trials with repeated measures and a baseline value.

  7. Power analysis for multivariate and repeated measures designs: a flexible approach using the SPSS MANOVA procedure. (United States)

    D'Amico, E J; Neilands, T B; Zambarano, R


    Although power analysis is an important component in the planning and implementation of research designs, it is often ignored. Computer programs for performing power analysis are available, but most have limitations, particularly for complex multivariate designs. An SPSS procedure is presented that can be used for calculating power for univariate, multivariate, and repeated measures models with and without time-varying and time-constant covariates. Three examples provide a framework for calculating power via this method: an ANCOVA, a MANOVA, and a repeated measures ANOVA with two or more groups. The benefits and limitations of this procedure are discussed.

  8. Repeatability of the Oxford Foot Model for Kinematic Gait Analysis of the Foot and Ankle

    NARCIS (Netherlands)

    van Hoeve, S.; Vos, J.; Weijers, P.; Verbruggen, J.; Willems, P.; Poeze, M.; Meijer, K.


    INTRODUCTION: Kinematic gait analysis via the multi-segmental Oxford foot model (OFM) may be a valuable addition to the biomechanical examination of the foot and ankle. The aim of this study is to assess the repeatability of the OFM in healthy subjects. METHODS: Nine healthy subjects, without a

  9. How do repeat suicide attempters differ from first timers? An exploratory record based analysis

    Directory of Open Access Journals (Sweden)

    Vikas Menon


    Full Text Available Background: Evidence indicates that repeat suicide attempters, as a group, may differ from 1st time attempters. The identification of repeat attempters is a powerful but underutilized clinical variable. Aims: In this research, we aimed to compare individuals with lifetime histories of multiple attempts with 1st time attempters to identify factors predictive of repeat attempts. Setting and Design: This was a retrospective record based study carried out at a teaching cum Tertiary Care Hospital in South India. Methods: Relevant data was extracted from the clinical records of 1st time attempters (n = 362 and repeat attempters (n = 61 presenting to a single Tertiary Care Center over a 4½ year period. They were compared on various sociodemographic and clinical parameters. The clinical measures included Presumptive Stressful Life Events Scale, Beck Hopelessness Scale, Coping Strategies Inventory – Short Form, and the Global Assessment of Functioning Scale. Statistical Analysis Used: First time attempters and repeaters were compared using appropriate inferential statistics. Logistic regression was used to identify independent predictors of repeat attempts. Results: The two groups did not significantly differ on sociodemographic characteristics. Repeat attempters were more likely to have given prior hints about their act (χ2 = 4.500, P = 0.034. In the final regression model, beck hopelessness score emerged as a significant predictor of repeat suicide attempts (odds ratio = 1.064, P = 0.020. Conclusion: Among suicide attempters presenting to the hospital, the presence of hopelessness is a predictor of repeat suicide attempts, independent of clinical depression. This highlights the importance of considering hopelessness in the assessment of suicidality with a view to minimize the risk of future attempts.

  10. Repeat film analysis and its implications for quality assurance in dental radiology: An institutional case study

    Directory of Open Access Journals (Sweden)

    Shruthi Acharya


    Full Text Available Context: The goal of any radiologist is to produce the highest quality diagnostic radiographs, while keeping patient exposure as low as reasonably achievable (ALARA. Aims: The aim of this study was to describe the reasons for radiograph rejections through a repeat film analysis in an Indian dental school. Settings and Design: An observational study conducted in the Department of Oral Medicine and Radiology, Manipal College of Dental Sciences, Manipal. Materials and Methods: During a 6-month study period, a total of 9,495 intra-oral radiographs and 2339 extraoral radiographs taken in the Radiology Department were subjected to repeat film analysis. Statistical Analysis Used: SPSS Version 16. Descriptive analysis used. Results: The results showed that the repeat rates were 7.1% and 5.86% for intraoral and extraoral radiographs, respectively. Among the causes for errors reported, positioning error (38.7% was the most common, followed by improper angulations (26.1%, and improper film placement (11.2% for intra-oral radiographs. The study found that the maximum frequency of repeats among extraoral radiographs was for panoramic radiographs (49% followed by lateral cephalogram (33%, and paranasal sinus view (14%. It was also observed that repeat rate of intraoral radiographs was highest for internees (44.7%, and undergraduate students (28.2%. Conclusions: The study pointed to a need for more targeted interventions to achieve the goal of keeping patient exposure ALARA in a dental school setting.

  11. Analysis of repeated measurement data in the clinical trials (United States)

    Singh, Vineeta; Rana, Rakesh Kumar; Singhal, Richa


    Statistics is an integral part of Clinical Trials. Elements of statistics span Clinical Trial design, data monitoring, analyses and reporting. A solid understanding of statistical concepts by clinicians improves the comprehension and the resulting quality of Clinical Trials. In biomedical research it has been seen that researcher frequently use t-test and ANOVA to compare means between the groups of interest irrespective of the nature of the data. In Clinical Trials we record the data on the patients more than two times. In such a situation using the standard ANOVA procedures is not appropriate as it does not consider dependencies between observations within subjects in the analysis. To deal with such types of study data Repeated Measure ANOVA should be used. In this article the application of One-way Repeated Measure ANOVA has been demonstrated by using the software SPSS (Statistical Package for Social Sciences) Version 15.0 on the data collected at four time points 0 day, 15th day, 30th day, and 45th day of multicentre clinical trial conducted on Pandu Roga (~Iron Deficiency Anemia) with an Ayurvedic formulation Dhatrilauha. PMID:23930038

  12. Characterization of Dutch Staphylococcus aureus from bovine mastitis using a Multiple Locus Variable Number Tandem Repeat Analysis

    NARCIS (Netherlands)

    Ikawaty, R.; Brouwer, E.C.; Jansen, M.D.; Duijkeren, van E.; Mevius, D.J.; Verhoef, J.; Fluit, A.C.


    Current typing methods for Staphylococcus aureus have important drawbacks. We evaluated a Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) scheme with 6 loci which lacks most drawbacks on 85 bovine mastitis isolates from The Netherlands. For each locus the number of repeat units (RU) was

  13. Repeatability of oral fluid collection methods for THC measurement

    NARCIS (Netherlands)

    Houwing, Sjoerd; Smink, Beitske E.; Legrand, Sara-Ann; Mathijssen, Rene P. M.; Verstraete, Alain G.; Brookhuis, Karel A.


    Study objectives: To determine the influence of sample collection for two different collection methods on THC concentrations and to compare THC concentrations collected by both methods. Methods: A total of 136 pairs of oral fluid samples from subjects who had recently smoked Cannabis were obtained

  14. Repeated dose titration versus age-based method in electroconvulsive therapy: a pilot study. (United States)

    Aten, Jan Jaap; Oudega, Mardien; van Exel, Eric; Stek, Max L; van Waarde, Jeroen A


    In electroconvulsive therapy (ECT), a dose titration method (DTM) was suggested to be more individualized and therefore more accurate than formula-based dosing methods. A repeated DTM (every sixth session and dose adjustment accordingly) was compared to an age-based method (ABM) regarding treatment characteristics, clinical outcome, and cognitive functioning after ECT. Thirty-nine unipolar depressed patients dosed using repeated DTM and 40 matched patients treated with ABM were compared. Montgomery-Åsberg Depression Rating Scale (MADRS) and Mini-Mental State Examination (MMSE) were assessed at baseline and at the end of the index course, as well as the total number of ECT sessions. Both groups were similar regarding age, sex, psychotic features, mean baseline MADRS, and median baseline MMSE. At the end of the index course, the two methods showed equal outcome (mean end MADRS, 11.6 ± 8.3 in DTM and 9.5 ± 7.6 in ABM (P = 0.26); median end MMSE, 28 (25-29) and 28 (25-29.8), respectively (P = 0.81). However, the median number of all ECT sessions differed 16 (11-22) in DTM versus 12 (10-14.8) in ABM; P = 0.02]. Using regression analysis, dosing method and age were independently associated with the total number of ECT sessions, with less sessions needed in ABM (P = 0.02) and in older patients (P = 0.001). In this comparative cohort study, ABM and DTM showed equal outcome for depression and cognition. However, the median ECT course duration in repeated DTM appeared longer. Additionally, higher age was associated with shorter ECT courses regardless of the dosing method. Further prospective studies are needed to confirm these findings.

  15. Repeatability of oral fluid collection methods for THC measurement.

    NARCIS (Netherlands)

    Houwing, S. Smink, B.E. Legrand, S.-A. Mathijssen, M.P.M. Verstraete, A.G. & Brookhuis, K.A.


    The study objective was to determine the influence of sample collection for two different collection methods on THC concentrations and to compare THC concentrations collected by both methods. A total of 136 pairs of oral fluid samples from subjects who had recently smoked Cannabis were obtained by

  16. Fine typing of methicillin-resistant Staphylococcus aureus isolates using direct repeat unit and staphylococcal interspersed repeat unit typing methods. (United States)

    Ho, Cheng-Mao; Ho, Mao-Wang; Li, Chi-Yuan; Lu, Jang-Jih


    Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated. A total of 157 MRSA isolates from four different regions in Taiwan were typed with five different molecular methods, including SCCmec typing, multilocus sequence typing (MLST), spa typing, mec-associated direct repeat unit (dru) copy number determination, and staphylococcal interspersed repeat unit (SIRU) profiling. There were four SCCmec types, eight MLST types, 15 spa types, 11 dru types, and 31 SIRU profiles. The most common type determined by each molecular typing method was SCCmec III (115 isolates, 73.2%), ST239 (99 isolates, 63.1%), t037 (107 isolates, 68.2%), 14 dru copies (76 isolates, 48.4%), and SIRU profile 3013722 (102 isolates, 65%), respectively. When using the combination of MLST, spa typing, and dru copy number, ST5-t002-4 (n = 8), ST239-t037-14 (n = 68), ST59-t437-9 (n = 9), and ST59-t437-11 (n = 6) were found to be the most common types of SCCmec types II (n = 9), III (n = 115), IV (n = 21), and VT (n = 11) isolates, respectively. SCCmec type III isolates were further classified into 11 dru types. Of the 21 SCCmec type IV isolates, 14 SIRU profiles were found. Seven SIRU patterns were observed in the 11 SCCmec type VT isolates. Different typing methods showed a similar Hunter-Gaston discrimination index among the 157 MRSA isolates. However, dru and SIRU typing methods had a better discriminatory power for SCCmec type III and SCCmec types IV and VT isolates, respectively, suggesting that dru and SIRU can be used to further type these isolates. Copyright © 2013. Published by Elsevier B.V.

  17. Detection-Discrimination Method for Multiple Repeater False Targets Based on Radar Polarization Echoes

    Directory of Open Access Journals (Sweden)

    Z. W. ZONG


    Full Text Available Multiple repeat false targets (RFTs, created by the digital radio frequency memory (DRFM system of jammer, are widely used in practical to effectively exhaust the limited tracking and discrimination resource of defence radar. In this paper, common characteristic of radar polarization echoes of multiple RFTs is used for target recognition. Based on the echoes from two receiving polarization channels, the instantaneous polarization radio (IPR is defined and its variance is derived by employing Taylor series expansion. A detection-discrimination method is designed based on probability grids. By using the data from microwave anechoic chamber, the detection threshold of the method is confirmed. Theoretical analysis and simulations indicate that the method is valid and feasible. Furthermore, the estimation performance of IPRs of RFTs due to the influence of signal noise ratio (SNR is also covered.

  18. The case for repeatable analysis with energy economy optimization models

    International Nuclear Information System (INIS)

    DeCarolis, Joseph F.; Hunter, Kevin; Sreepathi, Sarat


    Energy economy optimization (EEO) models employ formal search techniques to explore the future decision space over several decades in order to deliver policy-relevant insights. EEO models are a critical tool for decision-makers who must make near-term decisions with long-term effects in the face of large future uncertainties. While the number of model-based analyses proliferates, insufficient attention is paid to transparency in model development and application. Given the complex, data-intensive nature of EEO models and the general lack of access to source code and data, many of the assumptions underlying model-based analysis are hidden from external observers. This paper discusses the simplifications and subjective judgments involved in the model building process, which cannot be fully articulated in journal papers, reports, or model documentation. In addition, we argue that for all practical purposes, EEO model-based insights cannot be validated through comparison to real world outcomes. As a result, modelers are left without credible metrics to assess a model's ability to deliver reliable insight. We assert that EEO models should be discoverable through interrogation of publicly available source code and data. In addition, third parties should be able to run a specific model instance in order to independently verify published results. Yet a review of twelve EEO models suggests that in most cases, replication of model results is currently impossible. We provide several recommendations to help develop and sustain a software framework for repeatable model analysis.

  19. Analysis of CR1 Repeats in the Zebra Finch Genome

    Directory of Open Access Journals (Sweden)

    George E. Liu


    Full Text Available Most bird species have smaller genomes and fewer repeats than mammals. Chicken Repeat 1 (CR1 repeat is one of the most abundant families of repeats, ranging from ~133,000 to ~187,000 copies accounting for ~50 to ~80% of the interspersed repeats in the zebra finch and chicken genomes, respectively. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to multiple CR1 subfamilies in the chicken. In this study, we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the zebra finch genome. We identified and validated 34 CR1 subfamilies and further analyzed the correlation between these subfamilies. We also discovered 4 novel lineage-specific CR1 subfamilies in the zebra finch when compared to the chicken genome. We built various evolutionary trees of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

  20. Repeat profile analysis in an x-ray department

    International Nuclear Information System (INIS)

    Bassey, C.E.; Ojo, O.O.; Akpabio, I.


    The repeat profile of an x-ray department in a developing country was analysed monthly between July 1989 and June 1990. Results showed an average repeat rate of 3.7% for the period of study. The main causes of film repetition were: equipment fault, 33.9%; radiographer's fault, 27.4%; film fault, 19.3%; processing fault, 10.8% and patient's fault, 8.6%. The average repeat rate in the first 6 months of study reduced by 50% in the last 6 months. This was due to the effectiveness of implementation of corrective actions. The overall repeat rate was found to correlate well with both the equipment fault and radiographer's fault with correlation coefficients, r, of 0.94 and 0.91, respectively. It is expected that a further reduction in the repeat rate will be obtained after the introduction of quality assurance programmes. (author)

  1. Facile fabrication of controllable zinc oxide nanorod clusters on polyacrylonitrile nanofibers via repeatedly alternating immersion method

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Ying; Li, Xia; Yu, Hou-Yong, E-mail: [Zhejiang Sci-Tech University, The Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, College of Materials and Textiles (China); Hu, Guo-Liang; Yao, Ju-Ming, E-mail: [Zhejiang Sci-Tech University, National Engineering Lab for Textile Fiber Materials and Processing Technology (China)


    Polyacrylonitrile/zinc oxide (PAN/ZnO) composite nanofiber membranes with different ZnO morphologies were fabricated by repeatedly alternating hot–cold immersion and single alternating hot–cold immersion methods. The influence of the PAN/ZnCl{sub 2} ratio and different immersion methods on the morphology, microstructure, and properties of the nanofiber membranes was investigated by using field-emission scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) analysis, thermogravimetric analysis (TGA), and ultraviolet–visible (UV–Vis) spectroscopy. A possible mechanism for different morphologies of PAN/ZnO nanofiber membranes with different PAN/ZnCl{sub 2} ratio through different immersion processes was presented, and well-dispersed ZnO nanorod clusters with smallest average dimeter of 115 nm and hexagonal wurtzite structure were successfully anchored onto the PAN nanofiber surface for R-7/1 nanofiber membrane. Compared to S-5/1 prepared by single alternating hot–cold immersion method, the PAN/ZnO nanofiber membrane fabricated by repeatedly alternating hot–cold immersion method (especially for R-7/1) showed improved thermal stability and high photocatalytic activity for methylene blue (MB). Compared to S-5/1, decomposition temperature at 5% weight loss (T{sub 5%}) was increased by 43 °C from 282 to 325 °C for R-7/1; meanwhile, R-7/1 showed higher photocatalytic degradation ratio of approximately 100% (after UV light irradiation for 8 h) than 65% for S-5/1 even after irradiation for 14 h. Moreover, the degradation efficiency of R-7/1 with good reuse stability remained above 94% after 3 cycles.

  2. simple sequence repeat (SSR) markers in genetic analysis of

    African Journals Online (AJOL)



    1998). Cross- species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15:1275-1287.

  3. Analysis of genetic polymorphism of nine short tandem repeat loci in ...

    African Journals Online (AJOL)



    Mar 15, 2012 ... Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics. INTRODUCTION. Short tandem repeat (STR) is widely .... Data analysis. The exact test of Hardy-Weinberg equilibrium was conducted with. Arlequin version 3.5 software (Computational and Molecular.

  4. [Analysis of binary classification repeated measurement data with GEE and GLMMs using SPSS software]. (United States)

    An, Shengli; Zhang, Yanhong; Chen, Zheng


    To analyze binary classification repeated measurement data with generalized estimating equations (GEE) and generalized linear mixed models (GLMMs) using SPSS19.0. GEE and GLMMs models were tested using binary classification repeated measurement data sample using SPSS19.0. Compared with SAS, SPSS19.0 allowed convenient analysis of categorical repeated measurement data using GEE and GLMMs.

  5. Design and analysis of communication protocols for quantum repeater networks

    International Nuclear Information System (INIS)

    Jones, Cody; Kim, Danny; Rakher, Matthew T; Ladd, Thaddeus D; Kwiat, Paul G


    We analyze how the performance of a quantum-repeater network depends on the protocol employed to distribute entanglement, and we find that the choice of repeater-to-repeater link protocol has a profound impact on entanglement-distribution rate as a function of hardware parameters. We develop numerical simulations of quantum networks using different protocols, where the repeater hardware is modeled in terms of key performance parameters, such as photon generation rate and collection efficiency. These parameters are motivated by recent experimental demonstrations in quantum dots, trapped ions, and nitrogen-vacancy centers in diamond. We find that a quantum-dot repeater with the newest protocol (‘MidpointSource’) delivers the highest entanglement-distribution rate for typical cases where there is low probability of establishing entanglement per transmission, and in some cases the rate is orders of magnitude higher than other schemes. Our simulation tools can be used to evaluate communication protocols as part of designing a large-scale quantum network. (paper)

  6. Electromyographic analysis of repeated bouts of eccentric exercise. (United States)

    McHugh, M P; Connolly, D A; Eston, R G; Gartman, E J; Gleim, G W


    The repeated bout effect refers to the protective effect provided by a single bout of eccentric exercise against muscle damage from a similar subsequent bout. The aim of this study was to determine if the repeated bout was associated with an increase in motor unit activation relative to force production, an increased recruitment of slow-twitch motor units or increased motor unit synchronization. Surface electromyographic (EMG) signals were recorded from the hamstring muscles during two bouts of submaximal isokinetic (2.6 rad x s(-1)) eccentric (11 men, 9 women) or concentric (6 men, 4 women) contractions separated by 2 weeks. The EMG per unit torque and median frequency were analysed. The initial bout of eccentric exercise resulted in strength loss, pain and muscle tenderness, while the repeated eccentric bout resulted in a slight increase in strength, no pain and no muscle tenderness (bout x time effects, P exercise. The EMG per unit torque and median frequency were not different between the initial and repeated bouts of eccentric exercise. The EMG per unit torque and median frequency increased during both bouts of eccentric exercise (P < 0.01) but did not change during either concentric bout. In conclusion, there was no evidence that the repeated bout effect was due to a neural adaptation.

  7. Repeated dose titration versus age-based method in electroconvulsive therapy: a pilot study

    NARCIS (Netherlands)

    Aten, J.J.; Oudega, M.L.; van Exel, E.; Stek, M.L.; van Waarde, J.A.


    In electroconvulsive therapy (ECT), a dose titration method (DTM) was suggested to be more individualized and therefore more accurate than formula-based dosing methods. A repeated DTM (every sixth session and dose adjustment accordingly) was compared to an age-based method (ABM) regarding treatment

  8. Quantitative analysis and prediction of curvature in leucine-rich repeat proteins. (United States)

    Hindle, K Lauren; Bella, Jordi; Lovell, Simon C


    Leucine-rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein-protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large-scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine-rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at

  9. A rational repeating template method for synthesis of 2D hexagonally ordered mesoporous precious metals. (United States)

    Takai, Azusa; Doi, Yoji; Yamauchi, Yusuke; Kuroda, Kazuyuki


    A repeating template method is presented for the synthesis of mesoporous metals with 2D hexagonal mesostructures. First, a silica replica (i.e., silica nanorods arranged periodically) is prepared by using 2D hexagonally ordered mesoporous carbon as the template. After that, the obtained silica replica is used as the second template for the preparation of mesoporous ruthenium. After the ruthenium species are introduced into the silica replica, the ruthenium species are then reduced by a vapor-infiltration method by using the reducing agent dimethylamine borane. After the ruthenium deposition, the silica is chemically removed. Analysis by transmission and scanning electron microscopies, a nitrogen-adsorption-desorption isotherm, and small-angle X-ray scattering revealed that the mesoporous ruthenium had a 2D hexagonal mesostructure, although the mesostructural ordering is decreased compared to that of the original mesoporous carbon template. This method is widely applicable to other metal systems. By changing the metal species introduced into the silica replica, several mesoporous metals (palladium and platinum) can be synthesized. Ordered mesoporous ruthenium and palladium, which are not easily attainable by the soft-templating methods, can be prepared. This study has overcome the composition variation limitations of the soft-templating method. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Methodology for repeated load analysis of composite structures with embedded magnetic microwires

    Directory of Open Access Journals (Sweden)

    K. Semrád


    Full Text Available The article processes issue of strength of cyclically loaded composite structures with the possibility of contactless stress measuring inside a material. For this purpose a contactless tensile stress sensor using improved induction principle based on the magnetic microwires embedded in the composite structure has been developed. The methodology based on the E-N approach was applied for the analysis of the repeated load of the wing hinge connection, including finite element method (FEM fatigue strength analysis. The results proved that composites in comparison with the metal structures offer significant weight reduction of the small aircraft construction, whereas the required strength, stability and lifetime of the components are remained.

  11. Analysis of unknown cause subarachnoid hemorrhage with repeated negative angiogram

    International Nuclear Information System (INIS)

    Fujii, Mutsumi; Takasato, Yoshio; Masaoka, Hiroyuki; Ohta, Yoshihisa; Hayakawa, Takanori; Honma, Masato


    Seven hundred and fifty five cases of acute non-traumatic subarachnoid hemorrhage (SAH) were admitted to the department of neurosurgery of our hospital from July, 1995 to March, 2004. In 555 patients cerebral angiography was conducted but initial angiography was negative in 30 patients. Except 10 general condition poor patients, in 20 initial angiogram-negative patients were undergone repeated angiography. The cause of SAH could not be demonstrated in 13 cases. The SAH in perimesencephalic and non-perimesencephalic cisturns was seen in 7 and 6 cases, respectively. Occipital and/or neck pain on admission was statistically more common among patients with perimesencephalic SAH than those with non-perimesencephalic SAH (p=0.029), and the prognosis of perimesencephalic SAH was good. We conclude that repeat angiography should not be recommended in patients with perimesencephalic SAH. Patients with non-perimesencephalic SAH had a higher rate of complication. In the non-perimesencephalic group, 3 patients developed hydrocephalus and 3 patients had vasospasm, which were found by repeated angiography. Therefore, repeated angiography is recommended for better clinical outcome by early detection and management of serious complications in this group of patients. (author)

  12. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA). (United States)

    Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi


    The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO, leprosy remains endemic in many countries with approximately 250,000 new cases each year. The entire M. leprae genome has been mapped and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites). Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci. Variable number tandem repeat (VNTR) analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA) has been used to study leprosy evolution and transmission in several countries including China, Malawi, the Philippines, and Brazil. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS). The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions. The PCR products may be subjected to agarose gel electrophoresis to verify the

  13. Comparability and repeatability of three commonly used methods for measuring endurance capacity. (United States)

    Baxter-Gilbert, James; Mühlenhaupt, Max; Whiting, Martin J


    Measures of endurance (time to exhaustion) have been used to address a wide range of questions in ecomorphological and physiological research, as well as being used as a proxy for survival and fitness. Swimming, stationary (circular) track running, and treadmill running are all commonly used methods for measuring endurance. Despite the use of these methods across a broad range of taxa, how comparable these methods are to one another, and whether they are biologically relevant, is rarely examined. We used Australian water dragons (Intellagama lesueurii), a species that is morphologically adept at climbing, swimming, and running, to compare these three methods of endurance and examined if there is repeatability within and between trial methods. We found that time to exhaustion was not highly repeatable within a method, suggesting that single measures or a mean time to exhaustion across trials are not appropriate. Furthermore, we compared mean maximal endurance times among the three methods, and found that the two running methods (i.e., stationary track and treadmill) were similar, but swimming was distinctly different, resulting in lower mean maximal endurance times. Finally, an individual's endurance rank was not repeatable across methods, suggesting that the three endurance trial methods are not providing similar information about an individual's performance capacity. Overall, these results highlight the need to carefully match a measure of performance capacity with the study species and the research questions being asked so that the methods being used are behaviorally, ecologically, and physiologically relevant. © 2018 Wiley Periodicals, Inc.

  14. Repeatability analysis on LPFGs written by a CO2 laser (United States)

    Nespereira, Marta; Castro Alves, D.; Coelho, João. M. P.; Monteiro, Fernando; Abreu, Manuel; Rebordão, J. M.


    The physical mechanisms involved in the writing process of long period fiber gratings (LPFG) using mid-infrared radiation emitted by CO2 lasers limit the obtained characteristics, in particular the minimum period that can be achieved. In order to evaluate the performances of a new methodology developed by us, we analyzed its capability to produce gratings with different periods (from 600 μm down to 300 μm). We also present a repeatability study on the obtained LPFG characteristics (mainly the resonant wavelength and grating length) for several values of the repetition period.

  15. Utility of repeat testing of critical values: a Q-probes analysis of 86 clinical laboratories. (United States)

    Lehman, Christopher M; Howanitz, Peter J; Souers, Rhona; Karcher, Donald S


    A common laboratory practice is to repeat critical values before reporting the test results to the clinical care provider. This may be an unnecessary step that delays the reporting of critical test results without adding value to the accuracy of the test result. To determine the proportions of repeated chemistry and hematology critical values that differ significantly from the original value as defined by the participating laboratory, to determine the threshold differences defined by the laboratory as clinically significant, and to determine the additional time required to analyze the repeat test. Participants prospectively reviewed critical test results for 4 laboratory tests: glucose, potassium, white blood cell count, and platelet count. Participants reported the following information: initial and repeated test result; time initial and repeat results were first known to laboratory staff; critical result notification time; if the repeat result was still a critical result; if the repeat result was significantly different from the initial result, as judged by the laboratory professional or policy; significant difference threshold, as defined by the laboratory; the make and model of the instrument used for primary and repeat testing. Routine, repeat analysis of critical values is a common practice. Most laboratories did not formally define a significant difference between repeat results. Repeated results were rarely considered significantly different. Median repeated times were at least 17 to 21 minutes for 10% of laboratories. Twenty percent of laboratories reported at least 1 incident in the last calendar year of delayed result reporting that clinicians indicated had adversely affected patient care. Routine repeat analysis of automated chemistry and hematology critical values is unlikely to be clinically useful and may adversely affect patient care.

  16. Performance of thallium bromide semiconductor detectors produced by repeated Bridgman method

    International Nuclear Information System (INIS)

    Santos, Robinson Alves dos; Costa, Fabio Eduardo da; Martins, Joao Francisco Trencher; Hamada, Margarida M.


    TlBr crystals have been grown by the Repeated Bridgman method from commercial TlBr materials and characterized to be used as radiation detectors. We have shown that the Repeated Bridgman is effective to reduce the concentration of impurities in TlBr. It was observed that detectors fabricated from higher purity crystal exhibit significant improvement in performance compared to those produced from low purity crystals. However, problems still exist in TlBr detectors, due to the low charge carrier collection efficiency, which is probably caused by additional impurities or defects incorporated during crystal growth and detector fabrication processes. (author)

  17. Revisiting Slow Slip Events Occurrence in Boso Peninsula, Japan, Combining GPS Data and Repeating Earthquakes Analysis (United States)

    Gardonio, B.; Marsan, D.; Socquet, A.; Bouchon, M.; Jara, J.; Sun, Q.; Cotte, N.; Campillo, M.


    Slow slip events (SSEs) regularly occur near the Boso Peninsula, central Japan. Their time of recurrence has been decreasing from 6.4 to 2.2 years from 1996 to 2014. It is important to better constrain the slip history of this area, especially as models show that the recurrence intervals could become shorter prior to the occurrence of a large interplate earthquake nearby. We analyze the seismic waveforms of more than 2,900 events (M≥1.0) taking place in the Boso Peninsula, Japan, from 1 April 2004 to 4 November 2015, calculating the correlation and the coherence between each pair of events in order to define groups of repeating earthquakes. The cumulative number of repeating earthquakes suggests the existence of two slow slip events that have escaped detection so far. Small transient displacements observed in the time series of nearby GPS stations confirm these results. The detection scheme coupling repeating earthquakes and GPS analysis allow to detect small SSEs that were not seen before by classical methods. This work brings new information on the diversity of SSEs and demonstrates that the SSEs in Boso area present a more complex history than previously considered.

  18. D20S16 is a complex interspersed repeated sequence: Genetic and physical analysis of the locus

    Energy Technology Data Exchange (ETDEWEB)

    Bowden, D.W.; Krawchuk, M.D.; Howard, T.D. [Wake Forest Univ., Winston-Salem, NC (United States)] [and others


    The genomic structure of the D20S16 locus has been evaluated using genetic and physical methods. D20S16, originally detected with the probe CRI-L1214, is a highly informative, complex restriction fragment length polymorphism consisting of two separate allelic systems. The allelic systems have the characteristics of conventional VNTR polymorphisms and are separated by recombination ({theta} = 0.02, Z{sub max} = 74.82), as demonstrated in family studies. Most of these recombination events are meiotic crossovers and are maternal in origin, but two, including deletion of the locus in a cell line from a CEPH family member, occur without evidence for exchange of flanking markers. DNA sequence analysis suggests that the basis of the polymorphism is variable numbers of a 98-bp sequence tandemly repeated with 87 to 90% sequence similarity between repeats. The 98-bp repeat is a dimer of 49 bp sequence with 45 to 98% identity between the elements. In addition, nonpolymorphic genomic sequences adjacent to the polymorphic 98-bp repeat tracts are also repeated but are not polymorphic, i.e., show no individual to individual variation. Restriction enzyme mapping of cosmids containing the CRI-L1214 sequence suggests that there are multiple interspersed repeats of the CRI-L1214 sequence on chromosome 20. The results of dual-color fluorescence in situ hybridization experiments with interphase nuclei are also consistent with multiple repeats of an interspersed sequence on chromosome 20. 23 refs., 6 figs.

  19. A multi locus variable number of tandem repeat analysis (MLVA scheme for Streptococcus agalactiae genotyping

    Directory of Open Access Journals (Sweden)

    Mereghetti Laurent


    Full Text Available Abstract Background Multilocus sequence typing (MLST is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR analysis (MLVA applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping. Results We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R. Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains. Conclusions The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.

  20. Evaluation, including effects of storage and repeated freezing and thawing, of a method for measurement of urinary creatinine

    DEFF Research Database (Denmark)

    Garde, A H; Hansen, Åse Marie; Kristiansen, J


    The aims of this study were to elucidate to what extent storage and repeated freezing and thawing influenced the concentration of creatinine in urine samples and to evaluate the method for determination of creatinine in urine. The creatinine method was based on the well-known Jaffe's reaction...... and measured on a COBAS Mira autoanalyser from Roche. The main findings were that samples for analysis of creatinine should be kept at a temperature of -20 degrees C or lower and frozen and thawed only once. The limit of detection, determined as 3 x SD of 20 determinations of a sample at a low concentration (6...

  1. Position Paper: Applying Machine Learning to Software Analysis to Achieve Trusted, Repeatable Scientific Computing

    Energy Technology Data Exchange (ETDEWEB)

    Prowell, Stacy J [ORNL; Symons, Christopher T [ORNL


    Producing trusted results from high-performance codes is essential for policy and has significant economic impact. We propose combining rigorous analytical methods with machine learning techniques to achieve the goal of repeatable, trustworthy scientific computing.

  2. Repeated Time-to-event Analysis of Consecutive Analgesic Events in Postoperative Pain

    DEFF Research Database (Denmark)

    Juul, Rasmus Vestergaard; Rasmussen, Sten; Kreilgaard, Mads


    BACKGROUND: Reduction in consumption of opioid rescue medication is often used as an endpoint when investigating analgesic efficacy of drugs by adjunct treatment, but appropriate methods are needed to analyze analgesic consumption in time. Repeated time-to-event (RTTE) modeling is proposed as a way...... to describe analgesic consumption by analyzing the timing of consecutive analgesic events. METHODS: Retrospective data were obtained from 63 patients receiving standard analgesic treatment including morphine on request after surgery following hip fracture. Times of analgesic events up to 96 h after surgery...... were extracted from hospital medical records. Parametric RTTE analysis was performed with exponential, Weibull, or Gompertz distribution of analgesic events using NONMEM®, version 7.2 (ICON Development Solutions, USA). The potential influences of night versus day, sex, and age were investigated...

  3. Franchise Values in North American Professional Sports Leagues: Evidence from a Repeat Sales Method


    Brad R. Humphreys; Yang Seung Lee


    The paper develops a quality adjusted professional sports franchise price index for North America based on a repeat sale method. This index reflects trends in the general price of sports franchises holding local market, facility, and team characteristics constant. The price index exhibits considerable volatility but no upward trend over time, unlike previous quality adjusted price indexes based on hedonic models in the literature. The lack of an upward trend in this quality adjusted price ind...

  4. The genetic analysis of repeated measures I: Simplex models

    NARCIS (Netherlands)

    Molenaar, P.C.M.; Boomsma, D.I.


    Extends the simplex model to a model that may be used for the genetic and environmental analysis of covariance (ANCOVA) structures. This "double" simplex structure can be specified as a linear structural relationships model. It is shown that data that give rise to a simplex correlation structure,


    Energy Technology Data Exchange (ETDEWEB)

    Morello, G.; Waldmann, I. P.; Tinetti, G., E-mail: [Department of Physics and Astronomy, University College London, Gower Street, WC1E6BT (United Kingdom)


    The research of effective and reliable detrending methods for Spitzer data is of paramount importance for the characterization of exoplanetary atmospheres. To date, the totality of exoplanetary observations in the mid- and far-infrared, at wavelengths >3 μm, have been taken with Spitzer. In some cases, in past years, repeated observations and multiple reanalyses of the same data sets led to discrepant results, raising questions about the accuracy and reproducibility of such measurements. Morello et al. (2014, 2015) proposed a blind-source separation method based on the Independent Component Analysis of pixel time series (pixel-ICA) to analyze InfraRed Array Camera (IRAC) data, obtaining coherent results when applied to repeated transit observations previously debated in the literature. Here we introduce a variant to the pixel-ICA through the use of wavelet transform, wavelet pixel-ICA, which extends its applicability to low-signal-to-noise-ratio cases. We describe the method and discuss the results obtained over 12 eclipses of the exoplanet XO3b observed during the “Warm Spitzer” era in the 4.5 μm band. The final results are reported, in part, also in Ingalls et al. (2016), together with results obtained with other detrending methods, and over 10 synthetic eclipses that were analyzed for the “IRAC Data Challenge 2015.” Our results are consistent within 1σ with the ones reported in Wong et al. (2014) and with most of the results reported in Ingalls et al. (2016), which appeared on arXiv while this paper was under review. Based on many statistical tests discussed in Ingalls et al. (2016), the wavelet pixel-ICA method performs as well as or better than other state-of-art methods recently developed by other teams to analyze Spitzer/IRAC data, and, in particular, it appears to be the most repeatable and the most reliable, while reaching the photon noise limit, at least for the particular data set analyzed. Another strength of the ICA approach is its highest


    International Nuclear Information System (INIS)

    Morello, G.; Waldmann, I. P.; Tinetti, G.


    The research of effective and reliable detrending methods for Spitzer data is of paramount importance for the characterization of exoplanetary atmospheres. To date, the totality of exoplanetary observations in the mid- and far-infrared, at wavelengths >3 μm, have been taken with Spitzer. In some cases, in past years, repeated observations and multiple reanalyses of the same data sets led to discrepant results, raising questions about the accuracy and reproducibility of such measurements. Morello et al. (2014, 2015) proposed a blind-source separation method based on the Independent Component Analysis of pixel time series (pixel-ICA) to analyze InfraRed Array Camera (IRAC) data, obtaining coherent results when applied to repeated transit observations previously debated in the literature. Here we introduce a variant to the pixel-ICA through the use of wavelet transform, wavelet pixel-ICA, which extends its applicability to low-signal-to-noise-ratio cases. We describe the method and discuss the results obtained over 12 eclipses of the exoplanet XO3b observed during the “Warm Spitzer” era in the 4.5 μm band. The final results are reported, in part, also in Ingalls et al. (2016), together with results obtained with other detrending methods, and over 10 synthetic eclipses that were analyzed for the “IRAC Data Challenge 2015.” Our results are consistent within 1σ with the ones reported in Wong et al. (2014) and with most of the results reported in Ingalls et al. (2016), which appeared on arXiv while this paper was under review. Based on many statistical tests discussed in Ingalls et al. (2016), the wavelet pixel-ICA method performs as well as or better than other state-of-art methods recently developed by other teams to analyze Spitzer/IRAC data, and, in particular, it appears to be the most repeatable and the most reliable, while reaching the photon noise limit, at least for the particular data set analyzed. Another strength of the ICA approach is its highest

  7. Genetic analysis of repeated, biparental, diploid, hydatidiform moles

    DEFF Research Database (Denmark)

    Sunde, Lone; Vejerslev, Lars O.; Jensen, Mie Poulsen


    for the abnormal development can be envisaged, environmental as well as genetic. To conform to current ideas of molar pathogenesis, it is suggested that the present conceptuses might have arisen from imbalances in imprinted genomic regions. This could be a consequence of uniparental disomy in critical regions......A woman presented with five consecutive pregnancies displaying molar morphology. In the fifth pregnancy, a non-malformed, liveborn infant was delivered. Genetic analyses (RFLP analysis, cytogenetics, flow cytometry) were performed in pregnancies II-V. It was demonstrated that these pregnancies...... originated in separate conceptions, all conceptuses were diploid, and all had maternally as well as paternally derived genetic markers. By cytogenetic analysis, aberrant heteromorphisms were noted; no other abnormalities were observed in chromosome structure or in DNA sequence. Many different causes...

  8. Nonlinear analysis of sequence repeats of multi-domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail:


    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

  9. Repeatability, correlation and path analysis of physical and chemical characteristics of peach fruits

    Directory of Open Access Journals (Sweden)

    Rosana Gonçalves Pires Matias


    Full Text Available This study aimed to determine the number of measurements necessary to evaluate physical and chemical characteristics of peach fruits, study the relationships between them and their direct and indirect effects on the content of ascorbic acid and total carotenoids. The characteristics skin and pulp color, fruit weight, suture, equatorial and polar diameters, firmness, soluble solids (SS, titratable acidity (TA, SS/TA ratio, ascorbic acid and total carotenoids were evaluated in 39 cultivars of peach and 3 cultivars of nectarine from the orchard of the Universidade Federal de Viçosa. The repeatability coefficient was estimated by ANOVA and CPCOR. Phenotypic correlation coefficients (rf were estimated and, after the multicollinearity diagnostics, they were unfolded to direct and indirect effects of the explanatory variables on the response variable using path analysis. There was agreement on the magnitude of repeatability coefficients obtained by the two methods; however, they varied among the 14 characteristics. The highest correlations were found between FW, SD, ED and PD. Seven fruits are sufficient to evaluate the physical and chemical characteristics of peach with a correlation coefficient of 90%. The characteristics considered in the path diagrams (b* skin, hº skin, b* pulp, hº pulp, ED, PD, FIR, SS, SS/AT and TC are not the main determinants of the ascorbic acid. The yellow hue of the pulp (hº pulp has the potential to be used in indirect selection for total carotenoids.

  10. Welfare Risks of Repeated Application of On-Farm Killing Methods for Poultry

    Directory of Open Access Journals (Sweden)

    Jessica E. Martin


    Full Text Available Council Regulation (EC no. 1099/2009 on the protection of animals at the time of killing restricts the use of manual cervical dislocation in poultry on farms in the European Union (EU to birds weighing up to 3 kg and 70 birds per person per day. However, few studies have examined whether repeated application of manual cervical dislocation has welfare implications and whether these are dependent on individual operator skill or susceptibility to fatigue. We investigated the effects of repeated application (100 birds at a fixed killing rate of 1 bird per 2 min and multiple operators on two methods of killing of broilers, laying hens, and turkeys in commercial settings. We compared the efficacy and welfare impact of repeated application of cervical dislocation and a percussive killer (Cash Poultry Killer, CPK, using 12 male stockworkers on three farms (one farm per bird type. Both methods achieved over 96% kill success at the first attempt. The killing methods were equally effective for each bird type and there was no evidence of reduced performance with time and/or bird number. Both methods of killing caused a rapid loss of reflexes, indicating loss of brain function. There was more variation in reflex durations and post-mortem damage in birds killed by cervical dislocation than that found using CPK. High neck dislocation was associated with improved kill success and more rapid loss of reflexes. The CPK caused damage to multiple brain areas with little variation. Overall, the CPK was associated with faster abolition of reflexes, with fewer birds exhibiting them at all, suggestive of better welfare outcomes. However, technical difficulties with the CPK highlighted the advantages of cervical dislocation, which can be performed immediately with no equipment. At the killing rates tested, we did not find evidence to justify the current EU limit on the number of birds that one operator can kill on–farm by manual cervical dislocation.

  11. Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences. (United States)

    Zhang, Meiping; Rong, Ying; Lee, Mi-Kyung; Zhang, Yang; Stelly, David M; Zhang, Hong-Bin


    Cotton is the world's leading textile fiber crop and is also grown as a bioenergy and food crop. Knowledge of the phylogeny of closely related species and the genome origin and evolution of polyploid species is significant for advanced genomics research and breeding. We have reconstructed the phylogeny of the cotton genus, Gossypium L., and deciphered the genome origin and evolution of its five polyploid species by restriction fragment analysis of repeated sequences. Nuclear DNA of 84 accessions representing 35 species and all eight genomes of the genus were analyzed. The phylogenetic tree of the genus was reconstructed using the parsimony method on 1033 polymorphic repeated sequence restriction fragments. The genome origin of its polyploids was determined by calculating the diploid-polyploid restriction fragment correspondence (RFC). The tree is consistent with the morphological classification, genome designation and geographic distribution of the species at subgenus, section and subsection levels. Gossypium lobatum (D7) was unambiguously shown to have the highest RFC with the D-subgenomes of all five polyploids of the genus, while the common ancestor of Gossypium herbaceum (A1) and Gossypium arboreum (A2) likely contributed to the A-subgenomes of the polyploids. These results provide a comprehensive phylogenetic tree of the cotton genus and new insights into the genome origin and evolution of its polyploid species. The results also further demonstrate a simple, rapid and inexpensive method suitable for phylogenetic analysis of closely related species, especially congeneric species, and the inference of genome origin of polyploids that constitute over 70 % of flowering plants.

  12. [Analytical procedure of variable number of tandem repeats (VNTR) analysis and effective use of analysis results for tuberculosis control]. (United States)

    Hachisu, Yushi; Hashimoto, Ruiko; Kishida, Kazunori; Yokoyama, Eiji


    Variable number of tandem repeats (VNTR) analysis is one of the methods for molecular epidemiological studies of Mycobacterium tuberculosis. VNTR analysis is a method based on PCR, provides rapid highly reproducible results and higher strain discrimination power than the restriction fragment length polymorphism (RFLP) analysis widely used in molecular epidemiological studies of Mycobacterium tuberculosis. Genetic lineage compositions of Mycobacterium tuberculosis clinical isolates differ among the regions from where they are isolated, and allelic diversity at each locus also differs among the genetic lineages of Mycobacterium tuberculosis. Therefore, the combination of VNTR loci that can provide high discrimination capacity for analysis is not common in every region. The Japan Anti-Tuberculosis Association (JATA) 12 (15) reported a standard combination of VNTR loci for analysis in Japan, and the combination with hypervariable (HV) loci added to JATA12 (15), which has very high discrimination capacity, was also reported. From these reports, it is thought that data sharing between institutions and construction of a nationwide database will progress from now on. Using database construction of VNTR profiles, VNTR analysis has become an effective tool to trace the route of tuberculosis infection, and also helps in decision-making in the treatment course. However, in order to utilize the results of VNTR analysis effectively, it is important that each related organization cooperates closely, and analysis should be appropriately applied in the system in which accurate control and private information protection are ensured.

  13. Analyzing Repeated Measures Marginal Models on Sample Surveys with Resampling Methods

    Directory of Open Access Journals (Sweden)

    James D. Knoke


    Full Text Available Packaged statistical software for analyzing categorical, repeated measures marginal models on sample survey data with binary covariates does not appear to be available. Consequently, this report describes a customized SAS program which accomplishes such an analysis on survey data with jackknifed replicate weights for which the primary sampling unit information has been suppressed for respondent confidentiality. First, the program employs the Macro Language and the Output Delivery System (ODS to estimate the means and covariances of indicator variables for the response variables, taking the design into account. Then, it uses PROC CATMOD and ODS, ignoring the survey design, to obtain the design matrix and hypothesis test specifications. Finally, it enters these results into another run of CATMOD, which performs automated direct input of the survey design specifications and accomplishes the appropriate analysis. This customized SAS program can be employed, with minor editing, to analyze general categorical, repeated measures marginal models on sample surveys with replicate weights. Finally, the results of our analysis accounting for the survey design are compared to the results of two alternate analyses of the same data. This comparison confirms that such alternate analyses, which do not properly account for the design, do not produce useful results.

  14. Improvement of recovery and repeatability in liquid chromatography-mass spectrometry analysis of peptides

    NARCIS (Netherlands)

    van Midwoud, Paul M.; Rieux, Laurent; Bischoff, Rainer; Verpoorte, Elisabeth; Niederlander, Harm A. G.


    Poor repeatability of peak areas is a problem frequently encountered in peptide analysis with nanoLiquid Chromatography coupled on-line with Mass Spectrometry (nanoLC-MS). As a result, quantitative analysis will be seriously hampered unless the observed variability can be corrected in some way.

  15. [Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella]. (United States)

    Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin


    This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

  16. [Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea]. (United States)

    Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian


    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

  17. Testing Mean Differences among Groups: Multivariate and Repeated Measures Analysis with Minimal Assumptions. (United States)

    Bathke, Arne C; Friedrich, Sarah; Pauly, Markus; Konietschke, Frank; Staffen, Wolfgang; Strobl, Nicolas; Höller, Yvonne


    To date, there is a lack of satisfactory inferential techniques for the analysis of multivariate data in factorial designs, when only minimal assumptions on the data can be made. Presently available methods are limited to very particular study designs or assume either multivariate normality or equal covariance matrices across groups, or they do not allow for an assessment of the interaction effects across within-subjects and between-subjects variables. We propose and methodologically validate a parametric bootstrap approach that does not suffer from any of the above limitations, and thus provides a rather general and comprehensive methodological route to inference for multivariate and repeated measures data. As an example application, we consider data from two different Alzheimer's disease (AD) examination modalities that may be used for precise and early diagnosis, namely, single-photon emission computed tomography (SPECT) and electroencephalogram (EEG). These data violate the assumptions of classical multivariate methods, and indeed classical methods would not have yielded the same conclusions with regards to some of the factors involved.

  18. Comparison of Variable Number Tandem Repeat and Short Tandem Repeat Genetic Markers for Qualitative and Quantitative Chimerism Analysis Post Allogeneic Stem Cell Transplantation

    International Nuclear Information System (INIS)

    Mossallam, G.I.; Smith, A.G.; Mcfarland, C.


    Analysis of donor chimerism has become a routine procedure for the documentation of engraftment after allogeneic hematopoietic stem cell transplantation. Quantitative analysis of chimerism kinetics has been shown to predict graft failure or relapse. In this study, we compared the use of variable number tandem repeats (VNTR) and short tandem repeats (STR) as polymorphic genetic markers in chimerism analysis. This study included qualitative and quantitative assessment of both techniques to assess informative yield and sensitivity. Patients and Methods: We analyzed 206 samples representing 40 transplant recipients and their HLA identical sibling donors. A panel of six VNTR loci, 15 STR loci and 1 sex chromosome locus was used. Amplified VNTR products were visualized in an ethidium bromide stained gel. STR loci were amplified using fluorescent primers, and the products were analyzed by capillary electrophoresis. VNTR and STR analysis gave comparable qualitative results in the majority of cases. The incidence of mixed chimerism (Me) by STR analysis was 45% compared to 32% in cases evaluated by VNTR analysis. STR markers were more informative; several informative loci could be identified in all patients. Unique alleles for both patient and donor could be identified in all patients by STR versus 32/40 by VNTR analysis. The STR markers were also more sensitive in the detection of chimerism. The size of VNTR alleles and differences between the size of donor and recipient VNTR alleles affected the sensitivity of detection. With both techniques, quantitative assessment of chimerism showed some discrepancies between the estimated and the calculated percentage of donor DNA. Discordance between the two estimates was observed in 8/19 patients with Me. However, sequential monitoring of the relative band intensity of VNTR alleles offered some insight into the direction of change in engraftment over time. The higher yield of informative loci with STR and the automated measurement of

  19. Genotypic characterization by multi locus variable number of tandem repeats analysis international Bordetella pertussis vaccine strains

    Directory of Open Access Journals (Sweden)

    M. Fatah Moghadam


    Full Text Available Background: In 1930's first whole cell pertussis vaccines became available to the public heralding a dramatic success in overcoming the global burden of the disease. To date only a handful of B. pertussis strains have been used by international/local pertussis vaccine manufacturers. Inevitable well-documented genetic changes in the world population of this pathogen have prompted serious questions on suitability of traditional vaccine strains protect human against currently circulating wild isolates of Bordetella pertussis. Objective: Analyzing the genetic diversity within the most frequently-used vaccine strains of B. pertussis in the world Methods: A recently developed multi locus variable number of tandem repeats analysis (MLVA genotyping system along with a bioinforamtic piece of analysis was conducted on 11 strain / substrains of B137, B203 (10536, C393, Cs, E476, Tohama I, J445 (134, B202 and J446 (509 plus 2 sub-strains of 134 and 509 that are used at Razi institute for preparation of pertussis vaccine. In this study have used 6 individual loci of VNTR1, VNTR3a, VNTR3b, VNTR4, VNTR5 and VNTR6. Findings: Six distinct genotypes were recognized among the examined strains by comparing our data with the Dutch MLVA databank. These were all new and not reported before in the database. Conclusion: This observation reiterates on necessity for detection of predominant native strains to include in vaccine preparations suitable for different countries.

  20. Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia

    Directory of Open Access Journals (Sweden)

    Junjie Cui


    Full Text Available Bitter gourd (Momordica charantia is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus, watermelon (Citrullus lanatus, and melon (Cucumis melo genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

  1. Association analysis of a highly polymorphic CAG Repeat in the human potassium channel gene KCNN3 and migraine susceptibility

    Directory of Open Access Journals (Sweden)

    Ovcaric Mick


    Full Text Available Abstract Background Migraine is a polygenic multifactorial disease, possessing environmental and genetic causative factors with multiple involved genes. Mutations in various ion channel genes are responsible for a number of neurological disorders. KCNN3 is a neuronal small conductance calcium-activated potassium channel gene that contains two polyglutamine tracts, encoded by polymorphic CAG repeats in the gene. This gene plays a critical role in determining the firing pattern of neurons and acts to regulate intracellular calcium channels. Methods The present association study tested whether length variations in the second (more 3' polymorphic CAG repeat in exon 1 of the KCNN3 gene, are involved in susceptibility to migraine with and without aura (MA and MO. In total 423 DNA samples from unrelated individuals, of which 202 consisted of migraine patients and 221 non-migraine controls, were genotyped and analysed using a fluorescence labelled primer set on an ABI310 Genetic Analyzer. Allele frequencies were calculated from observed genotype counts for the KCNN3 polymorphism. Analysis was performed using standard contingency table analysis, incorporating the chi-squared test of independence and CLUMP analysis. Results Overall, there was no convincing evidence that KCNN3 CAG lengths differ between Caucasian migraineurs and controls, with no significant difference in the allelic length distribution of CAG repeats between the population groups (P = 0.090. Also the MA and MO subtypes did not differ significantly between control allelic distributions (P > 0.05. The prevalence of the long CAG repeat (>19 repeats did not reach statistical significance in migraineurs (P = 0.15, nor was there a significant difference between the MA and MO subgroups observed compared to controls (P = 0.46 and P = 0.09, respectively, or between MA vs MO (P = 0.40. Conclusion This association study provides no evidence that length variations of the second polyglutamine array in

  2. Deployment Repeatability (United States)


    evaluating the deployment repeatability builds upon the testing or analysis of deployment kinematics (Chapter 6) and adds repetition. Introduction...material yield or failure during a test. For the purposes of this chapter, zero shift will refer to permanent changes in the structure, while reversible ...the content of other chapters in this book: Gravity Compensation (Chapter 4) and Deployment Kinematics and Dynamics (Chapter 6). Repeating the

  3. Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

    International Nuclear Information System (INIS)

    Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles


    The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°

  4. Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus

    Directory of Open Access Journals (Sweden)

    Chermette René


    Full Text Available Abstract Background Multiple-locus variable-number tandem repeat (VNTR analysis (MLVA is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8 of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89. The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST. The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a

  5. The surface analysis methods

    International Nuclear Information System (INIS)

    Deville, J.P.


    Nowadays, there are a lot of surfaces analysis methods, each having its specificity, its qualities, its constraints (for instance vacuum) and its limits. Expensive in time and in investment, these methods have to be used deliberately. This article appeals to non specialists. It gives some elements of choice according to the studied information, the sensitivity, the use constraints or the answer to a precise question. After having recalled the fundamental principles which govern these analysis methods, based on the interaction between radiations (ultraviolet, X) or particles (ions, electrons) with matter, two methods will be more particularly described: the Auger electron spectroscopy (AES) and x-rays photoemission spectroscopy (ESCA or XPS). Indeed, they are the most widespread methods in laboratories, the easier for use and probably the most productive for the analysis of surface of industrial materials or samples submitted to treatments in aggressive media. (O.M.)

  6. The repeatability of three diagnostic methods (visual using ICDAS II, laser fluorescence, and radiographic) for early caries detection (United States)

    Sukmasari, S.; Lestari, W.; Ko, B. B.; Noh, Z.; Asmail, N.; Yaacob, N.


    Newly introduced ICDAS II as a visual method, laser fluorescence as another technique that have ability to quantify early mineral loss of tooth structure and intra oral radiograph, are methods can be used in the clinic. To provide standardization for comprehensive caries management at an early stage, all methods supposed to be tested between users. The objective of this research is to evaluate the repeatability of each system. It is a comparative cross sectional study using 100 extracted permanent teeth without obvious cavitation (premolar & molar) that were collected and stored in thymol solution. The teeth were embedded on the wax block and labeled with numbers. All 5 surfaces were examined by 5 examiners using visual (ICDAS II), laser fluorescence (LF) and radiographic examination. The data were then analyzed to measure intra and inter examiner repeatability using Cronbach’s alpha and inter-item correlation matrix. Intra-examiner repeatability for all examiners was >0.7. Chronbach’s a value for inter-examiner repeatability for ICDAS II was >0.8 on 3 surfaces except on buccal and lingual. LF exhibit repeatability of >0.8 on all surfaces. Radiograph shows a low value of inter examiner repeatability (students for inter-item correlation while the 2nd and 3rd reading of LF displays the best agreement. ICDAS II score favors more non-invasive treatment compared to LF. ICDAS II showed good repeatability except on buccal and lingual surfaces. In line with some of the previous study, ICDAS II is applicable for caries detection in daily clinical basis. Laser fluorescence exhibits the highest repeatability while the radiograph showed weak inter-examiner repeatability. Treatment decisions of ICDAS II propose more preventive treatment for early caries lesions compared to laser fluorescence.

  7. Masonry fireplace emissions test method: Repeatability and sensitivity to fueling protocol. (United States)

    Stern, C H; Jaasma, D R; Champion, M R


    A test method for masonry fireplaces has been evaluated during testing on six masonry fireplace configurations. The method determines carbon monoxide and particulate matter emission rates (g/h) and factors (g/kg) and does not require weighing of the appliance to determine the timing of fuel loading.The intralaboratory repeatability of the test method has been determined from multiple tests on the six fireplaces. For the tested fireplaces, the ratio of the highest to lowest measured PM rate averaged 1.17 and in no case was greater than 1.32. The data suggest that some of the variation is due to differences in fuel properties.The influence of fueling protocol on emissions has also been studied. A modified fueling protocol, tested in large and small fireplaces, reduced CO and PM emission factors by roughly 40% and reduced CO and PM rates from 0 to 30%. For both of these fireplaces, emission rates were less sensitive to fueling protocol than emission factors.

  8. Methods of Multivariate Analysis

    CERN Document Server

    Rencher, Alvin C


    Praise for the Second Edition "This book is a systematic, well-written, well-organized text on multivariate analysis packed with intuition and insight . . . There is much practical wisdom in this book that is hard to find elsewhere."-IIE Transactions Filled with new and timely content, Methods of Multivariate Analysis, Third Edition provides examples and exercises based on more than sixty real data sets from a wide variety of scientific fields. It takes a "methods" approach to the subject, placing an emphasis on how students and practitioners can employ multivariate analysis in real-life sit

  9. Molecular characterization of Leptospira sp by multilocus variable number tandem repeat analysis (MLVA from clinical samples: a case report

    Directory of Open Access Journals (Sweden)

    Hélène Pailhoriès


    Full Text Available Leptospirosis is a zoonotic infection for which diagnosis is difficult. It has appeared as a global emerging infectious disease over recent years. Genotype determination often requires a Leptospira strain obtained by culture, which is a long and fastidious technique. A method based on multilocus variable number tandem repeat analysis (MLVA to determine the genotype of Leptospira interrogans, performed directly on blood or urine samples, is proposed. This method was applied to a fatal case of leptospirosis for which the geographical origin of infection was unknown. This technique will allow a genotype to be obtained for L. interrogans, even when cultures remain negative.

  10. Repeated CT scans in trauma transfers: An analysis of indications, radiation dose exposure, and costs

    International Nuclear Information System (INIS)

    Hinzpeter, Ricarda; Sprengel, Kai; Wanner, Guido A.; Mildenberger, Peter; Alkadhi, Hatem


    Highlights: • Repetition of CT in trauma patients occurs relatively often. • Repetition of CT is mainly caused by inadequate image data transfer. • Potentially preventable CT examinations add radiation dose to patients. • Repeated CT is associated with excess costs to the health care system. - Abstract: Objectives: To identify the number of CT scans repeated in acute trauma patients receiving imaging before being referred to a trauma center, to define indications, and to assess radiation doses and costs of repeated CT. Methods: This retrospective study included all adult trauma patients transferred from other hospitals to a Level-I trauma center during 2014. Indications for repeated CT scans were categorized into: inadequate CT image data transfer, poor image quality, repetition of head CT after head injury together with completion to whole-body CT (WBCT), and follow-up of injury known from previous CT. Radiation doses from repeated CT were determined; costs were calculated using a nation-wide fee schedule. Results: Within one year, 85/298 (28.5%) trauma patients were transferred from another hospital because of severe head injury (n = 45,53%) and major body trauma (n = 23;27%) not manageable in the referring hospital, repatriation from a foreign country (n = 14;16.5%), and no ICU-capacity (n = 3;3.5%). Of these 85 patients, 74 (87%) had repeated CT in our center because of inadequate CT data transfer (n = 29;39%), repetition of head CT with completion to WBCT (n = 24;32.5%), and follow-up of known injury (n = 21;28.5%). None occurred because of poor image quality. Cumulative dose length product (DLP) and annual costs of potential preventable, repeated CT (inadequate data transfer) was 631mSv (81′304mGy*cm) and 35′233€, respectively. Conclusion: A considerable number of transferred trauma patients undergo potentially preventable, repeated CT, adding radiation dose to patients and costs to the health care system.

  11. Repeated CT scans in trauma transfers: An analysis of indications, radiation dose exposure, and costs

    Energy Technology Data Exchange (ETDEWEB)

    Hinzpeter, Ricarda, E-mail: [Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Raemistr. 100, Zurich CH-8091 (Switzerland); Sprengel, Kai, E-mail: [Division of Trauma Surgery, Department of Surgery, University Hospital Zurich, University of Zurich, Raemistr. 100, CH-8091 Zurich (Switzerland); Wanner, Guido A., E-mail: [Division of Trauma Surgery, Department of Surgery, University Hospital Zurich, University of Zurich, Raemistr. 100, CH-8091 Zurich (Switzerland); Department of General Surgery, Schwarzwald-Baar Klinikum, University of Freiburg, Klinikstr. 11, D-78052 Villingen-Schwenningen (Germany); Mildenberger, Peter, E-mail: [Department of Diagnostic and Interventional Radiology, University Hospital of Mainz, Langenbeckstr. 1, D-55131 Mainz (Germany); Alkadhi, Hatem, E-mail: [Institute of Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Raemistr. 100, Zurich CH-8091 (Switzerland)


    Highlights: • Repetition of CT in trauma patients occurs relatively often. • Repetition of CT is mainly caused by inadequate image data transfer. • Potentially preventable CT examinations add radiation dose to patients. • Repeated CT is associated with excess costs to the health care system. - Abstract: Objectives: To identify the number of CT scans repeated in acute trauma patients receiving imaging before being referred to a trauma center, to define indications, and to assess radiation doses and costs of repeated CT. Methods: This retrospective study included all adult trauma patients transferred from other hospitals to a Level-I trauma center during 2014. Indications for repeated CT scans were categorized into: inadequate CT image data transfer, poor image quality, repetition of head CT after head injury together with completion to whole-body CT (WBCT), and follow-up of injury known from previous CT. Radiation doses from repeated CT were determined; costs were calculated using a nation-wide fee schedule. Results: Within one year, 85/298 (28.5%) trauma patients were transferred from another hospital because of severe head injury (n = 45,53%) and major body trauma (n = 23;27%) not manageable in the referring hospital, repatriation from a foreign country (n = 14;16.5%), and no ICU-capacity (n = 3;3.5%). Of these 85 patients, 74 (87%) had repeated CT in our center because of inadequate CT data transfer (n = 29;39%), repetition of head CT with completion to WBCT (n = 24;32.5%), and follow-up of known injury (n = 21;28.5%). None occurred because of poor image quality. Cumulative dose length product (DLP) and annual costs of potential preventable, repeated CT (inadequate data transfer) was 631mSv (81′304mGy*cm) and 35′233€, respectively. Conclusion: A considerable number of transferred trauma patients undergo potentially preventable, repeated CT, adding radiation dose to patients and costs to the health care system.

  12. Recommendations for analysis of repeated-measures designs: testing and correcting for sphericity and use of manova and mixed model analysis. (United States)

    Armstrong, Richard A


    A common experimental design in ophthalmic research is the repeated-measures design in which at least one variable is a within-subject factor. This design is vulnerable to lack of 'sphericity' which assumes that the variances of the differences among all possible pairs of within-subject means are equal. Traditionally, this design has been analysed using a repeated-measures analysis of variance (RM-anova) but increasingly more complex methods such as multivariate anova (manova) and mixed model analysis (MMA) are being used. This article surveys current practice in the analysis of designs incorporating different factors in research articles published in three optometric journals, namely Ophthalmic and Physiological Optics (OPO), Optometry and Vision Science (OVS), and Clinical and Experimental Optometry (CXO), and provides advice to authors regarding the analysis of repeated-measures designs. Of the total sample of articles, 66% used a repeated-measures design. Of those articles using a repeated-measures design, 59% and 8% analysed the data using RM-anova or manova respectively and 33% used MMA. The use of MMA relative to RM-anova has increased significantly since 2009/10. A further search using terms to select those papers testing and correcting for sphericity ('Mauchly's test', 'Greenhouse-Geisser', 'Huynh and Feld') identified 66 articles, 62% of which were published from 2012 to the present. If the design is balanced without missing data then manova should be used rather than RM-anova as it gives better protection against lack of sphericity. If the design is unbalanced or with missing data then MMA is the method of choice. However, MMA is a more complex analysis and can be difficult to set up and run, and care should be taken first, to define appropriate models to be tested and second, to ensure that sample sizes are adequate. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

  13. Repeatability and reproducibility of Population Viability Analysis (PVA and the implications for threatened species management

    Directory of Open Access Journals (Sweden)

    Clare Morrison


    Full Text Available Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost. Population Viability Analysis (PVA is frequently used in population focused conservation prioritizations. The critical nature of many of these management decisions requires that PVA models are repeatable and reproducible to reliably rank species and/or populations quantitatively. This paper assessed the repeatability and reproducibility of a subset of previously published PVA models. We attempted to rerun baseline models from 90 publicly available PVA studies published between 2000-2012 using the two most common PVA modelling software programs, VORTEX and RAMAS-GIS. Forty percent (n = 36 failed, 50% (45 were both repeatable and reproducible, and 10% (9 had missing baseline models. Repeatability was not linked to taxa, IUCN category, PVA program version used, year published or the quality of publication outlet, suggesting that the problem is systemic within the discipline. Complete and systematic presentation of PVA parameters and results are needed to ensure that the scientific input into conservation planning is both robust and reliable, thereby increasing the chances of making decisions that are both beneficial and defensible. The implications for conservation triage may be far reaching if population viability models cannot be reproduced with confidence, thus undermining their intended value.

  14. Analysis of a kinetic multi-segment foot model. Part I: Model repeatability and kinematic validity. (United States)

    Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L


    Kinematic multi-segment foot models are still evolving, but have seen increased use in clinical and research settings. The addition of kinetics may increase knowledge of foot and ankle function as well as influence multi-segment foot model evolution; however, previous kinetic models are too complex for clinical use. In this study we present a three-segment kinetic foot model and thorough evaluation of model performance during normal gait. In this first of two companion papers, model reference frames and joint centers are analyzed for repeatability, joint translations are measured, segment rigidity characterized, and sample joint angles presented. Within-tester and between-tester repeatability were first assessed using 10 healthy pediatric participants, while kinematic parameters were subsequently measured on 17 additional healthy pediatric participants. Repeatability errors were generally low for all sagittal plane measures as well as transverse plane Hindfoot and Forefoot segments (median<3°), while the least repeatable orientations were the Hindfoot coronal plane and Hallux transverse plane. Joint translations were generally less than 2mm in any one direction, while segment rigidity analysis suggested rigid body behavior for the Shank and Hindfoot, with the Forefoot violating the rigid body assumptions in terminal stance/pre-swing. Joint excursions were consistent with previously published studies. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Nonparametric modeling and analysis of association between Huntington's disease onset and CAG repeats. (United States)

    Ma, Yanyuan; Wang, Yuanjia


    Huntington's disease (HD) is a neurodegenerative disorder with a dominant genetic mode of inheritance caused by an expansion of CAG repeats on chromosome 4. Typically, a longer sequence of CAG repeat length is associated with increased risk of experiencing earlier onset of HD. Previous studies of the association between HD onset age and CAG length have favored a logistic model, where the CAG repeat length enters the mean and variance components of the logistic model in a complex exponential-linear form. To relax the parametric assumption of the exponential-linear association to the true HD onset distribution, we propose to leave both mean and variance functions of the CAG repeat length unspecified and perform semiparametric estimation in this context through a local kernel and backfitting procedure. Motivated by including family history of HD information available in the family members of participants in the Cooperative Huntington's Observational Research Trial (COHORT), we develop the methodology in the context of mixture data, where some subjects have a positive probability of being risk free. We also allow censoring on the age at onset of disease and accommodate covariates other than the CAG length. We study the theoretical properties of the proposed estimator and derive its asymptotic distribution. Finally, we apply the proposed methods to the COHORT data to estimate the HD onset distribution using a group of study participants and the disease family history information available on their family members. Copyright © 2013 John Wiley & Sons, Ltd.

  16. Spoligotyping and variable number tandem repeat analysis of Mycobacterium bovis isolates from cattle in Brazil

    Directory of Open Access Journals (Sweden)

    Patrícia Martins Parreiras


    Full Text Available We performed spoligotyping and 12-mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTRs typing to characterise Mycobacterium bovis isolates collected from tissue samples of bovines with lesions suggestive for tuberculosis during slaughter inspection procedures in abattoirs in Brazil. High-quality genotypes were obtained with both procedures for 61 isolates that were obtained from 185 bovine tissue samples and all of these isolates were identified as M. bovis by conventional identification procedures. On the basis of the spoligotyping, 53 isolates were grouped into nine clusters and the remaining eight isolates were unique types, resulting in 17 spoligotypes. The majority of the Brazilian M. bovis isolates displayed spoligotype patterns that have been previously observed in strains isolated from cattle in other countries. MIRU-VNTR typing produced 16 distinct genotypes, with 53 isolates forming eight of the groups, and individual isolates with unique VNTR profiles forming the remaining eight groups. The allelic diversity of each VNTR locus was calculated and only two of the 12-MIRU-VNTR loci presented scores with either a moderate (0.4, MIRU16 or high (0.6, MIRU26 discriminatory index (h. Both typing methods produced similar discriminatory indexes (spoligotyping h = 0.85; MIRU-VNTR h = 0.86 and the combination of the two methods increased the h value to 0.94, resulting in 29 distinct patterns. These results confirm that spoligotyping and VNTR analysis are valuable tools for studying the molecular epidemiology of M. bovis infections in Brazil.

  17. Spatial Component Position in Total Hip Arthroplasty. Accuracy and repeatability with a new CT method

    International Nuclear Information System (INIS)

    Olivecrona, H.


    Purpose: 3D detection of centerpoints of prosthetic cup and head after total hip arthroplasty (THA) using CT. Material and Methods: Two CT examinations, 10 min apart, were obtained from each of 10 patients after THA. Two independent examiners placed landmarks in images of the prosthetic cup and head. All landmarking was repeated after 1 week. Centerpoints were calculated and compared. Results: Within volumes, all measurements of centerpoints of cup and head fell, with a 95% confidence, within one CT-voxel of any other measurement of the same object. Across two volumes, the mean error of distance between center of cup and prosthetic head was 1.4 mm (SD 0.73). Intra- and interobserver 95% accuracy limit was below 2 mm within and below 3 mm across volumes. No difference between intra- and interobserver measurements occurred. A formula for converting finite sets of point landmarks in the radiolucent tread of the cup to a centerpoint was stable. The percent difference of the landmark distances from a calculated spherical surface was within one CT-voxel. This data was normally distributed and not dependent on observer or trial. Conclusion: The true 3D position of the centers of cup and prosthetic head can be detected using CT. Spatial relationship between the components can be analyzed visually and numerically

  18. Spatial Component Position in Total Hip Arthroplasty. Accuracy and repeatability with a new CT method

    Energy Technology Data Exchange (ETDEWEB)

    Olivecrona, H. [Soedersjukhuset, Stockholm (Sweden). Dept. of Hand Surgery; Weidenhielm, L. [Karolinska Hospital, Stockholm (Sweden). Dept. of Orthopedics; Olivecrona, L. [Karolinska Hospital, Stockholm (Sweden). Dept. of Radiology; Noz, M.E. [New York Univ. School of Medicine, NY (United States). Dept. of Radiology; Maguire, G.Q. [Royal Inst. of Tech., Kista (Sweden). Inst. for Microelectronics and Information Technology; Zeleznik, M. P. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Radiation Oncology; Svensson, L. [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Mathematics; Jonson, T. [Eskadern Foeretagsutveckling AB, Goeteborg (Sweden)


    Purpose: 3D detection of centerpoints of prosthetic cup and head after total hip arthroplasty (THA) using CT. Material and Methods: Two CT examinations, 10 min apart, were obtained from each of 10 patients after THA. Two independent examiners placed landmarks in images of the prosthetic cup and head. All landmarking was repeated after 1 week. Centerpoints were calculated and compared. Results: Within volumes, all measurements of centerpoints of cup and head fell, with a 95% confidence, within one CT-voxel of any other measurement of the same object. Across two volumes, the mean error of distance between center of cup and prosthetic head was 1.4 mm (SD 0.73). Intra- and interobserver 95% accuracy limit was below 2 mm within and below 3 mm across volumes. No difference between intra- and interobserver measurements occurred. A formula for converting finite sets of point landmarks in the radiolucent tread of the cup to a centerpoint was stable. The percent difference of the landmark distances from a calculated spherical surface was within one CT-voxel. This data was normally distributed and not dependent on observer or trial. Conclusion: The true 3D position of the centers of cup and prosthetic head can be detected using CT. Spatial relationship between the components can be analyzed visually and numerically.

  19. New method for remote and repeatable monitoring of intraocular pressure variations. (United States)

    Margalit, Israel; Beiderman, Yevgeny; Skaat, Alon; Rosenfeld, Elkanah; Belkin, Michael; Tornow, Ralf-Peter; Mico, Vicente; Garcia, Javier; Zalevsky, Zeev


    We present initial steps toward a new measurement device enabling high-precision, noncontact remote and repeatable monitoring of intraocular pressure (IOP)-based on an innovative measurement principle. Using only a camera and a laser source, the device measures IOP by tracking the secondary speckle pattern trajectories produced by the reflection of an illuminating laser beam from the iris or the sclera. The device was tested on rabbit eyes using two different methods to modify IOP: via an infusion bag and via mechanical pressure. In both cases, the eyes were stimulated with increasing and decreasing ramps of the IOP. As IOP variations changed the speckle distributions reflected back from the eye, data were recorded under various optical configurations to define and optimize the best experimental configuration for the IOP extraction. The association between the data provided by our proposed device and that resulting from controlled modification of the IOP was assessed, revealing high correlation (R2=0.98) and sensitivity and providing a high-precision measurement (5% estimated error) for the best experimental configuration. Future steps will be directed toward applying the proposed measurement principle in clinical trials for monitoring IOP with human subjects.

  20. A repeatable and scalable fabrication method for sharp, hollow silicon microneedles (United States)

    Kim, H.; Theogarajan, L. S.; Pennathur, S.


    Scalability and manufacturability are impeding the mass commercialization of microneedles in the medical field. Specifically, microneedle geometries need to be sharp, beveled, and completely controllable, difficult to achieve with microelectromechanical fabrication techniques. In this work, we performed a parametric study using silicon etch chemistries to optimize the fabrication of scalable and manufacturable beveled silicon hollow microneedles. We theoretically verified our parametric results with diffusion reaction equations and created a design guideline for a various set of miconeedles (80-160 µm needle base width, 100-1000 µm pitch, 40-50 µm inner bore diameter, and 150-350 µm height) to show the repeatability, scalability, and manufacturability of our process. As a result, hollow silicon microneedles with any dimensions can be fabricated with less than 2% non-uniformity across a wafer and 5% deviation between different processes. The key to achieving such high uniformity and consistency is a non-agitated HF-HNO3 bath, silicon nitride masks, and surrounding silicon filler materials with well-defined dimensions. Our proposed method is non-labor intensive, well defined by theory, and straightforward for wafer scale mass production, opening doors to a plethora of potential medical and biosensing applications.

  1. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    of the transcriptome, 5’ end capture of RNA is combined with next-generation sequencing for high-throughput quantitative assessment of transcription start sites by two different methods. The methods presented here allow for functional investigation of coding as well as noncoding RNA and contribute to future...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA...

  2. High-Dimensional Multivariate Repeated Measures Analysis with Unequal Covariance Matrices (United States)

    Harrar, Solomon W.; Kong, Xiaoli


    In this paper, test statistics for repeated measures design are introduced when the dimension is large. By large dimension is meant the number of repeated measures and the total sample size grow together but either one could be larger than the other. Asymptotic distribution of the statistics are derived for the equal as well as unequal covariance cases in the balanced as well as unbalanced cases. The asymptotic framework considered requires proportional growth of the sample sizes and the dimension of the repeated measures in the unequal covariance case. In the equal covariance case, one can grow at much faster rate than the other. The derivations of the asymptotic distributions mimic that of Central Limit Theorem with some important peculiarities addressed with sufficient rigor. Consistent and unbiased estimators of the asymptotic variances, which make efficient use of all the observations, are also derived. Simulation study provides favorable evidence for the accuracy of the asymptotic approximation under the null hypothesis. Power simulations have shown that the new methods have comparable power with a popular method known to work well in low-dimensional situation but the new methods have shown enormous advantage when the dimension is large. Data from Electroencephalograph (EEG) experiment is analyzed to illustrate the application of the results. PMID:26778861

  3. Analysis of numerical methods

    CERN Document Server

    Isaacson, Eugene


    This excellent text for advanced undergraduates and graduate students covers norms, numerical solution of linear systems and matrix factoring, iterative solutions of nonlinear equations, eigenvalues and eigenvectors, polynomial approximation, and other topics. It offers a careful analysis and stresses techniques for developing new methods, plus many examples and problems. 1966 edition.

  4. Analysis of oligonucleotide array experiments with repeated measures using mixed models

    Directory of Open Access Journals (Sweden)

    Getchell Thomas V


    Full Text Available Abstract Background Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease or absence (Control of the disease, and brain regions including olfactory bulb (OB or cerebellum (CER. In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. Results In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH procedure of controlling false discovery rate (FDR at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the α-level (αnew = 0.0033 determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD procedure at the level of αnew to control the family-wise error rate (FWER for each gene examined. Conclusions A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

  5. In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

    Directory of Open Access Journals (Sweden)

    Evandro Vagner Tambarussi


    Full Text Available The availability of chloroplast genome (cpDNA sequences of Atropa belladonna, Nicotiana sylvestris, N.tabacum, N. tomentosiformis, Solanum bulbocastanum, S. lycopersicum and S. tuberosum, which are Solanaceae species,allowed us to analyze the organization of cpSSRs in their genic and intergenic regions. In general, the number of cpSSRs incpDNA ranged from 161 in S. tuberosum to 226 in N. tabacum, and the number of intergenic cpSSRs was higher than geniccpSSRs. The mononucleotide repeats were the most frequent in studied species, but we also identified di-, tri-, tetra-, pentaandhexanucleotide repeats. Multiple alignments of all cpSSRs sequences from Solanaceae species made the identification ofnucleotide variability possible and the phylogeny was estimated by maximum parsimony. Our study showed that the plastomedatabase can be exploited for phylogenetic analysis and biotechnological approaches.

  6. Multielemental segregation analysis of the thallium bromide impurities purified by repeated Bridgman technique

    International Nuclear Information System (INIS)

    Santos, Robinson A. dos; Hamada, Margarida M.; Costa, Fabio E. da; Gennari, Roseli F.; Martins, Joao F.T.; Marcondes, Renata M.; Mesquita, Carlos H. de


    TlBr crystals were purified and grown by the repeated Bridgman method from two commercial TlBr salts and characterized to be used as radiation detectors. To evaluate the purification efficiency, measurements of the impurity concentration were made after each growth, analyzing the trace impurities by inductively coupled plasma mass spectroscopy (ICP-MS). A significant decrease of the impurity concentration resulting from the purification number was observed. To evaluate the crystal as a radiation semiconductor detector, measurements of its resistivity and gamma-ray spectroscopy were carried out. The radiation response depended on the crystal purity. The repeated Bridgman technique improved the TlBr crystal quality used as a radiation detector. A compartmental model was proposed to fit the impurity concentration as a function of the repetition number of the Bridgman growth. (author)

  7. Repeatability of heart rate variability in congenital hypothyroidism as analysed by detrended fluctuation analysis

    International Nuclear Information System (INIS)

    Echeverría, J C; Solís, L I; Pérez, J E; Gaitán, M J; Mandujano, M; Sánchez, M C; González-Camarena, R; Rivera, I R


    The analysis of heart rate fluctuations, or heart rate variability (HRV), may be applied to explore children's neurodevelopment. However, previous studies have reported poor reliability (repeatability) of HRV measures in children at rest and during light exercise. Whether the reliability can be improved by controlling variables such as physical activity, breathing rate and tidal volume, or by selecting non-conventional techniques for analysing the data remains as an open question. We evaluated the short-term repeatability of RR-interval data from medicated children with congenital hypothyroidism (CH). The α 1 exponents, obtained by detrended fluctuation analysis (DFA), from the data of 21 children collected at two different sessions were compared. Elapsed days between sessions were 59 ± 33, and data were obtained during 10 min, trying to restrict the children's activity while being seated. We found statistical agreement between the means of α 1 exponents for each session (p = 0.94) and no bias with a low-coefficient variation (9.1%); an intraclass correlation coefficient ri = 0.48 ([0.14 0.72], 95% confidence interval) was also estimated. These findings, which were compared with results obtained by conventional time and frequency techniques, indicate the existence of agreement between the α 1 exponents obtained at each session, thereby providing support concerning the repeatability of HRV data as analysed by DFA in children with congenital hypothyroidism. Of particular interest was also the agreement found by using the central frequency of the high-frequency band and the parameter pNN20, both showing better or similar ri than α 1 (0.77 [0.57 0.89] and 0.51 [0.17 0.74], respectively), yet considerably better repeatability than other conventional time and frequency parameters

  8. Methods for Risk Analysis

    International Nuclear Information System (INIS)

    Alverbro, Karin


    Many decision-making situations today affect humans and the environment. In practice, many such decisions are made without an overall view and prioritise one or other of the two areas. Now and then these two areas of regulation come into conflict, e.g. the best alternative as regards environmental considerations is not always the best from a human safety perspective and vice versa. This report was prepared within a major project with the aim of developing a framework in which both the environmental aspects and the human safety aspects are integrated, and decisions can be made taking both fields into consideration. The safety risks have to be analysed in order to be successfully avoided and one way of doing this is to use different kinds of risk analysis methods. There is an abundance of existing methods to choose from and new methods are constantly being developed. This report describes some of the risk analysis methods currently available for analysing safety and examines the relationships between them. The focus here is mainly on human safety aspects

  9. Repeat participation in annual cross-sectional surveys of drug users and its implications for analysis. (United States)

    Agius, P A; Aitken, C K; Breen, C; Dietze, P M


    We sought to establish the extent of repeat participation in a large annual cross-sectional survey of people who inject drugs and assess its implications for analysis. We used "porn star names" (the name of each participant's first pet followed by the name of the first street in which they lived) to identify repeat participation in three Australian Illicit Drug Reporting System surveys. Over 2013-2015, 2468 porn star names (96.2%) appeared only once, 88 (3.4%) twice, and nine (0.4%) in all 3 years. We measured design effects, based on the between-cluster variability for selected estimates, of 1.01-1.07 for seven key variables. These values indicate that the complex sample is (e.g.) 7% less efficient in estimating prevalence of heroin use (ever) than a simple random sample, and 1% less efficient in estimating number of heroin overdoses (ever). Porn star names are a useful means of tracking research participants longitudinally while maintaining their anonymity. Repeat participation in the Australian Illicit Drug Reporting System is low (less than 5% per annum), meaning point-prevalence and effect estimation without correction for the lack of independence in observations is unlikely to seriously affect population inference.

  10. High repeatability from 3D experimental platform for quantitative analysis of cellular branch pattern formations. (United States)

    Hagiwara, Masaya; Nobata, Rina; Kawahara, Tomohiro


    Three-dimensional (3D) cell and tissue cultures more closely mimic biological environments than two-dimensional (2D) cultures and are therefore highly desirable in culture experiments. However, 3D cultures often fail to yield repeatable experimental results because of variation in the initial culture conditions, such as cell density and distribution in the extracellular matrix, and therefore reducing such variation is a paramount concern. Here, we present a 3D culture platform that demonstrates highly repeatable experimental results, obtained by controlling the initial cell cluster shape in the gel cube culture device. A micro-mould with the desired shape was fabricated by photolithography or machining, creating a 3D pocket in the extracellular matrix contained in the device. Highly concentrated human bronchial epithelial cells were then injected in the pocket so that the cell cluster shape matched the fabricated mould shape. Subsequently, the cubic device supplied multi-directional scanning, enabling high-resolution capture of the whole tissue structure with only a low-magnification lens. The proposed device significantly improved the repeatability of the developed branch pattern, and multi-directional scanning enabled quantitative analysis of the developed branch pattern formations. A mathematical simulation was also conducted to reveal the mechanisms of branch pattern formation. The proposed platform offers the potential to accelerate any research field that conducts 3D culture experiments, including tissue regeneration and drug development.

  11. Analysis of the Effect of Radio Frequency Interference on Repeat Track Airborne InSAR System

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    Ding Bin


    Full Text Available The SAR system operating at low frequency is susceptible to Radio Frequency Interference (RFI from television station, radio station, and some other civil electronic facilities. The presence of RFI degrades the SAR image quality, and obscures the targets in the scene. Furthermore, RFI can cause interferometric phase error in repeat track InSAR system. In order to analyze the effect of RFI on interferometric phase of InSAR, real measured RFI signal are added on cone simulated SAR echoes. The imaging and interferometric processing results of both the RFI-contaminated and raw data are given. The effect of real measured RFI signal on repeat track InSAR system is analyzed. Finally, the imaging and interferometric processing results of both with and without RFI suppressed of the P band airborne repeat track InSAR real data are presented, which demonstrates the efficiency of the RFI suppression method in terms of decreasing the interferometric phase errors caused by RFI.

  12. Dynamic changes in cellular infiltrates with repeated cutaneous vaccination: a histologic and immunophenotypic analysis

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    Schaefer Jochen T


    Full Text Available Abstract Background Melanoma vaccines have not been optimized. Adjuvants are added to activate dendritic cells (DCs and to induce a favourable immunologic milieu, however, little is known about their cellular and molecular effects in human skin. We hypothesized that a vaccine in incomplete Freund's adjuvant (IFA would increase dermal Th1 and Tc1-lymphocytes and mature DCs, but that repeated vaccination may increase regulatory cells. Methods During and after 6 weekly immunizations with a multipeptide vaccine, immunization sites were biopsied at weeks 0, 1, 3, 7, or 12. In 36 participants, we enumerated DCs and lymphocyte subsets by immunohistochemistry and characterized their location within skin compartments. Results Mature DCs aggregated with lymphocytes around superficial vessels, however, immature DCs were randomly distributed. Over time, there was no change in mature DCs. Increases in T and B-cells were noted. Th2 cells outnumbered Th1 lymphocytes after 1 vaccine 6.6:1. Eosinophils and FoxP3+ cells accumulated, especially after 3 vaccinations, the former cell population most abundantly in deeper layers. Conclusions A multipeptide/IFA vaccine may induce a Th2-dominant microenvironment, which is reversed with repeat vaccination. However, repeat vaccination may increase FoxP3+T-cells and eosinophils. These data suggest multiple opportunities to optimize vaccine regimens and potential endpoints for monitoring the effects of new adjuvants. Trail Registration Identifier: NCT00705640

  13. Development and validation of a single-tube multiple-locus variable number tandem repeat analysis for Klebsiella pneumoniae.

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    Antoinette A T P Brink

    Full Text Available Genotyping of Klebsiella pneumoniae is indispensable for management of nosocomial infections, monitoring of emerging strains--including extended-spectrum beta-lactamase (ESBL producers-, and general epidemiology. Such objectives require a high-resolution genotyping method with a fixed scheme that allows (1 long-term retrospective and prospective assessment, (2 objective result readout and (3 library storage for database development and exchangeable results. We have developed a multiple-locus variable number tandem repeat analysis (MLVA using a single-tube fluorescently primed multiplex PCR for 8 Variable Number Tandem Repeats (VNTRs and automated fragment size analysis. The type allocation scheme was optimized using 224 K. pneumoniae clinical isolates, which yielded 101 MLVA types. The method was compared to the gold standard multilocus sequence typing (MLST using a subset of these clinical isolates (n = 95 and found to be highly concordant, with at least as high a resolution but with considerably less hands-on time. Our results position this MLVA scheme as an appropriate, high-throughput and relatively low-cost tool for K. pneumoniae epidemiology.

  14. Method of signal analysis

    International Nuclear Information System (INIS)

    Berthomier, Charles


    A method capable of handling the amplitude and the frequency time laws of a certain kind of geophysical signals is described here. This method is based upon the analytical signal idea of Gabor and Ville, which is constructed either in the time domain by adding an imaginary part to the real signal (in-quadrature signal), or in the frequency domain by suppressing negative frequency components. The instantaneous frequency of the initial signal is then defined as the time derivative of the phase of the analytical signal, and his amplitude, or envelope, as the modulus of this complex signal. The method is applied to three types of magnetospheric signals: chorus, whistlers and pearls. The results obtained by analog and numerical calculations are compared to results obtained by classical systems using filters, i.e. based upon a different definition of the concept of frequency. The precision with which the frequency-time laws are determined leads then to the examination of the principle of the method and to a definition of instantaneous power density spectrum attached to the signal, and to the first consequences of this definition. In this way, a two-dimensional representation of the signal is introduced which is less deformed by the analysis system properties than the usual representation, and which moreover has the advantage of being obtainable practically in real time [fr

  15. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci Multiple Locus Variable-Number Tandem Repeats Analysis

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    Ciervo Alessandra


    Full Text Available Abstract Background The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR Analysis (MLVA assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. Results Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. Conclusion In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the

  16. Assessment of repeatability of composition of perfumed waters by high-performance liquid chromatography combined with numerical data analysis based on cluster analysis (HPLC UV/VIS - CA). (United States)

    Ruzik, L; Obarski, N; Papierz, A; Mojski, M


    High-performance liquid chromatography (HPLC) with UV/VIS spectrophotometric detection combined with the chemometric method of cluster analysis (CA) was used for the assessment of repeatability of composition of nine types of perfumed waters. In addition, the chromatographic method of separating components of the perfume waters under analysis was subjected to an optimization procedure. The chromatograms thus obtained were used as sources of data for the chemometric method of cluster analysis (CA). The result was a classification of a set comprising 39 perfumed water samples with a similar composition at a specified level of probability (level of agglomeration). A comparison of the classification with the manufacturer's declarations reveals a good degree of consistency and demonstrates similarity between samples in different classes. A combination of the chromatographic method with cluster analysis (HPLC UV/VIS - CA) makes it possible to quickly assess the repeatability of composition of perfumed waters at selected levels of probability. © 2014 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

  17. Methods for geochemical analysis (United States)

    Baedecker, Philip A.


    The laboratories for analytical chemistry within the Geologic Division of the U.S. Geological Survey are administered by the Office of Mineral Resources. The laboratory analysts provide analytical support to those programs of the Geologic Division that require chemical information and conduct basic research in analytical and geochemical areas vital to the furtherance of Division program goals. Laboratories for research and geochemical analysis are maintained at the three major centers in Reston, Virginia, Denver, Colorado, and Menlo Park, California. The Division has an expertise in a broad spectrum of analytical techniques, and the analytical research is designed to advance the state of the art of existing techniques and to develop new methods of analysis in response to special problems in geochemical analysis. The geochemical research and analytical results are applied to the solution of fundamental geochemical problems relating to the origin of mineral deposits and fossil fuels, as well as to studies relating to the distribution of elements in varied geologic systems, the mechanisms by which they are transported, and their impact on the environment.


    Kumkrong, Khurawan; Chankate, Phanita; Tonyoung, Wittawat; Intarapuk, Apiradee; Kerdsin, Anusak; Kalambaheti, Thareerat


    Brucellosis-induced abortion can result in significant economic loss to farm animals. Brucellosis can be transmitted to humans during slaughter of infected animals or via consumption of contaminated food products. Strain identification of Brucella isolates can reveal the route of transmission. Brucella strains were isolated from vaginal swabs of farm animal, cow milk and from human blood cultures. Multiplex PCR was used to identify Brucella species, and owing to high DNA homology among Brucella isolates, multiple-locus variable-number tandem repeat analysis (MLVA) based on the number of tandem repeats at 16 different genomic loci was used for strain identification. Multiplex PCR categorized the isolates into B. abortus (n = 7), B. melitensis (n = 37), B. suis (n = 3), and 5 of unknown Brucella spp. MLVA-16 clustering analysis differentiated the strains into various genotypes, with Brucella isolates from the same geographic region being closely related, and revealed that the Thai isolates were phylogenetically distinct from those in other countries, including within the Southeast Asian region. Thus, MLVA-16 typing has utility in epidemiological studies.

  19. Kinematic Analysis of a Six-Degrees-of-Freedom Model Based on ISB Recommendation: A Repeatability Analysis and Comparison with Conventional Gait Model. (United States)

    Żuk, Magdalena; Pezowicz, Celina


    Objective. The purpose of the present work was to assess the validity of a six-degrees-of-freedom gait analysis model based on the ISB recommendation on definitions of joint coordinate systems (ISB 6DOF) through a quantitative comparison with the Helen Hays model (HH) and repeatability assessment. Methods. Four healthy subjects were analysed with both marker sets: an HH marker set and four marker clusters in ISB 6DOF. A navigated pointer was used to indicate the anatomical landmark position in the cluster reference system according to the ISB recommendation. Three gait cycles were selected from the data collected simultaneously for the two marker sets. Results. Two protocols showed good intertrial repeatability, which apart from pelvic rotation did not exceed 2°. The greatest differences between protocols were observed in the transverse plane as well as for knee angles. Knee internal/external rotation revealed the lowest subject-to-subject and interprotocol repeatability and inconsistent patterns for both protocols. Knee range of movement in transverse plane was overestimated for the HH set (the mean is 34°), which could indicate the cross-talk effect. Conclusions. The ISB 6DOF anatomically based protocol enabled full 3D kinematic description of joints according to the current standard with clinically acceptable intertrial repeatability and minimal equipment requirements.

  20. Usefulness of repeat coronary angiography 24 hours after balloon angioplasty to evaluate early lminal deterioration and facilitate quantitative analysis

    NARCIS (Netherlands)

    G.R. Heyndrickx (Guy); G-J. Laarman (GertJan); H. Suryapranata (Harry); F. Zijlstra (Felix); P.W.J.C. Serruys (Patrick); D.P. Foley (David); A.A. van den Bos (Arjan); J.W. Deckers (Jaap)


    textabstractBecause of the unavoidable occurrence of vessel disruption after successful coronary balloon angioplasty, the reliability of quantitative angiographic analysis in that setting has been questioned. For this reason and the suggested occurrence of delayed elastic recoil, repeat angiography


    Directory of Open Access Journals (Sweden)

    A. L. Osipov


    Full Text Available The basic statistical methods used in conducting the genetic analysis of human traits. We studied by segregation analysis, linkage analysis and allelic associations. Developed software for the implementation of these methods support.

  2. A Method against Interrupted-Sampling Repeater Jamming Based on Energy Function Detection and Band-Pass Filtering

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    Hui Yuan


    Full Text Available Interrupted-sampling repeater jamming (ISRJ is a new kind of coherent jamming to the large time-bandwidth linear frequency modulation (LFM signal. Many jamming modes, such as lifelike multiple false targets and dense false targets, can be made through setting up different parameters. According to the “storage-repeater-storage-repeater” characteristics of the ISRJ and the differences in the time-frequency-energy domain between the ISRJ signal and the target echo signal, one new method based on the energy function detection and band-pass filtering is proposed to suppress the ISRJ. The methods mainly consist of two parts: extracting the signal segments without ISRJ and constructing band-pass filtering function with low sidelobe. The simulation results show that the method is effective in the ISRJ with different parameters.

  3. Repeatability and variation of region-of-interest methods using quantitative diffusion tensor MR imaging of the brain

    International Nuclear Information System (INIS)

    Hakulinen, Ullamari; Brander, Antti; Ryymin, Pertti; Öhman, Juha; Soimakallio, Seppo; Helminen, Mika; Dastidar, Prasun; Eskola, Hannu


    Diffusion tensor imaging (DTI) is increasingly used in various diseases as a clinical tool for assessing the integrity of the brain’s white matter. Reduced fractional anisotropy (FA) and an increased apparent diffusion coefficient (ADC) are nonspecific findings in most pathological processes affecting the brain’s parenchyma. At present, there is no gold standard for validating diffusion measures, which are dependent on the scanning protocols, methods of the softwares and observers. Therefore, the normal variation and repeatability effects on commonly-derived measures should be carefully examined. Thirty healthy volunteers (mean age 37.8 years, SD 11.4) underwent DTI of the brain with 3T MRI. Region-of-interest (ROI) -based measurements were calculated at eleven anatomical locations in the pyramidal tracts, corpus callosum and frontobasal area. Two ROI-based methods, the circular method (CM) and the freehand method (FM), were compared. Both methods were also compared by performing measurements on a DTI phantom. The intra- and inter-observer variability (coefficient of variation, or CV%) and repeatability (intra-class correlation coefficient, or ICC) were assessed for FA and ADC values obtained using both ROI methods. The mean FA values for all of the regions were 0.663 with the CM and 0.621 with the FM. For both methods, the FA was highest in the splenium of the corpus callosum. The mean ADC value was 0.727 ×10 -3 mm 2 /s with the CM and 0.747 ×10 -3 mm 2 /s with the FM, and both methods found the ADC to be lowest in the corona radiata. The CV percentages of the derived measures were < 13% with the CM and < 10% with the FM. In most of the regions, the ICCs were excellent or moderate for both methods. With the CM, the highest ICC for FA was in the posterior limb of the internal capsule (0.90), and with the FM, it was in the corona radiata (0.86). For ADC, the highest ICC was found in the genu of the corpus callosum (0.93) with the CM and in the uncinate

  4. Repeated attempted homicide by administration of drugs documented by hair analysis. (United States)

    Baillif-Couniou, Valérie; Bartoli, Christophe; Sastre, Caroline; Chèze, Marjorie; Deveaux, Marc; Léonetti, Georges; Pélissier-Alicot, Anne-Laure


    Attempted murder by repeated poisoning is quite rare. The authors describe the case of a 62-year-old man who was admitted to an intensive care unit (ICU) for neurological disturbances complicated by inhalation pneumopathy. He presented a loss of consciousness while his wife was visiting him at the ICU (H0). Forty-eight hours later (H48), police officers apprehended the patient's wife pouring a liquid into his fruit salad at the hospital. Toxicological analyses of a blood sample and the infusion equipment (H0), as well as the fruit salad and its container (H48), confirmed the attempted poisoning with cyamemazine (H0) and hydrochloric acid (H48). In order to evaluate the anteriority of poisonings, hair analysis was requested and the medical records of the 6 previous months were also examined. Two 6-cm brown hair strands were sampled and the victim's medical record was seized in order to determine the treatments he had been given during the previous six months. Segmental hair testing on two 6-cm brown hair was conducted by GC-MS, LC-DAD and LC-MS/MS (0-2/2-4/4-6 cm; pg/mg). Haloperidol (9200/1391/227), amitriptyline (7450/1850/3260), venlafaxine (332/560/260), that had never been part of the victim's treatment were detected, as well as some benzodiazepines (alprazolam, bromazepam, nordazepam); cyamemazine was also detected in all the segments (9960/1610/2367) though only a single dose administration was reported in the medical records. The toxicological analyses performed at H0 and H48 confirmed the homicide attempts in the ICU. In addition, comparison of the results in hair analysis with the medical records confirmed repeated poisoning attempts over the previous six months, and thus explain the origin of the disorders presented by the victim. This case serves to remind us that repeated attempted murder can be difficult to diagnose and that hair analysis can be an effective way to detect such attempts. Copyright © 2018. Published by Elsevier Ltd.

  5. At what price? A cost-effectiveness analysis comparing trial of labour after previous caesarean versus elective repeat caesarean delivery.

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    Christopher G Fawsitt

    Full Text Available BACKGROUND: Elective repeat caesarean delivery (ERCD rates have been increasing worldwide, thus prompting obstetric discourse on the risks and benefits for the mother and infant. Yet, these increasing rates also have major economic implications for the health care system. Given the dearth of information on the cost-effectiveness related to mode of delivery, the aim of this paper was to perform an economic evaluation on the costs and short-term maternal health consequences associated with a trial of labour after one previous caesarean delivery compared with ERCD for low risk women in Ireland. METHODS: Using a decision analytic model, a cost-effectiveness analysis (CEA was performed where the measure of health gain was quality-adjusted life years (QALYs over a six-week time horizon. A review of international literature was conducted to derive representative estimates of adverse maternal health outcomes following a trial of labour after caesarean (TOLAC and ERCD. Delivery/procedure costs derived from primary data collection and combined both "bottom-up" and "top-down" costing estimations. RESULTS: Maternal morbidities emerged in twice as many cases in the TOLAC group than the ERCD group. However, a TOLAC was found to be the most-effective method of delivery because it was substantially less expensive than ERCD (€ 1,835.06 versus € 4,039.87 per women, respectively, and QALYs were modestly higher (0.84 versus 0.70. Our findings were supported by probabilistic sensitivity analysis. CONCLUSIONS: Clinicians need to be well informed of the benefits and risks of TOLAC among low risk women. Ideally, clinician-patient discourse would address differences in length of hospital stay and postpartum recovery time. While it is premature advocate a policy of TOLAC across maternity units, the results of the study prompt further analysis and repeat iterations, encouraging future studies to synthesis previous research and new and relevant evidence under a single

  6. Cost-effectiveness analysis of repeat fine-needle aspiration for thyroid biopsies read as atypia of undetermined significance. (United States)

    Heller, Michael; Zanocco, Kyle; Zydowicz, Sara; Elaraj, Dina; Nayar, Ritu; Sturgeon, Cord


    The 2007 National Cancer Institute (NCI) conference on Thyroid Fine-Needle Aspiration (FNA) introduced the category atypia of undetermined significance (AUS) or follicular lesion of undetermined significance (FLUS). Repeat FNA in 3 to 6 months was recommended for low-risk patients. Compliance with these recommendations has been suboptimal. We hypothesized that repeat FNA would be more effective than diagnostic lobectomy, with decreased costs and improved rates of cancer detection. Cost-effectiveness analysis was performed in which we compared diagnostic lobectomy with repeat FNA. A Markov model was developed. Outcomes and probabilities were identified from literature review. Third-party payer costs were estimated in 2010 US dollars. Outcomes were weighted by use of the quality-of-life utility factors, yielding quality-adjusted life years (QALYs). Monte Carlo simulation and sensitivity analysis were used to examine the uncertainty of probability, cost, and utility estimates. The diagnostic lobectomy strategy cost $8,057 and produced 23.99 QALYs. Repeat FNA cost $2,462 and produced 24.05 QALYs. Repeat FNA was dominant until the cost of FNA increased to $6,091. Dominance of the repeat FNA strategy was not sensitive to the cost of operation or the complication rate. The NCI recommendations for repeat FNA regarding follow-up of AUS/FLUS results are cost-effective. Improving compliance with these guidelines should lead to less overall costs, greater quality of life, and fewer unnecessary operations. Copyright © 2012 Mosby, Inc. All rights reserved.

  7. Analysis of an "off-ladder" allele at the Penta D short tandem repeat locus. (United States)

    Yang, Y L; Wang, J G; Wang, D X; Zhang, W Y; Liu, X J; Cao, J; Yang, S L


    Kinship testing of a father and his son from Guangxi, China, the location of the Zhuang minority people, was performed using the PowerPlex® 18D System with a short tandem repeat typing kit. The results indicated that both the father and his son had an off-ladder allele at the Penta D locus, with a genetic size larger than that of the maximal standard allelic ladder. To further identify this locus, monogenic amplification, gene cloning, and genetic sequencing were performed. Sequencing analysis demonstrated that the fragment size of the Penta D-OL locus was 469 bp and the core sequence was [AAAGA]21, also called Penta D-21. The rare Penta D-21 allele was found to be distributed among the Zhuang population from the Guangxi Zhuang Autonomous Region of China; therefore, this study improved the range of DNA data available for this locus and enhanced our ability for individual identification of gene loci.

  8. Multiple-locus variable-number tandem-repeat analysis of pathogenic Yersinia enterocolitica in China.

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    Xin Wang

    Full Text Available The predominant bioserotypes of pathogenic Yersinia enterocolitica in China are 2/O: 9 and 3/O: 3; no pathogenic O: 8 strains have been found to date. Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA based on seven loci was able to distinguish 104 genotypes among 218 pathogenic Y. enterocolitica isolates in China and from abroad, showing a high resolution. The major pathogenic serogroups in China, O: 3 and O: 9, were divided into two clusters based on MLVA genotyping. The different distribution of Y. enterocolitica MLVA genotypes maybe due to the recent dissemination of specific clones of 2/O: 9 and 3/O: 3 strains in China. MLVA was a helpful tool for bacterial pathogen surveillance and investigation of pathogenic Y. enterocolitica outbreaks.

  9. Effects of Repeated-Sprint Training in Hypoxia on Sea-Level Performance: A Meta-Analysis. (United States)

    Brocherie, Franck; Girard, Olivier; Faiss, Raphaël; Millet, Grégoire P


    Repeated-sprint training in hypoxia (RSH) is a recent intervention regarding which numerous studies have reported effects on sea-level physical performance outcomes that are debated. No previous study has performed a meta-analysis of the effects of RSH. We systematically reviewed the literature and meta-analyzed the effects of RSH versus repeated-sprint training in normoxia (RSN) on key components of sea-level physical performance, i.e., best and mean (all sprint) performance during repeated-sprint exercise and aerobic capacity (i.e., maximal oxygen uptake [[Formula: see text

  10. Repeatability of quantitative 18F-FLT uptake measurements in solid tumors: an individual patient data multi-center meta-analysis. (United States)

    Kramer, G M; Liu, Y; de Langen, A J; Jansma, E P; Trigonis, I; Asselin, M-C; Jackson, A; Kenny, L; Aboagye, E O; Hoekstra, O S; Boellaard, R


    3'-deoxy-3'-[ 18 F]fluorothymidine ( 18 F-FLT) positron emission tomography (PET) provides a non-invasive method to assess cellular proliferation and response to antitumor therapy. Quantitative 18 F-FLT uptake metrics are being used for evaluation of proliferative response in investigational setting, however multi-center repeatability needs to be established. The aim of this study was to determine the repeatability of 18 F-FLT tumor uptake metrics by re-analyzing individual patient data from previously published reports using the same tumor segmentation method and repeatability metrics across cohorts. A systematic search in PubMed, and the Cochrane Library from inception-October 2016 yielded five 18 F-FLT repeatability cohorts in solid tumors. 18 F-FLT avid lesions were delineated using a 50% isocontour adapted for local background on test and retest scans. SUV max , SUV mean , SUV peak , proliferative volume and total lesion uptake (TLU) were calculated. Repeatability was assessed using the repeatability coefficient (RC = 1.96 × SD of test-retest differences), linear regression analysis, and the intra-class correlation coefficient (ICC). The impact of different lesion selection criteria was also evaluated. Images from four cohorts containing 30 patients with 52 lesions were obtained and analyzed (ten in breast cancer, nine in head and neck squamous cell carcinoma, and 33 in non-small cell lung cancer patients). A good correlation was found between test-retest data for all 18 F-FLT uptake metrics (R 2  ≥ 0.93; ICC ≥ 0.96). Best repeatability was found for SUV peak (RC: 23.1%), without significant differences in RC between different SUV metrics. Repeatability of proliferative volume (RC: 36.0%) and TLU (RC: 36.4%) was worse than SUV. Lesion selection methods based on SUV max  ≥ 4.0 improved the repeatability of volumetric metrics (RC: 26-28%), but did not affect the repeatability of SUV metrics. In multi-center studies

  11. Methods of nonlinear analysis

    CERN Document Server

    Bellman, Richard Ernest


    In this book, we study theoretical and practical aspects of computing methods for mathematical modelling of nonlinear systems. A number of computing techniques are considered, such as methods of operator approximation with any given accuracy; operator interpolation techniques including a non-Lagrange interpolation; methods of system representation subject to constraints associated with concepts of causality, memory and stationarity; methods of system representation with an accuracy that is the best within a given class of models; methods of covariance matrix estimation;methods for low-rank mat

  12. Variable-number-of-tandem-repeats analysis of genetic diversity in Pasteuria ramosa. (United States)

    Mouton, L; Ebert, D


    Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

  13. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E


    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  14. Genotyping analysis of Helicobacter pylori using multiple-locus variable-number tandem-repeats analysis in five regions of China and Japan

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    Zhang Jinyong


    Full Text Available Abstract Background H. pylori (Helicobacter pylori is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.

  15. An analysis of single amino acid repeats as use case for application specific background models

    Directory of Open Access Journals (Sweden)

    Sykacek Peter


    Full Text Available Abstract Background Sequence analysis aims to identify biologically relevant signals against a backdrop of functionally meaningless variation. Increasingly, it is recognized that the quality of the background model directly affects the performance of analyses. State-of-the-art approaches rely on classical sequence models that are adapted to the studied dataset. Although performing well in the analysis of globular protein domains, these models break down in regions of stronger compositional bias or low complexity. While these regions are typically filtered, there is increasing anecdotal evidence of functional roles. This motivates an exploration of more complex sequence models and application-specific approaches for the investigation of biased regions. Results Traditional Markov-chains and application-specific regression models are compared using the example of predicting runs of single amino acids, a particularly simple class of biased regions. Cross-fold validation experiments reveal that the alternative regression models capture the multi-variate trends well, despite their low dimensionality and in contrast even to higher-order Markov-predictors. We show how the significance of unusual observations can be computed for such empirical models. The power of a dedicated model in the detection of biologically interesting signals is then demonstrated in an analysis identifying the unexpected enrichment of contiguous leucine-repeats in signal-peptides. Considering different reference sets, we show how the question examined actually defines what constitutes the 'background'. Results can thus be highly sensitive to the choice of appropriate model training sets. Conversely, the choice of reference data determines the questions that can be investigated in an analysis. Conclusions Using a specific case of studying biased regions as an example, we have demonstrated that the construction of application-specific background models is both necessary and

  16. Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae

    Directory of Open Access Journals (Sweden)

    Lam Connie


    Full Text Available Abstract Background Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs analysis (MLVA to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae. Results MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus. Conclusions MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing.

  17. Imported brucellosis in Denmark: Molecular identification and multiple-locus variable number tandem repeat analysis (MLVA) genotyping of the bacteria

    DEFF Research Database (Denmark)

    Aftab, H.; Dargis, R.; Christensen, J. J.


    A polymerase chain reaction was used to identify Brucella species isolated from humans in Denmark. Consecutive analysis of referred bacteria and re-examination of historical isolates identified all as Brucella melitensis. Multiple-locus variable number tandem repeat analysis (MLVA) placed...... the isolates in the previously defined 'East Mediterranean' B. melitensis group....

  18. Molecular analysis of the eTG trinucleotide repeat in South African ...

    African Journals Online (AJOL)

    -4 When amplified, this trinucleotide repeat is responsible for DNA instability and molecular pathology. A similar mechanism of trinucleotide repeat expansion has been described in fragile X mental retardation syndrome. (CGG):·· spinobulbar muscular atrophy (CAG)' and, more. MRC Human Ecogenetics Research Unit, ...

  19. Narrative exposure therapy for posttraumatic stress disorder associated with repeated interpersonal trauma in patients with severe mental illness: a mixed methods design

    Directory of Open Access Journals (Sweden)

    Maria W. Mauritz


    Full Text Available Background: In the Netherlands, most patients with severe mental illness (SMI receive flexible assertive community treatment (FACT provided by multidisciplinary community mental health teams. SMI patients with comorbid posttraumatic stress disorder (PTSD are sometimes offered evidence-based trauma-focused treatment like eye movement desensitization reprocessing or prolonged exposure. There is a large amount of evidence for the effectiveness of narrative exposure therapy (NET within various vulnerable patient groups with repeated interpersonal trauma. Some FACT-teams provide NET for patients with comorbid PTSD, which is promising, but has not been specifically studied in SMI patients. Objectives: The primary aim is to evaluate NET in SMI patients with comorbid PTSD associated with repeated interpersonal trauma to get insight into whether (1 PTSD and dissociative symptoms changes and (2 changes occur in the present SMI symptoms, care needs, quality of life, global functioning, and care consumption. The second aim is to gain insight into patients’ experiences with NET and to identify influencing factors on treatment results. Methods: This study will have a mixed methods convergent design consisting of quantitative repeated measures and qualitative semi-structured in-depth interviews based on Grounded Theory. The study population will include adult SMI outpatients (n=25 with comorbid PTSD and receiving NET. The quantitative study parameters will be existence and severity of PTSD, dissociative, and SMI symptoms; care needs; quality of life; global functioning; and care consumption. In a longitudinal analysis, outcomes will be analyzed using mixed models to estimate the difference in means between baseline and repeated measurements. The qualitative study parameters will be experiences with NET and perceived factors for success or failure. Integration of quantitative and qualitative results will be focused on interpreting how qualitative results

  20. Multifunctional surface modification of silk fabric via graphene oxide repeatedly coating and chemical reduction method (United States)

    Cao, Jiliang; Wang, Chaoxia


    Multifunctional silk fabrics with electrical conductive, anti-ultraviolet and water repellent were successfully prepared by surface modification with graphene oxide (GO). The yellow-brown GO deposited on the surface of silk fabric was converted into graphitic black reduced graphene (RGO) by sodium hydrosulfite. The surface properties of silk fabrics were changed by repeatedly RGO coating process, which have been proved by SEM and XPS. The SEM results showed that the RGO sheets were successive form a continuously thin film on the surface of silk fabrics, and the deposition of GO or RGO also can be proved by XPS. The electrical conductivity was tested by electrical surface resistance value of the silk fabric, the surface resistance decreased with increasing of RGO surface modification times, and a low surface resistance value reached to 3.24 KΩ cm-1 after 9 times of modification, indicating the silk obtained excellent conductivity. The UPF value of one time GO modification silk fabric (silk-1RGO) was enhanced significantly to 24.45 in comparison to 10.40 of original silk. The contact angle of RGO coating silk samples was all above of 120°. The durability of RGO coated silk fabrics was tested by laundering. The electrical surface resistance of silk-4RGO (65.74 KΩ cm-1), silk-6RGO (15.54 KΩ cm-1) and silk-8RGO (3.86 KΩ cm-1) fabrics was up to 86.82, 22.30 and 6.57 KΩ cm-1 after 10 times of standard washing, respectively. The UPF value, contact angle and color differences of RGO modified silk fabric slightly changed before and after 10 times of standard washing. Therefore, the washing fastness of electric conduction, anti-ultraviolet and water repellent multifunctional silk fabrics was excellent.

  1. Film repeats in radiology department

    International Nuclear Information System (INIS)

    Suwan, A. Z.; Al-Shakharah, A. I


    During a one year period, 4910 radiographs of 55780 films were repeated. The objective of our study was to analyse and to classify the causes in order to minimize the repeats, cut the expenses and to provide optimal radiographs for accurate diagnosis. Analysis of the different factors revealed that, 43.6% of film repeats in our service were due to faults in exposure factors, centering comprises 15.9% of the repeats, while too much collimation was responsible for 7.6% of these repeats. All of which can be decreased by awareness and programmed training of technicians. Film blurring caused by patient motion was also responsible for 4.9% for radiographs reexamination, which can be minimized by detailed explanation to the patient and providing the necessary privacy. Fogging of X-Ray films by improper storage or inadequate handling or processing faults were responsible for 14.5% in repeats in our study. Methods and criteria for proper storage and handling of films were discussed. Recommendation for using modern day-light and laser processor has been high lighted. Artefacts are noticeably high in our cases, due to spinal dresses and frequent usage of precious metals for c osmotic purposes in this part of the world. The repeated films comprise 8.8% of all films We conclude that, the main factor responsible for repeats of up to 81.6% of cases was the technologists, thus emphasizing the importance of adequate training of the technologists. (authors). 15 refs., 9 figs., 1 table

  2. Social instigation and repeated aggressive confrontations in male Swiss mice: analysis of plasma corticosterone, CRF and BDNF levels in limbic brain areas

    Directory of Open Access Journals (Sweden)

    Paula Madeira Fortes


    Full Text Available Abstract Introduction: Agonistic behaviors help to ensure survival, provide advantage in competition, and communicate social status. The resident-intruder paradigm, an animal model based on male intraspecific confrontations, can be an ethologically relevant tool to investigate the neurobiology of aggressive behavior. Objectives: To examine behavioral and neurobiological mechanisms of aggressive behavior in male Swiss mice exposed to repeated confrontations in the resident intruder paradigm. Methods: Behavioral analysis was performed in association with measurements of plasma corticosterone of mice repeatedly exposed to a potential rival nearby, but inaccessible (social instigation, or to 10 sessions of social instigation followed by direct aggressive encounters. Moreover, corticotropin-releasing factor (CRF and brain-derived neurotrophic factor (BNDF were measured in the brain of these animals. Control mice were exposed to neither social instigation nor aggressive confrontations. Results: Mice exposed to aggressive confrontations exhibited a similar pattern of species-typical aggressive and non-aggressive behaviors on the first and the last session. Moreover, in contrast to social instigation only, repeated aggressive confrontations promoted an increase in plasma corticosterone. After 10 aggressive confrontation sessions, mice presented a non-significant trend toward reducing hippocampal levels of CRF, which inversely correlated with plasma corticosterone levels. Conversely, repeated sessions of social instigation or aggressive confrontation did not alter BDNF concentrations at the prefrontal cortex and hippocampus. Conclusion: Exposure to repeated episodes of aggressive encounters did not promote habituation over time. Additionally, CRF seems to be involved in physiological responses to social stressors.

  3. Can You Repeat That Please?: Using Monte Carlo Simulation in Graduate Quantitative Research Methods Classes (United States)

    Carsey, Thomas M.; Harden, Jeffrey J.


    Graduate students in political science come to the discipline interested in exploring important political questions, such as "What causes war?" or "What policies promote economic growth?" However, they typically do not arrive prepared to address those questions using quantitative methods. Graduate methods instructors must…

  4. Multivariate analysis: models and method

    International Nuclear Information System (INIS)

    Sanz Perucha, J.


    Data treatment techniques are increasingly used since computer methods result of wider access. Multivariate analysis consists of a group of statistic methods that are applied to study objects or samples characterized by multiple values. A final goal is decision making. The paper describes the models and methods of multivariate analysis

  5. Multivariate analysis methods in physics

    International Nuclear Information System (INIS)

    Wolter, M.


    A review of multivariate methods based on statistical training is given. Several multivariate methods useful in high-energy physics analysis are discussed. Selected examples from current research in particle physics are discussed, both from the on-line trigger selection and from the off-line analysis. Also statistical training methods are presented and some new application are suggested [ru

  6. A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming. (United States)

    Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der


    Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

  7. Methods in algorithmic analysis

    CERN Document Server

    Dobrushkin, Vladimir A


    …helpful to any mathematics student who wishes to acquire a background in classical probability and analysis … This is a remarkably beautiful book that would be a pleasure for a student to read, or for a teacher to make into a year's course.-Harvey Cohn, Computing Reviews, May 2010

  8. Communication Network Analysis Methods. (United States)

    Farace, Richard V.; Mabee, Timothy

    This paper reviews a variety of analytic procedures that can be applied to network data, discussing the assumptions and usefulness of each procedure when applied to the complexity of human communication. Special attention is paid to the network properties measured or implied by each procedure. Factor analysis and multidimensional scaling are among…

  9. Complementing Gender Analysis Methods. (United States)

    Kumar, Anant


    The existing gender analysis frameworks start with a premise that men and women are equal and should be treated equally. These frameworks give emphasis on equal distribution of resources between men and women and believe that this will bring equality which is not always true. Despite equal distribution of resources, women tend to suffer and experience discrimination in many areas of their lives such as the power to control resources within social relationships, and the need for emotional security and reproductive rights within interpersonal relationships. These frameworks believe that patriarchy as an institution plays an important role in women's oppression, exploitation, and it is a barrier in their empowerment and rights. Thus, some think that by ensuring equal distribution of resources and empowering women economically, institutions like patriarchy can be challenged. These frameworks are based on proposed equality principle which puts men and women in competing roles. Thus, the real equality will never be achieved. Contrary to the existing gender analysis frameworks, the Complementing Gender Analysis framework proposed by the author provides a new approach toward gender analysis which not only recognizes the role of economic empowerment and equal distribution of resources but suggests to incorporate the concept and role of social capital, equity, and doing gender in gender analysis which is based on perceived equity principle, putting men and women in complementing roles that may lead to equality. In this article the author reviews the mainstream gender theories in development from the viewpoint of the complementary roles of gender. This alternative view is argued based on existing literature and an anecdote of observations made by the author. While criticizing the equality theory, the author offers equity theory in resolving the gender conflict by using the concept of social and psychological capital.

  10. [An analysis of industrial accidents in the working field with a particular emphasis on repeated accidents]. (United States)

    Wakisaka, I; Yanagihashi, T; Tomari, T; Sato, M


    The present study is based on an analysis of routinely submitted reports of occupational accidents experienced by the workers of industrial enterprises under the jurisdiction of Kagoshima Labor Standard Office during a 5-year period 1983 to 1987. Officially notified injuries serious enough to keep employees away from their job for work at least 4 days were utilized in this study. Data was classified so as to give an observed frequency distribution for workers having any specified number of accidents. Also, the accident rate which is an indicator of the risk of accident was compared among different occupations, between age groups and between the sexes. Results obtained are as follows; 1) For the combined total of 6,324 accident cases for 8 types of occupation (Construction, Transportation, Mining & Quarrying, Forestry, Food manufacture, Lumber & Woodcraft, Manufacturing industry and Other business), the number of those who had at least one accident was 6,098, of which 5,837 were injured only once, 208 twice, 21 three times and 2 four times. When occupation type was fixed, however, the number of workers having one, two, three and four times of accidents were 5,895, 182, 19 and 2, respectively. This suggests that some workers are likely to have experienced repeated accidents in more than one type of occupation.(ABSTRACT TRUNCATED AT 250 WORDS)

  11. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis. (United States)

    Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi


    The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species. (United States)

    Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y


    The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

  13. Discovery and analysis of an active long terminal repeat-retrotransposable element in Aspergillus oryzae. (United States)

    Jie Jin, Feng; Hara, Seiichi; Sato, Atsushi; Koyama, Yasuji


    Wild-type Aspergillus oryzae RIB40 contains two copies of the AO090005001597 gene. We previously constructed A. oryzae RIB40 strain, RKuAF8B, with multiple chromosomal deletions, in which the AO090005001597 copy number was found to be increased significantly. Sequence analysis indicated that AO090005001597 is part of a putative 6,000-bp retrotransposable element, flanked by two long terminal repeats (LTRs) of 669 bp, with characteristics of retroviruses and retrotransposons, and thus designated AoLTR (A. oryzae LTR-retrotransposable element). AoLTR comprised putative reverse transcriptase, RNase H, and integrase domains. The deduced amino acid sequence alignment of AoLTR showed 94% overall identity with AFLAV, an A. flavus Tf1/sushi retrotransposon. Quantitative real-time RT-PCR showed that AoLTR gene expression was significantly increased in the RKuAF8B, in accordance with the increased copy number. Inverse PCR indicated that the full-length retrotransposable element was randomly integrated into multiple genomic locations. However, no obvious phenotypic changes were associated with the increased AoLTR gene copy number.

  14. Isolation and characterization of repeat elements of the oak genome and their application in population analysis

    International Nuclear Information System (INIS)

    Fluch, S.; Burg, K.


    Four minisatellite sequence elements have been identified and isolated from the genome of the oak species Quercus petraea and Quercus robur. Minisatellites 1 and 2 are putative members of repeat families, while minisatellites 3 and 4 show repeat length variation among individuals of test populations. A 590 base pair (bp) long element has also been identified which reveals individual-specific autoradiographic patterns when used as probe in Southern hybridisations of genomic oak DNA. (author)


    Directory of Open Access Journals (Sweden)

    Vladimíra OSADSKÁ


    Full Text Available In this paper, we review basic stochastic methods which can be used to extend state-of-the-art deterministic analytical methods for risk analysis. We can conclude that the standard deterministic analytical methods highly depend on the practical experience and knowledge of the evaluator and therefore, the stochastic methods should be introduced. The new risk analysis methods should consider the uncertainties in input values. We present how large is the impact on the results of the analysis solving practical example of FMECA with uncertainties modelled using Monte Carlo sampling.

  16. Power analysis for multivariate and repeated measurements designs via SPSS: correction and extension of D'Amico, Neilands, and Zambarano (2001). (United States)

    Osborne, Jason W


    D'Amico, Neilands, and Zambarano (2001) published SPSS syntax to perform power analyses for three complex procedures: ANCOVA, MANOVA, and repeated measures ANOVA. Unfortunately, the published SPSS syntax for performing the repeated measures analysis needed some minor revision in order to perform the analysis correctly. This article presents the corrected syntax that will successfully perform the repeated measures analysis and provides some guidance on modifying the syntax to customize the analysis.

  17. Creating multithemed ecological regions for macroscale ecology: Testing a flexible, repeatable, and accessible clustering method (United States)

    Cheruvelil, Kendra Spence; Yuan, Shuai; Webster, Katherine E.; Tan, Pang-Ning; Lapierre, Jean-Francois; Collins, Sarah M.; Fergus, C. Emi; Scott, Caren E.; Norton Henry, Emily; Soranno, Patricia A.; Filstrup, Christopher T.; Wagner, Tyler


    Understanding broad-scale ecological patterns and processes often involves accounting for regional-scale heterogeneity. A common way to do so is to include ecological regions in sampling schemes and empirical models. However, most existing ecological regions were developed for specific purposes, using a limited set of geospatial features and irreproducible methods. Our study purpose was to: (1) describe a method that takes advantage of recent computational advances and increased availability of regional and global data sets to create customizable and reproducible ecological regions, (2) make this algorithm available for use and modification by others studying different ecosystems, variables of interest, study extents, and macroscale ecology research questions, and (3) demonstrate the power of this approach for the research question—How well do these regions capture regional-scale variation in lake water quality? To achieve our purpose we: (1) used a spatially constrained spectral clustering algorithm that balances geospatial homogeneity and region contiguity to create ecological regions using multiple terrestrial, climatic, and freshwater geospatial data for 17 northeastern U.S. states (~1,800,000 km2); (2) identified which of the 52 geospatial features were most influential in creating the resulting 100 regions; and (3) tested the ability of these ecological regions to capture regional variation in water nutrients and clarity for ~6,000 lakes. We found that: (1) a combination of terrestrial, climatic, and freshwater geospatial features influenced region creation, suggesting that the oft-ignored freshwater landscape provides novel information on landscape variability not captured by traditionally used climate and terrestrial metrics; and (2) the delineated regions captured macroscale heterogeneity in ecosystem properties not included in region delineation—approximately 40% of the variation in total phosphorus and water clarity among lakes was at the regional

  18. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses (United States)

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.


    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  19. Basic methods of isotope analysis

    International Nuclear Information System (INIS)

    Ochkin, A.V.; Rozenkevich, M.B.


    The bases of the most applied methods of the isotope analysis are briefly presented. The possibilities and analytical characteristics of the mass-spectrometric, spectral, radiochemical and special methods of the isotope analysis, including application of the magnetic resonance, chromatography and refractometry, are considered [ru

  20. [Usefulness of the variable numbers of tandem repeats (VNTR) analysis for complex infections of Mycobacterium avium and Mycobacterium intracellulare]. (United States)

    Tsunematsu, Noriko; Goto, Mieko; Saiki, Yumiko; Baba, Michiko; Udagawa, Tadashi; Kazumi, Yuko


    The bacilli which were isolated from a patient suspected of the mixed infections with Mycobacterium avium and Mycobacterium intracellulare, were analyzed. The genotypes of M. avium in the sedimented fractions of treated sputum and in some colonies isolated from Ogawa medium were compared by the Variable Numbers of Tandem Repeats (VNTR). A woman, aged 57. Mycobacterial species isolated from some colonies by culture in 2004 and 2006 and from the treated sputum in 2006, were determined by DNA sequencing analysis of the 16S rRNA gene. Also, by using VNTR, the genotype of mycobacteria was analyzed. [Results] (1) The colony isolated from Ogawa medium in 2004 was monoclonal M. avium. (2) By VNTR analyses of specimens in 2006, multiple acid-fast bacteria were found in the sputum sediment and in isolated bacteria from Ogawa medium. (3) By analyses of 16S rRNA DNA sequence, M. avium and M. intracellulare were found in the colonies isolated from the sputum sediment and the Ogawa medium in 2006. (4) The same VNTR patterns were obtained in M. avium in 2004 and 2006 when single colony was analyzed. (5) From the showerhead and culvert of the bathroom in the patient's house, M. avium was not detected. By VNTR analyses, it was considered that the mixed infections of M. avium and M. intracellulare had been generated during treatment in this case. Therefore, in the case of suspected complex infection, VNTR analysis would be a useful genotyping method in M. avium complex infection.

  1. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome. (United States)

    Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele


    A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

  2. Probabilistic methods for rotordynamics analysis (United States)

    Wu, Y.-T.; Torng, T. Y.; Millwater, H. R.; Fossum, A. F.; Rheinfurth, M. H.


    This paper summarizes the development of the methods and a computer program to compute the probability of instability of dynamic systems that can be represented by a system of second-order ordinary linear differential equations. Two instability criteria based upon the eigenvalues or Routh-Hurwitz test functions are investigated. Computational methods based on a fast probability integration concept and an efficient adaptive importance sampling method are proposed to perform efficient probabilistic analysis. A numerical example is provided to demonstrate the methods.

  3. Statistical methods for conducting agreement (comparison of clinical tests) and precision (repeatability or reproducibility) studies in optometry and ophthalmology. (United States)

    McAlinden, Colm; Khadka, Jyoti; Pesudovs, Konrad


    The ever-expanding choice of ocular metrology and imaging equipment has driven research into the validity of their measurements. Consequently, studies of the agreement between two instruments or clinical tests have proliferated in the ophthalmic literature. It is important that researchers apply the appropriate statistical tests in agreement studies. Correlation coefficients are hazardous and should be avoided. The 'limits of agreement' method originally proposed by Altman and Bland in 1983 is the statistical procedure of choice. Its step-by-step use and practical considerations in relation to optometry and ophthalmology are detailed in addition to sample size considerations and statistical approaches to precision (repeatability or reproducibility) estimates. Ophthalmic & Physiological Optics © 2011 The College of Optometrists.

  4. Apraxia of Speech: Perceptual Analysis of Trisyllabic Word Productions across Repeated Sampling Occasions (United States)

    Mauszycki, Shannon C.; Wambaugh, Julie L.; Cameron, Rosalea M.


    Purpose: Early apraxia of speech (AOS) research has characterized errors as being variable, resulting in a number of different error types being produced on repeated productions of the same stimuli. Conversely, recent research has uncovered greater consistency in errors, but there are limited data examining sound errors over time (more than one…

  5. Genome-wide analysis of tandem repeats in plants and green algae (United States)

    Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig Echt; Jie Zhang; Chun Liang


    Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (, we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among...

  6. Device-independent secret-key-rate analysis for quantum repeaters (United States)

    Holz, Timo; Kampermann, Hermann; Bruß, Dagmar


    The device-independent approach to quantum key distribution (QKD) aims to establish a secret key between two or more parties with untrusted devices, potentially under full control of a quantum adversary. The performance of a QKD protocol can be quantified by the secret key rate, which can be lower bounded via the violation of an appropriate Bell inequality in a setup with untrusted devices. We study secret key rates in the device-independent scenario for different quantum repeater setups and compare them to their device-dependent analogon. The quantum repeater setups under consideration are the original protocol by Briegel et al. [Phys. Rev. Lett. 81, 5932 (1998), 10.1103/PhysRevLett.81.5932] and the hybrid quantum repeater protocol by van Loock et al. [Phys. Rev. Lett. 96, 240501 (2006), 10.1103/PhysRevLett.96.240501]. For a given repeater scheme and a given QKD protocol, the secret key rate depends on a variety of parameters, such as the gate quality or the detector efficiency. We systematically analyze the impact of these parameters and suggest optimized strategies.

  7. Design and analysis of effects of triplet repeat oligonucleotides in cell models for myotonic dystrophy

    NARCIS (Netherlands)

    Gonzalez-Barriga, A.; Mulders, S.A.M.; Giessen, J. van der; Hooijer, J.D.; Bijl, S.; Kessel, I.D.G. van; Beers, J. van; Deutekom, J.C. van; Fransen, J.A.M.; Wieringa, B.; Wansink, D.G.


    Myotonic dystrophy type 1 (DM1) is caused by DM protein kinase (DMPK) transcripts containing an expanded (CUG)n repeat. Antisense oligonucleotide (AON)-mediated suppression of these mutant RNAs is considered a promising therapeutic strategy for this severe disorder. Earlier, we identified a

  8. Large scale analysis of small repeats via mining of the human genome

    NARCIS (Netherlands)

    van den Berg, I.; Bosnacki, D.; Hilbers, P.A.J.


    Small repetitive sequences, called tandem repeats, are abundant throughout the human genome, both in coding and in non-coding regions. Their role is still mostly unknown, but at least 20 of those repetitive sequences have been related to neurodegenerative disorders. The mutational process that is

  9. Factors influencing repeated teenage pregnancy: a review and meta-analysis. (United States)

    Maravilla, Joemer C; Betts, Kim S; Couto E Cruz, Camila; Alati, Rosa


    Existing evidence of predictors of repeated teenage pregnancy has not been assessed rigorously. This systematic review provides a comprehensive evaluation of protective and risk factors that are associated with repeated teenage pregnancy through a metaanalytical consensus. We used PubMed, EMBASE, CINAHL, ProQuest, PsychINFO, ScienceDirect, Scopus, and Web of Science databases from 1997-2015 and the reference list of other relevant research papers and related reviews. Eligibility criteria included (1) epidemiologic studies that analyzed factors associated with repeated pregnancy or birth among adolescents pregnancy, and (2) experimental studies with an observational component that was adjusted for the intervention. We performed narrative synthesis of study characteristics, participant characteristics, study results, and quality assessment. We also conducted random-effects and quality-effects metaanalyses with meta-regression to obtain pooled odds ratios of identified factors and to determine sources of between-study heterogeneity. Twenty-six eligible epidemiologic studies, most from the United States (n=24), showed >47 factors with no evidence of publication bias for each metaanalysis. Use of contraception (pooled odds ratio, 0.60; 95% confidence interval, 0.35-1.02), particularly long-acting reversible contraceptives (pooled odds ratio, 0.19; 95% confidence interval, 0.08-0.45), considerably reduced repeated teenage pregnancy risk. Among studies about contraception, the number of follow-up visits (adjusted coefficient, 0.72; P=.102) and country of study (unadjusted coefficient, 2.57; permuted P=.071) explained between-study heterogeneity. Education-related factors, which included higher level of education (pooled odds ratio, 0.74; 95% confidence interval, 0.60-0.91) and school continuation (pooled odds ratio, 0.53; 95% confidence interval, 0.33-0.84), were found to be protective. Conversely, depression (pooled odds ratio, 1.46; 95% confidence interval, 1

  10. Analysis of Precision of Activation Analysis Method

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Nørgaard, K.


    The precision of an activation-analysis method prescribes the estimation of the precision of a single analytical result. The adequacy of these estimates to account for the observed variation between duplicate results from the analysis of different samples and materials, is tested by the statistic T...

  11. Development of a Tandem Repeat-Based Polymerase Chain Displacement Reaction Method for Highly Sensitive Detection of 'Candidatus Liberibacter asiaticus'. (United States)

    Lou, Binghai; Song, Yaqin; RoyChowdhury, Moytri; Deng, Chongling; Niu, Ying; Fan, Qijun; Tang, Yan; Zhou, Changyong


    Huanglongbing (HLB) is one of the most destructive diseases in citrus production worldwide. Early detection of HLB pathogens can facilitate timely removal of infected citrus trees in the field. However, low titer and uneven distribution of HLB pathogens in host plants make reliable detection challenging. Therefore, the development of effective detection methods with high sensitivity is imperative. This study reports the development of a novel method, tandem repeat-based polymerase chain displacement reaction (TR-PCDR), for the detection of 'Candidatus Liberibacter asiaticus', a widely distributed HLB-associated bacterium. A uniquely designed primer set (TR2-PCDR-F/TR2-PCDR-1R) and a thermostable Taq DNA polymerase mutant with strand displacement activity were used for TR-PCDR amplification. Performed in a regular thermal cycler, TR-PCDR could produce more than two amplicons after each amplification cycle. Sensitivity of the developed TR-PCDR was 10 copies of target DNA fragment. The sensitive level was proven to be 100× higher than conventional PCR and similar to real-time PCR. Data from the detection of 'Ca. L. asiaticus' with filed samples using the above three methods also showed similar results. No false-positive TR-PCDR amplification was observed from healthy citrus samples and water controls. These results thereby illustrated that the developed TR-PCDR method can be applied to the reliable, highly sensitive, and cost-effective detection of 'Ca. L. asiaticus'.

  12. Analysis of simple sequence repeats in rice bean (Vigna umbellata using an SSR-enriched library

    Directory of Open Access Journals (Sweden)

    Lixia Wang


    Full Text Available Rice bean (Vigna umbellata Thunb., a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%. Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%, and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker

  13. Analysis apparatus and method of analysis

    International Nuclear Information System (INIS)


    A continuous streaming method developed for the excution of immunoassays is described in this patent. In addition, a suitable apparatus for the method was developed whereby magnetic particles are automatically employed for the consecutive analysis of a series of liquid samples via the RIA technique

  14. Analysis of genetic relationships and identification of lily cultivars based on inter-simple sequence repeat markers. (United States)

    Cui, G F; Wu, L F; Wang, X N; Jia, W J; Duan, Q; Ma, L L; Jiang, Y L; Wang, J H


    Inter-simple sequence repeat (ISSR) markers were used to discriminate 62 lily cultivars of 5 hybrid series. Eight ISSR primers generated 104 bands in total, which all showed 100% polymorphism, and an average of 13 bands were amplified by each primer. Two software packages, POPGENE 1.32 and NTSYSpc 2.1, were used to analyze the data matrix. Our results showed that the observed number of alleles (NA), effective number of alleles (NE), Nei's genetic diversity (H), and Shannon's information index (I) were 1.9630, 1.4179, 0.2606, and 0.4080, respectively. The highest genetic similarity (0.9601) was observed between the Oriental x Trumpet and Oriental lilies, which indicated that the two hybrids had a close genetic relationship. An unweighted pair-group method with arithmetic means dendrogram showed that the 62 lily cultivars clustered into two discrete groups. The first group included the Oriental and OT cultivars, while the Asiatic, LA, and Longiflorum lilies were placed in the second cluster. The distribution of individuals in the principal component analysis was consistent with the clustering of the dendrogram. Fingerprints of all lily cultivars built from 8 primers could be separated completely. This study confirmed the effect and efficiency of ISSR identification in lily cultivars.

  15. Nonlinear programming analysis and methods

    CERN Document Server

    Avriel, Mordecai


    This text provides an excellent bridge between principal theories and concepts and their practical implementation. Topics include convex programming, duality, generalized convexity, analysis of selected nonlinear programs, techniques for numerical solutions, and unconstrained optimization methods.

  16. Chemical methods of rock analysis

    National Research Council Canada - National Science Library

    Jeffery, P. G; Hutchison, D


    A practical guide to the methods in general use for the complete analysis of silicate rock material and for the determination of all those elements present in major, minor or trace amounts in silicate...


    Directory of Open Access Journals (Sweden)

    Sorokin VM


    Full Text Available Stomach infection with Helicobacter pylori (H. pylori is the second most common infectious disease of humans. The severe pathological consequences of this infection include gastric and duodenal ulcer disease, the development of gastric mucosal atrophy, gastric carcinoma, and, more rarely, malignant tumors of the lymphoma. H. pylori infections cause very high morbidity and mortality and are of particular concern in developing countries, where H. pylori prevalences as high as 90% have been reported. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-Locus of Variable number of tandem repeat Analysis method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori isolates in Russia. MLVA of 4 VNTR loci with high discrimination power based on 10 candidates were performed on a collection of 22 strains of H. pylori which originated from Rostov region of Russia. This method provides a starting point on which improvements to the method and comparisons to other techniques can be made.

  18. CAG repeat polymorphisms in the androgen receptor and breast cancer risk in women: a meta-analysis of 17 studies

    Directory of Open Access Journals (Sweden)

    Mao Q


    Full Text Available Qixing Mao,1–3,* Mantang Qiu,1–3,* Gaochao Dong,3 Wenjie Xia,1–3 Shuai Zhang,1,3 Youtao Xu,1,3 Jie Wang,3 Yin Rong,1,3 Lin Xu,1,3 Feng Jiang1,3 1Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Institute of Jiangsu Province, 2Fourth Clinical College of Nanjing Medical University, 3Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing, People’s Republic of China *These authors contributed equally to this work Abstract: The association between polymorphic CAG repeats in the androgen receptor gene in women and breast cancer susceptibility has been studied extensively. However, the conclusions regarding this relationship remain conflicting. The purpose of this meta-analysis was to identify whether androgen receptor CAG repeat lengths were related to breast cancer susceptibility. The MEDLINE, PubMed, and EMBASE databases were searched through to December 2014 to identify eligible studies. Data and study quality were rigorously assessed by two investigators according to the Newcastle-Ottawa Quality Assessment Scale. The publication bias was assessed by the Begg’s test. Seventeen eligible studies were included in this meta-analysis. The overall analysis suggested no association between CAG polymorphisms and breast cancer risk (odds ratio [OR] 1.031, 95% confidence interval [CI] 0.855–1.245. However, in the subgroup analysis, we observed that long CAG repeats significantly increased the risk of breast cancer in the Caucasian population (OR 1.447, 95% CI 1.089–1.992. Additionally, the risk was significantly increased in Caucasian women carrying two alleles with CAG repeats ≥22 units compared with those with two shorter alleles (OR 1.315, 95% CI 1.014–1.707. These findings suggest that long CAG repeats increase the risk of breast cancer in Caucasian women. However, larger scale case-control studies are needed to validate our results. Keywords: androgen, CAG repeat polymorphism, women

  19. Repeat prenatal corticosteroid prior to preterm birth: a systematic review and individual participant data meta-analysis for the PRECISE study group (prenatal repeat corticosteroid international IPD study group: assessing the effects using the best level of evidence - study protocol

    Directory of Open Access Journals (Sweden)

    Crowther Caroline A


    Full Text Available Abstract Background The aim of this individual participant data (IPD meta-analysis is to assess whether the effects of repeat prenatal corticosteroid treatment given to women at risk of preterm birth to benefit their babies are modified in a clinically meaningful way by factors related to the women or the trial protocol. Methods/Design The Prenatal Repeat Corticosteroid International IPD Study Group: assessing the effects using the best level of Evidence (PRECISE Group will conduct an IPD meta-analysis. The PRECISE International Collaborative Group was formed in 2010 and data collection commenced in 2011. Eleven trials with up to 5,000 women and 6,000 infants are eligible for the PRECISE IPD meta-analysis. The primary study outcomes for the infants will be serious neonatal outcome (defined by the PRECISE International IPD Study Group as one of death (foetal, neonatal or infant; severe respiratory disease; severe intraventricular haemorrhage (grade 3 and 4; chronic lung disease; necrotising enterocolitis; serious retinopathy of prematurity; and cystic periventricular leukomalacia; use of respiratory support (defined as mechanical ventilation or continuous positive airways pressure or other respiratory support; and birth weight (Z-scores. For the children, the primary study outcomes will be death or any neurological disability (however defined by trialists at childhood follow up and may include developmental delay or intellectual impairment (developmental quotient or intelligence quotient more than one standard deviation below the mean, cerebral palsy (abnormality of tone with motor dysfunction, blindness (for example, corrected visual acuity worse than 6/60 in the better eye or deafness (for example, hearing loss requiring amplification or worse. For the women, the primary outcome will be maternal sepsis (defined as chorioamnionitis; pyrexia after trial entry requiring the use of antibiotics; puerperal sepsis; intrapartum fever requiring the use

  20. Development of a Method to Compensate for Signal Quality Variations in Repeated Auditory Event-Related Potential Recordings (United States)

    Paukkunen, Antti K. O.; Leminen, Miika M.; Sepponen, Raimo


    Reliable measurements are mandatory in clinically relevant auditory event-related potential (AERP)-based tools and applications. The comparability of the results gets worse as a result of variations in the remaining measurement error. A potential method is studied that allows optimization of the length of the recording session according to the concurrent quality of the recorded data. In this way, the sufficiency of the trials can be better guaranteed, which enables control of the remaining measurement error. The suggested method is based on monitoring the signal-to-noise ratio (SNR) and remaining measurement error which are compared to predefined threshold values. The SNR test is well defined, but the criterion for the measurement error test still requires further empirical testing in practice. According to the results, the reproducibility of average AERPs in repeated experiments is improved in comparison to a case where the number of recorded trials is constant. The test-retest reliability is not significantly changed on average but the between-subject variation in the value is reduced by 33–35%. The optimization of the number of trials also prevents excessive recordings which might be of practical interest especially in the clinical context. The efficiency of the method may be further increased by implementing online tools that improve data consistency. PMID:20407635


    Directory of Open Access Journals (Sweden)

    Marija Viljevac


    Full Text Available The objective of this study was to investigate changes in photosynthetic efficiency applying repeated measures ANOVA using the photosynthetic performance index (PIABS of the JIP-test as a vitality parameter in seven genotypes of sour cherry (Prunus cerasus, L. during 10 days of continuous water deficit. Both univariate and multivariate ANOVA repeated measures revealed highly significant time effect (Days and its subsequent interactions with genotype and water deficit. However, the multivariate Pillai’s trace test detected the interaction Time × Genotype × Water deficit as not significant. According to the Tukey’s Studentized Range (HSD test, differences between the control and genotypes exposed to water stress became significant on the fourth day of the experiment, indicating that the plants on the average, began to lose their photosynthetic efficiency four days after being exposed to water shortage. It corroborates previous findings in other species that PIABS is very sensitive tool for detecting drought stress.

  2. Hysteresis analysis of graphene transistor under repeated test and gate voltage stress

    International Nuclear Information System (INIS)

    Yang Jie; Jia Kunpeng; Su Yajuan; Zhao Chao; Chen Yang


    The current transport characteristic is studied systematically based on a back-gate graphene field effect transistor, under repeated test and gate voltage stress. The interface trapped charges caused by the gate voltage sweep process screens the gate electric field, and results in the neutral point voltage shift between the forth and back sweep direction. In the repeated test process, the neutral point voltage keeps increasing with test times in both forth and back sweeps, which indicates the existence of interface trapped electrons residual and accumulation. In gate voltage stress experiment, the relative neutral point voltage significantly decreases with the reducing of stress voltage, especially in −40 V, which illustrates the driven-out phenomenon of trapped electrons under negative voltage stress. (semiconductor devices)

  3. Analysis of genetic polymorphism of nine short tandem repeat loci in ...

    African Journals Online (AJOL)

    This study was carried out to investigate the genetic polymorphism of nine short tandem repeat (STR) loci including D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364 and D22GATA198B05 in Chinese Han population of Henan province and to assess its value in forensic science.

  4. Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models

    International Nuclear Information System (INIS)

    Teng, S.; Tebby, C.; Barcellini-Couget, S.; De Sousa, G.; Brochot, C.; Rahmani, R.; Pery, A.R.R.


    Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro – in vivo extrapolation need to be developed. However, most in vitro tests only assess short-term effects and consider static endpoints which hinder extrapolation to realistic human exposure scenarios where concentration in target organs is varies over time. Thanks to impedance metrics, real-time cell viability monitoring for repeated exposure has become possible. We recently constructed biokinetic/toxicodynamic models (BK/TD) to analyze such data (Teng et al., 2015) for three hepatotoxic cosmetic ingredients: coumarin, isoeugenol and benzophenone-2. In the present study, we aim to apply these models to analyze the dynamics of mixture impedance data using the concepts of concentration addition and independent action. Metabolic interactions between the mixture components were investigated, characterized and implemented in the models, as they impacted the actual cellular exposure. Indeed, cellular metabolism following mixture exposure induced a quick disappearance of the compounds from the exposure system. We showed that isoeugenol substantially decreased the metabolism of benzophenone-2, reducing the disappearance of this compound and enhancing its in vitro toxicity. Apart from this metabolic interaction, no mixtures showed any interaction, and all binary mixtures were successfully modeled by at least one model based on exposure to the individual compounds. - Highlights: • We could predict cell response over repeated exposure to mixtures of cosmetics. • Compounds acted independently on the cells. • Metabolic interactions impacted exposure concentrations to the compounds.

  5. Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models

    Energy Technology Data Exchange (ETDEWEB)

    Teng, S.; Tebby, C. [Models for Toxicology and Ecotoxicology Unit, INERIS, Parc Technologique Alata, BP 2, 60550 Verneuil-en-Halatte (France); Barcellini-Couget, S. [ODESIA Neosciences, Sophia Antipolis, 400 route des chappes, 06903 Sophia Antipolis (France); De Sousa, G. [INRA, ToxAlim, 400 route des Chappes, BP, 167 06903 Sophia Antipolis, Cedex (France); Brochot, C. [Models for Toxicology and Ecotoxicology Unit, INERIS, Parc Technologique Alata, BP 2, 60550 Verneuil-en-Halatte (France); Rahmani, R. [INRA, ToxAlim, 400 route des Chappes, BP, 167 06903 Sophia Antipolis, Cedex (France); Pery, A.R.R., E-mail: [AgroParisTech, UMR 1402 INRA-AgroParisTech Ecosys, 78850 Thiverval Grignon (France); INRA, UMR 1402 INRA-AgroParisTech Ecosys, 78850 Thiverval Grignon (France)


    Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro – in vivo extrapolation need to be developed. However, most in vitro tests only assess short-term effects and consider static endpoints which hinder extrapolation to realistic human exposure scenarios where concentration in target organs is varies over time. Thanks to impedance metrics, real-time cell viability monitoring for repeated exposure has become possible. We recently constructed biokinetic/toxicodynamic models (BK/TD) to analyze such data (Teng et al., 2015) for three hepatotoxic cosmetic ingredients: coumarin, isoeugenol and benzophenone-2. In the present study, we aim to apply these models to analyze the dynamics of mixture impedance data using the concepts of concentration addition and independent action. Metabolic interactions between the mixture components were investigated, characterized and implemented in the models, as they impacted the actual cellular exposure. Indeed, cellular metabolism following mixture exposure induced a quick disappearance of the compounds from the exposure system. We showed that isoeugenol substantially decreased the metabolism of benzophenone-2, reducing the disappearance of this compound and enhancing its in vitro toxicity. Apart from this metabolic interaction, no mixtures showed any interaction, and all binary mixtures were successfully modeled by at least one model based on exposure to the individual compounds. - Highlights: • We could predict cell response over repeated exposure to mixtures of cosmetics. • Compounds acted independently on the cells. • Metabolic interactions impacted exposure concentrations to the compounds.

  6. Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs (United States)

    M.N. lslam-Faridi; C.D. Nelson; S.P. DiFazio; L.E. Gunter; G.A. Tuskan


    The 185-285 rDNA and 55 rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 185-285 rDNA sites and one 55 rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis-type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones...

  7. Seismic design and analysis methods

    International Nuclear Information System (INIS)

    Varpasuo, P.


    Seismic load is in many areas of the world the most important loading situation from the point of view of structural strength. Taking this into account it is understandable, that there has been a strong allocation of resources in the seismic analysis during the past ten years. In this study there are three areas of the center of gravity: (1) Random vibrations; (2) Soil-structure interaction and (3) The methods for determining structural response. The solution of random vibration problems is clarified with the aid of applications in this study and from the point of view of mathematical treatment and mathematical formulations it is deemed sufficient to give the relevant sources. In the soil-structure interaction analysis the focus has been the significance of frequency dependent impedance functions. As a result it was obtained, that the description of the soil with the aid of frequency dependent impedance functions decreases the structural response and it is thus always the preferred method when compared to more conservative analysis types. From the methods to determine the C structural response the following four were tested: (1) The time history method; (2) The complex frequency-response method; (3) Response spectrum method and (4) The equivalent static force method. The time history appeared to be the most accurate method and the complex frequency-response method did have the widest area of application. (orig.). (14 refs., 35 figs.)

  8. Effect of repeated sterilization by different methods on strength of carbon fiber rods used in external fixator systems. (United States)

    Unal, Omer Kays; Poyanli, Oguz Sukru; Unal, Ulku Sur; Mutlu, Hasan Huseyin; Ozkut, Afsar Timucin; Esenkaya, Irfan


    We set out to reveal the effects of repeated sterilization, using different methods, on the carbon fiber rods of external fixator systems. We used a randomized set of forty-four unused, unsterilized, and identical carbon fiber rods (11 × 200 mm), randomly assigned to two groups: unsterilized (US) (4 rods) and sterilized (40 rods). The sterilized rods were divided into two groups, those sterilized in an autoclave (AC) and by hydrogen peroxide (HP). These were further divided into five subgroups based on the number of sterilization repetition to which the fibers were subjected (25-50-75-100-200). A bending test was conducted to measure the maximum bending force (MBF), maximum deflection (MD), flexural strength (FS), maximum bending moment (MBM) and bending rigidity (BR). We also measured the surface roughness of the rods. An increase in the number of sterilization repetition led to a decrease in MBF, MBM, FS, BR, but increased MD and surface roughness (p < 0.01). The effect of the number of sterilization repetition was more prominent in the HP group. This study revealed that the sterilization method and number of sterilization repetition influence the strength of the carbon fiber rods. Increasing the number of sterilization repetition degrades the strength and roughness of the rods.

  9. Analysis of real-time mixture cytotoxicity data following repeated exposure using BK/TD models. (United States)

    Teng, S; Tebby, C; Barcellini-Couget, S; De Sousa, G; Brochot, C; Rahmani, R; Pery, A R R


    Cosmetic products generally consist of multiple ingredients. Thus, cosmetic risk assessment has to deal with mixture toxicity on a long-term scale which means it has to be assessed in the context of repeated exposure. Given that animal testing has been banned for cosmetics risk assessment, in vitro assays allowing long-term repeated exposure and adapted for in vitro - in vivo extrapolation need to be developed. However, most in vitro tests only assess short-term effects and consider static endpoints which hinder extrapolation to realistic human exposure scenarios where concentration in target organs is varies over time. Thanks to impedance metrics, real-time cell viability monitoring for repeated exposure has become possible. We recently constructed biokinetic/toxicodynamic models (BK/TD) to analyze such data (Teng et al., 2015) for three hepatotoxic cosmetic ingredients: coumarin, isoeugenol and benzophenone-2. In the present study, we aim to apply these models to analyze the dynamics of mixture impedance data using the concepts of concentration addition and independent action. Metabolic interactions between the mixture components were investigated, characterized and implemented in the models, as they impacted the actual cellular exposure. Indeed, cellular metabolism following mixture exposure induced a quick disappearance of the compounds from the exposure system. We showed that isoeugenol substantially decreased the metabolism of benzophenone-2, reducing the disappearance of this compound and enhancing its in vitro toxicity. Apart from this metabolic interaction, no mixtures showed any interaction, and all binary mixtures were successfully modeled by at least one model based on exposure to the individual compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Genetic diversity and geographic differentiation analysis of duckweed using inter-simple sequence repeat markers. (United States)

    Xue, Huiling; Xiao, Yao; Jin, Yanling; Li, Xinbo; Fang, Yang; Zhao, Hai; Zhao, Yun; Guan, Jiafa


    Duckweed, with rapid growth rate and high starch content, is a new alternate feedstock for bioethanol production. The genetic diversity among 27 duckweed populations of seven species in genus Lemna and Spirodela from China and Vietnam was analyzed by ISSR-PCR. Eight ISSR primers generating a reproducible amplification banding pattern had been screened. 89 polymorphic bands were scored out of the 92 banding patterns of 16 Lemna populations, accounting for 96.74% of the polymorphism. 98 polymorphic bands of 11 Spirodela populations were scored out of 99 banding patterns, and the polymorphism was 98.43%. The genetic distance of Lemna varied from 0.127 to 0.784, and from 0.138 to 0.902 for Spirodela, which indicated a high level of genetic variation among the populations studied. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis corresponded well with the genetic distance. Populations from Sichuan China grouped together and so did the populations from Vietnam, which illuminated populations collected from the same region clustered into one group. Especially, the only one population from Tibet was included in subgroup A2 alone. Clustering analysis indicated that the geographic differentiation of collected sites correlated closely with the genetic differentiation of duckweeds. The results suggested that geographic differentiation had great influence on genetic diversity of duckweed in China and Vietnam at the regional scale. This study provided primary guidelines for collection, conservation, characterization of duckweed resources for bioethanol production etc.

  11. "Focused introspection" during naturally increased diuresis: description and repeatability of a method to study bladder sensation non-invasively. (United States)

    De Wachter, Stefan G G; Heeringa, Rhea; Van Koeveringe, Gommert A; Winkens, Bjorn; Van Kerrebroeck, Philip E V; Gillespie, James I


    To present and describe a non-invasive method to study the origin and development of bladder filling sensation and to evaluate the repeatability of the method. Eighteen volunteers participated in the study and were given a water loading protocol consisting of 1,000 ml water intake 1 hr before the session and 200 ml every 10 min during the session. Protocol 1: To evaluate diuresis rate, seven participants were asked to void every 15 min and the voided volume was measured. Protocol 2: Eleven volunteers graded bladder sensation on regular time points, on an empty graph with time on the X-axis and intensity of sensation on the Y-axis. The protocol ended at absolute need to void (maximal intensity) and voided volumes were measured. This protocol was conducted three times with a 10 days interval. Protocol 1: The diuresis rate was not different during the sessions and showed no variation over the studied time period (P = 0.2). Protocol 2: For an individual, the diuresis rate was not different between the sessions. The curves in all patients showed a continuously increasing bladder intensity. In seven participants the curve was convex, in the other four, the curve was sigmoidal. For each individual the pattern was constant during the three sessions. A strict water loading protocol induces a constant diuresis. This allows individuals to draw an introspection bladder sensation curve with a specific shape, which can be used as a method to study the development of bladder sensation non-invasively. © 2013 Wiley Periodicals, Inc.

  12. Analysis of the finescale timing of repeated signals: does shell rapping in hermit crabs signal stamina? (United States)

    Briffa; Elwood


    Hermit crabs, Pagurus bernhardus, sometimes exchange shells after a period of shell rapping, when the initiating or attacking crab brings its shell rapidly and repeatedly into contact with the shell of the noninitiator or defender in a series of bouts. Bouts are separated by pauses, and raps within bouts are separated by very short periods called 'gaps'. Since within-contest variation is missed when signals are studied by averaging performance rates over entire contests, we analysed the fine within-bout structure of this repeated, aggressive signal. We found that the pattern is consistent with high levels of fatigue in initiators. The duration of the gaps between individual raps increased both within bouts and from bout to bout, and we conclude that this activity is costly to perform. Furthermore, long pauses between bouts is correlated with increased vigour of rapping in the subsequent bout, which suggests that the pause allows for recovery from fatigue induced by rapping. These between-bout pauses may be assessed by noninitiators and provide a signal of stamina. Copyright 2000 The Association for the Study of Animal Behaviour.

  13. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.). (United States)

    Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen


    Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

  14. Variability and repeatability analysis of plantar pressure during gait in older people. (United States)

    Franco, Pedro S; Silva, Caio Borella P da; Rocha, Emmanuel S da; Carpes, Felipe P


    Repeatability and variability of the plantar pressure during walking are important components in the clinical assessment of the elderly. However, there is a lack of information on the uniformity of plantar pressure patterns in the elderly. To analyze the repeatability and variability in plantar pressure considering mean, peak and asymmetries during aged gait. Plantar pressure was monitored in four different days for ten elderly subjects (5 female), with mean±standard-deviation age of 73±6 years, walking barefoot at preferred speed. Data were compared between steps for each day and between different days. Mean and peak plantar pressure values were similar between the different days of evaluation. Asymmetry indexes were similar between the different days evaluated. Plantar pressure presented a consistent pattern in the elderly. However, the asymmetry indexes observed suggest that the elderly are exposed to repetitive asymmetric loading during locomotion. Such result requires further investigation, especially concerning the role of these asymmetries for development of articular injuries. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

  15. Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

    Directory of Open Access Journals (Sweden)

    Marwa H Saied

    Full Text Available Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. Two genes (SPHKAP and DPP6 with significantly methylated promoters were of interest and further analysis of their expression showed them to be repressed in AML. We also demonstrated considerable cytogenetic subtype specificity in the methylomes affecting different genomic features. Significantly distinct patterns of hypomethylation of certain interspersed repeat elements were associated with cytogenetic subtypes. The methylation patterns of members of the SINE family tightly clustered all leukemic patients with an enrichment of Alu repeats with a high CpG density (P<0.0001. We were able to demonstrate significant inverse correlation between intragenic interspersed repeat sequence methylation and gene expression with SINEs showing the strongest inverse correlation (R(2 = 0.7. We conclude that the alterations in DNA methylation that accompany the development of AML affect not only the promoters, but also the non-promoter genomic features, with significant demethylation of certain interspersed repeat DNA elements being associated with AML cytogenetic subtypes. MeDIP-seq data were validated using bisulfite pyrosequencing and the Infinium array.

  16. One-time versus repeated abutment connection for platform-switched implant: A systematic review and meta-analysis. (United States)

    Wang, Qing-Qing; Dai, Ruoxi; Cao, Chris Ying; Fang, Hui; Han, Min; Li, Quan-Li


    This review aims to compare peri-implant tissue changes in terms of clinical and radiographic aspects of implant restoration protocol using one-time abutment to repeated abutment connection in platform switched implant. A structured search strategy was applied to three electronic databases, namely, Pubmed, Embase and Web of Science. Eight eligible studies, including seven randomised controlled studies and one controlled clinical study, were identified in accordance with inclusion/exclusion criteria. Outcome measures included peri-implant bone changes (mm), peri-implant soft tissue changes (mm), probing depth (mm) and postsurgical complications. Six studies were pooled for meta-analysis on bone tissue, three for soft tissue, two for probing depth and four for postsurgical complications. A total of 197 implants were placed in one-time abutment group, whereas 214 implants were included in repeated abutment group. The implant systems included Global implants, Ankylos, JDEvolution (JdentalCare), Straumann Bone level and Conelog-Screwline. One-time abutment group showed significantly better outcomes than repeated abutment group, as measured in the standardised differences in mean values (fixed- and random-effect model): vertical bone change (0.41, 3.23) in 6 months, (1.51, 14.81) in 12 months and (2.47, 2.47) in 3 years and soft tissue change (0.21, 0.23). No significant difference was observed in terms of probing depth and complications. Our meta-analysis revealed that implant restoration protocol using one-time abutment is superior to repeated abutment for platform switched implant because of less bone resorption and soft tissue shifts in former. However, future randomised clinical trials should be conducted to further confirm these findings because of the small samples and the limited quality of the original research.

  17. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics. (United States)

    Muller, Leslie; Fornecker, Luc; Van Dorsselaer, Alain; Cianférani, Sarah; Carapito, Christine


    Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats. (United States)

    Ma, S J; Sa, K J; Hong, T K; Lee, J K


    In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.


    Directory of Open Access Journals (Sweden)



    Full Text Available Audit sampling involves the application of audit procedures to less than 100% of items within an account balance or class of transactions. Our article aims to study audit sampling in audit of financial statements. As an audit technique largely used, in both its statistical and nonstatistical form, the method is very important for auditors. It should be applied correctly for a fair view of financial statements, to satisfy the needs of all financial users. In order to be applied correctly the method must be understood by all its users and mainly by auditors. Otherwise the risk of not applying it correctly would cause loose of reputation and discredit, litigations and even prison. Since there is not a unitary practice and methodology for applying the technique, the risk of incorrectly applying it is pretty high. The SWOT analysis is a technique used that shows the advantages, disadvantages, threats and opportunities. We applied SWOT analysis in studying the sampling method, from the perspective of three players: the audit company, the audited entity and users of financial statements. The study shows that by applying the sampling method the audit company and the audited entity both save time, effort and money. The disadvantages of the method are difficulty in applying and understanding its insight. Being largely used as an audit method and being a factor of a correct audit opinion, the sampling method’s advantages, disadvantages, threats and opportunities must be understood by auditors.

  20. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.

    Directory of Open Access Journals (Sweden)

    Andrew J Alverson


    Full Text Available The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean, and show that despite its unexceptional size (401,262 nt, the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38-297 nt repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.

  1. Development of new multilocus variable number of tandem repeat analysis (MLVA) for Listeria innocua and its application in a food processing plant. (United States)

    Takahashi, Hajime; Ohshima, Chihiro; Nakagawa, Miku; Thanatsang, Krittaporn; Phraephaisarn, Chirapiphat; Chaturongkasumrit, Yuphakhun; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon


    Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE). The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories.

  2. Development of new multilocus variable number of tandem repeat analysis (MLVA for Listeria innocua and its application in a food processing plant.

    Directory of Open Access Journals (Sweden)

    Hajime Takahashi

    Full Text Available Listeria innocua is an important hygiene indicator bacterium in food industries because it behaves similar to Listeria monocytogenes, which is pathogenic to humans. PFGE is often used to characterize bacterial strains and to track contamination source. However, because PFGE is an expensive, complicated, time-consuming protocol, and poses difficulty in data sharing, development of a new typing method is necessary. MLVA is a technique that identifies bacterial strains on the basis of the number of tandem repeats present in the genome varies depending on the strains. MLVA has gained attention due to its high reproducibility and ease of data sharing. In this study, we developed a MLVA protocol to assess L. innocua and evaluated it by tracking the contamination source of L. innocua in an actual food manufacturing factory by typing the bacterial strains isolated from the factory. Three VNTR regions of the L. innocua genome were chosen for use in the MLVA. The number of repeat units in each VNTR region was calculated based on the results of PCR product analysis using capillary electrophoresis (CE. The calculated number of repetitions was compared with the results of the gene sequence analysis to demonstrate the accuracy of the CE repeat number analysis. The developed technique was evaluated using 60 L. innocua strains isolated from a food factory. These 60 strains were classified into 11 patterns using MLVA. Many of the strains were classified into ST-6, revealing that this MLVA strain type can contaminate each manufacturing process in the factory. The MLVA protocol developed in this study for L. innocua allowed rapid and easy analysis through the use of CE. This technique was found to be very useful in hygiene control in factories because it allowed us to track contamination sources and provided information regarding whether the bacteria were present in the factories.

  3. [Clinical outcomes and economic analysis of two ovulation induction protocols in patients undergoing repeated IVF/ICSI cycles]. (United States)

    Chen, Xiao; Geng, Ling; Li, Hong


    To compare the clinical outcomes and cost-effectiveness of luteal phase down-regulation with gonadotrophin-releasing hormone (GnRH) agonist protocol and GnRH antagonist protocol in patients undergoing repeated in vitro fertilization and intracytoplasmic sperm injection (IVF-ICSI) cycles. A retrospective analysis of clinical outcomes and costs was conducted among 198 patients undergoing repeated IVF-ICSI cycles, including 109 receiving luteal phase down-regulation with GnRH agonist protocol (group A) and 89 receiving GnRH antagonist protocol (group B). The numbers of oocytes retrieved and good embryos, clinical pregnancy rate, abortion rate, the live birth rate, mean total cost, and the cost-effective ratio were compared between the two groups. In patients undergoing repeated IVF-ICSI cycles, the two protocols produced no significant differences in the number of good embryos, clinical pregnancy rate, abortion rate, or twin pregnancy rate. Compared with group B, group A had better clinical outcomes though this difference was not statistically significant. The number of retrieved oocytes was significantly greater and live birth rate significantly higher in group A than in group B (9.13=4.98 vs 7.11=4.74, and 20.2% vs 9.0%, respectively). Compared with group B, group A had higher mean total cost per cycle but lower costs for each oocyte retrieved (2729.11 vs 3038.60 RMB yuan), each good embryo (8867.19 vs 9644.85 RMB yuan), each clinical pregnancy (77598.06 vs 96139.85 RMB yuan). For patients undergoing repeated IVF/ICSI cycle, luteal phase down-regulation with GnRH agonist protocol produces good clinical outcomes with also good cost-effectiveness in spite an unsatisfactory ovarian reserve.

  4. Multiple-locus variable-number tandem repeat analysis of Neisseria meningitidis yields groupings similar to those obtained by multilocus sequence typing.

    NARCIS (Netherlands)

    Schouls, Leo M; Ende, Arie van der; Damen, Marjolein; Pol, Ingrid van de


    We identified many variable-number tandem repeat (VNTR) loci in the genomes of Neisseria meningitidis serogroups A, B, and C and utilized a number of these loci to develop a multiple-locus variable-number tandem repeat analysis (MLVA). Eighty-five N. meningitidis serogroup B and C isolates obtained

  5. Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs

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    Halling Shirley M


    Full Text Available Abstract Background Currently, there are very few tools available for subtyping Brucella isolates for epidemiological trace-back. Subtyping is difficult because of the genetic homogeneity within the genus. Sequencing of the genomes from three Brucella species has facilitated the search for DNA sequence variability. Recently, hypervariability among short tandem repeat sequences has been exploited for strain-typing of several bacterial pathogens. Results An eight-base pair tandem repeat sequence was discovered in nine genomic loci of the B. abortus genome. Eight loci were hypervariable among the three Brucella species. A PCR-based method was developed to identify the number of repeat units (alleles at each locus, generating strain-specific fingerprints. None of the loci exhibited species- or biovar-specific alleles. Sometimes, a species or biovar contained a specific allele at one or more loci, but the allele also occurred in other species or biovars. The technique successfully differentiated the type strains for all Brucella species and biovars, among unrelated B. abortus biovar 1 field isolates in cattle, and among B. abortus strains isolated from bison and elk. Isolates from the same herd or from short-term in vitro passage exhibited little or no variability in fingerprint pattern. Sometimes, isolates from an animal would have multiple alleles at a locus, possibly from mixed infections in enzootic areas, residual disease from incomplete depopulation of an infected herd or molecular evolution within the strain. Therefore, a mixed population or a pool of colonies from each animal and/or tissue was tested. Conclusion This paper describes a new method for fingerprinting Brucella isolates based on multi-locus characterization of a variable number, eight-base pair, tandem repeat. We have named this technique "HOOF-Prints" for Hypervariable Octameric Oligonucleotide Finger-Prints. The technique is highly discriminatory among Brucella species, among

  6. Variable Number of Tandem Repeats (VNTR) analysis of Flavobacterium psychrophilum from salmonids in Chile and Norway. (United States)

    Apablaza, Patricia; Brevik, Øyvind J; Mjøs, Svein; Valdebenito, Samuel; Ilardi, Pedro; Battaglia, Juan; Dalsgaard, Inger; Nylund, Are


    Flavobacterium psychrophilum causes serious fish diseases such RTFS and BCWD, affecting the aquaculture industry worldwide. Commercial vaccines are not available and control of the disease depends on the use of antibiotics. Reliable methods for detection and identification of different isolates of this bacterium could play an important role in the development of good management strategies. The aim of this study was to identify genetic markers for discrimination between isolates. A selection of eight VNTRs from 53 F. psychrophilum isolates from Norway, Chile, Denmark and Scotland were analyzed. The results were compared with previous work on the same pathogen using MLST for genetic differentiation. The VNTR analysis gave a separation between the F. psychrophilum isolates supporting the results of previous MLST work. A higher diversity was found among the Chilean isolates compared to those from Norway, which suggests a more homogenous reservoir in Norway. Transgenerational transmission of F. psychrophilum from other countries, exporting salmon embryos to Chile, may explain the differences in diversity. The same transmission mechanisms could also explain the wide geographical distribution of identical isolates in Norway. But, this could also be a result of movement of smolts and embryos. The selected VNTRs are stable genetic markers and no variation was observed after several passages on agar plates at different temperatures. These VNTRs are important additions for genotyping of F. psychrophilum isolates. Future studies on VNTRs of F. psychrophilum should include isolates from more host species from a wider geographical area. To get a more robust genotyping the VNTRs should be used in concert with MLST. Future studies of isolates with high and low virulence should focus on identifying virulence markers using VTNRs and MLST.

  7. Theoretical conformational analysis of the tetrasaccharide repeating units of the O-antigenic polysaccharide of Shigella flexneri

    International Nuclear Information System (INIS)

    Lipkind, G.M.; Kochetkov, N.K.


    A theoretical conformational analysis has been made of the four tetrasaccharide repeating units of the polysaccharide of Shigella flexneri, serotype Y. The interdependence of the conformation states of the neighboring disaccharide units and the oligosaccharides has been investigated. The distribution of the tetrasaccharides over the conformations in solution obtained by calculating the free energies of the optimum structures is given. It has been shown that a substantial correction of the results relating to oligosaccharide chains is achieved when the entropy factors is taken into account

  8. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿† (United States)

    Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo


    Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from PMID:21147956

  9. Flows method in global analysis

    International Nuclear Information System (INIS)

    Duong Minh Duc.


    We study the gradient flows method for W r,p (M,N) where M and N are Riemannian manifold and r may be less than m/p. We localize some global analysis problem by constructing gradient flows which only change the value of any u in W r,p (M,N) in a local chart of M. (author). 24 refs

  10. Diversity of Salmonella enterica serovar Typhi strains collected from india using variable number tandem repeat (VNTR)-PCR analysis. (United States)

    Sankar, Sathish; Kuppanan, Suresh; Nandagopal, Balaji; Sridharan, Gopalan


    Typhoid fever is endemic in India, and a seasonal increase of cases is observed annually. In spite of effective therapies and the availability of vaccines, morbidity is widespread owing to the circulation of multiple genetic variants, frequent migration of asymptomatic carriers, unhygienic food practices and the emergence of multidrug resistance and thus continues to be a major public health problem in developing countries, particularly in India. Classical methods of strain typing such as pulsed-field gel electrophoresis, ribotyping, random amplification of polymorphic DNA and amplified fragment length polymorphism are either laborious and technically complicated or less discriminatory. We investigated the molecular diversity of Indian strains of Salmonella enterica serovar Typhi (S. Typhi) isolated from humans from different parts of India to establish the molecular epidemiology of the organism using the variable number tandem repeat (VNTR)-PCR analysis. The electrophoretic band pattern was analysed using the GelCompar II software program. Of the 94 strains tested for three VNTRs loci, 75 VNTR genotypes were obtained. Of the three VNTRs tested in this study, VNTR1 was amplified in all the strains except one and found to be predominant. VNTR2 was amplified only in 57 strains with a Simpson diversity index of 0.93 indicating the high variability of this region within the strains. VNTR3 was amplified in 90 strains. The discriminatory power of this typing tool has been greatly enhanced by this VNTR2 region as the other two regions could not discriminate strains significantly. In our study, about 55 % of the strains amplified all three VNTR regions and 39 % of the strains lacked the VNTR2 region. Among the three VNTR regions tested, the majority of the strains produced similar banding pattern for any two regions grouped into a cluster. The strains grouped as a genotype were from the same geographical location. Strains collected from each geographical region were also

  11. Simple Sequence Repeat Analysis of Selected NSIC-registered Coffee Varieties in the Philippines

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    Daisy May C. Santos


    Full Text Available Coffee (Coffea sp. is an important commercial crop worldwide. Three species of coffee are used as beverage, namely Coffea arabica, C. canephora, and C. liberica. Coffea arabica L. is the most cultivated among the three coffee species due to its taste quality, rich aroma, and low caffeine content. Despite its inferior taste and aroma, C. canephora Pierre ex A. Froehner, which has the highest caffeine content, is the second most widely cultivated because of its resistance to coffee diseases. On the other hand, C. liberica W.Bull ex Hierncomes is characterized by its very strong taste and flavor. The Philippines used to be a leading exporter of coffee until coffee rust destroyed the farms in Batangas, home of the famous Kapeng Barako. The country has been attempting to revive the coffee industry by focusing on the production of specialty coffee with registered varieties on the National Seed Industry Council (NSIC. Correct identification and isolation of pure coffee beans are the main factors that determine coffee’s market value. Local farms usually misidentify and mix coffee beans of different varieties, leading to the depreciation of their value. This study used simple sequence repeat (SSR markers to evaluate and distinguish Philippine NSIC-registered coffee species and varieties. The neighbor-joining tree generated using PAUP showed high bootstrap support, separating C. arabica, C. canephora, and C. liberica from each other. Among the twenty primer pairs used, seven were able to distinguish C. arabica, nine for C. liberica, and one for C. canephora.

  12. Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer

    International Nuclear Information System (INIS)

    Spink, Barbara C.; Bloom, Michael S.; Wu, Susan; Sell, Stewart; Schneider, Erasmus; Ding, Xinxin; Spink, David C.


    The aryl hydrocarbon receptor (AhR) regulates expression of numerous genes, including those of the CYP1 gene family. With the goal of determining factors that control AHR gene expression, our studies are focused on the role of the short tandem repeat polymorphism, (GGGGC) n , located in the proximal promoter of the human AHR gene. When luciferase constructs containing varying GGGGC repeats were transfected into cancer cell lines derived from the lung, colon, and breast, the number of GGGGC repeats affected AHR promoter activity. The number of GGGGC repeats was determined in DNA from 327 humans and from 38 samples representing 5 species of non-human primates. In chimpanzees and 3 species of macaques, only (GGGGC) 2 alleles were observed; however, in western gorilla, (GGGGC) n alleles with n = 2, 4, 5, 6, 7, and 8 were identified. In all human populations examined, the frequency of (GGGGC) n was n = 4 > 5 ≫ 2, 6. When frequencies of the (GGGGC) n alleles in DNA from patients with lung, colon, or breast cancer were evaluated, the occurrence of (GGGGC) 2 was found to be 8-fold more frequent among lung cancer patients in comparison with its incidence in the general population, as represented by New York State neonates. Analysis of matched tumor and non-tumor DNA samples from the same individuals provided no evidence of microsatellite instability. These studies indicate that the (GGGGC) n short tandem repeats are inherited, and that the (GGGGC) 2 allele in the AHR proximal promoter region should be further investigated with regard to its potential association with lung cancer susceptibility. - Highlights: • The AHR proximal promoter contains a polymorphism, (GGGGC) n , where n = 4 > 5 ≫ 2, 6 • Matched tumor and non-tumor DNA did not show (GGGGC) n microsatellite instability • AHR promoter activity of a construct with (GGGGC) 2 was lower than that of (GGGGC) 4 • The frequency of (GGGGC) 2 in lung cancer patients was 8-fold higher than in neonates • The

  13. Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer

    Energy Technology Data Exchange (ETDEWEB)

    Spink, Barbara C. [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Bloom, Michael S. [Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Wu, Susan [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Sell, Stewart; Schneider, Erasmus [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Ding, Xinxin [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States); Spink, David C., E-mail: [Wadsworth Center, New York State Department of Health, Albany, NY 12201 (United States); Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201 (United States)


    The aryl hydrocarbon receptor (AhR) regulates expression of numerous genes, including those of the CYP1 gene family. With the goal of determining factors that control AHR gene expression, our studies are focused on the role of the short tandem repeat polymorphism, (GGGGC){sub n}, located in the proximal promoter of the human AHR gene. When luciferase constructs containing varying GGGGC repeats were transfected into cancer cell lines derived from the lung, colon, and breast, the number of GGGGC repeats affected AHR promoter activity. The number of GGGGC repeats was determined in DNA from 327 humans and from 38 samples representing 5 species of non-human primates. In chimpanzees and 3 species of macaques, only (GGGGC){sub 2} alleles were observed; however, in western gorilla, (GGGGC){sub n} alleles with n = 2, 4, 5, 6, 7, and 8 were identified. In all human populations examined, the frequency of (GGGGC){sub n} was n = 4 > 5 ≫ 2, 6. When frequencies of the (GGGGC){sub n} alleles in DNA from patients with lung, colon, or breast cancer were evaluated, the occurrence of (GGGGC){sub 2} was found to be 8-fold more frequent among lung cancer patients in comparison with its incidence in the general population, as represented by New York State neonates. Analysis of matched tumor and non-tumor DNA samples from the same individuals provided no evidence of microsatellite instability. These studies indicate that the (GGGGC){sub n} short tandem repeats are inherited, and that the (GGGGC){sub 2} allele in the AHR proximal promoter region should be further investigated with regard to its potential association with lung cancer susceptibility. - Highlights: • The AHR proximal promoter contains a polymorphism, (GGGGC){sub n}, where n = 4 > 5 ≫ 2, 6 • Matched tumor and non-tumor DNA did not show (GGGGC){sub n} microsatellite instability • AHR promoter activity of a construct with (GGGGC){sub 2} was lower than that of (GGGGC){sub 4} • The frequency of (GGGGC){sub 2} in lung

  14. Deformation analysis of the repeated positional surveys in the undermined localities using web applications and WMS map services

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    Milan Talich


    Full Text Available The XML web application for on-line calculations of deformation analysis from the repeated positional surveys using Internet service and data is described. Parameters of deformation field (strain tensors, total dilatations are determined in a grid network covering the zone of interest. Displacement vectors from repeated measurements at given points of a geodetic network represent the imput data of calculation. The calculation is based on application of the theory of continuum mechanics and its fundamental prerequisite is homogeneity of the researched territory.The application currently utilizes the Web Map Services - WMS for the graphic presentation of calculated results as GIS. This service for example enables on-line thematic map composition as defined by the user in the window of Internet explorer based on data given by servers of WMS service. Thus the user does not need to own any geographic data to create his/her GIS.Furthermore there are also given application examples of the repeated geodetic surveys used in the field at localities in the forefront of ČSA giant quarry at Komořany and in the undermined territory in Ostrava region. The examples show the independence of calculated values of tensors from rotation and translation of the coordinate systems in practise. This fact gives the evidence that the deformation analysis is more objective dynamic indicator in the researched area and not only the calculus and representation of point displacement vectors. After registration this application is at all interested persons disposal to on-line calculations via the Internet.

  15. Repeating Marx

    DEFF Research Database (Denmark)

    Fuchs, Christian; Monticelli, Lara


    This introduction sets out the context of the special issue “Karl Marx @ 200: Debating Capitalism & Perspectives for the Future of Radical Theory”, which was published on the occasion of Marx’s bicentenary on 5 May 2018. First, we give a brief overview of contemporary capitalism’s development...... and its crises. Second, we argue that it is important to repeat Marx today. Third, we reflect on lessons learned from 200 years of struggles for alternatives to capitalism. Fourth, we give an overview of the contributions in this special issue. Taken together, the contributions in this special issue show...... that Marx’s theory and politics remain key inspirations for understanding exploitation and domination in 21st-century society and for struggles that aim to overcome these phenomena and establishing a just and fair society. We need to repeat Marx today....

  16. Deployment Repeatability (United States)


    large cohort of trials to spot unusual cases. However, deployment repeatability is inherently a nonlinear phenomenon, which makes modeling difficult...and GEMS tip position were both tracked during ground testing by a laser target tracking system. Earlier SAILMAST testing in 2005 [8] used...recalls the strategy used by SRTM, where a constellation of lights was installed at the tip of the boom and a modified star tracker was used to track tip

  17. The influence of learning methods on collaboration: prior repeated retrieval enhances retrieval organization, abolishes collaborative inhibition, and promotes post-collaborative memory. (United States)

    Congleton, Adam R; Rajaram, Suparna


    Research on collaborative memory has unveiled the counterintuitive yet robust phenomenon that collaboration impairs group recall. A candidate explanation for this collaborative inhibition effect is the disruption of people's idiosyncratic retrieval strategies during collaboration, and it is hypothesized that employing methods that improve one's organization protects against retrieval disruption. Here it is investigated how one's learning method during the study phase--defined as either repeatedly studying or repeatedly retrieving information--influences retrieval organization and what effects this has on collaborative recall and post-collaborative individual recall. Results show that repeated retrieval consistently eliminated collaborative inhibition. This enabled participants to gain the most from re-exposure to materials recalled by their partners that they themselves did not recall and led to improvements in their individual memory following collaboration. This repeated retrieval advantage stemmed from the preferential manner in which this learning method strengthened retrieval organization. Findings are also discussed that reveal a relationship between retrieval organization and the interaction observed between learning method and short versus long delay seen in the testing effect literature. Finally, results show that the elusive benefits of cross-cuing during collaboration may be best detected with a longer study-test delay. Together, these findings illuminate when and how collaboration can enhance memory.

  18. Experimental Analysis for Factors Affecting the Repeatability of Plastics Injection Molding Tests on the Self-developed Apparatus

    Directory of Open Access Journals (Sweden)

    Yugang Huang


    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 To improve the repeatability of the injection molding test result, the affecting factors were investigated by means of experiments. Besides the traditional processing parameter, the factors of test conditions were also considered. In order to focus on the molding process rather than the molded part, the curve measurement of the melt pressure at the entrance to the nozzle was used as the output characteristic. Experiments for polypropylene (PP showed that the injected volume was the key processing parameter. Within the test conditions, the injection number is the most important factor. According to the analysis the operating procedure was improved effectively. Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Doi: 10.12777/ijse.5.1.6-11 [How to cite this article: Huang, Y., Li, D., Liu, Y. (2013. Experimental Analysis for Factors Affecting the Repeatability of Plastics Injection Molding Tests on the Self-developed Apparatus. International Journal of Science and Engineering, 5(1,6-11. Doi: 10.12777/ijse.5.1.6-11]

  19. An approach for evaluating the repeatability of rapid wetland assessment methods: The effects of training and experience (United States)

    We sampled 92 wetlands from four different basins in the United States to quantify observer repeatability in rapid wetland condition assessment using the Delaware Rapid Assessment Protocol (DERAP). In the Inland Bays basin of Delaware, 58 wetland sites were sampled by multiple ob...

  20. [Polymorphism analysis of 20 autosomal short-tandem repeat loci in southern Chinese Han population]. (United States)

    Chen, Ling; Lu, Hui-Jie; DU, Wei-An; Qiu, Ping-Ming; Liu, Chao


    To evaluate the value of PowerPlex ® 21 System (Promega) and study the genetic polymorphism of its 20 short-tandem repeat (STR) loci in southern Chinese Han population. We conducted genotyping experiments using PowerPlex ® 21 System on 20 autosomal STR loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA) in 2367 unrelated Chinese Han individuals living in South China. The allele frequencies and parameters commonly used in forensic science were statistically analyzed in these individuals and compared with the reported data of other populations. The PowerPlex ® 21 System had a power of discrimination (PD) ranging from 0.7839 to 0.9852 and a power of exclusion (PE) ranging from 0.2974 to 0.8099 for the 20 loci. No significant deviation from Hardy-Weinberg expectations was found for all the loci except for D5S818. This southern Chinese Han population had significant differences in the allele frequencies from 8 ethnic groups reported in China, and showed significant differences at 8 to 20 STR foci from 5 foreign populations. The allele frequency at the locus D1S1656 in this southern Chinese Han population differed significantly from those in the 5 foreign populations and from 3 reported Han populations in Beijing, Zhejiang Province and Fujian Province of China. The neighbor-joining phylogenetictree showed clustering of all the Asian populations in one branch, while the northern Italian and Argentina populations clustered in a separate branch. This southern Chinese Han population had the nearest affinity with the Yi ethnic population in Yunnan Province of China. The 20 STR loci are highly polymorphic in this southern Chinese Han population, suggesting the value of this set of STR loci in forensic personal identification, paternity testing and anthropological study.

  1. Data Analysis Methods for Paleogenomics

    DEFF Research Database (Denmark)

    Avila Arcos, Maria del Carmen

    (Danmarks Grundforskningfond) 'Centre of Excellence in GeoGenetics' grant, with additional funding provided by the Danish Council for Independent Research 'Sapere Aude' programme. The thesis comprises five chapters, all of which represent different projects that involved the analysis of massive amounts......, thanks to the introduction of NGS and the implementation of data analysis methods specific for each project. Chapters 1 to 3 have been published in peer-reviewed journals and Chapter 4 is currently in review. Chapter 5 consists of a manuscript describing initial results of an ongoing research project......The work presented in this thesis is the result of research carried out during a three-year PhD at the Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, under supervision of Professor Tom Gilbert. The PhD was funded by the Danish National Research Foundation...

  2. Variable Number of Tandem Repeats (VNTR) analysis of Flavobacterium psychrophilum from salmonids in Chile and Norway

    DEFF Research Database (Denmark)

    Apablaza, Patricia; Brevik, Oyvind J.; Mjos, Svein


    Background: Flavobacterium psychrophilum causes serious fish diseases such RTFS and BCWD, affecting the aquaculture industry worldwide. Commercial vaccines are not available and control of the disease depends on the use of antibiotics. Reliable methods for detection and identification of differen...

  3. Multiple‐locus variable‐number tandem repeat analysis of Salmonella enterica subsp. enterica serovar Dublin

    DEFF Research Database (Denmark)

    Kjeldsen, M. K.; Torpdahl, M.; Campos, J.


    Salmonella serovar Dublin causes disease in cattle and leads to considerable production losses. In humans, severe invasive disease and high mortality rates are reported. The presently available typing methods provide insufficient discrimination within Salm. Dublin for epidemiological investigatio...

  4. A New Boron Analysis Method

    Energy Technology Data Exchange (ETDEWEB)

    Weitman, J; Daaverhoeg, N; Farvolden, S


    In connection with fast neutron (n, {alpha}) cross section measurements a novel boron analysis method has been developed. The boron concentration is inferred from the mass spectrometrically determined number of helium atoms produced in the thermal and epithermal B-10 (n, {alpha}) reaction. The relation between helium amount and boron concentration is given, including corrections for self shielding effects and background levels. Direct and diffusion losses of helium are calculated and losses due to gettering, adsorption and HF-ionization in the release stage are discussed. A series of boron determinations is described and the results are compared with those obtained by other methods, showing excellent agreement. The lower limit of boron concentration which can be measured varies with type of sample. In e.g. steel, concentrations below 10-5 % boron in samples of 0.1-1 gram may be determined.

  5. Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers. (United States)

    Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu


    Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

  6. Cyclic elastic analysis of a PWR nozzle subjected to a repeated thermal shock

    International Nuclear Information System (INIS)

    Locci, J.M.; Prost, J.P.


    In the primary piping system of a PWR nuclear power plant, some nozzles are subjected to strong thermal shocks due to sudden thermal variations in the internal water flow. The thermal gradients are sufficiently high to induce general elastic plastic behaviour. The design of these nozzles using the simplified elastic plastic analysis given in the ASME III Code NB-3200 generally leads to a very high usage factor. The aim of this work is to show by giving an example that a complete cyclic elastic plastic analysis makes it possible to considerably reduce the usage factor. (orig.)

  7. The genetic analysis of repeated measures II: The Karhunen-Loeve expansion.

    NARCIS (Netherlands)

    Molenaar, P.C.M.; Boomsma, D.I.


    Outlines the Karhunen-Loeve (N. Ahmed and K. R. Rao, 1975) approach to the genetic analysis of time series of arbitrary length and with arbitrary covariance function. This approach is based on the simultaneous eigenvalue decomposition of the covariance matrices of the original time series obtained


    Directory of Open Access Journals (Sweden)

    Ivan Valeriu


    Full Text Available Keeping a company in the top performing players in the relevant market depends not only on its ability to develop continually, sustainably and balanced, to the standards set by the customer and competition, but also on the ability to protect its strategic information and to know in advance the strategic information of the competition. In addition, given that economic markets, regardless of their profile, enable interconnection not only among domestic companies, but also between domestic companies and foreign companies, the issue of economic competition moves from the national economies to the field of interest of regional and international economic organizations. The stakes for each economic player is to keep ahead of the competition and to be always prepared to face market challenges. Therefore, it needs to know as early as possible, how to react to others’ strategy in terms of research, production and sales. If a competitor is planning to produce more and cheaper, then it must be prepared to counteract quickly this movement. Competitive intelligence helps to evaluate the capabilities of competitors in the market, legally and ethically, and to develop response strategies. One of the main goals of the competitive intelligence is to acknowledge the role of early warning and prevention of surprises that could have a major impact on the market share, reputation, turnover and profitability in the medium and long term of a company. This paper presents some aspects of competitive intelligence, mainly in terms of information analysis and intelligence generation. Presentation is theoretical and addresses a structured method of information analysis - scenarios method – in a version that combines several types of analysis in order to reveal some interconnecting aspects of the factors governing the activity of a company.

  9. Rule-of-thumb adjustment of sample sizes to accommodate dropouts in a two-stage analysis of repeated measurements. (United States)

    Overall, John E; Tonidandel, Scott; Starbuck, Robert R


    Recent contributions to the statistical literature have provided elegant model-based solutions to the problem of estimating sample sizes for testing the significance of differences in mean rates of change across repeated measures in controlled longitudinal studies with differentially correlated error and missing data due to dropouts. However, the mathematical complexity and model specificity of these solutions make them generally inaccessible to most applied researchers who actually design and undertake treatment evaluation research in psychiatry. In contrast, this article relies on a simple two-stage analysis in which dropout-weighted slope coefficients fitted to the available repeated measurements for each subject separately serve as the dependent variable for a familiar ANCOVA test of significance for differences in mean rates of change. This article is about how a sample of size that is estimated or calculated to provide desired power for testing that hypothesis without considering dropouts can be adjusted appropriately to take dropouts into account. Empirical results support the conclusion that, whatever reasonable level of power would be provided by a given sample size in the absence of dropouts, essentially the same power can be realized in the presence of dropouts simply by adding to the original dropout-free sample size the number of subjects who would be expected to drop from a sample of that original size under conditions of the proposed study.

  10. Effect of exercise order on the number of repeats and training volume in the tri-set training method

    Directory of Open Access Journals (Sweden)

    Waynne Ferreira de Faria


    Full Text Available DOI:   Although the tri-set system is widely adopted by athletes and experienced weight training practitioners aimed at optimizing the metabolic overload, there are still few works in literature on the effect of exercise order manipulation on this training system. Therefore, this work was aimed at investigating the effect of exercise order manipulation on the number of repeats and training volume using the tri-set system for lower limbs. This is a randomized cross-over design study. The experimental group consisted of 14 healthy men (23.53 ± 5.40 years; 24.51 ± 2.96 kg/m2. Subjects were submitted to two experimental sessions at different exercise order for lower limbs: Sequence A: squat on guided bar, leg press 45° and bilateral leg extension; sequence B: bilateral leg extension, leg press 45° and squat on guided bar. Three sets to volitional fatigue in all exercises were performed, with intensity of 75% 1RM. Superiority for sequence B in the total number of repeats (70.14 ± 13 vs 60.93 ± 7.94 repeats, p = 0.004 and total training volume (9129.64 ± 2830.05 vs 8238.29 ± 2354.20 kg, p = 0.014 was observed. Based on the above, the performance of single-joint exercises before multi-joint exercises in the tri-set system adopted for lower limbs induced higher number of repeats and total training volume.

  11. Comparison of the capillary and agarose electrophoresis based multiple locus VNTR (variable number of tandem repeats) analysis (MLVA) on Mycobacterium bovis isolates. (United States)

    Jenkins, A O; Venter, E H; Hutamo, K; Godfroid, J


    Electrophoretic techniques that can be used for genotyping of bacterial pathogens ranges from manual, low-cost, agarose gels to high-throughput capillary electrophoresis sequencing machines. These two methods are currently employed in the electrophoresis of PCR products used in multiple locus VNTR (variable number of tandem repeats) analysis (MLVA), i.e. the agarose electrophoresis (AE) and the capillary electrophoresis (CE). Some authors have suggested that clusters generated by AE are less reliable than those generated by CE and that the latter is a more sensitive technique than the former when typing Mycobacterium tuberculosis complex (MTC) isolates. Because such a claim could have significant consequences for investigators in this field, a comparison was made on 19 Belgian Mycobacterium bovis strains which had previously been genotyped using CE VNTR analysis. The VNTR profiles of the CE VNTR analysis were compared with those obtained by AE VNTR analysis at 14 VNTR loci. Our results indicated that there were no differences in copy numbers at all loci tested when the copy numbers obtained by the AE VNTR analysis were compared with those obtained by CE VNTR analysis. The use of AE VNTR analysis in mycobacterial genotyping does not alter the sensitivity of the MLVA technique compared with the CE VNTR analysis. The AE VNTR can therefore be regarded as a viable alternative in moderately equipped laboratories that cannot afford the expensive equipment required for CE VNTR analysis and data obtained by AE VNTR analysis can be shared between laboratories which use the CE VNTR method. (c) 2010 Elsevier B.V. All rights reserved.

  12. Gravimetric and titrimetric methods of analysis

    International Nuclear Information System (INIS)

    Rives, R.D.; Bruks, R.R.


    Gravimetric and titrimetric methods of analysis are considered. Methods of complexometric titration are mentioned, as well as methods of increasing sensitivity in titrimetry. Gravimetry and titrimetry are applied during analysis for traces of geological materials

  13. The relationship between visitor spending and repeat visits: An analysis of spectators at the Old Mutual Two Oceans Marathon

    Directory of Open Access Journals (Sweden)

    M. Kruger


    Full Text Available Purpose: The purpose of this research is to determine the relationship between visitor spending patterns, and previous and planned return visits as well as demographic and trip characteristics of supporters to the Old Mutual Two Oceans Marathon held annually in Cape Town. Problem investigated: Spectator sport is a significant segment of the tourism industry which also has a considerable economic impact on host communities. For this reason, communities and destinations have recognised and attempt to capitalise on hosting large sporting events. In this regard visitor spending is crucial since information concerning the latter can provide sport event organisers to focus their marketing efforts to attract optimal economic benefits. In addition, the relationship of previous visits to a sport event and intended re-visits to visitor spending has received increasing attention since it is believed that repeat visitation is associated with higher levels of expenditure. However limited attention is currently being paid to the relationship between spectator spending patterns and previous and planned return visits in a South African sport spectator context even though the latter has a direct impact on the future sustainability of an event. Methodology: A supporter survey was done for the first time in 2010 (30 March - 2 April 2010 at the event and 430 questionnaires were completed. Factor analysis and regression analysis are used to analyse the data and to identify the relationship between repeat visits and visitor spending patterns. Findings: Results from this study shows that it is predominantly socio-demographic variables that influence travel behaviour. The significant socio-demographic determinants that influence spending per person are gender, language and province of origin while the only behavioural determinant was group size. The results also revealed that there is no significant relationship between spectator spending, repeat attendance and

  14. In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

    Directory of Open Access Journals (Sweden)

    Andrea Vásquez


    Full Text Available We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava’s SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp. It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava’s genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution.

  15. Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations. (United States)

    Soltyszewski, Ireneusz; Plocienniczak, Andrzej; Fabricius, Hans Ake; Kornienko, Igor; Vodolazhsky, Dmitrij; Parson, Walther; Hradil, Roman; Schmitter, Hermann; Ivanov, Pavel; Kuzniar, Piotr; Malyarchuk, Boris A; Grzybowski, Tomasz; Woźniak, Marcin; Henke, Jurgen; Henke, Lotte; Olkhovets, Sergiv; Voitenko, Vladimir; Lagus, Vita; Ficek, Andrej; Minárik, Gabriel; de Knijff, Peter; Rebała, Krzysztof; Wysocka, Joanna; Kapińska, Ewa; Cybulska, Lidia; Mikulich, Alexei I; Tsybovsky, Iosif S; Szczerkowska, Zofia; Krajewski, Paweł; Ploski, Rafał


    The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling. We found homogeneity of present day Poland and consistent differences between Polish and German populations which contrasted with relative similarities between Russian and German populations. These discrepancies between genetic and geographic distances were confirmed by analysis of an independent data set on Y chromosome STRs. Migrations of Goths, Viking influences, German settlements in the region of Volga river and/or forced population resettlements and other events related to World War II are the historic events which might have caused these finding.

  16. Isolation of human simple repeat loci by hybridization selection. (United States)

    Armour, J A; Neumann, R; Gobert, S; Jeffreys, A J


    We have isolated short tandem repeat arrays from the human genome, using a rapid method involving filter hybridization to enrich for tri- or tetranucleotide tandem repeats. About 30% of clones from the enriched library cross-hybridize with probes containing trimeric or tetrameric tandem arrays, facilitating the rapid isolation of large numbers of clones. In an initial analysis of 54 clones, 46 different tandem arrays were identified. Analysis of these tandem repeat loci by PCR showed that 24 were polymorphic in length; substantially higher levels of polymorphism were displayed by the tetrameric repeat loci isolated than by the trimeric repeats. Primary mapping of these loci by linkage analysis showed that they derive from 17 chromosomes, including the X chromosome. We anticipate the use of this strategy for the efficient isolation of tandem repeats from other sources of genomic DNA, including DNA from flow-sorted chromosomes, and from other species.

  17. Repeatability of Cryogenic Multilayer Insulation (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.


    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five Glenn Research Center (GRC) provided coupons with 25 layers was shown to be +/- 8.4% whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0%. A second group of 10 coupons has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  18. NMR Analysis of Amide Hydrogen Exchange Rates in a Pentapeptide-Repeat Protein from A. thaliana. (United States)

    Xu, Shenyuan; Ni, Shuisong; Kennedy, Michael A


    At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown. Given its unusual structure, we investigated the biophysical properties of At2g44920 as a representative of the β-helix family to determine if it had exceptional global stability, backbone dynamics, or amide hydrogen exchange rates. Circular dichroism measurements yielded a melting point of 62.8°C, indicating unexceptional global thermal stability. Nuclear spin relaxation measurements indicated that the Rfr-fold core was rigid with order parameters ranging from 0.7 to 0.9. At2g44920 exhibited a striking range of amide hydrogen exchange rates spanning 10 orders of magnitude, with lifetimes ranging from minutes to several months. A weak correlation was found among hydrogen exchange rates, hydrogen bonding energies, and amino acid solvent-accessible areas. Analysis of contributions from fast (approximately picosecond to nanosecond) backbone dynamics to amide hydrogen exchange rates revealed that the average order parameter of amides undergoing fast exchange was significantly smaller compared to those undergoing slow exchange. Importantly, the activation energies for amide hydrogen exchange were found to be generally higher for the slowest exchanging amides in the central Rfr coil and decreased toward the terminal coils. This could be explained by assuming that the concerted motions of two preceding or following coils required for hydrogen bond disruption and amide hydrogen exchange have a higher activation energy

  19. Comparison of serum creatine kinase estimation with short tandem repeats based linkage analysis in carriers and affected children of duchenne muscular dystrophy

    International Nuclear Information System (INIS)

    Hashim, R.; Ahmad, S.; Sattar, A.; Khan, F.A.


    Background: Duchenne Muscular Dystrophy (DMD) is an X-linked recessive lethal, genetic disorder characterised by progressive weakness of skeletal muscles which is untreatable and transmitted to males by carrier females. Advances in laboratory techniques now focus direct mutational analysis as the most reliable and indirect analysis based on Short Tandem Repeats (STR) based linkage analysis as feasible, inexpensive, and efficient method for carrier detection and prenatal diagnosis. The objective of this study was to compare the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic efficiency of Serum Creatine Kinase (SCK) with Short Tandem Repeats (STR based linkage analysis in carriers and affected children of Duchenne Muscular Dystrophy. Methods: The study was carried out from Dec 2006 to Dec 2007 in families having index clinical cases of DMD who were referred from different hospitals for evaluation/workup of DMD. SCK was done as a preliminary investigation in all index cases. The PCR assay with STR based linkage analysis with Intron 44, 45, 49 and 50 of DMD gene were performed in all families. Six families were informative with Intron 44 of DMD gene and one family was non-informative with all four intronic markers of DMD. SCK analyses were done in all the family members and compared with PCR analysis in informative families. SCK was not performed on Chorionic villous sample (CVS) done for prenatal diagnosis of DMD, and CVS and non-informative family members were excluded from the study. Results: In carriers of DMD, the sensitivity and negative predictive value of SCK were 33.3%, and specificity and positive predictive were 100% with diagnostic efficiency of 50%. In affected cases of DMD the sensitivity and negative predictive value of SCK were 100%, and specificity and positive predictive were 91% and 88.8% respectively and diagnostic efficiency of 94.1%. Conclusion: The SCK is an excellent screening test for

  20. Analysis methods (from 301 to 351)

    International Nuclear Information System (INIS)

    Analysis methods of materials used in the nuclear field (uranium, plutonium and their compounds, zirconium, magnesium, water...) and determination of impurities. Only reliable methods are selected [fr

  1. The PCA3 test for guiding repeat biopsy of prostate cancer and its cut-off score: a systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Yong Luo


    Full Text Available The specificity of prostate-specific antigen (PSA for early intervention in repeat biopsy is unsatisfactory. Prostate cancer antigen 3 (PCA3 may be more accurate in outcome prediction than other methods for the early detection of prostate cancer (PCa. However, the results were inconsistent in repeated biopsies. Therefore, we performed a systematic review and meta-analysis to evaluate the role of PCA3 in outcome prediction. A systematic bibliographic search was conducted for articles published before April 2013, using PubMed, Medline, Web of Science, Embase and other databases from health technology assessment agencies. The quality of the studies was assessed on the basis of QUADAS criteria. Eleven studies of diagnostic tests with moderate to high quality were selected. A meta-analysis was carried out to synthesize the results. The results of the meta-analyses were heterogeneous among studies. We performed a subgroup analysis (with or without inclusion of high-grade prostatic intraepithelial neoplasia (HGPIN and atypical small acinar proliferation (ASAP. Using a PCA3 cutoff of 20 or 35, in the two sub-groups, the global sensitivity values were 0.93 or 0.80 and 0.79 or 0.75, specificities were 0.65 or 0.44 and 0.78 or 0.70, positive likelihood ratios were 1.86 or 1.58 and 2.49 or 1.78, negative likelihood ratios were 0.81 or 0.43 and 0.91 or 0.82 and diagnostic odd ratios (ORs were 5.73 or 3.45 and 7.13 or 4.11, respectively. The areas under the curve (AUCs of the summary receiver operating characteristic curve were 0.85 or 0.72 and 0.81 or 0.69, respectively. PCA3 can be used for repeat biopsy of the prostate to improve accuracy of PCa detection. Unnecessary biopsies can be avoided by using a PCa cutoff score of 20.

  2. DTI analysis methods : Voxel-based analysis

    NARCIS (Netherlands)

    Van Hecke, Wim; Leemans, Alexander; Emsell, Louise


    Voxel-based analysis (VBA) of diffusion tensor imaging (DTI) data permits the investigation of voxel-wise differences or changes in DTI metrics in every voxel of a brain dataset. It is applied primarily in the exploratory analysis of hypothesized group-level alterations in DTI parameters, as it does

  3. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats. (United States)

    Seman, Ali; Sapawi, Azizian Mohd; Salleh, Mohd Zaki


    Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84-1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data.

  4. Bayesian methods for data analysis

    CERN Document Server

    Carlin, Bradley P.


    Approaches for statistical inference Introduction Motivating Vignettes Defining the Approaches The Bayes-Frequentist Controversy Some Basic Bayesian Models The Bayes approach Introduction Prior Distributions Bayesian Inference Hierarchical Modeling Model Assessment Nonparametric Methods Bayesian computation Introduction Asymptotic Methods Noniterative Monte Carlo Methods Markov Chain Monte Carlo Methods Model criticism and selection Bayesian Modeling Bayesian Robustness Model Assessment Bayes Factors via Marginal Density Estimation Bayes Factors

  5. Substoichiometric method in the simple radiometric analysis

    International Nuclear Information System (INIS)

    Ikeda, N.; Noguchi, K.


    The substoichiometric method is applied to simple radiometric analysis. Two methods - the standard reagent method and the standard sample method - are proposed. The validity of the principle of the methods is verified experimentally in the determination of silver by the precipitation method, or of zinc by the ion-exchange or solvent-extraction method. The proposed methods are simple and rapid compared with the conventional superstoichiometric method. (author)

  6. Repeatability of Brain Volume Measurements Made with the Atlas-based Method from T1-weighted Images Acquired Using a 0.4 Tesla Low Field MR Scanner. (United States)

    Goto, Masami; Suzuki, Makoto; Mizukami, Shinya; Abe, Osamu; Aoki, Shigeki; Miyati, Tosiaki; Fukuda, Michinari; Gomi, Tsutomu; Takeda, Tohoru


    An understanding of the repeatability of measured results is important for both the atlas-based and voxel-based morphometry (VBM) methods of magnetic resonance (MR) brain volumetry. However, many recent studies that have investigated the repeatability of brain volume measurements have been performed using static magnetic fields of 1-4 tesla, and no study has used a low-strength static magnetic field. The aim of this study was to investigate the repeatability of measured volumes using the atlas-based method and a low-strength static magnetic field (0.4 tesla). Ten healthy volunteers participated in this study. Using a 0.4 tesla magnetic resonance imaging (MRI) scanner and a quadrature head coil, three-dimensional T 1 -weighted images (3D-T 1 WIs) were obtained from each subject, twice on the same day. VBM8 software was used to construct segmented normalized images [gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) images]. The regions-of-interest (ROIs) of GM, WM, CSF, hippocampus (HC), orbital gyrus (OG), and cerebellum posterior lobe (CPL) were generated using WFU PickAtlas. The percentage change was defined as[100 × (measured volume with first segmented image - mean volume in each subject)/(mean volume in each subject)]The average percentage change was calculated as the percentage change in the 6 ROIs of the 10 subjects. The mean of the average percentage changes for each ROI was as follows: GM, 0.556%; WM, 0.324%; CSF, 0.573%; HC, 0.645%; OG, 1.74%; and CPL, 0.471%. The average percentage change was higher for the orbital gyrus than for the other ROIs. We consider that repeatability of the atlas-based method is similar between 0.4 and 1.5 tesla MR scanners. To our knowledge, this is the first report to show that the level of repeatability with a 0.4 tesla MR scanner is adequate for the estimation of brain volume change by the atlas-based method.

  7. Umbilical cord Wharton's jelly repeated culture system: a new device and method for obtaining abundant mesenchymal stem cells for bone tissue engineering.

    Directory of Open Access Journals (Sweden)

    Zhengqi Chang

    Full Text Available To date, various types of cells for seeding regenerative scaffolds have been used for bone tissue engineering. Among seed cells, the mesenchymal stem cells derived from human umbilical cord Wharton's jelly (hUCMSCs represent a promising candidate and hold potential for bone tissue engineering due to the the lack of ethical controversies, accessibility, sourced by non-invasive procedures for donors, a reduced risk of contamination, osteogenic differentiation capacities, and higher immunomodulatory capacity. However, the current culture methods are somewhat complicated and inefficient and often fail to make the best use of the umbilical cord (UC tissues. Moreover, these culture processes cannot be performed on a large scale and under strict quality control. As a result, only a small quantity of cells can be harvested using the current culture methods. To solve these problems, we designed and evaluated an UC Wharton's jelly repeated culture device. Using this device, hUCMSCs were obtained from the repeated cultures and their quantities and biological characteristics were compared. We found that using our culture device, which retained all tissue blocks on the bottom of the dish, the total number of obtained cells increased 15-20 times, and the time required for the primary passage was reduced. Moreover, cells harvested from the repeated cultures exhibited no significant difference in their immunophenotype, potential for multilineage differentiation, or proliferative, osteoinductive capacities, and final osteogenesis. The application of the repeated culture frame (RCF not only made full use of the Wharton's jelly but also simplified and specified the culture process, and thus, the culture efficiency was significantly improved. In summary, abundant hUCMSCs of dependable quality can be acquired using the RCF.

  8. Repeatability of riparian vegetation sampling methods: how useful are these techniques for broad-scale, long-term monitoring? (United States)

    Marc C. Coles-Ritchie; Richard C. Henderson; Eric K. Archer; Caroline Kennedy; Jeffrey L. Kershner


    Tests were conducted to evaluate variability among observers for riparian vegetation data collection methods and data reduction techniques. The methods are used as part of a largescale monitoring program designed to detect changes in riparian resource conditions on Federal lands. Methods were evaluated using agreement matrices, the Bray-Curtis dissimilarity metric, the...

  9. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

    Directory of Open Access Journals (Sweden)

    Perumal Sampath

    Full Text Available Miniature inverted-repeat transposable elements (MITEs are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5 were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1 were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.

  10. Genetic diversity analysis of cyanogenic potential (CNp) of root among improved genotypes of cassava using simple sequence repeat markers. (United States)

    Moyib, O K; Mkumbira, J; Odunola, O A; Dixon, A G


    Cyanogenic potential (CNp) of cassava constitutes a serious problem for over 500 million people who rely on the crop as their main source of calories. Genetic diversity is a key to successful crop improvement for breeding new improved variability for target traits. Forty-three improved genotypes of cassava developed by International Institute of Tropical Agriculture (ITA), Ibadan, were characterized for CNp trait using 35 Simple Sequence.Repeat (SSR) markers. Essential colorimetry picric test was used for evaluation of CNp on a color scale of 1 to 14. The CNp scores obtained ranged from 3 to 9, with a mean score of 5.48 (+/- 0.09) based on Statistical Analysis System (SAS) package. TMS M98/ 0068 (4.0 +/- 0.25) was identified as the best genotype with low CNp while TMS M98/0028 (7.75 +/- 0.25) was the worst. The 43 genotypes were assigned into 7 phenotypic groups based on rank-sum analysis in SAS. Dissimilarity analysis representatives for windows generated a phylogenetic tree with 5 clusters which represented hybridizing groups. Each of the clusters (except 4) contained low CNp genotypes that could be used for improving the high CNp genotypes in the same or near cluster. The scatter plot of the genotypes showed that there was little or no demarcation for phenotypic CNp groupings in the molecular groupings. The result of this study demonstrated that SSR markers are powerful tools for the assessment of genetic variability, and proper identification and selection of parents for genetic improvement of low CNp trait among the IITA cassava collection.

  11. Chemical methods of rock analysis

    National Research Council Canada - National Science Library

    Jeffery, P. G; Hutchison, D


    .... Such methods include those based upon spectrophotometry, flame emission spectrometry and atomic absorption spectroscopy, as well as gravimetry, titrimetry and the use of ion-selective electrodes...

  12. Analysis of the a genome genetic diversity among brassica napus, b. rapa and b. juncea accessions using specific simple sequence repeat markers

    International Nuclear Information System (INIS)

    Tian, H.; Yan, J.; Zhang, R.; Guo, Y.; Hu, S.; Channa, S.A.


    This investigation was aimed at evaluating the genetic diversity of 127 accessions among Brassica napus, B. rapa, and B. juncea by using 15 pairs of the A genome specific simple sequence repeat primers. These 127 accessions could be clearly separated into three groups by cluster analysis, principal component analysis, and population structure analysis separately, and the results analyzed by the three methods were very similar. Group I comprised of mainly B. napus accessions and the most of B. juncea accessions formed Group II, Group III included nearly all of the B. rapa accessions. The result showed that 36.86% of the variance was due to significant differences among populations of species, indicated that abundance genetic diversity existed among the A genome of B. napus, B. rapa, and B. juncea accessions. B. napus, B. rapa, and B. juncea have the abundant genetic diversity in the A genome, and some elite genes can be used to broaden the genetic base of them, especially for B. napus, in future rapeseed breeding program. (author)

  13. A method for nonlinear exponential regression analysis (United States)

    Junkin, B. G.


    A computer-oriented technique is presented for performing a nonlinear exponential regression analysis on decay-type experimental data. The technique involves the least squares procedure wherein the nonlinear problem is linearized by expansion in a Taylor series. A linear curve fitting procedure for determining the initial nominal estimates for the unknown exponential model parameters is included as an integral part of the technique. A correction matrix was derived and then applied to the nominal estimate to produce an improved set of model parameters. The solution cycle is repeated until some predetermined criterion is satisfied.

  14. Probabilistic methods in combinatorial analysis

    CERN Document Server

    Sachkov, Vladimir N


    This 1997 work explores the role of probabilistic methods for solving combinatorial problems. These methods not only provide the means of efficiently using such notions as characteristic and generating functions, the moment method and so on but also let us use the powerful technique of limit theorems. The basic objects under investigation are nonnegative matrices, partitions and mappings of finite sets, with special emphasis on permutations and graphs, and equivalence classes specified on sequences of finite length consisting of elements of partially ordered sets; these specify the probabilist

  15. Methods in quantitative image analysis. (United States)

    Oberholzer, M; Ostreicher, M; Christen, H; Brühlmann, M


    The main steps of image analysis are image capturing, image storage (compression), correcting imaging defects (e.g. non-uniform illumination, electronic-noise, glare effect), image enhancement, segmentation of objects in the image and image measurements. Digitisation is made by a camera. The most modern types include a frame-grabber, converting the analog-to-digital signal into digital (numerical) information. The numerical information consists of the grey values describing the brightness of every point within the image, named a pixel. The information is stored in bits. Eight bits are summarised in one byte. Therefore, grey values can have a value between 0 and 256 (2(8)). The human eye seems to be quite content with a display of 5-bit images (corresponding to 64 different grey values). In a digitised image, the pixel grey values can vary within regions that are uniform in the original scene: the image is noisy. The noise is mainly manifested in the background of the image. For an optimal discrimination between different objects or features in an image, uniformity of illumination in the whole image is required. These defects can be minimised by shading correction [subtraction of a background (white) image from the original image, pixel per pixel, or division of the original image by the background image]. The brightness of an image represented by its grey values can be analysed for every single pixel or for a group of pixels. The most frequently used pixel-based image descriptors are optical density, integrated optical density, the histogram of the grey values, mean grey value and entropy. The distribution of the grey values existing within an image is one of the most important characteristics of the image. However, the histogram gives no information about the texture of the image. The simplest way to improve the contrast of an image is to expand the brightness scale by spreading the histogram out to the full available range. Rules for transforming the grey value

  16. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. (United States)

    Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming


    Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

  17. Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013. (United States)

    Tian, Guo-Zhong; Cui, Bu-Yun; Piao, Dong-Ri; Zhao, Hong-Yan; Li, Lan-Yu; Liu, Xi; Xiao, Pei; Zhao, Zhong-Zhi; Xu, Li-Qing; Jiang, Hai; Li, Zhen-Jun


    Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. IDOP-D-16-00101.

  18. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong


    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  19. Moyer's method of mixed dentition analysis: a meta-analysis ...

    African Journals Online (AJOL)

    The applicability of tables derived from the data Moyer used to other ethnic groups has ... This implies that Moyer's method of prediction may have population variations. ... Key Words: meta-analysis, mixed dentition analysis, Moyer's method

  20. Repeat syphilis has a different immune response compared with initial syphilis: an analysis of biomarker kinetics in two cohorts. (United States)

    Kenyon, Chris; Tsoumanis, Achilleas; Osbak, Kara; Van Esbroeck, Marjan; Florence, Eric; Crucitti, Tania; Kestens, Luc


    We aimed to asses if there are differences in the clinical presentation and immune response of repeat as compared with initial syphilis. Prospective study: we prospectively recruited all patients with a new diagnosis of syphilis and tested their plasma for a range of cytochemokines and rapid plasma reagin (RPR) at baseline pretreatment and 6 months following therapy. Retrospective study: we compared RPR assay response kinetics between initial and repeat syphilis in persons attending our HIV/STI clinic from 1993 to 2016. Prospective study: a total of 91 individuals, 36 with initial syphilis and 55 with repeat syphilis, were included in the study. At baseline visit, those with initial syphilis were more likely to be symptomatic and have higher levels of interleukin-10 than repeaters. At baseline, median RPR titres were higher in the repeat than the initial infection groups. Repeaters were less likely than those with initial infections to serorevert to a negative RPR and be serofast (<4-fold RPR titre decline) at 6 months.Retrospective study: syphilis was diagnosed in 1027/43 870 individuals tested. At diagnosis, repeaters had higher RPR titres and a stepwise increase in RPR titre with number of syphilis episodes. They had a different RPR test response kinetic: they were less likely to be serofast and to serorevert than initial syphilis at 6 and 12 months. No individuals with four or more previous episodes of syphilis seroreverted. Repeat syphilis has a different clinical presentation and immunological response to initial infection. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  1. The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species. (United States)

    Zhang, Yanzhen; Ma, Ji; Yang, Bingxian; Li, Ruyi; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Zhang, Lin


    Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Applying critical analysis - main methods

    Directory of Open Access Journals (Sweden)

    Miguel Araujo Alonso


    Full Text Available What is the usefulness of critical appraisal of literature? Critical analysis is a fundamental condition for the correct interpretation of any study that is subject to review. In epidemiology, in order to learn how to read a publication, we must be able to analyze it critically. Critical analysis allows us to check whether a study fulfills certain previously established methodological inclusion and exclusion criteria. This is frequently used in conducting systematic reviews although eligibility criteria are generally limited to the study design. Critical analysis of literature and be done implicitly while reading an article, as in reading for personal interest, or can be conducted in a structured manner, using explicit and previously established criteria. The latter is done when formally reviewing a topic.

  3. Analysis of tandem repeat units of the promoter of capsanthin/capsorubin synthase (Ccs) gene in pepper fruit. (United States)

    Tian, Shi-Lin; Li, Zheng; Li, Li; Shah, S N M; Gong, Zhen-Hui


    Capsanthin/capsorubin synthase ( Ccs ) gene is a key gene that regulates the synthesis of capsanthin and the development of red coloration in pepper fruits. There are three tandem repeat units in the promoter region of Ccs , but the potential effects of the number of repetitive units on the transcriptional regulation of Ccs has been unclear. In the present study, expression vectors carrying different numbers of repeat units of the Ccs promoter were constructed, and the transient expression of the β-glucuronidase ( GUS ) gene was used to detect differences in expression levels associated with the promoter fragments. These repeat fragments and the plant expression vector PBI121 containing the 35s CaMV promoter were ligated to form recombinant vectors that were transfected into Agrobacterium tumefaciens GV3101. A fluorescence spectrophotometer was used to analyze the expression associated with the various repeat units. It was concluded that the constructs containing at least one repeat were associated with GUS expression, though they did not differ from one another. This repeating unit likely plays a role in transcription and regulation of Ccs expression.

  4. An overview of longitudinal data analysis methods for neurological research. (United States)

    Locascio, Joseph J; Atri, Alireza


    The purpose of this article is to provide a concise, broad and readily accessible overview of longitudinal data analysis methods, aimed to be a practical guide for clinical investigators in neurology. In general, we advise that older, traditional methods, including (1) simple regression of the dependent variable on a time measure, (2) analyzing a single summary subject level number that indexes changes for each subject and (3) a general linear model approach with a fixed-subject effect, should be reserved for quick, simple or preliminary analyses. We advocate the general use of mixed-random and fixed-effect regression models for analyses of most longitudinal clinical studies. Under restrictive situations or to provide validation, we recommend: (1) repeated-measure analysis of covariance (ANCOVA), (2) ANCOVA for two time points, (3) generalized estimating equations and (4) latent growth curve/structural equation models.

  5. An Overview of Longitudinal Data Analysis Methods for Neurological Research

    Directory of Open Access Journals (Sweden)

    Joseph J. Locascio


    Full Text Available The purpose of this article is to provide a concise, broad and readily accessible overview of longitudinal data analysis methods, aimed to be a practical guide for clinical investigators in neurology. In general, we advise that older, traditional methods, including (1 simple regression of the dependent variable on a time measure, (2 analyzing a single summary subject level number that indexes changes for each subject and (3 a general linear model approach with a fixed-subject effect, should be reserved for quick, simple or preliminary analyses. We advocate the general use of mixed-random and fixed-effect regression models for analyses of most longitudinal clinical studies. Under restrictive situations or to provide validation, we recommend: (1 repeated-measure analysis of covariance (ANCOVA, (2 ANCOVA for two time points, (3 generalized estimating equations and (4 latent growth curve/structural equation models.

  6. Trial Sequential Methods for Meta-Analysis (United States)

    Kulinskaya, Elena; Wood, John


    Statistical methods for sequential meta-analysis have applications also for the design of new trials. Existing methods are based on group sequential methods developed for single trials and start with the calculation of a required information size. This works satisfactorily within the framework of fixed effects meta-analysis, but conceptual…

  7. Intellectual Data Analysis Method for Evaluation of Virtual Teams

    Directory of Open Access Journals (Sweden)

    Sandra Strigūnaitė


    Full Text Available The purpose of the article is to present a method for virtual team performance evaluation based on intelligent team member collaboration data analysis. The motivation for the research is based on the ability to create an evaluation method that is similar to ambiguous expert evaluations. The concept of the hierarchical fuzzy rule based method aims to evaluate the data from virtual team interaction instances related to implementation of project tasks. The suggested method is designed for project managers or virtual team leaders to help in virtual teamwork evaluation that is based on captured data analysis. The main point of the method is the ability to repeat human thinking and expert valuation process for data analysis by applying fuzzy logic: fuzzy sets, fuzzy signatures and fuzzy rules. The fuzzy set principle used in the method allows evaluation criteria numerical values to transform into linguistic terms and use it in constructing fuzzy rules. Using a fuzzy signature is possible in constructing a hierarchical criteria structure. This structure helps to solve the problem of exponential increase of fuzzy rules including more input variables. The suggested method is aimed to be applied in the virtual collaboration software as a real time teamwork evaluation tool. The research shows that by applying fuzzy logic for team collaboration data analysis it is possible to get evaluations equal to expert insights. The method includes virtual team, project task and team collaboration data analysis. The advantage of the suggested method is the possibility to use variables gained from virtual collaboration systems as fuzzy rules inputs. Information on fuzzy logic based virtual teamwork collaboration evaluation has evidence that can be investigated in the future. Also the method can be seen as the next virtual collaboration software development step.

  8. Hybrid methods for cybersecurity analysis :

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Warren Leon,; Dunlavy, Daniel M.


    Early 2010 saw a signi cant change in adversarial techniques aimed at network intrusion: a shift from malware delivered via email attachments toward the use of hidden, embedded hyperlinks to initiate sequences of downloads and interactions with web sites and network servers containing malicious software. Enterprise security groups were well poised and experienced in defending the former attacks, but the new types of attacks were larger in number, more challenging to detect, dynamic in nature, and required the development of new technologies and analytic capabilities. The Hybrid LDRD project was aimed at delivering new capabilities in large-scale data modeling and analysis to enterprise security operators and analysts and understanding the challenges of detection and prevention of emerging cybersecurity threats. Leveraging previous LDRD research e orts and capabilities in large-scale relational data analysis, large-scale discrete data analysis and visualization, and streaming data analysis, new modeling and analysis capabilities were quickly brought to bear on the problems in email phishing and spear phishing attacks in the Sandia enterprise security operational groups at the onset of the Hybrid project. As part of this project, a software development and deployment framework was created within the security analyst work ow tool sets to facilitate the delivery and testing of new capabilities as they became available, and machine learning algorithms were developed to address the challenge of dynamic threats. Furthermore, researchers from the Hybrid project were embedded in the security analyst groups for almost a full year, engaged in daily operational activities and routines, creating an atmosphere of trust and collaboration between the researchers and security personnel. The Hybrid project has altered the way that research ideas can be incorporated into the production environments of Sandias enterprise security groups, reducing time to deployment from months and

  9. Use of multiple-locus variable-number tandem-repeats analysis (MLVA) typing to characterize Salmonella Typhimurium DT41 broiler breeder infections

    DEFF Research Database (Denmark)

    Litrup, E.; Christensen, H.; Nordentoft, Steen


    To characterize isolates of Salmonella Typhimurium DT41 obtained from infected flocks of broiler breeders by multiple-locus variable-number tandem-repeats analysis (MLVA) and compare results with a diverse strain collection from Germany and United Kingdom and isolates from Danish patients. A total...

  10. Microparticle analysis system and method (United States)

    Morrison, Dennis R. (Inventor)


    A device for analyzing microparticles is provided which includes a chamber with an inlet and an outlet for respectively introducing and dispensing a flowing fluid comprising microparticles, a light source for providing light through the chamber and a photometer for measuring the intensity of light transmitted through individual microparticles. The device further includes an imaging system for acquiring images of the fluid. In some cases, the device may be configured to identify and determine a quantity of the microparticles within the fluid. Consequently, a method for identifying and tracking microparticles in motion is contemplated herein. The method involves flowing a fluid comprising microparticles in laminar motion through a chamber, transmitting light through the fluid, measuring the intensities of the light transmitted through the microparticles, imaging the fluid a plurality of times and comparing at least some of the intensities of light between different images of the fluid.

  11. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers. (United States)

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D


    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  12. Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example

    Directory of Open Access Journals (Sweden)

    Benner Steven A


    Full Text Available Abstract Background Blocks of duplicated genomic DNA sequence longer than 1000 base pairs are known as low copy repeats (LCRs. Identified by their sequence similarity, LCRs are abundant in the human genome, and are interesting because they may represent recent adaptive events, or potential future adaptive opportunities within the human lineage. Sequence analysis tools are needed, however, to decide whether these interpretations are likely, whether a particular set of LCRs represents nearly neutral drift creating junk DNA, or whether the appearance of LCRs reflects assembly error. Here we investigate an LCR family containing the sulfotransferase (SULT 1A genes involved in drug metabolism, cancer, hormone regulation, and neurotransmitter biology as a first step for defining the problems that those tools must manage. Results Sequence analysis here identified a fourth sulfotransferase gene, which may be transcriptionally active, located on human chromosome 16. Four regions of genomic sequence containing the four human SULT1A paralogs defined a new LCR family. The stem hominoid SULT1A progenitor locus was identified by comparative genomics involving complete human and rodent genomes, and a draft chimpanzee genome. SULT1A expansion in hominoid genomes was followed by positive selection acting on specific protein sites. This episode of adaptive evolution appears to be responsible for the dopamine sulfonation function of some SULT enzymes. Each of the conclusions that this bioinformatic analysis generated using data that has uncertain reliability (such as that from the chimpanzee genome sequencing project has been confirmed experimentally or by a "finished" chromosome 16 assembly, both of which were published after the submission of this manuscript. Conclusion SULT1A genes expanded from one to four copies in hominoids during intra-chromosomal LCR duplications, including (apparently one after the divergence of chimpanzees and humans. Thus, LCRs may

  13. Performance of bias-correction methods for exposure measurement error using repeated measurements with and without missing data. (United States)

    Batistatou, Evridiki; McNamee, Roseanne


    It is known that measurement error leads to bias in assessing exposure effects, which can however, be corrected if independent replicates are available. For expensive replicates, two-stage (2S) studies that produce data 'missing by design', may be preferred over a single-stage (1S) study, because in the second stage, measurement of replicates is restricted to a sample of first-stage subjects. Motivated by an occupational study on the acute effect of carbon black exposure on respiratory morbidity, we compare the performance of several bias-correction methods for both designs in a simulation study: an instrumental variable method (EVROS IV) based on grouping strategies, which had been recommended especially when measurement error is large, the regression calibration and the simulation extrapolation methods. For the 2S design, either the problem of 'missing' data was ignored or the 'missing' data were imputed using multiple imputations. Both in 1S and 2S designs, in the case of small or moderate measurement error, regression calibration was shown to be the preferred approach in terms of root mean square error. For 2S designs, regression calibration as implemented by Stata software is not recommended in contrast to our implementation of this method; the 'problematic' implementation of regression calibration although substantially improved with use of multiple imputations. The EVROS IV method, under a good/fairly good grouping, outperforms the regression calibration approach in both design scenarios when exposure mismeasurement is severe. Both in 1S and 2S designs with moderate or large measurement error, simulation extrapolation severely failed to correct for bias. Copyright © 2012 John Wiley & Sons, Ltd.

  14. Infinitesimal methods of mathematical analysis

    CERN Document Server

    Pinto, J S


    This modern introduction to infinitesimal methods is a translation of the book Métodos Infinitesimais de Análise Matemática by José Sousa Pinto of the University of Aveiro, Portugal and is aimed at final year or graduate level students with a background in calculus. Surveying modern reformulations of the infinitesimal concept with a thoroughly comprehensive exposition of important and influential hyperreal numbers, the book includes previously unpublished material on the development of hyperfinite theory of Schwartz distributions and its application to generalised Fourier transforms and harmon

  15. Development of advanced MCR task analysis methods

    International Nuclear Information System (INIS)

    Na, J. C.; Park, J. H.; Lee, S. K.; Kim, J. K.; Kim, E. S.; Cho, S. B.; Kang, J. S.


    This report describes task analysis methodology for advanced HSI designs. Task analyses was performed by using procedure-based hierarchical task analysis and task decomposition methods. The results from the task analysis were recorded in a database. Using the TA results, we developed static prototype of advanced HSI and human factors engineering verification and validation methods for an evaluation of the prototype. In addition to the procedure-based task analysis methods, workload estimation based on the analysis of task performance time and analyses for the design of information structure and interaction structures will be necessary

  16. Current status of methods for shielding analysis

    International Nuclear Information System (INIS)

    Engle, W.W.


    Current methods used in shielding analysis and recent improvements in those methods are discussed. The status of methods development is discussed based on needs cited at the 1977 International Conference on Reactor Shielding. Additional areas where methods development is needed are discussed

  17. Analysis of the repeatability of the exhaust pollutants emission research results for cold and hot starts under controlled driving cycle conditions. (United States)

    Jaworski, Artur; Kuszewski, Hubert; Ustrzycki, Adam; Balawender, Krzysztof; Lejda, Kazimierz; Woś, Paweł


    Measurement of car engines exhaust pollutants emissions is very important because of their harmful effects on the environment. This article presents the assessment of repeatability of the passenger car engine exhaust pollutants emission research results obtained in the conditions of a chassis dynamometer. The research was conducted in a climate chamber, enabling the temperature conditions to be determined from - 20 to + 30 °C. The emission of CO, CH 4 , CO 2 , NO X , THC, and NMHC was subjected to the analysis. The aim of the research is to draw attention to the accuracy of the pollutant emission research results in driving cycles, and the comparison of pollutant emission results and their repeatability obtained in successive NEDC cycles under cold and hot start conditions. The results of the analysis show that, in the case of a small number of measurements, the results repeatability analysis is necessary for a proper interpretation of the pollutant emission results on the basis of the mean value. According to the authors' judgment, it is beneficial to determine the coefficient of variation for a more complete assessment of exhaust emission result repeatability obtained from a small number of measurements. This parameter is rarely presented by the authors of papers on exhaust components emission research.

  18. Fast and accurate algorithm for repeated optical trapping simulations on arbitrarily shaped particles based on boundary element method

    International Nuclear Information System (INIS)

    Xu, Kai-Jiang; Pan, Xiao-Min; Li, Ren-Xian; Sheng, Xin-Qing


    In optical trapping applications, the optical force should be investigated within a wide range of parameter space in terms of beam configuration to reach the desirable performance. A simple but reliable way of conducting the related investigation is to evaluate optical forces corresponding to all possible beam configurations. Although the optical force exerted on arbitrarily shaped particles can be well predicted by boundary element method (BEM), such investigation is time costing because it involves many repetitions of expensive computation, where the forces are calculated from the equivalent surface currents. An algorithm is proposed to alleviate the difficulty by exploiting our previously developed skeletonization framework. The proposed algorithm succeeds in reducing the number of repetitions. Since the number of skeleton beams is always much less than that of beams in question, the computation can be very efficient. The proposed algorithm is accurate because the skeletonization is accuracy controllable. - Highlights: • A fast and accurate algorithm is proposed in terms of boundary element method to reduce the number of repetitions of computing the optical forces from the equivalent currents. • The algorithm is accuracy controllable because the accuracy of the associated rank-revealing process is well-controlled. • The accelerate rate can reach over one thousand because the number of skeleton beams can be very small. • The algorithm can be applied to other methods, e.g., FE-BI.

  19. Reducing repeat pregnancies in adolescence: applying realist principles as part of a mixed-methods systematic review to explore what works, for whom, how and under what circumstances. (United States)

    Charles, Joanna M; Rycroft-Malone, Jo; Aslam, Rabeea'h; Hendry, Maggie; Pasterfield, Diana; Whitaker, Rhiannon


    Previous research has demonstrated emotional, psychological and educational harm to young mothers following unintended conceptions. The UK has one of the highest rates of pregnancies in adolescence in Western Europe with a high proportion of these being repeat pregnancies, making it a topic of interest for public health policy makers, and health and social care practitioners. As part of a wider mixed-methods systematic review, realist principles were applied to synthesise evidence about interventions aiming to reduce repeat pregnancies in adolescence. A multi-streamed, mixed-methods systematic review was conducted searching 11 major electronic databases and 9 additional databases from 1995 onwards, using key terms such as pregnancy, teen or adolescent. The principles of realist synthesis were applied to all included literature to uncover theories about what works, for whom, how and in what context. Initial theory areas were developed through evidence scoping, group discussion by the authors and stakeholder engagement to uncover context + mechanism = outcome (CMO) configurations and related narratives. The searches identified 8,664 documents initially, and 403 in repeat searches, filtering to 81 included studies, including qualitative studies, randomised controlled trials, quantitative studies and grey literature. Three CMO configurations were developed. The individual experiences of young mothers' triggered self-efficacy, notions of perceived risks, susceptibility and benefits of pregnancy, resulting in the adolescent taking control of their fertility and sexual encounters. The choice between motherhood and other goals triggered notions of motivations, resulting in the adolescent managing their expectations of motherhood and controlling their fertility and sexual encounters. Barriers and facilitators to accessing services triggered notions of connectedness and self-determination; resulting in interventions that are tailored so they are relevant to young

  20. A multi-segment foot model based on anatomically registered technical coordinate systems: method repeatability and sensitivity in pediatric planovalgus feet. (United States)

    Saraswat, Prabhav; MacWilliams, Bruce A; Davis, Roy B; D'Astous, Jacques L


    Several multisegment foot models have been proposed and some have been used to study foot pathologies. These models have been tested and validated on typically developed populations; however application of such models to feet with significant deformities presents an additional set of challenges. For the first time, in this study, a multisegment foot model is tested for repeatability in a population of children with symptomatic abnormal feet. The results from this population are compared to the same metrics collected from an age matched (8-14 years) typically developing population. The modified Shriners Hospitals for Children, Greenville (mSHCG) foot model was applied to ten typically developing children and eleven children with planovalgus feet by two clinicians. Five subjects in each group were retested by both clinicians after 4-6 weeks. Both intra-clinician and inter-clinician repeatability were evaluated using static and dynamic measures. A plaster mold method was used to quantify variability arising from marker placement error. Dynamic variability was measured by examining trial differences from the same subjects when multiple clinicians carried out the data collection multiple times. For hindfoot and forefoot angles, static and dynamic variability in both groups was found to be less than 4° and 6° respectively. The mSHCG model strategy of minimal reliance on anatomical markers for dynamic measures and inherent flexibility enabled by separate anatomical and technical coordinate systems resulted in a model equally repeatable in typically developing and planovalgus populations. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. A method for rapid similarity analysis of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Liu Na


    Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

  2. Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture (United States)

    West, Phillip B [Idaho Falls, ID; Novascone, Stephen R [Idaho Falls, ID; Wright, Jerry P [Idaho Falls, ID


    Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture are described. According to one embodiment, an earth analysis method includes engaging a device with the earth, analyzing the earth in a single substantially lineal direction using the device during the engaging, and providing information regarding a subsurface feature of the earth using the analysis.

  3. Parametric Methods for Order Tracking Analysis

    DEFF Research Database (Denmark)

    Nielsen, Jesper Kjær; Jensen, Tobias Lindstrøm


    Order tracking analysis is often used to find the critical speeds at which structural resonances are excited by a rotating machine. Typically, order tracking analysis is performed via non-parametric methods. In this report, however, we demonstrate some of the advantages of using a parametric method...

  4. Boston Type 1 Keratoprosthesis versus Repeat Donor Keratoplasty for Corneal Graft Failure: A Systematic Review and Meta-analysis. (United States)

    Ahmad, Sumayya; Mathews, Priya M; Lindsley, Kristina; Alkharashi, Majed; Hwang, Frank S; Ng, Sueko M; Aldave, Anthony J; Akpek, Esen Karamursel


    To compare repeat penetrating keratoplasty (PK) with Boston type I keratoprosthesis (KPro) implantation for full-thickness donor corneal graft failure. Previous donor graft failure is a common indication for both PK and KPro implantation. Selection of the surgical procedure is entirely dependent on the surgeon because there are no studies available for guidance. Therefore, a systematic review was undertaken to examine vision, device retention, graft clarity, and postoperative glaucoma and infection outcomes after repeat PK versus KPro implantation. Articles with data regarding repeat PK published between 1990 and 2014 were identified in PubMed, EMBASE, the Latin American and Caribbean Health Sciences Literature Database, and the Cochrane Central Register of Controlled Trials and were reviewed. Results were compared with a retrospective review of consecutive, nonrandomized, longitudinal case series of KPro implantations performed at 5 tertiary care centers in the United States. Visual acuity at 2 years was the primary outcome measure. The proportion of clear grafts in the repeat PK group, device retention in the KPro group, and the development of postoperative glaucoma and infection were secondary outcome measures. The search strategy identified 17 128 articles in the PK analysis. After screening, 26 studies (21 case series and 5 cohort studies) were included in the review. Pooled analysis of the 26 unique studies demonstrated a 42% (95% confidence interval [CI], 30%-56%) likelihood of maintaining 20/200 or better at 2 years after repeat PK, compared with an 80% (95% CI, 68%-88%) probability with KPro implantation. The probability of maintaining a clear graft at 5 years was 47% (95% CI, 40%-54%) after repeat PK, whereas the probability of retention of the KPro at 5 years was 75% (95% CI, 64%-84%). The rate of progression of glaucoma at 3 years was 25% (95% CI, 10%-44%) after repeat PK and 30% in the KPro cohort. These results demonstrate favorable outcomes of KPro

  5. Clinical oversight and the avoidance of repeat induced abortion. (United States)

    Jacovetty, Erica L; Clare, Camille A; Squire, Mary-Beatrice; Kubal, Keshar P; Liou, Sherry; Inchiosa, Mario A


    To evaluate the impact of patient counseling, demographics, and contraceptive methods on repeat induced abortion in women attending family planning clinics. A retrospective chart review of repeat induced abortions was performed. The analysis included patients with an initial induced abortion obtained between January 1, 2001, and March 31, 2014, at New York City Health + Hospitals/Metropolitan. The duration of involvement in the family planning program, the use of contraceptive interventions, and 18 patient factors were analyzed for their correlation with the incidence of repeat induced abortions per year of follow-up. A decreased rate of repeat induced abortions was associated with a longer duration of clinical oversight (r 2 =0.449, Pabortions. By determining the patient characteristics that most influence repeat induced abortion rates, providers can best choose the most efficacious method of contraception available. © 2018 International Federation of Gynecology and Obstetrics.

  6. Elective repeat cesarean delivery compared with trial of labor after a prior cesarean delivery: a propensity score analysis

    NARCIS (Netherlands)

    Kok, N.; Ruiter, L.; Lindeboom, R.; de Groot, C.; Pajkrt, E.; Mol, B. W.; Kazemier, B. M.


    To determine neonatal and short term maternal outcomes according to intentional mode of delivery following a cesarean delivery (CD). Women pregnant after CD between January 2000 and December 2007 were categorized according to whether they had an elective repeat CD (ERCD) or a Trial of Labor (TOL).

  7. Structure-Function Analysis of Cf-9, a Receptor-Like Protein with Extracytoplasmic Leucine-Rich Repeats

    NARCIS (Netherlands)

    Hoorn, van der R.A.L.; Wulff, B.B.H.; Rivas, S.; Durrant, M.C.; Ploeg, van der A.; Wit, de P.J.G.M.; Jones, J.D.G.


    The tomato (Lycopersicon pimpinellifolium) resistance protein Cf-9 belongs to a large class of plant proteins with extracytoplasmic Leu-rich repeats (eLRRs). eLRR proteins play key roles in plant defense and development, mainly as receptor-like proteins or receptor-like kinases, conferring

  8. Repeatability of visual acuity measurement. (United States)

    Raasch, T W; Bailey, I L; Bullimore, M A


    This study investigates features of visual acuity chart design and acuity testing scoring methods which affect the validity and repeatability of visual acuity measurements. Visual acuity was measured using the Sloan and British Standard letter series, and Landolt rings. Identifiability of the different letters as a function of size was estimated, and expressed in the form of frequency-of-seeing curves. These functions were then used to simulate acuity measurements with a variety of chart designs and scoring criteria. Systematic relationships exist between chart design parameters and acuity score, and acuity score repeatability. In particular, an important feature of a chart, that largely determines the repeatability of visual acuity measurement, is the amount of size change attributed to each letter. The methods used to score visual acuity performance also affect repeatability. It is possible to evaluate acuity score validity and repeatability using the statistical principles discussed here.

  9. The delayed neutron method of uranium analysis

    International Nuclear Information System (INIS)

    Wall, T.


    The technique of delayed neutron analysis (DNA) is discussed. The DNA rig installed on the MOATA reactor, the assay standards and the types of samples which have been assayed are described. Of the total sample throughput of about 55,000 units since the uranium analysis service began, some 78% has been concerned with analysis of uranium ore samples derived from mining and exploration. Delayed neutron analysis provides a high sensitivity, low cost uranium analysis method for both uranium exploration and other applications. It is particularly suitable for analysis of large batch samples and for non-destructive analysis over a wide range of matrices. 8 refs., 4 figs., 3 tabs

  10. Analysis of Dextromethorphan and Dextrorphan in Skeletal Remains Following Differential Microclimate Exposure: Comparison of Acute vs. Repeated Drug Exposure. (United States)

    Morrison, Lucas M; Unger, Kirk A; Watterson, James H


    Analysis of dextromethorphan (DXM) and its metabolite dextrorphan (DXT) in skeletal remains of rats following acute (ACU, 75 mg/kg, IP, n = 10) or three repeated (REP, 25 mg/kg, IP, n = 10, 40-min interval) doses of DXM is described. Following dosing and euthanasia, rats decomposed outdoors to skeleton in two different microclimate environments (n = 5 ACU and n = 5 REP at each site): Site A (shaded forest microenvironment) and Site B (rocky substrate exposed to direct sunlight, 600 m from Site A). Two drug-free rats at each site served as negative controls. Skeletal elements (vertebrae, ribs, pelvic girdles, femora, tibiae, skulls and scapulae) were recovered, pulverized and underwent methanolic microwave assisted extraction (MAE). Extracts were analyzed by GC-MS following clean-up by solid-phase extraction (SPE). Drug levels, expressed as mass-normalized response ratios and the ratios of DXT and DXM levels (RRDXT/RRDXM) were compared between drug exposures, microclimate sites, and across skeletal elements. DXM levels differed significantly (P < 0.05) between corresponding bone elements across exposure groups (5/7-site A; 4/7-site B), but no significant differences in DXT levels were observed between corresponding elements. RRDXT/RRDXM differed significantly (P < 0.05) between corresponding bone elements across exposure groups (6/7-site A; 5/7-site B). No significant differences were observed in levels of DXM, DXT or RRDXT/RRDXM between corresponding elements from either group between sites. When data from all bone elements was pooled, levels of DXM and RRDXT/RRDXM differed significantly between exposure groups at each site, while those of DXT did not. For both exposure groups, comparison of pooled data between sites showed no significant differences in levels of DXM, DXT or RRDXT/RRDXM. Different decomposition microclimates did not impede the discrimination of DXM exposure patterns from the analyses of DXM, DXT and RRDXT/RRDXM in bone samples. © The Author 2017

  11. Radiochemistry and nuclear methods of analysis

    International Nuclear Information System (INIS)

    Ehmann, W.D.; Vance, D.


    This book provides both the fundamentals of radiochemistry as well as specific applications of nuclear techniques to analytical chemistry. It includes such areas of application as radioimmunoassay and activation techniques using very short-lined indicator radionuclides. It emphasizes the current nuclear methods of analysis such as neutron activation PIXE, nuclear reaction analysis, Rutherford backscattering, isotope dilution analysis and others

  12. Computational methods in power system analysis

    CERN Document Server

    Idema, Reijer


    This book treats state-of-the-art computational methods for power flow studies and contingency analysis. In the first part the authors present the relevant computational methods and mathematical concepts. In the second part, power flow and contingency analysis are treated. Furthermore, traditional methods to solve such problems are compared to modern solvers, developed using the knowledge of the first part of the book. Finally, these solvers are analyzed both theoretically and experimentally, clearly showing the benefits of the modern approach.

  13. Constructing an Intelligent Patent Network Analysis Method

    Directory of Open Access Journals (Sweden)

    Chao-Chan Wu


    Full Text Available Patent network analysis, an advanced method of patent analysis, is a useful tool for technology management. This method visually displays all the relationships among the patents and enables the analysts to intuitively comprehend the overview of a set of patents in the field of the technology being studied. Although patent network analysis possesses relative advantages different from traditional methods of patent analysis, it is subject to several crucial limitations. To overcome the drawbacks of the current method, this study proposes a novel patent analysis method, called the intelligent patent network analysis method, to make a visual network with great precision. Based on artificial intelligence techniques, the proposed method provides an automated procedure for searching patent documents, extracting patent keywords, and determining the weight of each patent keyword in order to generate a sophisticated visualization of the patent network. This study proposes a detailed procedure for generating an intelligent patent network that is helpful for improving the efficiency and quality of patent analysis. Furthermore, patents in the field of Carbon Nanotube Backlight Unit (CNT-BLU were analyzed to verify the utility of the proposed method.

  14. A multi-segment foot model based on anatomically registered technical coordinate systems: method repeatability in pediatric feet. (United States)

    Saraswat, Prabhav; MacWilliams, Bruce A; Davis, Roy B


    Several multi-segment foot models to measure the motion of intrinsic joints of the foot have been reported. Use of these models in clinical decision making is limited due to lack of rigorous validation including inter-clinician, and inter-lab variability measures. A model with thoroughly quantified variability may significantly improve the confidence in the results of such foot models. This study proposes a new clinical foot model with the underlying strategy of using separate anatomic and technical marker configurations and coordinate systems. Anatomical landmark and coordinate system identification is determined during a static subject calibration. Technical markers are located at optimal sites for dynamic motion tracking. The model is comprised of the tibia and three foot segments (hindfoot, forefoot and hallux) and inter-segmental joint angles are computed in three planes. Data collection was carried out on pediatric subjects at two sites (Site 1: n=10 subjects by two clinicians and Site 2: five subjects by one clinician). A plaster mold method was used to quantify static intra-clinician and inter-clinician marker placement variability by allowing direct comparisons of marker data between sessions for each subject. Intra-clinician and inter-clinician joint angle variability were less than 4°. For dynamic walking kinematics, intra-clinician, inter-clinician and inter-laboratory variability were less than 6° for the ankle and forefoot, but slightly higher for the hallux. Inter-trial variability accounted for 2-4° of the total dynamic variability. Results indicate the proposed foot model reduces the effects of marker placement variability on computed foot kinematics during walking compared to similar measures in previous models. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Evaluation of a highly discriminating multiplex multi-locus variable-number of tandem-repeats (MLVA) analysis for Vibrio cholerae. (United States)

    Olsen, Jaran S; Aarskaug, Tone; Skogan, Gunnar; Fykse, Else Marie; Ellingsen, Anette Bauer; Blatny, Janet M


    Vibrio cholerae is the etiological agent of cholera and may be used in bioterror actions due to the easiness of its dissemination, and the public fear for acquiring the cholera disease. A simple and highly discriminating method for connecting clinical and environmental isolates of V. cholerae is needed in microbial forensics. Twelve different loci containing variable numbers of tandem-repeats (VNTRs) were evaluated in which six loci were polymorphic. Two multiplex reactions containing PCR primers targeting these six VNTRs resulted in successful DNA amplification of 142 various environmental and clinical V. cholerae isolates. The genetic distribution inside the V. cholerae strain collection was used to evaluate the discriminating power (Simpsons Diversity Index=0.99) of this new MLVA analysis, showing that the assay have a potential to differentiate between various strains, but also to identify those isolates which are collected from a common V. cholerae outbreak. This work has established a rapid and highly discriminating MLVA assay useful for track back analyses and/or forensic studies of V. cholerae infections.

  16. Text analysis methods, text analysis apparatuses, and articles of manufacture (United States)

    Whitney, Paul D; Willse, Alan R; Lopresti, Charles A; White, Amanda M


    Text analysis methods, text analysis apparatuses, and articles of manufacture are described according to some aspects. In one aspect, a text analysis method includes accessing information indicative of data content of a collection of text comprising a plurality of different topics, using a computing device, analyzing the information indicative of the data content, and using results of the analysis, identifying a presence of a new topic in the collection of text.

  17. Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for Typing Mycobacterium avium with Mycobacterial Interspersed Repetitive-Unit-VNTR and IS1245 Restriction Fragment Length Polymorphism Typing▿ †


    Inagaki, Takayuki; Nishimori, Kei; Yagi, Tetsuya; Ichikawa, Kazuya; Moriyama, Makoto; Nakagawa, Taku; Shibayama, Takami; Uchiya, Kei-ichi; Nikai, Toshiaki; Ogawa, Kenji


    Mycobacterium avium complex (MAC) infections are increasing annually in various countries, including Japan, but the route of transmission and pathophysiology of the infection remain unclear. Currently, a variable-number tandem-repeat (VNTR) typing method using the Mycobacterium avium tandem repeat (MATR) loci (MATR-VNTR) is employed in Japan for epidemiological studies using clinical isolates of M. avium. In this study, the usefulness of this MATR-VNTR typing method was compared with that of ...

  18. Nuclear analysis methods. Rudiments of radiation protection

    International Nuclear Information System (INIS)

    Roth, E.


    The nuclear analysis methods are generally used to analyse radioactive elements but they can be used also for chemical analysis, with fields such analysis and characterization of traces. The principles of radiation protection are explained (ALARA), the biological effects of ionizing radiations are given, elements and units used in radiation protection are reminded in tables. A part of this article is devoted to how to use radiation protection in a nuclear analysis laboratory. (N.C.)

  19. DNA polymorphisms in cuban varieties of avocado (persea americana mill.) as detected by inverse sequence tagged repeat (ISTR) analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, M; Fuentes, J L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Rodriguez, N N; Cueto, J [Max Planck Institut fur Zuchtungsforschung (MPIZ), Koln (Germany); Becker, D; Rohde, W [Instituto de Investigaciones en Fruticultura Tropical (IIFT). C. Habana (Cuba)


    A survey of the genetic diversity among commercial Cuban avocado varieties was initiated using ISTR analysis. ISTR markers were efficient in detecting polymorphisms among the genotypes. The obtained dissimilarities values ranged from 0.24 between var. Suardia and Hass to 1.00 between Lula and Los Moros or CHI-3 with an average dissimilarity of 0.78. A cluster analysis was performed based on dissimilarity using UPGMA as the clustering method. The efficiency of UPGMA in estimating genetic relationships between varieties was corroborated by the cophenetic correlation coefficients, which indicated that the distortion degree in the relationship of the estimated dissimilarities was minimal. Ecological groups were not adequately represented in the dendrogram. Thus, West Indians, Guatemalan and Mexican genotypes were positioned across the dendrogram. The utility of ISTR for genotype identification and assessment of genetic diversity in commercial avocado varieties is discussed.

  20. DNA polymorphisms in cuban varieties of avocado (persea americana mill.) as detected by inverse sequence tagged repeat (ISTR) analysis

    International Nuclear Information System (INIS)

    Ramirez, M; Fuentes, J. L.; Rodriguez, N.N.; Cueto, J.; Becker, D.; Rohde, W.


    A survey of the genetic diversity among commercial Cuban avocado varieties was initiated using ISTR analysis. ISTR markers were efficient in detecting polymorphisms among the genotypes. The obtained dissimilarities values ranged from 0.24 between var. Suardia and Hass to 1.00 between Lula and Los Moros or CHI-3 with an average dissimilarity of 0.78. A cluster analysis was performed based on dissimilarity using UPGMA as the clustering method. The efficiency of UPGMA in estimating genetic relationships between varieties was corroborated by the cophenetic correlation coefficients, which indicated that the distortion degree in the relationship of the estimated dissimilarities was minimal. Ecological groups were not adequately represented in the dendrogram. Thus, West Indians, Guatemalan and Mexican genotypes were positioned across the dendrogram. The utility of ISTR for genotype identification and assessment of genetic diversity in commercial avocado varieties is discussed

  1. [Rapid, simple genotyping method by the variable numbers of tandem repeats (VNTR) for Mycobacterium tuberculosis isolates in Japan--analytical procedure of JATA (12)-VNTR]. (United States)

    Maeda, Shinji; Murase, Yoshiro; Mitarai, Satoshi; Sugawara, Isamu; Kato, Seiya


    The discriminatory power of each locus in variable numbers of tandem repeats (VNTR) analyses was evaluated for development of the genotyping method of Mycobacterium tuberculosis (TB) in Japan. By using 325 TB strains collected from whole Japan and 24 mass infection cases (74 isolates), IS6110 restriction fragment length polymorphism (RFLP), spoligotyping and VNTR (35 loci) were analyzed. We excluded 4 loci (VNTRs 2163a, 3232, 3820, and 4120) and selected in top 12 loci (VNTRs 0424, 0960, 1955, 2074, 2163b, 2372, 2996, 3155, 3192, 3336, 4052, and 4156). The cluster rate of IS6110 RFLP was higher than that of 12-locus [Japan Anti-Tuberculosis Association (JATA)] VNTR. And in comparison of the discriminatory power of 12-locus JATA VNTR and that of Supply (15)-VNTR, the JATA (12)-VNTR was superior, even though less loci analyses. Therefore, this JATA (12)-VNTR could be used for TB genotyping in areas where Beijing strains are prevalent.

  2. A pretreatment method for grain size analysis of red mudstones (United States)

    Jiang, Zaixing; Liu, Li'an


    Traditional sediment disaggregation methods work well for loose mud sediments, but not for tightly cemented mudstones by ferric oxide minerals. In this paper, a new pretreatment method for analyzing the grain size of red mudstones is presented. The experimental samples are Eocene red mudstones from the Dongying Depression, Bohai Bay Basin. The red mudstones are composed mainly of clay minerals, clastic sediments and ferric oxides that make the mudstones red and tightly compacted. The procedure of the method is as follows. Firstly, samples of the red mudstones were crushed into fragments with a diameter of 0.6-0.8 mm in size; secondly, the CBD (citrate-bicarbonate-dithionite) treatment was used to remove ferric oxides so that the cementation of intra-aggregates and inter-aggregates became weakened, and then 5% dilute hydrochloric acid was added to further remove the cements; thirdly, the fragments were further ground with a rubber pestle; lastly, an ultrasonicator was used to disaggregate the samples. After the treatment, the samples could then be used for grain size analysis or for other geological analyses of sedimentary grains. Compared with other pretreatment methods for size analysis of mudstones, this proposed method is more effective and has higher repeatability.

  3. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Legionella pneumophila and Development of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿ (United States)

    Pourcel, Christine; Visca, Paolo; Afshar, Baharak; D'Arezzo, Silvia; Vergnaud, Gilles; Fry, Norman K.


    The utility of a genotypic typing assay for Legionella pneumophila was investigated. A multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) scheme using PCR and agarose gel electrophoresis is proposed based on eight minisatellite markers. Panels of well-characterized strains were examined in a multicenter analysis to validate the assay and to compare its performance to that of other genotyping assays. Excellent typeability, reproducibility, stability, and epidemiological concordance were observed. The MLVA type or profile is composed of a string of allele numbers, corresponding to the number of repeats at each VNTR locus, separated by commas, in a predetermined order. A database containing information from 99 L. pneumophila serogroup 1 strains and four strains of other serogroups and their MLVA profiles, which can be queried online, is available from PMID:17251393

  4. Safety of Repeated Yttrium-90 Radioembolization

    International Nuclear Information System (INIS)

    Lam, Marnix G. E. H.; Louie, John D.; Iagaru, Andrei H.; Goris, Michael L.; Sze, Daniel Y.


    Purpose: Repeated radioembolization (RE) treatments carry theoretically higher risk of radiation-induced hepatic injury because of the liver’s cumulative memory of previous exposure. We performed a retrospective safety analysis on patients who underwent repeated RE. Methods: From 2004 to 2011, a total of 247 patients were treated by RE. Eight patients (5 men, 3 women, age range 51–71 years) underwent repeated treatment of a targeted territory, all with resin microspheres (SIR-Spheres; Sirtex, Lane Cove, Australia). Adverse events were graded during a standardized follow-up. In addition, the correlation between the occurrence of RE-induced liver disease (REILD) and multiple variables was investigated in univariate and multivariate analyses in all 247 patients who received RE. Results: Two patients died shortly after the second treatment (at 84 and 107 days) with signs and symptoms of REILD. Both patients underwent whole liver treatment twice (cumulative doses 3.08 and 2.66 GBq). The other 6 patients demonstrated only minor toxicities after receiving cumulative doses ranging from 2.41 to 3.88 GBq. All patients experienced objective tumor responses. In the whole population, multifactorial analysis identified three risk factors associated with REILD: repeated RE (p = 0.036), baseline serum total bilirubin (p = 0.048), and baseline serum aspartate aminotransferase (p = 0.043). Repeated RE proved to be the only independent risk factor for REILD in multivariate analysis (odds ratio 9.6; p = 0.002). Additionally, the administered activity per target volume (in GBq/L) was found to be an independent risk factor for REILD, but only in whole liver treatments (p = 0.033). Conclusion: The risk of REILD appears to be elevated for repeated RE. Objective tumor responses were observed, but establishment of safety limits will require improvement in dosimetric measurement and prediction

  5. Safety of Repeated Yttrium-90 Radioembolization

    Energy Technology Data Exchange (ETDEWEB)

    Lam, Marnix G. E. H.; Louie, John D. [Stanford University School of Medicine, Division of Interventional Radiology (United States); Iagaru, Andrei H.; Goris, Michael L. [Stanford University School of Medicine, Division of Nuclear Medicine (United States); Sze, Daniel Y., E-mail: [Stanford University School of Medicine, Division of Interventional Radiology (United States)


    Purpose: Repeated radioembolization (RE) treatments carry theoretically higher risk of radiation-induced hepatic injury because of the liver's cumulative memory of previous exposure. We performed a retrospective safety analysis on patients who underwent repeated RE. Methods: From 2004 to 2011, a total of 247 patients were treated by RE. Eight patients (5 men, 3 women, age range 51-71 years) underwent repeated treatment of a targeted territory, all with resin microspheres (SIR-Spheres; Sirtex, Lane Cove, Australia). Adverse events were graded during a standardized follow-up. In addition, the correlation between the occurrence of RE-induced liver disease (REILD) and multiple variables was investigated in univariate and multivariate analyses in all 247 patients who received RE. Results: Two patients died shortly after the second treatment (at 84 and 107 days) with signs and symptoms of REILD. Both patients underwent whole liver treatment twice (cumulative doses 3.08 and 2.66 GBq). The other 6 patients demonstrated only minor toxicities after receiving cumulative doses ranging from 2.41 to 3.88 GBq. All patients experienced objective tumor responses. In the whole population, multifactorial analysis identified three risk factors associated with REILD: repeated RE (p = 0.036), baseline serum total bilirubin (p = 0.048), and baseline serum aspartate aminotransferase (p = 0.043). Repeated RE proved to be the only independent risk factor for REILD in multivariate analysis (odds ratio 9.6; p = 0.002). Additionally, the administered activity per target volume (in GBq/L) was found to be an independent risk factor for REILD, but only in whole liver treatments (p = 0.033). Conclusion: The risk of REILD appears to be elevated for repeated RE. Objective tumor responses were observed, but establishment of safety limits will require improvement in dosimetric measurement and prediction.

  6. Microlocal methods in the analysis of the boundary element method

    DEFF Research Database (Denmark)

    Pedersen, Michael


    The application of the boundary element method in numerical analysis is based upon the use of boundary integral operators stemming from multiple layer potentials. The regularity properties of these operators are vital in the development of boundary integral equations and error estimates. We show...

  7. Statistical methods for categorical data analysis

    CERN Document Server

    Powers, Daniel


    This book provides a comprehensive introduction to methods and models for categorical data analysis and their applications in social science research. Companion website also available, at

  8. Development of Ultraviolet Spectrophotometric Method for Analysis ...

    African Journals Online (AJOL)


    Method for Analysis of Lornoxicam in Solid Dosage. Forms. Sunit Kumar Sahoo ... testing. Mean recovery was 100.82 % for tablets. Low values of % RSD indicate .... Saharty E, Refaat YS, Khateeb ME. Stability-. Indicating. Spectrophotometric.

  9. Some remarks on the influence of temperature-variations, non-linearities, repeatability and ageing on modal-analysis for structural health monitoring of real bridges

    Directory of Open Access Journals (Sweden)

    Maas Stefan


    Full Text Available Structural Health Monitoring (SHM intends to identify damage by changes of characteristics as for instance the modal parameters. The eigenfrequencies, mode-shapes and damping-values are either directly used as damage indicators or the changes of derived parameters are analysed, such as e.g. flexibilities or updated finite element models. One common way is a continuous monitoring under environmental excitation forces, such as wind or traffic, i.e. the so-called output-only modal analysis. Alternatively, a forced measured external excitation in distinct time-intervals may be used for input-output modal analysis. Both methods are limited by the precision or the repeatability under real-life conditions at site. The paper will summarize several field tests of artificially step-by-step damaged bridges prior to their final demolishment and it will show the changes of eigenfrequencies due to induced artificial damage. Additionally, some results of a monitoring campaign of a healthy bridge in Luxembourg are presented. Reinforced concrete shows non-linear behaviour in the sense that modal parameters depend on the excitation force amplitude, i.e. higher forces lead often to lower eigenfrequencies than smaller forces. Furthermore, the temperature of real bridges is neither constant in space nor in time, while for instance the stiffness of asphalt is strongly dependant on it. Finally, ageing as such can also change a bridge’s stiffness and its modal parameters, e.g. because creep and shrinkage of concrete or ageing of elastomeric bearing pads influence their modulus of elasticity. These effects cannot be considered as damage, though they influence the measurement of modal parameters and hinder damage detection.

  10. New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations (United States)

    Guinard, Jérémy; Latreille, Anne; Guérin, Fabien; Poussier, Stéphane


    ABSTRACT Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to R. pseudosolanacearum phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology and population genetics of this bacterium are poorly understood. Until now, the genetic structure of the RSSC has been analyzed on the worldwide and regional scales. Emerging questions regarding evolutionary forces in RSSC adaptation to hosts now require genetic markers that are able to monitor RSSC field populations. In this study, we aimed to evaluate the multilocus variable-number tandem-repeat analysis (MLVA) approach for its ability to discriminate genetically close phylotype I strains and for population genetics studies. We developed a new MLVA scheme (MLVA-7) allowing us to genotype 580 R. pseudosolanacearum phylotype I strains extracted from susceptible and resistant hosts and from different habitats (stem, soil, and rhizosphere). Based on specificity, polymorphism, and the amplification success rate, we selected seven fast-evolving variable-number tandem-repeat (VNTR) markers. The newly developed MLVA-7 scheme showed higher discriminatory power than the previously published MLVA-13 scheme when applied to collections sampled from the same location on different dates and to collections from different locations on very small scales. Our study provides a valuable tool for fine-scale monitoring and microevolution-related study of R. pseudosolanacearum phylotype I populations. IMPORTANCE Understanding the evolutionary dynamics of adaptation of plant pathogens to new hosts or ecological niches has become a key point for the development of innovative disease management strategies, including durable resistance. Whereas the molecular mechanisms underlying virulence or pathogenicity changes have been studied thoroughly, the

  11. An introduction to numerical methods and analysis

    CERN Document Server

    Epperson, James F


    Praise for the First Edition "". . . outstandingly appealing with regard to its style, contents, considerations of requirements of practice, choice of examples, and exercises.""-Zentralblatt MATH "". . . carefully structured with many detailed worked examples.""-The Mathematical Gazette The Second Edition of the highly regarded An Introduction to Numerical Methods and Analysis provides a fully revised guide to numerical approximation. The book continues to be accessible and expertly guides readers through the many available techniques of numerical methods and analysis. An Introduction to

  12. Hypothesis analysis methods, hypothesis analysis devices, and articles of manufacture (United States)

    Sanfilippo, Antonio P [Richland, WA; Cowell, Andrew J [Kennewick, WA; Gregory, Michelle L [Richland, WA; Baddeley, Robert L [Richland, WA; Paulson, Patrick R [Pasco, WA; Tratz, Stephen C [Richland, WA; Hohimer, Ryan E [West Richland, WA


    Hypothesis analysis methods, hypothesis analysis devices, and articles of manufacture are described according to some aspects. In one aspect, a hypothesis analysis method includes providing a hypothesis, providing an indicator which at least one of supports and refutes the hypothesis, using the indicator, associating evidence with the hypothesis, weighting the association of the evidence with the hypothesis, and using the weighting, providing information regarding the accuracy of the hypothesis.

  13. Relating Actor Analysis Methods to Policy Problems

    NARCIS (Netherlands)

    Van der Lei, T.E.


    For a policy analyst the policy problem is the starting point for the policy analysis process. During this process the policy analyst structures the policy problem and makes a choice for an appropriate set of methods or techniques to analyze the problem (Goeller 1984). The methods of the policy

  14. Evaluation of the Repeatability of the Delta Q Duct Leakage Testing TechniqueIncluding Investigation of Robust Analysis Techniques and Estimates of Weather Induced Uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Dickerhoff, Darryl; Walker, Iain


    The DeltaQ test is a method of estimating the air leakage from forced air duct systems. Developed primarily for residential and small commercial applications it uses the changes in blower door test results due to forced air system operation. Previous studies established the principles behind DeltaQ testing, but raised issues of precision of the test, particularly for leaky homes on windy days. Details of the measurement technique are available in an ASTM Standard (ASTM E1554-2007). In order to ease adoption of the test method, this study answers questions regarding the uncertainty due to changing weather during the test (particularly changes in wind speed) and the applicability to low leakage systems. The first question arises because the building envelope air flows and pressures used in the DeltaQ test are influenced by weather induced pressures. Variability in wind induced pressures rather than temperature difference induced pressures dominates this effect because the wind pressures change rapidly over the time period of a test. The second question needs to answered so that DeltaQ testing can be used in programs requiring or giving credit for tight ducts (e.g., California's Building Energy Code (CEC 2005)). DeltaQ modeling biases have been previously investigated in laboratory studies where there was no weather induced changes in envelope flows and pressures. Laboratory work by Andrews (2002) and Walker et al. (2004) found biases of about 0.5% of forced air system blower flow and individual test uncertainty of about 2% of forced air system blower flow. The laboratory tests were repeated by Walker and Dickerhoff (2006 and 2008) using a new ramping technique that continuously varied envelope pressures and air flows rather than taking data at pre-selected pressure stations (as used in ASTM E1554-2003 and other previous studies). The biases and individual test uncertainties for ramping were found to be very close (less than 0.5% of air handler flow) to those

  15. Method and equipment for the analysis of gases

    International Nuclear Information System (INIS)

    Bailitis, E.


    The density of the gas is determined by the average molecular velocity. The gas and the reference gas flow at known pressure from one volume to the other through a Knudsen-flow, where for example, the pressure increase is measured. After a spontaneous change of the cross section of the Knudsen-flow the measurement is repeated and for example the density is determined from the measured values. A SIMS-Auger-vacuum chamber serves as device after the installation of two secondary valves. The tested gas is CCl 4 for example. The measurement method is also suitable for the gas analysis of coal gassing by means of the determination of the molecular weight. (RW) [de

  16. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France


    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  17. Nodal method for fast reactor analysis

    International Nuclear Information System (INIS)

    Shober, R.A.


    In this paper, a nodal method applicable to fast reactor diffusion theory analysis has been developed. This method has been shown to be accurate and efficient in comparison to highly optimized finite difference techniques. The use of an analytic solution to the diffusion equation as a means of determining accurate coupling relationships between nodes has been shown to be highly accurate and efficient in specific two-group applications, as well as in the current multigroup method

  18. At what price? A cost-effectiveness analysis comparing trial of labour after previous Caesarean versus elective repeat Caesarean delivery.

    LENUS (Irish Health Repository)

    Fawsitt, Christopher G


    Elective repeat caesarean delivery (ERCD) rates have been increasing worldwide, thus prompting obstetric discourse on the risks and benefits for the mother and infant. Yet, these increasing rates also have major economic implications for the health care system. Given the dearth of information on the cost-effectiveness related to mode of delivery, the aim of this paper was to perform an economic evaluation on the costs and short-term maternal health consequences associated with a trial of labour after one previous caesarean delivery compared with ERCD for low risk women in Ireland.

  19. Analysis of short tandem repeat (STR) polymorphisms by the powerplex 16 system and capillary electrophoresis: application to forensic practice.


    Okamoto, Osamu; Yamamoto, Yuji; Inagaki, Sachiyo; Yoshitome, Kei; ishikawa, Takaki; Imabayashi, Kiyomi; Miyaishi, Satoru; Ishizu, Hideo


    Allele and genotype frequencies for 15 short tandem repeat (STR) polymorphisms--D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA--in a Japanese population were estimated. No deviations of the observed allele frequency from Hardy-Weinberg equilibrium expectations were found for any of the systems studied. Between 2 new pentanucleotide STR loci, Penta E and Penta D, for which there is only limited data regarding the allelic di...

  20. Inelastic analysis methods for piping systems

    International Nuclear Information System (INIS)

    Boyle, J.T.; Spence, J.


    The analysis of pipework systems which operate in an environment where local inelastic strains are evident is one of the most demanding problems facing the stress analyst in the nuclear field. The spatial complexity of even the most modest system makes a detailed analysis using finite element techniques beyond the scope of current computer technology. For this reason the emphasis has been on simplified methods. It is the aim of this paper to provide a reasonably complete, state-of-the-art review of inelastic pipework analysis methods and to attempt to highlight areas where reliable information is lacking and further work is needed. (orig.)

  1. Telomerase Repeated Amplification Protocol (TRAP). (United States)

    Mender, Ilgen; Shay, Jerry W


    Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al. , 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC - counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al. , 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

  2. Excitation methods for energy dispersive analysis

    International Nuclear Information System (INIS)

    Jaklevic, J.M.


    The rapid development in recent years of energy dispersive x-ray fluorescence analysis has been based primarily on improvements in semiconductor detector x-ray spectrometers. However, the whole analysis system performance is critically dependent on the availability of optimum methods of excitation for the characteristic x rays in specimens. A number of analysis facilities based on various methods of excitation have been developed over the past few years. A discussion is given of the features of various excitation methods including charged particles, monochromatic photons, and broad-energy band photons. The effects of the excitation method on background and sensitivity are discussed from both theoretical and experimental viewpoints. Recent developments such as pulsed excitation and polarized photons are also discussed

  3. Economic analysis of human papillomavirus triage, repeat cytology, and immediate colposcopy in management of women with minor cytological abnormalities in Sweden. (United States)

    Ostensson, Ellinor; Fröberg, Maria; Hjerpe, Anders; Zethraeus, Niklas; Andersson, Sonia


    To assess the cost-effectiveness of using human papillomavirus testing (HPV triage) in the management of women with minor cytological abnormalities in Sweden. An economic analysis based on a clinical trial, complemented with data from published meta-analyses on accuracy of HPV triage. The study takes perspective of the Swedish healthcare system. The Swedish population-based cervical cancer screening program. A decision analytic model was constructed to evaluate cost-effectiveness of HPV triage compared to repeat cytology and immediate colposcopy with biopsy, stratifying by index cytology (ASCUS = atypical squamous cells of undetermined significance, and LSIL = low-grade squamous intraepithelial lesion) and age (23-60 years, cytological abnormalities. Today, immediate colposcopy with biopsy is a cost-effective alternative compared to HPV triage and repeat cytology.

  4. Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics

    Directory of Open Access Journals (Sweden)

    Janet M. Doolittle-Hall


    Full Text Available Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV, hepatitis B virus (HBV or Merkel cell polyomavirus (MCPyV. These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures.

  5. Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junin arenavirus envelope glycoprotein

    International Nuclear Information System (INIS)

    York, Joanne; Agnihothram, Sudhakar S.; Romanowski, Victor; Nunberg, Jack H.


    The G2 fusion subunit of the Junin virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. We have investigated the role of these heptad-repeat regions and, specifically, the importance of the putative interhelical a and d position sidechains by using alanine-scanning mutagenesis. All the mutant glycoproteins were expressed and transported to the cell surface. Proteolytic maturation at the subtilisin kexin isozyme-1/site-1-protease (SKI-1/S1P) cleavage site was observed in all but two of the mutants. Among the adequately cleaved mutant glycoproteins, four positions in the N-terminal region (I333, L336, L347 and L350) and two positions in the C-terminal region (R392 and W395) were shown to be important determinants of cell-cell fusion. Taken together, our results indicate that α-helical coiled-coil structures are likely critical in promoting arenavirus membrane fusion. These findings support the inclusion of the arenavirus GP-C among the Class I viral fusion proteins and suggest pharmacologic and immunologic strategies for targeting arenavirus infection and hemorrhagic fever

  6. Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR Marker Resources for Diversity Analysis of Mango (Mangifera indica L.

    Directory of Open Access Journals (Sweden)

    Natalie L. Dillon


    Full Text Available In this study, a collection of 24,840 expressed sequence tags (ESTs generated from five mango (Mangifera indica L. cDNA libraries was mined for EST-based simple sequence repeat (SSR markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

  7. A strategy for evaluating pathway analysis methods. (United States)

    Yu, Chenggang; Woo, Hyung Jun; Yu, Xueping; Oyama, Tatsuya; Wallqvist, Anders; Reifman, Jaques


    Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Furthermore, previous evaluation strategies that have focused on defining 'true answers' are unable to systematically and objectively assess PA methods under a wide range of conditions. In this work, we propose a novel strategy for evaluating PA methods independently of any gold standard, either established or assumed. The strategy involves the use of two mutually complementary metrics, recall and discrimination. Recall measures the consistency of the perturbed pathways identified by applying a particular analysis method to an original large dataset and those identified by the same method to a sub-dataset of the original dataset. In contrast, discrimination measures specificity-the degree to which the perturbed pathways identified by a particular method to a dataset from one experiment differ from those identifying by the same method to a dataset from a different experiment. We used these metrics and 24 datasets to evaluate six widely used PA methods. The results highlighted the common challenge in reliably identifying significant pathways from small datasets. Importantly, we confirmed the effectiveness of our proposed dual-metric strategy by showing that previous comparative studies corroborate the performance evaluations of the six methods obtained by our strategy. Unlike any previously proposed strategy for evaluating the performance of PA methods, our dual-metric strategy does not rely on any ground truth

  8. Instrumental methods of analysis, 7th edition

    International Nuclear Information System (INIS)

    Willard, H.H.; Merritt, L.L. Jr.; Dean, J.A.; Settle, F.A. Jr.


    The authors have prepared an organized and generally polished product. The book is fashioned to be used as a textbook for an undergraduate instrumental analysis course, a supporting textbook for graduate-level courses, and a general reference work on analytical instrumentation and techniques for professional chemists. Four major areas are emphasized: data collection and processing, spectroscopic instrumentation and methods, liquid and gas chromatographic methods, and electrochemical methods. Analytical instrumentation and methods have been updated, and a thorough citation of pertinent recent literature is included

  9. Multiple-locus variable-number tandem repeat analysis of Leptospira interrogans and Leptospira borgpetersenii isolated from small feral and wild mammals in East Asia. (United States)

    Koizumi, Nobuo; Izumiya, Hidemasa; Mu, Jung-Jung; Arent, Zbigniew; Okano, Shou; Nakajima, Chie; Suzuki, Yasuhiko; Mizutani Muto, Maki; Tanikawa, Tsutomu; Taylor, Kyle R; Komatsu, Noriyuki; Yoshimatsu, Kumiko; Thi Thu Ha, Hoang; Ohnishi, Makoto


    Leptospira spp. are the causative agents of a worldwide zoonosis, leptospirosis, maintained by various mammals. Each Leptospira serovar is frequently associated with a particular maintenance host, and recently, Leptospira genotype-host association has also been suggested to limit serovars to restricted areas. We investigated the molecular characteristics of L. interrogans and L. borgpetersenii which were isolated from small feral and wild animals in four East Asian states using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA using 11 loci was performed on 110 L. interrogans serogroups from Japan (79 strains of 5 serogroups from 3 animal species), Philippines (21; 3; 2), Taiwan (7; 2; 3), and Vietnam (3; 1; 1). A MLVA method using 4 loci for L. borgpetersenii was established and performed on 52 isolates from Japan (26; 3; 7), Philippines (13; 1; 2), and Taiwan (13; 1; 3). In L. interrogans, serogroups Autumnalis and Hebdomadis appeared more genetically diverse than serogroups Bataviae, Grippotyphosa, Icterohaemorrhagiae, Pomona, or Pyrogenes. The former serogroup strains with the exception of one Hebdomadis strain were isolated from Apodemus speciosus while all the latter serogroup strains with the exception of Grippotyphosa were isolated from Rattus norvegicus. L. borgpetersenii was isolated from at least 11 animal species while L. interrogans was isolated from five species, which might suggest a wider host range for L. borgpetersenii. Broad host preference in a single genotype was also observed, which colonized not only different species of the same genera but also multiple animal genera. This study demonstrates that there may be variability in the range of genetic diversity among different Leptospira serogroups, which may be attributed to maintenance host animals and environmental factors. Copyright © 2015. Published by Elsevier B.V.

  10. Repeatability of road pavement condition assessment based on three-dimensional analysis of linear accelerations of vehicles (United States)

    Staniek, Marcin


    The article provides a discussion concerning a tool used for road pavement condition assessment based on signals of linear accelerations recorded with high sampling frequency for typical vehicles traversing the road network under real-life road traffic conditions. Specific relationships have been established for the sake of road pavement condition assessment, including identification of road sections of poor technical condition. The data thus acquired have been verified with regard to repeatability of estimated road pavement assessment indices. The data make it possible to describe the road network status against an area in which users of the system being developed move. What proves to be crucial in the assessment process is the scope of the data set based on multiple transfers within the road network.

  11. Limitations of systemic accident analysis methods

    Directory of Open Access Journals (Sweden)

    Casandra Venera BALAN


    Full Text Available In terms of system theory, the description of complex accidents is not limited to the analysis of the sequence of events / individual conditions, but highlights nonlinear functional characteristics and frames human or technical performance in relation to normal functioning of the system, in safety conditions. Thus, the research of the system entities as a whole is no longer an abstraction of a concrete situation, but an exceeding of the theoretical limits set by analysis based on linear methods. Despite the issues outlined above, the hypothesis that there isn’t a complete method for accident analysis is supported by the nonlinearity of the considered function or restrictions, imposing a broad vision of the elements introduced in the analysis, so it can identify elements corresponding to nominal parameters or trigger factors.

  12. Application of Software Safety Analysis Methods

    International Nuclear Information System (INIS)

    Park, G. Y.; Hur, S.; Cheon, S. W.; Kim, D. H.; Lee, D. Y.; Kwon, K. C.; Lee, S. J.; Koo, Y. H.


    A fully digitalized reactor protection system, which is called the IDiPS-RPS, was developed through the KNICS project. The IDiPS-RPS has four redundant and separated channels. Each channel is mainly composed of a group of bistable processors which redundantly compare process variables with their corresponding setpoints and a group of coincidence processors that generate a final trip signal when a trip condition is satisfied. Each channel also contains a test processor called the ATIP and a display and command processor called the COM. All the functions were implemented in software. During the development of the safety software, various software safety analysis methods were applied, in parallel to the verification and validation (V and V) activities, along the software development life cycle. The software safety analysis methods employed were the software hazard and operability (Software HAZOP) study, the software fault tree analysis (Software FTA), and the software failure modes and effects analysis (Software FMEA)

  13. Spatial analysis statistics, visualization, and computational methods

    CERN Document Server

    Oyana, Tonny J


    An introductory text for the next generation of geospatial analysts and data scientists, Spatial Analysis: Statistics, Visualization, and Computational Methods focuses on the fundamentals of spatial analysis using traditional, contemporary, and computational methods. Outlining both non-spatial and spatial statistical concepts, the authors present practical applications of geospatial data tools, techniques, and strategies in geographic studies. They offer a problem-based learning (PBL) approach to spatial analysis-containing hands-on problem-sets that can be worked out in MS Excel or ArcGIS-as well as detailed illustrations and numerous case studies. The book enables readers to: Identify types and characterize non-spatial and spatial data Demonstrate their competence to explore, visualize, summarize, analyze, optimize, and clearly present statistical data and results Construct testable hypotheses that require inferential statistical analysis Process spatial data, extract explanatory variables, conduct statisti...

  14. Advanced analysis methods in particle physics

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C.; /Fermilab


    Each generation of high energy physics experiments is grander in scale than the previous - more powerful, more complex and more demanding in terms of data handling and analysis. The spectacular performance of the Tevatron and the beginning of operations of the Large Hadron Collider, have placed us at the threshold of a new era in particle physics. The discovery of the Higgs boson or another agent of electroweak symmetry breaking and evidence of new physics may be just around the corner. The greatest challenge in these pursuits is to extract the extremely rare signals, if any, from huge backgrounds arising from known physics processes. The use of advanced analysis techniques is crucial in achieving this goal. In this review, I discuss the concepts of optimal analysis, some important advanced analysis methods and a few examples. The judicious use of these advanced methods should enable new discoveries and produce results with better precision, robustness and clarity.

  15. Ocular surface sensitivity repeatability with Cochet-Bonnet esthesiometer. (United States)

    Chao, Cecilia; Stapleton, Fiona; Badarudin, Ezailina; Golebiowski, Blanka


    To determine the repeatability of ocular surface threshold measurements using the Cochet-Bonnet esthesiometer on the same day and 3 months apart. Two separate studies were conducted to determine the repeatability of ocular surface threshold measurements made on the same day (n = 20 subjects) and 3 months apart (n = 29 subjects). The Cochet-Bonnet esthesiometer was used to measure corneal and inferior conjunctival thresholds using the ascending method of limits. The pressure exerted by the Cochet-Bonnet esthesiometer was determined using an analytical balance, for both the 0.08- and 0.12-mm-diameter filaments. This calibration was then used to convert filament length measurements to pressure. Repeatability was determined using a Bland and Altman analysis. The pressure exerted at each filament length differed between the two filament diameters. The measured pressure also differed from values provided by the manufacturer. Repeatability of threshold measurements at the central cornea was shown to be good, with better repeatability for same-day measurements (coefficient of repeatability [CoR] = ±0.23 g/mm²) than for those 3 months apart (CoR = ±0.52 g/mm²). Threshold measurements at the inferior conjunctiva, in contrast, were poorly repeatable (CoR = ±12.78 g/mm²). Cochet-Bonnet esthesiometry is repeatable when performed on the central cornea on the same day and 3 months apart, but this instrument is not recommended for conjunctival threshold measurements.

  16. Review of strain buckling: analysis methods

    International Nuclear Information System (INIS)

    Moulin, D.


    This report represents an attempt to review the mechanical analysis methods reported in the literature to account for the specific behaviour that we call buckling under strain. In this report, this expression covers all buckling mechanisms in which the strains imposed play a role, whether they act alone (as in simple buckling under controlled strain), or whether they act with other loadings (primary loading, such as pressure, for example). Attention is focused on the practical problems relevant to LMFBR reactors. The components concerned are distinguished by their high slenderness ratios and by rather high thermal levels, both constant and variable with time. Conventional static buckling analysis methods are not always appropriate for the consideration of buckling under strain. New methods must therefore be developed in certain cases. It is also hoped that this review will facilitate the coding of these analytical methods to aid the constructor in his design task and to identify the areas which merit further investigation

  17. The SCA1 (Spinocerebellar ataxia type 1 and MJD (Machado-Joseph disease CAG repeats in normal individuals: segregation analysis and allele frequencies

    Directory of Open Access Journals (Sweden)

    Cláudia Emília Vieira Wiezel


    Full Text Available Spinocerebellar ataxia type 1 (SCA1 and Machado-Joseph disease (MJD/SCA3 are autosomal dominant neurodegenerative diseases caused by expansions of a CAG trinucleotide repeat in the SCA1 and MJD genes. These expanded sequences are unstable upon transmission, leading to an intergeneration increase in the number of repeats (dynamic mutation. The transmission of the CAG repeat was studied in normal mother-father-child trios, referred for paternity testing (SCA1, n = 367; MJD, n = 879. No segregation distortion was detected. The CAG allele frequencies were determined in 330 unrelated individuals (fathers from couples tested for paternity. The allele frequency distributions did not differ from those previously reported for European populations. The estimated values for the statistic parameters indicating diversity at the SCA1 locus did not differ much from those reported previously for other STRs in the Brazilian population, while those for the MJD locus were close to or higher than the maximum values of previous reports. This shows that SCA1 and MJD are highly informative loci for applications in genetic and population studies and for forensic analysis.

  18. Analysis of mixed data methods & applications

    CERN Document Server

    de Leon, Alexander R


    A comprehensive source on mixed data analysis, Analysis of Mixed Data: Methods & Applications summarizes the fundamental developments in the field. Case studies are used extensively throughout the book to illustrate interesting applications from economics, medicine and health, marketing, and genetics. Carefully edited for smooth readability and seamless transitions between chaptersAll chapters follow a common structure, with an introduction and a concluding summary, and include illustrative examples from real-life case studies in developmental toxicolog

  19. Scope-Based Method Cache Analysis

    DEFF Research Database (Denmark)

    Huber, Benedikt; Hepp, Stefan; Schoeberl, Martin


    The quest for time-predictable systems has led to the exploration of new hardware architectures that simplify analysis and reasoning in the temporal domain, while still providing competitive performance. For the instruction memory, the method cache is a conceptually attractive solution, as it req......The quest for time-predictable systems has led to the exploration of new hardware architectures that simplify analysis and reasoning in the temporal domain, while still providing competitive performance. For the instruction memory, the method cache is a conceptually attractive solution...

  20. Effect of repeated transsphenoidal surgery in recurrent or residual pituitary adenomas: A systematic review and meta-analysis (United States)

    Heringer, Lindolfo Carlos; de Oliveira, Matheus Fernandes; Rotta, José Marcus; Botelho, Ricardo Vieira


    Background: Recurrent or residual pituitary adenomas previously treated by transsphenoidal surgery are not uncommon. There are no strongly established guidelines to perform treatment of such cases. The objective of this study is to elucidate the effect of transsphenoidal reoperation in residual or recurrent pituitary adenomas. Methods: We made a systematic review of the literature to elucidate this effect through electronic search in MEDLINE/PubMed and Cochrane Central database. PRISMA statement was used as a basis for this systematic review and analysis of the risk of bias was made according to the Grading of Recommendations, Assessment, Development and Evaluation recommendations. Results: In this review, fifteen studies were finally pooled analyzed. Although remission rates (RRs) and follow-up periods varied widely, from 149 patients with growth hormone-secreting tumors the mean RR was 44.5%, from 273 patients with adrenocorticotropic hormone-secreting tumors the mean RR was 55.5% and among 173 patients with nonsecreting tumors, RR was 76.1%. There was significant higher RR in nonsecreting tumors. Mean follow-up was 32.1 months. No difference was found between microscopic and endoscopic techniques. Conclusions: A second transsphenoidal surgery is accompanied by a chance of remission in approximately half of cases with secreting tumors. In nonsecreting ones, success is higher. PMID:26958420

  1. Quantitative analysis method for ship construction quality

    Directory of Open Access Journals (Sweden)

    FU Senzong


    Full Text Available The excellent performance of a ship is assured by the accurate evaluation of its construction quality. For a long time, research into the construction quality of ships has mainly focused on qualitative analysis due to a shortage of process data, which results from limited samples, varied process types and non-standardized processes. Aiming at predicting and controlling the influence of the construction process on the construction quality of ships, this article proposes a reliability quantitative analysis flow path for the ship construction process and fuzzy calculation method. Based on the process-quality factor model proposed by the Function-Oriented Quality Control (FOQC method, we combine fuzzy mathematics with the expert grading method to deduce formulations calculating the fuzzy process reliability of the ordinal connection model, series connection model and mixed connection model. The quantitative analysis method is applied in analyzing the process reliability of a ship's shaft gear box installation, which proves the applicability and effectiveness of the method. The analysis results can be a useful reference for setting key quality inspection points and optimizing key processes.

  2. Very low frequency earthquakes (VLFEs) detected during episodic tremor and slip (ETS) events in Cascadia using a match filter method indicate repeating events (United States)

    Hutchison, A. A.; Ghosh, A.


    Very low frequency earthquakes (VLFEs) occur in transitional zones of faults, releasing seismic energy in the 0.02-0.05 Hz frequency band over a 90 s duration and typically have magntitudes within the range of Mw 3.0-4.0. VLFEs can occur down-dip of the seismogenic zone, where they can transfer stress up-dip potentially bringing the locked zone closer to a critical failure stress. VLFEs also occur up-dip of the seismogenic zone in a region along the plate interface that can rupture coseismically during large megathrust events, such as the 2011 Tohoku-Oki earthquake [Ide et al., 2011]. VLFEs were first detected in Cascadia during the 2011 episodic tremor and slip (ETS) event, occurring coincidentally with tremor [Ghosh et al., 2015]. However, during the 2014 ETS event, VLFEs were spatially and temporally asynchronous with tremor activity [Hutchison and Ghosh, 2016]. Such contrasting behaviors remind us that the mechanics behind such events remain elusive, yet they are responsible for the largest portion of the moment release during an ETS event. Here, we apply a match filter method using known VLFEs as template events to detect additional VLFEs. Using a grid-search centroid moment tensor inversion method, we invert stacks of the resulting match filter detections to ensure moment tensor solutions are similar to that of the respective template events. Our ability to successfully employ a match filter method to VLFE detection in Cascadia intrinsically indicates that these events can be repeating, implying that the same asperities are likely responsible for generating multiple VLFEs.

  3. Piping dynamic analysis by the synthesis method

    International Nuclear Information System (INIS)

    Bezler, P.; Curreri, J.R.


    Since piping systems are a frequent source of noise and vibrations, their efficient dynamic analysis is imperative. As an alternate to more conventional analyses methods, an application of the synthesis method to piping vibrations analyses is demonstrated. Specifically, the technique is illustrated by determining the normal modes and natural frequencies of a composite bend from the normal mode and natural frequency data of two component parts. A comparison of the results to those derived for the composite bend by other techniques is made

  4. Probabilistic Analysis Methods for Hybrid Ventilation

    DEFF Research Database (Denmark)

    Brohus, Henrik; Frier, Christian; Heiselberg, Per

    This paper discusses a general approach for the application of probabilistic analysis methods in the design of ventilation systems. The aims and scope of probabilistic versus deterministic methods are addressed with special emphasis on hybrid ventilation systems. A preliminary application...... of stochastic differential equations is presented comprising a general heat balance for an arbitrary number of loads and zones in a building to determine the thermal behaviour under random conditions....

  5. Repeated intravenous administration of gadobutrol does not lead to increased signal intensity on unenhanced T1-weighted images - a voxel-based whole brain analysis

    Energy Technology Data Exchange (ETDEWEB)

    Langner, Soenke; Kromrey, Marie-Luise [University Medicine Greifswald, Institute of Diagnostic Radiology and Neuroradiology, Greifswald (Germany); Kuehn, Jens-Peter [University Medicine Greifswald, Institute of Diagnostic Radiology and Neuroradiology, Greifswald (Germany); University Hospital, Carl Gustav Carus University Dresden, Institute for Radiology, Dresden (Germany); Grothe, Matthias [University Medicine Greifswald, Department of Neurology, Greifswald (Germany); Domin, Martin [University Medicine Greifswald, Functional Imaging Unit, Institute of Diagnostic Radiology and Neuroradiology, Greifswald (Germany)


    To identify a possible association between repeated intravenous administration of gadobutrol and increased signal intensity in the grey and white matter using voxel-based whole-brain analysis. In this retrospective single-centre study, 217 patients with a clinically isolated syndrome underwent baseline brain magnetic resonance imaging and at least one annual follow-up examination with intravenous administration of 0.1 mmol/kg body weight of gadobutrol. Using the ''Diffeomorphic Anatomical Registration using Exponentiated Lie algebra'' (DARTEL) normalisation process, tissue templates for grey matter (GM), white matter (WM), and cerebrospinal fluid (CSF) were calculated, as were GM-CSF and WM-CSF ratios. Voxel-based whole-brain analysis was used to calculate the signal intensity for each voxel in each data set. Paired t-test was applied to test differences to baseline MRI for significance. Voxel-based whole-brain analysis demonstrated no significant changes in signal intensity of grey and white matter after up to five gadobutrol administrations. There was no significant change in GM-CSF and grey WM-CSF ratios. Voxel-based whole-brain analysis did not demonstrate increased signal intensity of GM and WM on unenhanced T1-weighted images after repeated gadobutrol administration. The molecular structure of gadolinium-based contrast agent preparations may be an essential factor causing SI increase on unenhanced T1-weighted images. (orig.)

  6. Repeat Gamma Knife Radiosurgery for Trigeminal Neuralgia

    International Nuclear Information System (INIS)

    Aubuchon, Adam C.; Chan, Michael D.; Lovato, James F.; Balamucki, Christopher J.; Ellis, Thomas L.; Tatter, Stephen B.; McMullen, Kevin P.; Munley, Michael T.; Deguzman, Allan F.; Ekstrand, Kenneth E.; Bourland, J. Daniel; Shaw, Edward G.


    Purpose: Repeat gamma knife stereotactic radiosurgery (GKRS) for recurrent or persistent trigeminal neuralgia induces an additional response but at the expense of an increased incidence of facial numbness. The present series summarized the results of a repeat treatment series at Wake Forest University Baptist Medical Center, including a multivariate analysis of the data to identify the prognostic factors for treatment success and toxicity. Methods and Materials: Between January 1999 and December 2007, 37 patients underwent a second GKRS application because of treatment failure after a first GKRS treatment. The mean initial dose in the series was 87.3 Gy (range, 80–90). The mean retreatment dose was 84.4 Gy (range, 60–90). The dosimetric variables recorded included the dorsal root entry zone dose, pons surface dose, and dose to the distal nerve. Results: Of the 37 patients, 81% achieved a >50% pain relief response to repeat GKRS, and 57% experienced some form of trigeminal dysfunction after repeat GKRS. Two patients (5%) experienced clinically significant toxicity: one with bothersome numbness and one with corneal dryness requiring tarsorraphy. A dorsal root entry zone dose at repeat treatment of >26.6 Gy predicted for treatment success (61% vs. 32%, p = .0716). A cumulative dorsal root entry zone dose of >84.3 Gy (72% vs. 44%, p = .091) and a cumulative pons surface dose of >108.5 Gy (78% vs. 44%, p = .018) predicted for post-GKRS numbness. The presence of any post-GKRS numbness predicted for a >50% decrease in pain intensity (100% vs. 60%, p = .0015). Conclusion: Repeat GKRS is a viable treatment option for recurrent trigeminal neuralgia, although the patient assumes a greater risk of nerve dysfunction to achieve maximal pain relief.

  7. Repeat Gamma Knife Radiosurgery for Trigeminal Neuralgia

    Energy Technology Data Exchange (ETDEWEB)

    Aubuchon, Adam C., E-mail: [Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC (United States); Chan, Michael D. [Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC (United States); Lovato, James F. [Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC (United States); Balamucki, Christopher J. [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Ellis, Thomas L.; Tatter, Stephen B. [Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC (United States); McMullen, Kevin P.; Munley, Michael T.; Deguzman, Allan F.; Ekstrand, Kenneth E.; Bourland, J. Daniel; Shaw, Edward G. [Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC (United States)


    Purpose: Repeat gamma knife stereotactic radiosurgery (GKRS) for recurrent or persistent trigeminal neuralgia induces an additional response but at the expense of an increased incidence of facial numbness. The present series summarized the results of a repeat treatment series at Wake Forest University Baptist Medical Center, including a multivariate analysis of the data to identify the prognostic factors for treatment success and toxicity. Methods and Materials: Between January 1999 and December 2007, 37 patients underwent a second GKRS application because of treatment failure after a first GKRS treatment. The mean initial dose in the series was 87.3 Gy (range, 80-90). The mean retreatment dose was 84.4 Gy (range, 60-90). The dosimetric variables recorded included the dorsal root entry zone dose, pons surface dose, and dose to the distal nerve. Results: Of the 37 patients, 81% achieved a >50% pain relief response to repeat GKRS, and 57% experienced some form of trigeminal dysfunction after repeat GKRS. Two patients (5%) experienced clinically significant toxicity: one with bothersome numbness and one with corneal dryness requiring tarsorraphy. A dorsal root entry zone dose at repeat treatment of >26.6 Gy predicted for treatment success (61% vs. 32%, p = .0716). A cumulative dorsal root entry zone dose of >84.3 Gy (72% vs. 44%, p = .091) and a cumulative pons surface dose of >108.5 Gy (78% vs. 44%, p = .018) predicted for post-GKRS numbness. The presence of any post-GKRS numbness predicted for a >50% decrease in pain intensity (100% vs. 60%, p = .0015). Conclusion: Repeat GKRS is a viable treatment option for recurrent trigeminal neuralgia, although the patient assumes a greater risk of nerve dysfunction to achieve maximal pain relief.

  8. Validation of chimerism in pediatric recipients of allogeneic hematopoietic stem cell transplantation (HSCT) a comparison between two methods: real-time PCR (qPCR) vs. variable number tandem repeats PCR (VNTR PCR). (United States)

    Kletzel, Morris; Huang, Wei; Olszewski, Marie; Khan, Sana


    Post-hematopoietic stem cell transplantation (HSCT) chimerism monitoring is important to assess relapse and therapeutic intervention. The purpose of our study is to compare two methods variable number tandem repeats (VNTR) vs. quantitative real- time polymerase chain reaction (qPCR) in terms of determining chimerism. 127 (peripheral blood n=112, bone marrow n=15) samples were simultaneously tested by VNTR using APO-B, D1S80, D1S111, D17S30, gene loci SRY and ZP3 and qPCR using 34 assays (CA001-CA034) that are designed to a bi-allelic insertion/deletion (indel) polymorphism in the human genome. Samples were separated in three subsets: total WBC, T-cell and Myeloid cells. Extraction of DNA was performed then quantified. We analyzed column statistics, paired t-test and regression analysis for both methods. There was complete correlation between the two methods. The simplicity and rapidity of the test results from the qPCR method is more efficient and accurate to assess chimerism.

  9. Chemical analysis by nuclear methods. v. 2

    International Nuclear Information System (INIS)

    Alfassi, Z.B.


    'Chemical analysis by Nuclear Methods' is an effort of some renowned authors in field of nuclear chemistry and radiochemistry which is compiled by Alfassi, Z.B. and translated into Farsi version collected in two volumes. The second volume consists of the following chapters: Detecting ion recoil scattering and elastic scattering are dealt in the eleventh chapter, the twelfth chapter is devoted to nuclear reaction analysis using charged particles, X-ray emission is discussed at thirteenth chapter, the fourteenth chapter is about using ion microprobes, X-ray fluorescence analysis is discussed in the fifteenth chapter, alpha, beta and gamma ray scattering in chemical analysis are dealt in chapter sixteen, Moessbauer spectroscopy and positron annihilation are discussed in chapter seventeen and eighteen; The last two chapters are about isotope dilution analysis and radioimmunoassay

  10. Numerical methods in software and analysis

    CERN Document Server

    Rice, John R


    Numerical Methods, Software, and Analysis, Second Edition introduces science and engineering students to the methods, tools, and ideas of numerical computation. Introductory courses in numerical methods face a fundamental problem-there is too little time to learn too much. This text solves that problem by using high-quality mathematical software. In fact, the objective of the text is to present scientific problem solving using standard mathematical software. This book discusses numerous programs and software packages focusing on the IMSL library (including the PROTRAN system) and ACM Algorithm

  11. Calibration of micro-thermal analysis for the detection of glass transition temperatures and melting points: repeatability and reproducibility

    NARCIS (Netherlands)

    Fischer, H.R.


    Micro-thermal analysis (μTATM) is a technique in which thermal analysis is performed on surfaces of test specimens on a small (ca. 2×2 μm) scale. Like any thermal analysis technique, interpretation of results benefits from accurate temperature information and knowledge of the precision of the

  12. Nonlinear structural analysis using integrated force method

    Indian Academy of Sciences (India)

    A new formulation termed the Integrated Force Method (IFM) was proposed by Patnaik ... nated ``Structure (nY m)'' where (nY m) are the force and displacement degrees of ..... Patnaik S N, Yadagiri S 1976 Frequency analysis of structures.

  13. Modern methods of wine quality analysis

    Directory of Open Access Journals (Sweden)

    Галина Зуфарівна Гайда


    Full Text Available  In this paper physical-chemical and enzymatic methods of quantitative analysis of the basic wine components were reviewed. The results of own experiments were presented for the development of enzyme- and cell-based amperometric sensors on ethanol, lactate, glucose, arginine

  14. Analysis of three variable number terminal repeat loci is sufficient to characterize the deoxyribonucleic acid fingerprints of a panel of human tumor cell lines. (United States)

    Anding, Allyson L; Reiss, Tanika; Germain, Glen S


    Using primers for the MCT118, YNZ22, and COL2A1 loci in polymerase chain reaction analysis we could distinguish among the approximately 20 cell lines routinely maintained in our laboratory. We also demonstrated that the cell line NB-1691 (a neuroblastoma) and its xenograft had an identical number of repeats at two loci. Rh30 (a rhabdomyosarcoma) made resistant to rapamycin was identical to its parent line and to a subline that had reverted to sensitivity after it was cultured without rapamycin in the medium.

  15. Computerized Analysis of Verbal Fluency: Normative Data and the Effects of Repeated Testing, Simulated Malingering, and Traumatic Brain Injury.

    Directory of Open Access Journals (Sweden)

    David L Woods

    Full Text Available In verbal fluency (VF tests, subjects articulate words in a specified category during a short test period (typically 60 s. Verbal fluency tests are widely used to study language development and to evaluate memory retrieval in neuropsychiatric disorders. Performance is usually measured as the total number of correct words retrieved. Here, we describe the properties of a computerized VF (C-VF test that tallies correct words and repetitions while providing additional lexical measures of word frequency, syllable count, and typicality. In addition, the C-VF permits (1 the analysis of the rate of responding over time, and (2 the analysis of the semantic relationships between words using a new method, Explicit Semantic Analysis (ESA, as well as the established semantic clustering and switching measures developed by Troyer et al. (1997. In Experiment 1, we gathered normative data from 180 subjects ranging in age from 18 to 82 years in semantic ("animals" and phonemic (letter "F" conditions. The number of words retrieved in 90 s correlated with education and daily hours of computer-use. The rate of word production declined sharply over time during both tests. In semantic conditions, correct-word scores correlated strongly with the number of ESA and Troyer-defined semantic switches as well as with an ESA-defined semantic organization index (SOI. In phonemic conditions, ESA revealed significant semantic influences in the sequence of words retrieved. In Experiment 2, we examined the test-retest reliability of different measures across three weekly tests in 40 young subjects. Different categories were used for each semantic ("animals", "parts of the body", and "foods" and phonemic (letters "F", "A", and "S" condition. After regressing out the influences of education and computer-use, we found that correct-word z-scores in the first session did not differ from those of the subjects in Experiment 1. Word production was uniformly greater in semantic than

  16. Multiple predictor smoothing methods for sensitivity analysis

    International Nuclear Information System (INIS)

    Helton, Jon Craig; Storlie, Curtis B.


    The use of multiple predictor smoothing methods in sampling-based sensitivity analyses of complex models is investigated. Specifically, sensitivity analysis procedures based on smoothing methods employing the stepwise application of the following nonparametric regression techniques are described: (1) locally weighted regression (LOESS), (2) additive models, (3) projection pursuit regression, and (4) recursive partitioning regression. The indicated procedures are illustrated with both simple test problems and results from a performance assessment for a radioactive waste disposal facility (i.e., the Waste Isolation Pilot Plant). As shown by the example illustrations, the use of smoothing procedures based on nonparametric regression techniques can yield more informative sensitivity analysis results than can be obtained with more traditional sensitivity analysis procedures based on linear regression, rank regression or quadratic regression when nonlinear relationships between model inputs and model predictions are present

  17. Economic analysis of alternative LLW disposal methods

    International Nuclear Information System (INIS)

    Foutes, C.E.


    The Environmental Protection Agency (EPA) has evaluated the costs and benefits of alternative disposal technologies as part of its program to develop generally applicable environmental standards for the land disposal of low-level radioactive waste (LLW). Costs, population health effects and Critical Population Group (CPG) exposures resulting from alternative waste treatment and disposal methods were developed and input into the analysis. The cost-effectiveness analysis took into account a number of waste streams, hydrogeologic and climatic region settings, and waste treatment and disposal methods. Total costs of each level of a standard included costs for packaging, processing, transportation, and burial of waste. Benefits are defined in terms of reductions in the general population health risk (expected fatal cancers and genetic effects) evaluated over 10,000 years. A cost-effectiveness ratio, was calculated for each alternative standard. This paper describes the alternatives considered and preliminary results of the cost-effectiveness analysis

  18. Reliability and risk analysis methods research plan

    International Nuclear Information System (INIS)


    This document presents a plan for reliability and risk analysis methods research to be performed mainly by the Reactor Risk Branch (RRB), Division of Risk Analysis and Operations (DRAO), Office of Nuclear Regulatory Research. It includes those activities of other DRAO branches which are very closely related to those of the RRB. Related or interfacing programs of other divisions, offices and organizations are merely indicated. The primary use of this document is envisioned as an NRC working document, covering about a 3-year period, to foster better coordination in reliability and risk analysis methods development between the offices of Nuclear Regulatory Research and Nuclear Reactor Regulation. It will also serve as an information source for contractors and others to more clearly understand the objectives, needs, programmatic activities and interfaces together with the overall logical structure of the program

  19. Multiple predictor smoothing methods for sensitivity analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Helton, Jon Craig; Storlie, Curtis B.


    The use of multiple predictor smoothing methods in sampling-based sensitivity analyses of complex models is investigated. Specifically, sensitivity analysis procedures based on smoothing methods employing the stepwise application of the following nonparametric regression techniques are described: (1) locally weighted regression (LOESS), (2) additive models, (3) projection pursuit regression, and (4) recursive partitioning regression. The indicated procedures are illustrated with both simple test problems and results from a performance assessment for a radioactive waste disposal facility (i.e., the Waste Isolation Pilot Plant). As shown by the example illustrations, the use of smoothing procedures based on nonparametric regression techniques can yield more informative sensitivity analysis results than can be obtained with more traditional sensitivity analysis procedures based on linear regression, rank regression or quadratic regression when nonlinear relationships between model inputs and model predictions are present.

  20. Spectroscopic Chemical Analysis Methods and Apparatus (United States)

    Hug, William F. (Inventor); Reid, Ray D. (Inventor); Bhartia, Rohit (Inventor); Lane, Arthur L. (Inventor)


    Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted along with photoluminescence spectroscopy (i.e. fluorescence and/or phosphorescence spectroscopy) to provide high levels of sensitivity and specificity in the same instrument.

  1. Computational methods for nuclear criticality safety analysis

    International Nuclear Information System (INIS)

    Maragni, M.G.


    Nuclear criticality safety analyses require the utilization of methods which have been tested and verified against benchmarks results. In this work, criticality calculations based on the KENO-IV and MCNP codes are studied aiming the qualification of these methods at the IPEN-CNEN/SP and COPESP. The utilization of variance reduction techniques is important to reduce the computer execution time, and several of them are analysed. As practical example of the above methods, a criticality safety analysis for the storage tubes for irradiated fuel elements from the IEA-R1 research has been carried out. This analysis showed that the MCNP code is more adequate for problems with complex geometries, and the KENO-IV code shows conservative results when it is not used the generalized geometry option. (author)

  2. Improving resolution of public health surveillance for human Salmonella enterica serovar Typhimurium infection: 3 years of prospective multiple-locus variable-number tandem-repeat analysis (MLVA

    Directory of Open Access Journals (Sweden)

    Sintchenko Vitali


    Full Text Available Abstract Background Prospective typing of Salmonella enterica serovar Typhimurium (STM by multiple-locus variable-number tandem-repeat analysis (MLVA can assist in identifying clusters of STM cases that might otherwise have gone unrecognised, as well as sources of sporadic and outbreak cases. This paper describes the dynamics of human STM infection in a prospective study of STM MLVA typing for public health surveillance. Methods During a three-year period between August 2007 and September 2010 all confirmed STM isolates were fingerprinted using MLVA as part of the New South Wales (NSW state public health surveillance program. Results A total of 4,920 STM isolates were typed and a subset of 4,377 human isolates was included in the analysis. The STM spectrum was dominated by a small number of phage types, including DT170 (44.6% of all isolates, DT135 (13.9%, DT9 (10.8%, DT44 (4.5% and DT126 (4.5%. There was a difference in the discriminatory power of MLVA types within endemic phage types: Simpson's index of diversity ranged from 0.109 and 0.113 for DTs 9 and 135 to 0.172 and 0.269 for DTs 170 and 44, respectively. 66 distinct STM clusters were observed ranging in size from 5 to 180 cases and in duration from 4 weeks to 25 weeks. 43 clusters had novel MLVA types and 23 represented recurrences of previously recorded MLVA types. The diversity of the STM population remained relatively constant over time. The gradual increase in the number of STM cases during the study was not related to significant changes in the number of clusters or their size. 667 different MLVA types or patterns were observed. Conclusions Prospective MLVA typing of STM allows the detection of community outbreaks and demonstrates the sustained level of STM diversity that accompanies the increasing incidence of human STM infections. The monitoring of novel and persistent MLVA types offers a new benchmark for STM surveillance. A part of this study was presented at the MEEGID

  3. The relationship of sugar to population-level diabetes prevalence: an econometric analysis of repeated cross-sectional data. (United States)

    Basu, Sanjay; Yoffe, Paula; Hills, Nancy; Lustig, Robert H


    While experimental and observational studies suggest that sugar intake is associated with the development of type 2 diabetes, independent of its role in obesity, it is unclear whether alterations in sugar intake can account for differences in diabetes prevalence among overall populations. Using econometric models of repeated cross-sectional data on diabetes and nutritional components of food from 175 countries, we found that every 150 kcal/person/day increase in sugar availability (about one can of soda/day) was associated with increased diabetes prevalence by 1.1% (p <0.001) after testing for potential selection biases and controlling for other food types (including fibers, meats, fruits, oils, cereals), total calories, overweight and obesity, period-effects, and several socioeconomic variables such as aging, urbanization and income. No other food types yielded significant individual associations with diabetes prevalence after controlling for obesity and other confounders. The impact of sugar on diabetes was independent of sedentary behavior and alcohol use, and the effect was modified but not confounded by obesity or overweight. Duration and degree of sugar exposure correlated significantly with diabetes prevalence in a dose-dependent manner, while declines in sugar exposure correlated with significant subsequent declines in diabetes rates independently of other socioeconomic, dietary and obesity prevalence changes. Differences in sugar availability statistically explain variations in diabetes prevalence rates at a population level that are not explained by physical activity, overweight or obesity.

  4. Serological analysis of human anti-human antibody responses in colon cancer patients treated with repeated doses of humanized monoclonal antibody A33. (United States)

    Ritter, G; Cohen, L S; Williams, C; Richards, E C; Old, L J; Welt, S


    Mouse monoclonal antibody A33 (mAb A33) recognizes a M(r) 43,000 cell surface glycoprotein (designated A33) expressed in human colonic epithelium and colon cancer but absent from most other normal tissues. In patients, mAb A33 localizes with high specificity to colon cancer and is retained for up to 6 weeks in the cancer but cleared rapidly from normal colon (5-6 days). As a carrier of (125)I or (131)I, mAb A33 has shown antitumor activity. Induction of strong human anti-mouse antibody (immunoglobulin; HAMA) responses in patients, however, limits the use of the murine mAb A33 to very few injections. A humanized version of this antibody (huAb A33) has been prepared for Phase I and II clinical studies in patients with colon cancer. In those studies, immunogenicity of huAb A33 has been monitored using a novel, highly sensitive BIACORE method, which allows measurement of human anti-human antibodies (HAHAs) without the use of secondary reagents. We found that 63% (26 of 41) of the patients treated with repeated doses of huAb A33 developed HAHAs against a conformational antigenic determinant located in the V(L) and V(H) regions of huAb A33. Detailed serological analysis showed two distinct types of HAHAs. HAHA of type I (49% of patients) was characterized by an early onset with peak HAHA levels after 2 weeks of treatment, which declined with ongoing huAb A33 treatment. HAHA of type II (17% of patients) was characterized by a typically later onset of HAHA than in type I and by progressively increasing HAHA levels with each subsequent huAb A33 administration. Colon cancer patients with type I HAHAs did not develop infusion-related adverse events. In contrast, HAHA of type II was indicative of infusion-related adverse events. By using this new method, we were able to distinguish these two types of HAHAs in patients while on antibody treatment, allowing patients to be removed from study prior to the onset of severe infusion-related adverse events.

  5. PIXE - a new method for elemental analysis

    International Nuclear Information System (INIS)

    Johansson, S.A.E.


    With elemental analysis we mean the determination of which chemical elements are present in a sample and of their concentration. This is an old and important problem in chemistry. The earliest methods were purely chemical and many such methods are still used. However, various methods based on physical principles have gradually become more and more important. One such method is neutron activation. When the sample is bombarded with neutrons it becomes radioactive and the various radioactive isotopes produced can be identified by the radiation they emit. From the measured intensity of the radiation one can calculate how much of a certain element that is present in the sample. Another possibility is to study the light emitted when the sample is excited in various ways. A spectroscopic investigation of the light can identify the chemical elements and allows also a determination of their concentration in the sample. In the same way, if a sample can be brought to emit X-rays, this radiation is also characteristic for the elements present and can be used to determine the elemental concentration. One such X-ray method which has been developed recently is PIXE. The name is an acronym for Particle Induced X-ray Emission and indicates the principle of the method. Particles in this context means heavy, charged particles such as protons and a-particles of rather high energy. Hence, in PIXE-analysis the sample is irradiated in the beam of an accelerator and the emitted X-rays are studied. (author)

  6. Dependability Analysis Methods For Configurable Software

    International Nuclear Information System (INIS)

    Dahll, Gustav; Pulkkinen, Urho


    Configurable software systems are systems which are built up by standard software components in the same way as a hardware system is built up by standard hardware components. Such systems are often used in the control of NPPs, also in safety related applications. A reliability analysis of such systems is therefore necessary. This report discusses what configurable software is, and what is particular with respect to reliability assessment of such software. Two very commonly used techniques in traditional reliability analysis, viz. failure mode, effect and criticality analysis (FMECA) and fault tree analysis are investigated. A real example is used to illustrate the discussed methods. Various aspects relevant to the assessment of the software reliability in such systems are discussed. Finally some models for quantitative software reliability assessment applicable on configurable software systems are described. (author)

  7. Demographic and practice factors predicting repeated non-attendance in primary care: a national retrospective cohort analysis

    Directory of Open Access Journals (Sweden)

    David A Ellis, PhD


    Full Text Available Summary: Background: Addressing the causes of low engagement in health care is a prerequisite for reducing health inequalities. People who miss multiple appointments are an under-researched group who might have substantial unmet health needs. Individual-level patterns of missed general practice appointments might thus provide a risk marker for vulnerability and poor health outcomes. We sought to ascertain the contributions of patient and practice factors to the likelihood of missing general practice appointments. Methods: For this national retrospective cohort analysis, we extracted UK National Health Service general practice data that were routinely collected across Scotland between Sept 5, 2013, and Sept 5, 2016. We calculated the per-patient number of missed appointments from individual appointments and investigated the risk of missing a general practice appointment using a negative binomial model offset by number of appointments made. We then analysed the effect of patient-level factors (including age, sex, and socioeconomic status and practice-level factors (including appointment availability and geographical location on the risk of missing appointments. Findings: The full dataset included information from 909 073 patients, of whom 550 083 were included in the analysis after processing. We observed that 104 461 (19·0% patients missed more than two appointments in the 3 year study period. After controlling for the number of appointments made, patterns of non-attendance could be differentiated, with patients who were aged 16–30 years (relative risk ratio [RRR] 1·21, 95% CI 1·19–1·23 or older than 90 years (2·20, 2·09–2·29, and of low socioeconomic status (Scottish Index of Multiple Deprivation decile 1: RRR 2·27, 2·22–2·31 significantly more likely to miss multiple appointments. Men missed fewer appointments overall than women, but were somewhat more likely to miss appointments

  8. Multivariate linear models and repeated measurements revisited

    DEFF Research Database (Denmark)

    Dalgaard, Peter


    Methods for generalized analysis of variance based on multivariate normal theory have been known for many years. In a repeated measurements context, it is most often of interest to consider transformed responses, typically within-subject contrasts or averages. Efficiency considerations leads...... to sphericity assumptions, use of F tests and the Greenhouse-Geisser and Huynh-Feldt adjustments to compensate for deviations from sphericity. During a recent implementation of such methods in the R language, the general structure of such transformations was reconsidered, leading to a flexible specification...

  9. Cask crush pad analysis using detailed and simplified analysis methods

    International Nuclear Information System (INIS)

    Uldrich, E.D.; Hawkes, B.D.


    A crush pad has been designed and analyzed to absorb the kinetic energy of a hypothetically dropped spent nuclear fuel shipping cask into a 44-ft. deep cask unloading pool at the Fluorinel and Storage Facility (FAST). This facility, located at the Idaho Chemical Processing Plant (ICPP) at the Idaho national Engineering and Environmental Laboratory (INEEL), is a US Department of Energy site. The basis for this study is an analysis by Uldrich and Hawkes. The purpose of this analysis was to evaluate various hypothetical cask drop orientations to ensure that the crush pad design was adequate and the cask deceleration at impact was less than 100 g. It is demonstrated herein that a large spent fuel shipping cask, when dropped onto a foam crush pad, can be analyzed by either hand methods or by sophisticated dynamic finite element analysis using computer codes such as ABAQUS. Results from the two methods are compared to evaluate accuracy of the simplified hand analysis approach

  10. Advanced Analysis Methods in High Energy Physics

    Energy Technology Data Exchange (ETDEWEB)

    Pushpalatha C. Bhat


    During the coming decade, high energy physics experiments at the Fermilab Tevatron and around the globe will use very sophisticated equipment to record unprecedented amounts of data in the hope of making major discoveries that may unravel some of Nature's deepest mysteries. The discovery of the Higgs boson and signals of new physics may be around the corner. The use of advanced analysis techniques will be crucial in achieving these goals. The author discusses some of the novel methods of analysis that could prove to be particularly valuable for finding evidence of any new physics, for improving precision measurements and for exploring parameter spaces of theoretical models.

  11. Spatial Analysis Methods of Road Traffic Collisions

    DEFF Research Database (Denmark)

    Loo, Becky P. Y.; Anderson, Tessa Kate

    Spatial Analysis Methods of Road Traffic Collisions centers on the geographical nature of road crashes, and uses spatial methods to provide a greater understanding of the patterns and processes that cause them. Written by internationally known experts in the field of transport geography, the book...... outlines the key issues in identifying hazardous road locations (HRLs), considers current approaches used for reducing and preventing road traffic collisions, and outlines a strategy for improved road safety. The book covers spatial accuracy, validation, and other statistical issues, as well as link...

  12. Simple gas chromatographic method for furfural analysis. (United States)

    Gaspar, Elvira M S M; Lopes, João F


    A new, simple, gas chromatographic method was developed for the direct analysis of 5-hydroxymethylfurfural (5-HMF), 2-furfural (2-F) and 5-methylfurfural (5-MF) in liquid and water soluble foods, using direct immersion SPME coupled to GC-FID and/or GC-TOF-MS. The fiber (DVB/CAR/PDMS) conditions were optimized: pH effect, temperature, adsorption and desorption times. The method is simple and accurate (RSDfurfurals will contribute to characterise and quantify their presence in the human diet.

  13. Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity

    Directory of Open Access Journals (Sweden)

    Norio Matsushima


    Full Text Available The NOD-like receptors (NLRs and Toll-like receptors (TLRs are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids. The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side.

  14. Neutron activation analysis: principle and methods

    International Nuclear Information System (INIS)

    Reddy, A.V.R.; Acharya, R.


    Neutron activation analysis (NAA) is a powerful isotope specific nuclear analytical technique for simultaneous determination of elemental composition of major, minor and trace elements in diverse matrices. The technique is capable of yielding high analytical sensitivity and low detection limits (ppm to ppb). Due to high penetration power of neutrons and gamma rays, NAA experiences negligible matrix effects in the samples of different origins. Depending on the sample matrix and element of interest NAA technique is used non-destructively, known as instrumental neutron activation analysis (INAA), or through chemical NAA methods. The present article describes principle of NAA, different methods and gives a overview some applications in the fields like environment, biology, geology, material sciences, nuclear technology and forensic sciences. (author)

  15. Digital dream analysis: a revised method. (United States)

    Bulkeley, Kelly


    This article demonstrates the use of a digital word search method designed to provide greater accuracy, objectivity, and speed in the study of dreams. A revised template of 40 word search categories, built into the website of the Sleep and Dream Database (SDDb), is applied to four "classic" sets of dreams: The male and female "Norm" dreams of Hall and Van de Castle (1966), the "Engine Man" dreams discussed by Hobson (1988), and the "Barb Sanders Baseline 250" dreams examined by Domhoff (2003). A word search analysis of these original dream reports shows that a digital approach can accurately identify many of the same distinctive patterns of content found by previous investigators using much more laborious and time-consuming methods. The results of this study emphasize the compatibility of word search technologies with traditional approaches to dream content analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Numerical methods and analysis of multiscale problems

    CERN Document Server

    Madureira, Alexandre L


    This book is about numerical modeling of multiscale problems, and introduces several asymptotic analysis and numerical techniques which are necessary for a proper approximation of equations that depend on different physical scales. Aimed at advanced undergraduate and graduate students in mathematics, engineering and physics – or researchers seeking a no-nonsense approach –, it discusses examples in their simplest possible settings, removing mathematical hurdles that might hinder a clear understanding of the methods. The problems considered are given by singular perturbed reaction advection diffusion equations in one and two-dimensional domains, partial differential equations in domains with rough boundaries, and equations with oscillatory coefficients. This work shows how asymptotic analysis can be used to develop and analyze models and numerical methods that are robust and work well for a wide range of parameters.

  17. Qualitative data analysis a methods sourcebook

    CERN Document Server

    Miles, Matthew B; Saldana, Johnny


    The Third Edition of Miles & Huberman's classic research methods text is updated and streamlined by Johnny SaldaNa, author of The Coding Manual for Qualitative Researchers. Several of the data display strategies from previous editions are now presented in re-envisioned and reorganized formats to enhance reader accessibility and comprehension. The Third Edition's presentation of the fundamentals of research design and data management is followed by five distinct methods of analysis: exploring, describing, ordering, explaining, and predicting. Miles and Huberman's original research studies are profiled and accompanied with new examples from SaldaNa's recent qualitative work. The book's most celebrated chapter, "Drawing and Verifying Conclusions," is retained and revised, and the chapter on report writing has been greatly expanded, and is now called "Writing About Qualitative Research." Comprehensive and authoritative, Qualitative Data Analysis has been elegantly revised for a new generation of qualitative r...

  18. An exergy method for compressor performance analysis

    Energy Technology Data Exchange (ETDEWEB)

    McGovern, J A; Harte, S [Trinity Coll., Dublin (Ireland)


    An exergy method for compressor performance analysis is presented. The purpose of this is to identify and quantify defects in the use of a compressor`s shaft power. This information can be used as the basis for compressor design improvements. The defects are attributed to friction, irreversible heat transfer, fluid throttling, and irreversible fluid mixing. They are described, on a common basis, as exergy destruction rates and their locations are identified. The method can be used with any type of positive displacement compressor. It is most readily applied where a detailed computer simulation program is available for the compressor. An analysis of an open reciprocating refrigeration compressor that used R12 refrigerant is given as an example. The results that are presented consist of graphs of the instantaneous rates of exergy destruction according to the mechanisms involved, a pie chart of the breakdown of the average shaft power wastage by mechanism, and a pie chart with a breakdown by location. (author)

  19. Methods for genetic linkage analysis using trisomies.


    Feingold, E; Lamb, N E; Sherman, S L


    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of "susceptibility" ...

  20. Machine Learning Methods for Production Cases Analysis (United States)

    Mokrova, Nataliya V.; Mokrov, Alexander M.; Safonova, Alexandra V.; Vishnyakov, Igor V.


    Approach to analysis of events occurring during the production process were proposed. Described machine learning system is able to solve classification tasks related to production control and hazard identification at an early stage. Descriptors of the internal production network data were used for training and testing of applied models. k-Nearest Neighbors and Random forest methods were used to illustrate and analyze proposed solution. The quality of the developed classifiers was estimated using standard statistical metrics, such as precision, recall and accuracy.

  1. Safety relief valve alternate analysis method

    International Nuclear Information System (INIS)

    Adams, R.H.; Javid, A.; Khatua, T.P.


    An experimental test program was started in the United States in 1976 to define and quantify Safety Relief Valve (SRV) phenomena in General Electric Mark I Suppression Chambers. The testing considered several discharged devices and was used to correlate SRV load prediction models. The program was funded by utilities with Mark I containments and has resulted in a detailed SRV load definition as a portion of the Mark I containment program Load Definition Report (LDR). The (USNRC) has reviewed and approved the LDR SRV load definition. In addition, the USNRC has permitted calibration of structural models used for predicting torus response to SRV loads. Model calibration is subject to confirmatory in-plant testing. The SRV methodology given in the LDR requires that transient dynamic pressures be applied to a torus structural model that includes a fluid added mass matrix. Preliminary evaluations of torus response have indicated order of magnitude conservatisms, with respect to test results, which could result in unrealistic containment modifications. In addition, structural response trends observed in full-scale tests between cold pipe, first valve actuation and hot pipe, subsequent valve actuation conditions have not been duplicated using current analysis methods. It was suggested by others that an energy approach using current fluid models be utilized to define loads. An alternate SRV analysis method is defined to correct suppression chamber structural response to a level that permits economical but conservative design. Simple analogs are developed for the purpose of correcting the analytical response obtained from LDR analysis methods. Analogs evaluated considered forced vibration and free vibration structural response. The corrected response correlated well with in-plant test response. The correlation of the analytical model at test conditions permits application of the alternate analysis method at design conditions. (orig./HP)

  2. Analysis and comparison of biometric methods


    Zatloukal, Filip


    The thesis deals with biometrics and biometric systems and the possibility to use these systems in the enterprise. Aim of this study is an analysis and description of selected types of biometric identification methods and their advantages and shortcomings. The work is divided into two parts. The first part is theoretical, describes the basic concepts of biometrics, biometric identification criteria, currently used identification systems, the ways of biometric systems use, performance measurem...

  3. Statistical trend analysis methods for temporal phenomena

    International Nuclear Information System (INIS)

    Lehtinen, E.; Pulkkinen, U.; Poern, K.


    We consider point events occurring in a random way in time. In many applications the pattern of occurrence is of intrinsic interest as indicating a trend or some other systematic feature in the rate of occurrence. The purpose of this report is to survey briefly different statistical trend analysis methods and illustrate their applicability to temporal phenomena in particular. The trend testing of point events is usually seen as the testing of the hypotheses concerning the intensity of the occurrence of events. When the intensity function is parametrized, the testing of trend is a typical parametric testing problem. In industrial applications the operational experience generally does not suggest any specified model and method in advance. Therefore, and particularly, if the Poisson process assumption is very questionable, it is desirable to apply tests that are valid for a wide variety of possible processes. The alternative approach for trend testing is to use some non-parametric procedure. In this report we have presented four non-parametric tests: The Cox-Stuart test, the Wilcoxon signed ranks test, the Mann test, and the exponential ordered scores test. In addition to the classical parametric and non-parametric approaches we have also considered the Bayesian trend analysis. First we discuss a Bayesian model, which is based on a power law intensity model. The Bayesian statistical inferences are based on the analysis of the posterior distribution of the trend parameters, and the probability of trend is immediately seen from these distributions. We applied some of the methods discussed in an example case. It should be noted, that this report is a feasibility study rather than a scientific evaluation of statistical methods, and the examples can only be seen as demonstrations of the methods

  4. Statistical trend analysis methods for temporal phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Lehtinen, E.; Pulkkinen, U. [VTT Automation, (Finland); Poern, K. [Poern Consulting, Nykoeping (Sweden)


    We consider point events occurring in a random way in time. In many applications the pattern of occurrence is of intrinsic interest as indicating a trend or some other systematic feature in the rate of occurrence. The purpose of this report is to survey briefly different statistical trend analysis methods and illustrate their applicability to temporal phenomena in particular. The trend testing of point events is usually seen as the testing of the hypotheses concerning the intensity of the occurrence of events. When the intensity function is parametrized, the testing of trend is a typical parametric testing problem. In industrial applications the operational experience generally does not suggest any specified model and method in advance. Therefore, and particularly, if the Poisson process assumption is very questionable, it is desirable to apply tests that are valid for a wide variety of possible processes. The alternative approach for trend testing is to use some non-parametric procedure. In this report we have presented four non-parametric tests: The Cox-Stuart test, the Wilcoxon signed ranks test, the Mann test, and the exponential ordered scores test. In addition to the classical parametric and non-parametric approaches we have also considered the Bayesian trend analysis. First we discuss a Bayesian model, which is based on a power law intensity model. The Bayesian statistical inferences are based on the analysis of the posterior distribution of the trend parameters, and the probability of trend is immediately seen from these distributions. We applied some of the methods discussed in an example case. It should be noted, that this report is a feasibility study rather than a scientific evaluation of statistical methods, and the examples can only be seen as demonstrations of the methods. 14 refs, 10 figs.

  5. Analysis Method for Integrating Components of Product

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jun Ho [Inzest Co. Ltd, Seoul (Korea, Republic of); Lee, Kun Sang [Kookmin Univ., Seoul (Korea, Republic of)


    This paper presents some of the methods used to incorporate the parts constituting a product. A new relation function concept and its structure are introduced to analyze the relationships of component parts. This relation function has three types of information, which can be used to establish a relation function structure. The relation function structure of the analysis criteria was established to analyze and present the data. The priority components determined by the analysis criteria can be integrated. The analysis criteria were divided based on their number and orientation, as well as their direct or indirect characteristic feature. This paper presents a design algorithm for component integration. This algorithm was applied to actual products, and the components inside the product were integrated. Therefore, the proposed algorithm was used to conduct research to improve the brake discs for bicycles. As a result, an improved product similar to the related function structure was actually created.

  6. Analysis Method for Integrating Components of Product

    International Nuclear Information System (INIS)

    Choi, Jun Ho; Lee, Kun Sang


    This paper presents some of the methods used to incorporate the parts constituting a product. A new relation function concept and its structure are introduced to analyze the relationships of component parts. This relation function has three types of information, which can be used to establish a relation function structure. The relation function structure of the analysis criteria was established to analyze and present the data. The priority components determined by the analysis criteria can be integrated. The analysis criteria were divided based on their number and orientation, as well as their direct or indirect characteristic feature. This paper presents a design algorithm for component integration. This algorithm was applied to actual products, and the components inside the product were integrated. Therefore, the proposed algorithm was used to conduct research to improve the brake discs for bicycles. As a result, an improved product similar to the related function structure was actually created.

  7. Probabilistic methods in fire-risk analysis

    International Nuclear Information System (INIS)

    Brandyberry, M.D.


    The first part of this work outlines a method for assessing the frequency of ignition of a consumer product in a building and shows how the method would be used in an example scenario utilizing upholstered furniture as the product and radiant auxiliary heating devices (electric heaters, wood stoves) as the ignition source. Deterministic thermal models of the heat-transport processes are coupled with parameter uncertainty analysis of the models and with a probabilistic analysis of the events involved in a typical scenario. This leads to a distribution for the frequency of ignition for the product. In second part, fire-risk analysis as currently used in nuclear plants is outlines along with a discussion of the relevant uncertainties. The use of the computer code COMPBRN is discussed for use in the fire-growth analysis along with the use of response-surface methodology to quantify uncertainties in the code's use. Generalized response surfaces are developed for temperature versus time for a cable tray, as well as a surface for the hot gas layer temperature and depth for a room of arbitrary geometry within a typical nuclear power plant compartment. These surfaces are then used to simulate the cable tray damage time in a compartment fire experiment


    Directory of Open Access Journals (Sweden)



    Full Text Available ABSTRACT Repeatability analysis has been used to study traits in several crops, assisting in the definition of the minimum number needed to evaluate genotypes more efficiently and with less time and resource consumption. So far, however, no repeatability studies on cactus pear have been found in the literature. The objective of this study was to determine the coefficient of repeatability for cactus pear fruits traits and the minimum number of evaluations (fruit that can provide acceptable accuracy for the prediction of the true value. The experiment was conducted at the Federal Institute of Bahia/Campus Guanambi, with 150 fruits collected from three municipalities in the state of Bahia. The coefficients of repeatability were estimated by the methods of analysis of variance, principal components based on the covariance (PCCV and correlation (PCC matrices, and structural analysis based on the correlation matrix (SA. The analysis of variance showed that, except for fruit diameter, the effect of the production site (municipality was significant for all traits evaluated. The PCCV method was proven the most suitable for studying the repeatability of quality traits of cactus pear fruits. Seven fruits were required to determine, with 90% confidence, the traits length, diameter, fruit firmness, skin thickness, number of seeds, fruit mass, bark mass, pulp mass, pH, titratable acidity, soluble solids, SS/AT ratio, and pulp yield.

  9. An unconventional method of quantitative microstructural analysis

    International Nuclear Information System (INIS)

    Rastani, M.


    The experiment described here introduces a simple methodology which could be used to replace the time-consuming and expensive conventional methods of metallographic and quantitative analysis of thermal treatment effect on microstructure. The method is ideal for the microstructural evaluation of tungsten filaments and other wire samples such as copper wire which can be conveniently coiled. Ten such samples were heat treated by ohmic resistance at temperatures which were expected to span the recrystallization range. After treatment, the samples were evaluated in the elastic recovery test. The normalized elastic recovery factor was defined in terms of these deflections. Experimentally it has shown that elastic recovery factor depends on the degree of recrystallization. In other words this factor is used to determine the fraction of unrecrystallized material. Because the elastic recovery method examines the whole filament rather than just one section through the filament as in metallographical method, it more accurately measures the degree of recrystallization. The method also takes a considerably shorter time and cost compared to the conventional method

  10. Homotopy analysis method for neutron diffusion calculations

    International Nuclear Information System (INIS)

    Cavdar, S.


    The Homotopy Analysis Method (HAM), proposed in 1992 by Shi Jun Liao and has been developed since then, is based on a fundamental concept in differential geometry and topology, the homotopy. It has proved useful for problems involving algebraic, linear/non-linear, ordinary/partial differential and differential-integral equations being an analytic, recursive method that provides a series sum solution. It has the advantage of offering a certain freedom for the choice of its arguments such as the initial guess, the auxiliary linear operator and the convergence control parameter, and it allows us to effectively control the rate and region of convergence of the series solution. HAM is applied for the fixed source neutron diffusion equation in this work, which is a part of our research motivated by the question of whether methods for solving the neutron diffusion equation that yield straightforward expressions but able to provide a solution of reasonable accuracy exist such that we could avoid analytic methods that are widely used but either fail to solve the problem or provide solutions through many intricate expressions that are likely to contain mistakes or numerical methods that require powerful computational resources and advanced programming skills due to their very nature or intricate mathematical fundamentals. Fourier basis are employed for expressing the initial guess due to the structure of the problem and its boundary conditions. We present the results in comparison with other widely used methods of Adomian Decomposition and Variable Separation.

  11. Detector Simulation: Data Treatment and Analysis Methods

    CERN Document Server

    Apostolakis, J


    Detector Simulation in 'Data Treatment and Analysis Methods', part of 'Landolt-Börnstein - Group I Elementary Particles, Nuclei and Atoms: Numerical Data and Functional Relationships in Science and Technology, Volume 21B1: Detectors for Particles and Radiation. Part 1: Principles and Methods'. This document is part of Part 1 'Principles and Methods' of Subvolume B 'Detectors for Particles and Radiation' of Volume 21 'Elementary Particles' of Landolt-Börnstein - Group I 'Elementary Particles, Nuclei and Atoms'. It contains the Section '4.1 Detector Simulation' of Chapter '4 Data Treatment and Analysis Methods' with the content: 4.1 Detector Simulation 4.1.1 Overview of simulation Uses of detector simulation 4.1.2 Stages and types of simulation Tools for event generation and detector simulation Level of simulation and computation time Radiation effects and background studies 4.1.3 Components of detector simulation Geometry modeling External fields Intro...

  12. Data Analysis Methods for Library Marketing (United States)

    Minami, Toshiro; Kim, Eunja

    Our society is rapidly changing to information society, where the needs and requests of the people on information access are different widely from person to person. Library's mission is to provide its users, or patrons, with the most appropriate information. Libraries have to know the profiles of their patrons, in order to achieve such a role. The aim of library marketing is to develop methods based on the library data, such as circulation records, book catalogs, book-usage data, and others. In this paper we discuss the methodology and imporatnce of library marketing at the beginning. Then we demonstrate its usefulness through some examples of analysis methods applied to the circulation records in Kyushu University and Guacheon Library, and some implication that obtained as the results of these methods. Our research is a big beginning towards the future when library marketing is an unavoidable tool.

  13. Multiple-locus variant-repeat assay (MLVA) is a useful tool for molecular epidemiologic analysis of Streptococcus agalactiae strains causing bovine mastitis. (United States)

    Radtke, Andreas; Bruheim, Torkjel; Afset, Jan Egil; Bergh, Kåre


    Group B streptococci (GBS) were considered a major cause of mastitis in cattle until preventive measures succeeded in controlling the disease in the 1970s and 1980s. During the last 5-6 years an increasing number of cases have been observed in some Scandinavian countries. A total of 187 GBS isolates from mastitis cases were collected from 119 animals in 34 Norwegian farms in the period from April 2007 to November 2010. 133 (71%) of the isolates were from farms with automated milking systems. The strains underwent typing of capsular polysaccharides (CPS) and surface proteins, and were analyzed by multi-locus variable repeat assay (MLVA) to investigate the epidemiological relationship of strains within and between farms. The GBS strains were differentiated into 12 types by CPS and surface protein analysis, with CPS types V (54%) and IV (34%) predominating. MLVA was superior to CPS and protein typing for strain differentiation, resolving the 187 strains into 37 types. In 29 of 34 farms all GBS strains had identical MLVA profiles specific for each farm. However, in one farm represented with 48 isolates, four MLVA variants with differences in one repeat locus were observed during the almost 3-year long collection period. Similar variations were observed at four other farms. This might reflect the stability of repeat loci under in vivo conditions. Farms with automated milking systems were overrepresented in this material. In conclusion, the five-loci MLVA allowed rapid high-resolution genotyping of the bovine GBS strains within and between farms. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Development of QSAR models using artificial neural network analysis for risk assessment of repeated-dose, reproductive, and developmental toxicities of cosmetic ingredients. (United States)

    Hisaki, Tomoka; Aiba Née Kaneko, Maki; Yamaguchi, Masahiko; Sasa, Hitoshi; Kouzuki, Hirokazu


    Use of laboratory animals for systemic toxicity testing is subject to strong ethical and regulatory constraints, but few alternatives are yet available. One possible approach to predict systemic toxicity of chemicals in the absence of experimental data is quantitative structure-activity relationship (QSAR) analysis. Here, we present QSAR models for prediction of maximum "no observed effect level" (NOEL) for repeated-dose, developmental and reproductive toxicities. NOEL values of 421 chemicals for repeated-dose toxicity, 315 for reproductive toxicity, and 156 for developmental toxicity were collected from Japan Existing Chemical Data Base (JECDB). Descriptors to predict toxicity were selected based on molecular orbital (MO) calculations, and QSAR models employing multiple independent descriptors as the input layer of an artificial neural network (ANN) were constructed to predict NOEL values. Robustness of the models was indicated by the root-mean-square (RMS) errors after 10-fold cross-validation (0.529 for repeated-dose, 0.508 for reproductive, and 0.558 for developmental toxicity). Evaluation of the models in terms of the percentages of predicted NOELs falling within factors of 2, 5 and 10 of the in-vivo-determined NOELs suggested that the model is applicable to both general chemicals and the subset of chemicals listed in International Nomenclature of Cosmetic Ingredients (INCI). Our results indicate that ANN models using in silico parameters have useful predictive performance, and should contribute to integrated risk assessment of systemic toxicity using a weight-of-evidence approach. Availability of predicted NOELs will allow calculation of the margin of safety, as recommended by the Scientific Committee on Consumer Safety (SCCS).

  15. Toxicological characteristics of petroleum products repeated exposure

    Directory of Open Access Journals (Sweden)

    V.M. Rubin


    Full Text Available Abstract. The ability of petroleum products to initiate cumulative effects was assessed in experimental intragastric admission to male albino rats for one month. The analysis of skin-resorptive effects was performed using "test-tube" method on the skin of rats’ tails. It has been established that petroleum products can penetrate the intact skin and, with repeated admission, cause a general toxic effect. There were reductions bodyweights, the negative effect on the function of the kidneys and liver, changes of hematological parameters, as well as activation of the antioksidatnoy system. Repeated intragastric administration does not lead to the death of the animals testifying to the lack of accumulation capacity for petroleum products at the level of functional mortal effects, the cumulation coefficient being > 5.1. Negative impact on urinary function and hepatobiliary system, changes in hematological parameters and activation of the «lipid peroxidation – antioksidant defense» were observed.

  16. Phosphorus analysis in milk samples by neutron activation analysis method

    International Nuclear Information System (INIS)

    Oliveira, R.M. de; Cunha, I.I.L.


    The determination of phosphorus in milk samples by instrumental thermal neutron activation analysis is described. The procedure involves a short irradiation in a nuclear reactor and measurement of the beta radiation emitted by phosphorus - 32 after a suitable decay period. The sources of error were studied and the established method was applied to standard reference materials of known phosphorus content. (author)

  17. Association Analysis of Simple Sequence Repeat (SSR Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb..

    Directory of Open Access Journals (Sweden)

    Yanhong Lou

    Full Text Available Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia, were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR markers. The panel displayed significant variation in spike count per plant (SCP and spike weight (SW. However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single

  18. MO-DE-207B-11: Reliability of PET/CT Radiomics Features in Functional and Morphological Components of NSCLC Lesions: A Repeatability Analysis in a Prospective Multicenter Cohort

    Energy Technology Data Exchange (ETDEWEB)

    Desseroit, M [INSERM, LaTIM UMR 1101, Brest (France); EE DACTIM, CHU de Poitiers, Poitiers (France); Tixier, F; Cheze Le Rest, C [EE DACTIM, CHU de Poitiers, Poitiers (France); Majdoub, M; Visvikis, D; Hatt, M [INSERM, LaTIM UMR 1101, Brest (France); Weber, W [Memorial Sloan Kettering Cancer Center, New-york, NY (United States); Siegel, B [Washington University School of Medicine, St Louis, MO (United States)


    Purpose: The goal of this study was to evaluate the repeatability of radiomics features (intensity, shape and heterogeneity) in both PET and low-dose CT components of test-retest FDG-PET/CT images in a prospective multicenter cohort of 74 NSCLC patients from ACRIN 6678 and a similar Merck trial. Methods: Seventy-four patients with stage III-IV NCSLC were prospectively included. The primary tumor and up to 3 additional lesions per patient were analyzed. The Fuzzy Locally Adaptive Bayesian algorithm was used to automatically delineate metabolically active volume (MAV) in PET. The 3D SlicerTM software was exploited to delineate anatomical volumes (AV) in CT. Ten intensity first-order features, as well as 26 textural features and four 3D shape descriptors were calculated from tumour volumes in both modalities. The repeatability of each metric was assessed by Bland-Altman analysis. Results: One hundred and five lesions (primary tumors and nodal or distant metastases) were delineated and characterized. The MAV and AV determination had a repeatability of −1.4±11.0% and −1.2±18.7% respectively. Several shape and heterogeneity features were found to be highly or moderately repeatable (e.g., sphericity, co-occurrence entropy or intensity size-zone matrix zone percentage), whereas others were confirmed as unreliable with much higher variability (more than twice that of the corresponding volume determination). Conclusion: Our results in this large multicenter cohort with more than 100 measurements confirm the PET findings in previous studies (with <30 lesions). In addition, our study is the first to explore the repeatability of radiomics features in the low-dose CT component of PET/CT acquisitions (previous studies considered dosimetry CT, CE-CT or CBCT). Several features were identified as reliable in both PET and CT components and could be used to build prognostic models. This work has received a French government support granted to the CominLabs excellence laboratory

  19. Coordination in continuously repeated games

    NARCIS (Netherlands)

    Weeren, A.J.T.M.; Schumacher, J.M.; Engwerda, J.C.


    In this paper we propose a model to describe the effectiveness of coordination in a continuously repeated two-player game. We study how the choice of a decision rule by a coordinator affects the strategic behavior of the players, resulting in more or less cooperation. Our model requires the analysis

  20. Discontinuous Patterns of Cigarette Smoking From Ages 18 to 50 in the United States: A Repeated-Measures Latent Class Analysis. (United States)

    Terry-McElrath, Yvonne M; O'Malley, Patrick M; Johnston, Lloyd D


    Effective cigarette smoking prevention and intervention programming is enhanced by accurate understanding of developmental smoking pathways across the life span. This study investigated within-person patterns of cigarette smoking from ages 18 to 50 among a US national sample of high school graduates, focusing on identifying ages of particular importance for smoking involvement change. Using data from approximately 15,000 individuals participating in the longitudinal Monitoring the Future study, trichotomous measures of past 30-day smoking obtained at 11 time points were modeled using repeated-measures latent class analyses. Sex differences in latent class structure and membership were examined. Twelve latent classes were identified: three characterized by consistent smoking patterns across age (no smoking; smoking developing effective smoking prevention and intervention programming. This study examined cigarette smoking among a national longitudinal US sample of high school graduates from ages 18 to 50 and identified distinct latent classes characterized by patterns of movement between no cigarette use, light-to-moderate smoking, and the conventional definition of heavy smoking at 11 time points via repeated-measures latent class analysis. Membership probabilities for each smoking class were estimated, and critical ages of susceptibility to change in smoking behaviors were identified. © The Author 2017. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail:

  1. The Utility of Repeat Culture in Fungal Corneal Ulcer Management: A Secondary Analysis of the MUTT-I Randomized Clinical Trial. (United States)

    Ray, Kathryn J; Lalitha, Prajna; Prajna, N Venkatesh; Rajaraman, Revathi; Krishnan, Tiruvengada; Srinivasan, Muthiah; Ryg, Peter; McLeod, Stephen; Acharya, Nisha R; Lietman, Thomas M; Rose-Nussbaumer, Jennifer


    To determine whether patients who had a positive repeated culture was predictive of worse clinical outcome than those who achieved microbiological cure at 6 days in the Mycotic Ulcer Treatment Trial I (MUTT-I). Secondary analysis from a multicenter, double-masked, randomized clinical trial. setting: Multiple hospital sites of the Aravind Eye Care System, India. Patients with culture-positive filamentous fungal ulcers and visual acuity of 20/40 to 20/400 reexamined 6 days after initiation of treatment. Corneal scraping and cultures were obtained from study participants at day 6 after enrollment. We assessed 3-month best spectacle-corrected visual acuity (BSCVA), 3-month infiltrate/scar size, corneal perforation, and re-epithelialization rates stratified by culture positivity at day 6. Of the 323 patients with smear-positive ulcers enrolled in MUTT-I, 299 (92.6%) were scraped and cultured 6 days after enrollment. Repeat culture positivity was 31% (92/299). Among patients who tested positive at enrollment, those with positive 6-day cultures had significantly worse 3-month BSCVA (0.39 logMAR; 95% confidence interval [CI]: 0.24-0.44; P cure on culture is a predictor of clinical response to treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter pittii and Development of an Optimized Multiple-Locus VNTR Analysis Typing Scheme. (United States)

    Hu, Yuan; Li, Bo Qing; Jin, Da Zhi; He, Li Hua; Tao, Xiao Xia; Zhang, Jian Zhong


    To develop a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Acinetobacter pittii typing. Polymorphic VNTRs were searched by Tandem Repeats Finder. The distribution and polymorphism of each VNTR locus were analyzed in all the A. pittii genomes deposited in the NCBI genome database by BLAST and were evaluated with a collection of 20 well-characterized clinical A. pittii strains and one reference strain. The MLVA assay was compared with pulsed-field gel electrophoresis (PFGE) for discriminating A. pittii isolates. Ten VNTR loci were identified upon bioinformatic screening of A. pittii genomes, but only five of them showed full amplifiability and good polymorphism. Therefore, an MLVA assay composed of five VNTR loci was developed. The typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. Compared with PFGE, the new optimized MLVA typing scheme provided the same and even greater discrimination. Compared with PFGE, MLVA typing is a faster and more standardized alternative for studying the genetic relatedness of A. pittii isolates in disease surveillance and outbreak investigation. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  3. Methods of charged-particle activation analysis

    International Nuclear Information System (INIS)

    Chaudhri, M. Anwar; Chaudhri, M. Nasir; Jabbar, Q.; Nadeem, Q.


    The accuracy of Chaudhri's method for charged-particle activation analysis published in J. Radioanal. Chem. (1977) v. 37 p. 243 has been further demonstrated by extensive calculations. The nuclear reactions 12 C(d,n) 13 N, 63 Cu( 3 He,p) 65 Zn, 107 Ag(α,n) 110 In and 208 Pb(d,p) 209 Pb, the cross sections of which were easily available, have been examined for the detection of 12 C, 63 Cu, 107 Ag and 208 Pb, respectively, in matrices of Cu, Zr and Pb, at the bombarding energies of 4 - 22 MeV. The 'standard' is assumed to be in a carbon matrix. It has been clearly demonstrated that Chaudhri's method, which makes the charged particle activation analysis as simple as neutron activation analysis, provides results which are almost identical to, or only about 1-2 % different, from the results obtained using the full 'Activity Equation' involving solving complex integrals. It is valid even when the difference in the average atomic weights of matrices of the standard and the sample is large. (author)

  4. Development and analysis of finite volume methods

    International Nuclear Information System (INIS)

    Omnes, P.


    This document is a synthesis of a set of works concerning the development and the analysis of finite volume methods used for the numerical approximation of partial differential equations (PDEs) stemming from physics. In the first part, the document deals with co-localized Godunov type schemes for the Maxwell and wave equations, with a study on the loss of precision of this scheme at low Mach number. In the second part, discrete differential operators are built on fairly general, in particular very distorted or nonconforming, bidimensional meshes. These operators are used to approach the solutions of PDEs modelling diffusion, electro and magneto-statics and electromagnetism by the discrete duality finite volume method (DDFV) on staggered meshes. The third part presents the numerical analysis and some a priori as well as a posteriori error estimations for the discretization of the Laplace equation by the DDFV scheme. The last part is devoted to the order of convergence in the L2 norm of the finite volume approximation of the solution of the Laplace equation in one dimension and on meshes with orthogonality properties in two dimensions. Necessary and sufficient conditions, relatively to the mesh geometry and to the regularity of the data, are provided that ensure the second-order convergence of the method. (author)

  5. Creep analysis by the path function method

    International Nuclear Information System (INIS)

    Akin, J.E.; Pardue, R.M.


    The finite element method has become a common analysis procedure for the creep analysis of structures. The most recent programs are designed to handle a general class of material properties and are able to calculate elastic, plastic, and creep components of strain under general loading histories. The constant stress approach is too crude a model to accurately represent the actual behaviour of the stress for large time steps. The true path of a point in the effective stress-effective strain (sigmasup(e)-epsilonsup(c)) plane is often one in which the slope is rapidly changing. Thus the stress level quickly moves away from the initial stress level and then gradually approaches the final one. The result is that the assumed constant stress level quickly becomes inaccurate. What is required is a better method of approximation of the true path in the sigmasup(e)-epsilonsup(c) space. The method described here is called the path function approach because it employs an assumed function to estimate the motion of points in the sigmasup(e)-epsilonsup(c) space. (Auth.)

  6. Earthquake Hazard Analysis Methods: A Review (United States)

    Sari, A. M.; Fakhrurrozi, A.


    One of natural disasters that have significantly impacted on risks and damage is an earthquake. World countries such as China, Japan, and Indonesia are countries located on the active movement of continental plates with more frequent earthquake occurrence compared to other countries. Several methods of earthquake hazard analysis have been done, for example by analyzing seismic zone and earthquake hazard micro-zonation, by using Neo-Deterministic Seismic Hazard Analysis (N-DSHA) method, and by using Remote Sensing. In its application, it is necessary to review the effectiveness of each technique in advance. Considering the efficiency of time and the accuracy of data, remote sensing is used as a reference to the assess earthquake hazard accurately and quickly as it only takes a limited time required in the right decision-making shortly after the disaster. Exposed areas and possibly vulnerable areas due to earthquake hazards can be easily analyzed using remote sensing. Technological developments in remote sensing such as GeoEye-1 provide added value and excellence in the use of remote sensing as one of the methods in the assessment of earthquake risk and damage. Furthermore, the use of this technique is expected to be considered in designing policies for disaster management in particular and can reduce the risk of natural disasters such as earthquakes in Indonesia.

  7. The leucine-rich repeat structure. (United States)

    Bella, J; Hindle, K L; McEwan, P A; Lovell, S C


    The leucine-rich repeat is a widespread structural motif of 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucines. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. Thousands of protein sequences containing leucine-rich repeats have been identified by automatic annotation methods. Three-dimensional structures of leucine-rich repeat domains determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. As the essential structural principles become well established, the leucine-rich repeat architecture is emerging as an attractive framework for structural prediction and protein engineering. This review presents an update of the current understanding of leucine-rich repeat structure at the primary, secondary, tertiary and quaternary levels and discusses specific examples from recently determined three-dimensional structures.

  8. Sensitivity analysis of the Two Geometry Method

    International Nuclear Information System (INIS)

    Wichers, V.A.


    The Two Geometry Method (TGM) was designed specifically for the verification of the uranium enrichment of low enriched UF 6 gas in the presence of uranium deposits on the pipe walls. Complications can arise if the TGM is applied under extreme conditions, such as deposits larger than several times the gas activity, small pipe diameters less than 40 mm and low pressures less than 150 Pa. This report presents a comprehensive sensitivity analysis of the TGM. The impact of the various sources of uncertainty on the performance of the method is discussed. The application to a practical case is based on worst case conditions with regards to the measurement conditions, and on realistic conditions with respect to the false alarm probability and the non detection probability. Monte Carlo calculations were used to evaluate the sensitivity for sources of uncertainty which are experimentally inaccessible. (orig.)

  9. Blood proteins analysis by Raman spectroscopy method (United States)

    Artemyev, D. N.; Bratchenko, I. A.; Khristoforova, Yu. A.; Lykina, A. A.; Myakinin, O. O.; Kuzmina, T. P.; Davydkin, I. L.; Zakharov, V. P.


    This work is devoted to study the possibility of plasma proteins (albumin, globulins) concentration measurement using Raman spectroscopy setup. The blood plasma and whole blood were studied in this research. The obtained Raman spectra showed significant variation of intensities of certain spectral bands 940, 1005, 1330, 1450 and 1650 cm-1 for different protein fractions. Partial least squares regression analysis was used for determination of correlation coefficients. We have shown that the proposed method represents the structure and biochemical composition of major blood proteins.

  10. Moessbauer lineshape analysis by the DISPA method

    International Nuclear Information System (INIS)

    Miglierini, M.; Sitek, J.


    To evaluate the Moessbauer spectral parameters and hence, the structural and magnetic properties the lineshape should be known. A plot of dispersion versus absorption (DISPA plot) for a pure Lorentzian gives a perfect circle. Directions and magnitudes of DISPA distortions from this reference circle point out the kind of line-broadening mechanism observed. A possibility of the application of the DISPA technique in the Moessbauer lineshape analysis is dealt with in this paper. The method is verified on Moessbauer spectra of sodium nitroprusside, natural iron, and stainless steel. The lineshape of an amorphous metallic alloy Fe 40 Ni 40 B 20 is studied by means of the DISPA plots. (author)

  11. Electromagnetic compatibility methods, analysis, circuits, and measurement

    CERN Document Server

    Weston, David A


    Revised, updated, and expanded, Electromagnetic Compatibility: Methods, Analysis, Circuits, and Measurement, Third Edition provides comprehensive practical coverage of the design, problem solving, and testing of electromagnetic compatibility (EMC) in electrical and electronic equipment and systems. This new edition provides novel information on theory, applications, evaluations, electromagnetic computational programs, and prediction techniques available. With sixty-nine schematics providing examples for circuit level electromagnetic interference (EMI) hardening and cost effective EMI problem solving, this book also includes 1130 illustrations and tables. Including extensive data on components and their correct implementation, the myths, misapplication, misconceptions, and fallacies that are common when discussing EMC/EMI will also be addressed and corrected.

  12. Method and apparatus for simultaneous spectroelectrochemical analysis (United States)

    Chatterjee, Sayandev; Bryan, Samuel A; Schroll, Cynthia A; Heineman, William R


    An apparatus and method of simultaneous spectroelectrochemical analysis is disclosed. A transparent surface is provided. An analyte solution on the transparent surface is contacted with a working electrode and at least one other electrode. Light from a light source is focused on either a surface of the working electrode or the analyte solution. The light reflected from either the surface of the working electrode or the analyte solution is detected. The potential of the working electrode is adjusted, and spectroscopic changes of the analyte solution that occur with changes in thermodynamic potentials are monitored.

  13. A multiple-locus variable-number tandem repeat analysis (MLVA) of Listeria monocytogenes isolated from Norwegian salmon-processing factories and from listeriosis patients. (United States)

    Lunestad, B T; Truong, T T T; Lindstedt, B-A


    The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

  14. Coloured Petri Nets: Basic Concepts, Analysis Methods and Practical Use. Vol. 2, Analysis Methods

    DEFF Research Database (Denmark)

    Jensen, Kurt

    ideas behind the analysis methods are described as well as the mathematics on which they are based and also how the methods are supported by computer tools. Some parts of the volume are theoretical while others are application oriented. The purpose of the volume is to teach the reader how to use......This three-volume work presents a coherent description of the theoretical and practical aspects of coloured Petri nets (CP-nets). The second volume contains a detailed presentation of the analysis methods for CP-nets. They allow the modeller to investigate dynamic properties of CP-nets. The main...... the formal analysis methods, which does not require a deep understanding of the underlying mathematical theory....

  15. Economic analysis of alternative LLW disposal methods

    International Nuclear Information System (INIS)

    Foutes, C.E.; Queenan, C.J. III


    The Environmental Protection Agency (EPA) has evaluated the costs and benefits of alternative disposal technologies as part of its program to develop generally applicable environmental standards for the land disposal of low-level radioactive waste (LLW). Costs, population health effects and Critical Population Group (CPG) exposures resulting from alternative waste treatment and disposal methods were evaluated both in absolute terms and also relative to a base case (current practice). Incremental costs of the standard included costs for packaging, processing, transportation, and burial of waste. Benefits are defined in terms of reductions in the general population health risk (expected fatal cancers and genetic effects) evaluated over 10,000 years. A cost-effectiveness ratio, defined as the incremental cost per avoided health effect, was calculated for each alternative standard. The cost-effectiveness analysis took into account a number of waste streams, hydrogeologic and climatic region settings, and waste treatment and disposal methods. This paper describes the alternatives considered and preliminary results of the cost-effectiveness analysis. 15 references, 7 figures, 3 tables

  16. Analysis of methods. [information systems evolution environment (United States)

    Mayer, Richard J. (Editor); Ackley, Keith A.; Wells, M. Sue; Mayer, Paula S. D.; Blinn, Thomas M.; Decker, Louis P.; Toland, Joel A.; Crump, J. Wesley; Menzel, Christopher P.; Bodenmiller, Charles A.


    Information is one of an organization's most important assets. For this reason the development and maintenance of an integrated information system environment is one of the most important functions within a large organization. The Integrated Information Systems Evolution Environment (IISEE) project has as one of its primary goals a computerized solution to the difficulties involved in the development of integrated information systems. To develop such an environment a thorough understanding of the enterprise's information needs and requirements is of paramount importance. This document is the current release of the research performed by the Integrated Development Support Environment (IDSE) Research Team in support of the IISEE project. Research indicates that an integral part of any information system environment would be multiple modeling methods to support the management of the organization's information. Automated tool support for these methods is necessary to facilitate their use in an integrated environment. An integrated environment makes it necessary to maintain an integrated database which contains the different kinds of models developed under the various methodologies. In addition, to speed the process of development of models, a procedure or technique is needed to allow automatic translation from one methodology's representation to another while maintaining the integrity of both. The purpose for the analysis of the modeling methods included in this document is to examine these methods with the goal being to include them in an integrated development support environment. To accomplish this and to develop a method for allowing intra-methodology and inter-methodology model element reuse, a thorough understanding of multiple modeling methodologies is necessary. Currently the IDSE Research Team is investigating the family of Integrated Computer Aided Manufacturing (ICAM) DEFinition (IDEF) languages IDEF(0), IDEF(1), and IDEF(1x), as well as ENALIM, Entity

  17. Application of pulse spectro- zonal luminescent method for the rapid method of material analysis

    International Nuclear Information System (INIS)

    Lisitsin, V.M.; Oleshko, V.I.; Yakovlev, A.N.


    Full text: The scope of luminescent methods of the analysis covers enough a big around of substances as the luminescence can be excited in overwhelming majority of nonmetals. Analytical opportunities of luminescent methods can be essentially expanded by use of pulse excitation and registration of spectra of a luminescence with the time resolved methods. The most perspective method is to use pulses of high-current electron beams with the nanosecond duration for excitation from the following reasons: excitation is carried out ionizing, deeply enough by a penetrating radiation; the pulse of radiation has high capacity, up to 10 8 W, but energy no more than 1 J; the pulse of radiation has the nanosecond duration. Electrons with energy in 300-400 keV will penetrate on depth into some tenth shares of mm, i.e. they create volumetric excitation of a sample. Therefore the luminescence raised by an electronic beam has the information about volumetric properties of substance. High density of excitation allow to find out and study the centers (defects) having a small yield of a luminescence, to analyze the weakly luminescent objects. Occurrence of the new effects is possible useful to analyze of materials. There is an opportunity of reception of the information from change of spectral structure of a luminescence during the time after the ending of a pulse of excitation and kinetic characteristics of attenuation of luminescence. The matter is the energy of radiation is absorbed mainly by a matrix, then electronic excitations one is transferred the centers of a luminescence (defects) of a lattice. Therefore during the time after creation electronic excitations the spectrum of a luminescence can repeatedly change, transferring the information on the centers (defects) which are the most effective radiators at present time. Hence, the study of change of spectra of radiation during the time allows providing an additional way of discrimination of the information on the centers of a

  18. X-ray analysis of the effect of the 5-HT3 receptor antagonist granisetron on gastrointestinal motility in rats repeatedly treated with the antitumoral drug cisplatin. (United States)

    Vera, Gema; López-Pérez, Ana Esther; Martínez-Villaluenga, María; Cabezos, Pablo Antonio; Abalo, Raquel


    Cancer chemotherapy is associated with the development of numerous adverse effects, including nausea, emesis and other alterations in gastrointestinal (GI) motility. The administration of 5-HT3 receptor antagonists has provided a clinical advance in the treatment of chemotherapy-induced vomiting but these drugs lose efficacy throughout chronic treatment. The effects of these drugs in experimental animals under chronic administration are not well known. Our aim was to study, using radiographic methods, the effect of the 5-HT3 receptor antagonist granisetron on GI dysmotility induced in the rat by repeated cisplatin administration. First, invasive methods were used to select a dose of granisetron capable of reducing increased stomach weight due to acute cisplatin administration (6 mg/kg, ip). Second, rats received two intraperitoneal (ip) injections once a week for 4 weeks: granisetron (1 mg/kg, ip) or saline and, thirty min later, saline or cisplatin (2 mg/kg, ip). Body weight gain was measured throughout treatment. Radiological techniques were used to determine the acute (after first dose) and chronic (after last dose) effects of cisplatin and/or granisetron on GI motility. Repeated cisplatin-induced weight loss which granisetron did not prevent. Gastric emptying was delayed after the first cisplatin administration. Granisetron completely prevented this effect. After weekly administration, cisplatin-induced gastric dysmotility was enhanced and granisetron was not capable of completely preventing this effect. Granisetron prevents gastric emptying alterations, but its efficacy decreases throughout antineoplastic treatment. This might be due to the enhanced effect of cisplatin.

  19. Chapter 11. Community analysis-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.


    Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

  20. Repeatability and number of growing seasons for the selection of custard apple progenies

    Directory of Open Access Journals (Sweden)

    Julio César Do Vale


    Full Text Available This study aimed to estimate the repeatability coefficient and determine the minimum number of samplesrequired for effective selection for yield of custard apple. Twenty progenies were evaluated in randomized blocks, fivereplications and four plants per plot. The fruits were collected, counted and weighed every two days of the year. Estimates ofthe repeatability coefficients were obtained by the methods of analysis of variance - ANOVA and principal components - PC.The estimates from the repeatability analysis of biennial data are higher than those based on individual years. The estimatesof the PC method were accurate even in the first harvest, unlike ANOVA. Four biennia were sufficient to ensure effectiveprogeny selection of custard apple.

  1. Cleanup standards and pathways analysis methods

    International Nuclear Information System (INIS)

    Devgun, J.S.


    Remediation of a radioactively contaminated site requires that certain regulatory criteria be met before the site can be released for unrestricted future use. Since the ultimate objective of remediation is to protect the public health and safety, residual radioactivity levels remaining at a site after cleanup must be below certain preset limits or meet acceptable dose or risk criteria. Release of a decontaminated site requires proof that the radiological data obtained from the site meet the regulatory criteria for such a release. Typically release criteria consist of a composite of acceptance limits that depend on the radionuclides, the media in which they are present, and federal and local regulations. In recent years, the US Department of Energy (DOE) has developed a pathways analysis model to determine site-specific soil activity concentration guidelines for radionuclides that do not have established generic acceptance limits. The DOE pathways analysis computer code (developed by Argonne National Laboratory for the DOE) is called RESRAD (Gilbert et al. 1989). Similar efforts have been initiated by the US Nuclear Regulatory Commission (NRC) to develop and use dose-related criteria based on genetic pathways analyses rather than simplistic numerical limits on residual radioactivity. The focus of this paper is radionuclide contaminated soil. Cleanup standards are reviewed, pathways analysis methods are described, and an example is presented in which RESRAD was used to derive cleanup guidelines

  2. 3D analysis methods - Study and seminar

    International Nuclear Information System (INIS)

    Daaviittila, A.


    The first part of the report results from a study that was performed as a Nordic co-operation activity with active participation from Studsvik Scandpower and Westinghouse Atom in Sweden, and VTT in Finland. The purpose of the study was to identify and investigate the effects rising from using the 3D transient com-puter codes in BWR safety analysis, and their influence on the transient analysis methodology. One of the main questions involves the critical power ratio (CPR) calculation methodology. The present way, where the CPR calculation is per-formed with a separate hot channel calculation, can be artificially conservative. In the investigated cases, no dramatic minimum CPR effect coming from the 3D calculation is apparent. Some cases show some decrease in the transient change of minimum CPR with the 3D calculation, which confirms the general thinking that the 1D calculation is conservative. On the other hand, the observed effect on neutron flux behaviour is quite large. In a slower transient the 3D effect might be stronger. The second part of the report is a summary of a related seminar that was held on the 3D analysis methods. The seminar was sponsored by the Reactor Safety part (NKS-R) of the Nordic Nuclear Safety Research Programme (NKS). (au)

  3. Generalized Analysis of a Distribution Separation Method

    Directory of Open Access Journals (Sweden)

    Peng Zhang


    Full Text Available Separating two probability distributions from a mixture model that is made up of the combinations of the two is essential to a wide range of applications. For example, in information retrieval (IR, there often exists a mixture distribution consisting of a relevance distribution that we need to estimate and an irrelevance distribution that we hope to get rid of. Recently, a distribution separation method (DSM was proposed to approximate the relevance distribution, by separating a seed irrelevance distribution from the mixture distribution. It was successfully applied to an IR task, namely pseudo-relevance feedback (PRF, where the query expansion model is often a mixture term distribution. Although initially developed in the context of IR, DSM is indeed a general mathematical formulation for probability distribution separation. Thus, it is important to further generalize its basic analysis and to explore its connections to other related methods. In this article, we first extend DSM’s theoretical analysis, which was originally based on the Pearson correlation coefficient, to entropy-related measures, including the KL-divergence (Kullback–Leibler divergence, the symmetrized KL-divergence and the JS-divergence (Jensen–Shannon divergence. Second, we investigate the distribution separation idea in a well-known method, namely the mixture model feedback (MMF approach. We prove that MMF also complies with the linear combination assumption, and then, DSM’s linear separation algorithm can largely simplify the EM algorithm in MMF. These theoretical analyses, as well as further empirical evaluation results demonstrate the advantages of our DSM approach.

  4. DNA fingerprinting of Shiga-toxin producing Escherichia coli O157 based on Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA

    Directory of Open Access Journals (Sweden)

    Vardund Traute


    Full Text Available Abstract Background The ability to react early to possible outbreaks of Escherichia coli O157:H7 and to trace possible sources relies on the availability of highly discriminatory and reliable techniques. The development of methods that are fast and has the potential for complete automation is needed for this important pathogen. Methods In all 73 isolates of shiga-toxin producing E. coli O157 (STEC were used in this study. The two available fully sequenced STEC genomes were scanned for tandem repeated stretches of DNA, which were evaluated as polymorphic markers for isolate identification. Results The 73 E. coli isolates displayed 47 distinct patterns and the MLVA assay was capable of high discrimination between the E. coli O157 strains. The assay was fast and all the steps can be automated. Conclusion The findings demonstrate a novel high discriminatory molecular typing method for the important pathogen E. coli O157 that is fast, robust and offers many advantages compared to current methods.

  5. Method development for trace and ultratrace analysis

    International Nuclear Information System (INIS)



    Method development, that is, selection of a mode of chromatography and the right column and mobile-phase combination for trace and ultratrace analysis, requires several main considerations. The method should be useful for resolving various trace and ultratrace components present in the sample. If the nature of these components is known, the choice of method may be straightforward, that is, a selection can be made from the following modes of HPLC: (1) adsorption chromatography; (2) normal-phase chromatography; (3) reversed-phase chromatography; (4) ion-pair chromatography; (5) ion-exchange chromatography; (6) ion chromatography. Unfortunately, the nature of all of the components is frequently unknown. However, several intelligent judgments can be made on the nature of impurities. This chapter deals with some basic approaches to mobile-phase selection and optimization. More detailed information may be found in basic texts. Techniques for separation of high-molecular-weight compounds (macromolecules) and chiral compounds may be found elsewhere. Mainly compounds with molecular weight lower than 2,000 are discussed here. 123 refs

  6. Novel Method of Production Decline Analysis (United States)

    Xie, Shan; Lan, Yifei; He, Lei; Jiao, Yang; Wu, Yong


    ARPS decline curves is the most commonly used in oil and gas field due to its minimal data requirements and ease application. And prediction of production decline which is based on ARPS analysis rely on known decline type. However, when coefficient index are very approximate under different decline type, it is difficult to directly recognize decline trend of matched curves. Due to difficulties above, based on simulation results of multi-factor response experiments, a new dynamic decline prediction model is introduced with using multiple linear regression of influence factors. First of all, according to study of effect factors of production decline, interaction experimental schemes are designed. Based on simulated results, annual decline rate is predicted by decline model. Moreover, the new method is applied in A gas filed of Ordos Basin as example to illustrate reliability. The result commit that the new model can directly predict decline tendency without needing recognize decline style. From arithmetic aspect, it also take advantage of high veracity. Finally, the new method improves the evaluation method of gas well production decline in low permeability gas reservoir, which also provides technical support for further understanding of tight gas field development laws.

  7. Phylogenetic analysis using parsimony and likelihood methods. (United States)

    Yang, Z


    The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were

  8. External event analysis methods for NUREG-1150

    International Nuclear Information System (INIS)

    Bohn, M.P.; Lambright, J.A.


    The US Nuclear Regulatory Commission is sponsoring probabilistic risk assessments of six operating commercial nuclear power plants as part of a major update of the understanding of risk as provided by the original WASH-1400 risk assessments. In contrast to the WASH-1400 studies, at least two of the NUREG-1150 risk assessments will include an analysis of risks due to earthquakes, fires, floods, etc., which are collectively known as eternal events. This paper summarizes the methods to be used in the external event analysis for NUREG-1150 and the results obtained to date. The two plants for which external events are being considered are Surry and Peach Bottom, a PWR and BWR respectively. The external event analyses (through core damage frequency calculations) were completed in June 1989, with final documentation available in September. In contrast to most past external event analyses, wherein rudimentary systems models were developed reflecting each external event under consideration, the simplified NUREG-1150 analyses are based on the availability of the full internal event PRA systems models (event trees and fault trees) and make use of extensive computer-aided screening to reduce them to sequence cut sets important to each external event. This provides two major advantages in that consistency and scrutability with respect to the internal event analysis is achieved, and the full gamut of random and test/maintenance unavailabilities are automatically included, while only those probabilistically important survive the screening process. Thus, full benefit of the internal event analysis is obtained by performing the internal and external event analyses sequentially

  9. Comparing sensitivity analysis methods to advance lumped watershed model identification and evaluation

    Directory of Open Access Journals (Sweden)

    Y. Tang


    Full Text Available This study seeks to identify sensitivity tools that will advance our understanding of lumped hydrologic models for the purposes of model improvement, calibration efficiency and improved measurement schemes. Four sensitivity analysis methods were tested: (1 local analysis using parameter estimation software (PEST, (2 regional sensitivity analysis (RSA, (3 analysis of variance (ANOVA, and (4 Sobol's method. The methods' relative efficiencies and effectiveness have been analyzed and compared. These four sensitivity methods were applied to the lumped Sacramento soil moisture accounting model (SAC-SMA coupled with SNOW-17. Results from this study characterize model sensitivities for two medium sized watersheds within the Juniata River Basin in Pennsylvania, USA. Comparative results for the 4 sensitivity methods are presented for a 3-year time series with 1 h, 6 h, and 24 h time intervals. The results of this study show that model parameter sensitivities are heavily impacted by the choice of analysis method as well as the model time interval. Differences between the two adjacent watersheds also suggest strong influences of local physical characteristics on the sensitivity methods' results. This study also contributes a comprehensive assessment of the repeatability, robustness, efficiency, and ease-of-implementation of the four sensitivity methods. Overall ANOVA and Sobol's method were shown to be superior to RSA and PEST. Relative to one another, ANOVA has reduced computational requirements and Sobol's method yielded more robust sensitivity rankings.

  10. Revisiting the TALE repeat. (United States)

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng


    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  11. Reconfigurable multiport EPON repeater (United States)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio


    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  12. Spectral Analysis Methods of Social Networks

    Directory of Open Access Journals (Sweden)

    P. G. Klyucharev


    Full Text Available Online social networks (such as Facebook, Twitter, VKontakte, etc. being an important channel for disseminating information are often used to arrange an impact on the social consciousness for various purposes - from advertising products or services to the full-scale information war thereby making them to be a very relevant object of research. The paper reviewed the analysis methods of social networks (primarily, online, based on the spectral theory of graphs. Such methods use the spectrum of the social graph, i.e. a set of eigenvalues of its adjacency matrix, and also the eigenvectors of the adjacency matrix.Described measures of centrality (in particular, centrality based on the eigenvector and PageRank, which reflect a degree of impact one or another user of the social network has. A very popular PageRank measure uses, as a measure of centrality, the graph vertices, the final probabilities of the Markov chain, whose matrix of transition probabilities is calculated on the basis of the adjacency matrix of the social graph. The vector of final probabilities is an eigenvector of the matrix of transition probabilities.Presented a method of dividing the graph vertices into two groups. It is based on maximizing the network modularity by computing the eigenvector of the modularity matrix.Considered a method for detecting bots based on the non-randomness measure of a graph to be computed using the spectral coordinates of vertices - sets of eigenvector components of the adjacency matrix of a social graph.In general, there are a number of algorithms to analyse social networks based on the spectral theory of graphs. These algorithms show very good results, but their disadvantage is the relatively high (albeit polynomial computational complexity for large graphs.At the same time it is obvious that the practical application capacity of the spectral graph theory methods is still underestimated, and it may be used as a basis to develop new methods.The work

  13. Quantum repeated games revisited

    International Nuclear Information System (INIS)

    Frąckiewicz, Piotr


    We present a scheme for playing quantum repeated 2 × 2 games based on Marinatto and Weber’s approach to quantum games. As a potential application, we study the twice repeated Prisoner’s Dilemma game. We show that results not available in the classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games proposed by Iqbal and Toor. We point out the drawbacks that make their results unacceptable. (paper)

  14. Method and tool for network vulnerability analysis (United States)

    Swiler, Laura Painton [Albuquerque, NM; Phillips, Cynthia A [Albuquerque, NM


    A computer system analysis tool and method that will allow for qualitative and quantitative assessment of security attributes and vulnerabilities in systems including computer networks. The invention is based on generation of attack graphs wherein each node represents a possible attack state and each edge represents a change in state caused by a single action taken by an attacker or unwitting assistant. Edges are weighted using metrics such as attacker effort, likelihood of attack success, or time to succeed. Generation of an attack graph is accomplished by matching information about attack requirements (specified in "attack templates") to information about computer system configuration (contained in a configuration file that can be updated to reflect system changes occurring during the course of an attack) and assumed attacker capabilities (reflected in "attacker profiles"). High risk attack paths, which correspond to those considered suited to application of attack countermeasures given limited resources for applying countermeasures, are identified by finding "epsilon optimal paths."

  15. Quantitative Risk Analysis: Method And Process

    Directory of Open Access Journals (Sweden)

    Anass BAYAGA


    Full Text Available Recent and past studies (King III report, 2009: 73-75; Stoney 2007;Committee of Sponsoring Organisation-COSO, 2004, Bartell, 2003; Liebenberg and Hoyt, 2003; Reason, 2000; Markowitz 1957 lament that although, the introduction of quantifying risk to enhance degree of objectivity in finance for instance was quite parallel to its development in the manufacturing industry, it is not the same in Higher Education Institution (HEI. In this regard, the objective of the paper was to demonstrate the methods and process of Quantitative Risk Analysis (QRA through likelihood of occurrence of risk (phase I. This paper serves as first of a two-phased study, which sampled hundred (100 risk analysts in a University in the greater Eastern Cape Province of South Africa.The analysis of likelihood of occurrence of risk by logistic regression and percentages were conducted to investigate whether there were a significant difference or not between groups (analyst in respect of QRA.The Hosmer and Lemeshow test was non-significant with a chi-square(X2 =8.181; p = 0.300, which indicated that there was a good model fit, since the data did not significantly deviate from the model. The study concluded that to derive an overall likelihood rating that indicated the probability that a potential risk may be exercised within the construct of an associated threat environment, the following governing factors must be considered: (1 threat source motivation and capability (2 nature of the vulnerability (3 existence and effectiveness of current controls (methods and process.

  16. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.). (United States)

    Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling


    Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Preliminary hazard analysis using sequence tree method

    International Nuclear Information System (INIS)

    Huang Huiwen; Shih Chunkuan; Hung Hungchih; Chen Minghuei; Yih Swu; Lin Jiinming


    A system level PHA using sequence tree method was developed to perform Safety Related digital I and C system SSA. The conventional PHA is a brainstorming session among experts on various portions of the system to identify hazards through discussions. However, this conventional PHA is not a systematic technique, the analysis results strongly depend on the experts' subjective opinions. The analysis quality cannot be appropriately controlled. Thereby, this research developed a system level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. Two major phases are included in this sequence tree based technique. The first phase uses a table to analyze each event in SAR Chapter 15 for a specific safety related I and C system, such as RPS. The second phase uses sequence tree to recognize what I and C systems are involved in the event, how the safety related systems work, and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. In the sequence tree, the defense-in-depth echelons, including Control echelon, Reactor trip echelon, ESFAS echelon, and Indication and display echelon, are arranged to construct the sequence tree structure. All the related I and C systems, include digital system and the analog back-up systems are allocated in their specific echelon. By this system centric sequence tree based analysis, not only preliminary hazard can be identified systematically, the vulnerability of the nuclear power plant can also be recognized. Therefore, an effective simplified D3 evaluation can be performed as well. (author)


    International Nuclear Information System (INIS)

    Christopher J. Koroneos; Dimitrios C. Rovas


    All human activities are related with the energy consumption. Energy requirements will continue to rise, due to the modern life and the developing countries growth. Most of the energy demand emanates from fossil fuels. Fossil fuels combustion has negative environmental impacts, with the CO 2 production to be dominating. The fulfillment of the Kyoto protocol criteria requires the minimization of CO 2 emissions. Thus the management of the CO 2 emissions is an urgent matter. The use of appliances with low energy use and the adoption of an energy policy that prevents the unnecessary energy use, can play lead to the reduction of carbon emissions. A different route is the introduction of ''clean'' energy sources, such as renewable energy sources. Last but not least, the development of carbon sequestration methods can be promising technique with big future potential. The objective of this work is the analysis and comparison of different carbon sequestration and deposit methods. Ocean deposit, land ecosystems deposit, geological formations deposit and radical biological and chemical approaches will be analyzed

  19. Recent improvement of the resonance analysis methods

    International Nuclear Information System (INIS)

    Sirakov, I.; Lukyanov, A.


    By the use of a two-step method called Combined, the R-matrix Wigner-Eisenbud representation in the resonance reaction theory has been converted into other equivalent representations (parameterizations) of the collision matrix with Poles in E domain. Two of them called Capture Elimination (CE) and Reaction Elimination (RE) representation respectively, have energy independent parameters and are both rigorous and applicable. The CE representation is essentially a generalization of the Reich-Moore (RM) formalism. The RE representation, in turn, offers some distinct advantages when analyzing fissile nuclei. The latter does not require any approximation for the capture channels and does not need any assumption about the number of fission channels in contrast to the RM representation. Unlike the RM parameters the RE ones are uniquely determined for applications in the resonance analysis. When given in the RE representation, neutron cross sections of fissile nuclei in the resolved resonance region are presented through simple scalar expressions without the need of matrix inversion. Various computer codes have been developed to demonstrate the viability of the new method. The RM parameters of the fissile nuclei have been converted into equivalent RE parameters implying the RM assumptions (REFINE code). Conversely, the RE parameters have been converted into corresponding RM parameters when one fission channel is present and the RM parameter set is unique, e.g. Pu-239, J =1 (REVERSE code). To further enhance the flexibility of the proposed method the obtained RE parameters have been converted into equivalent Generalized Pole parameters (REFILE code), which are parameters of the rigorous pole expansion of the collision matrix in √E domain. equi valent sets of RM, RE and GP parameters of 239 Pu are given as an example. It has been pointed out that all the advantages of the newly proposed representation can be implemented through an independent evaluation of the RE resonance

  20. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

    Directory of Open Access Journals (Sweden)

    Shirasawa Kenta


    Full Text Available Abstract Background Peanut (Arachis hypogaea is an autogamous allotetraploid legume (2n = 4x = 40 that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. Results The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2% of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. Conclusions In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (

  1. Molecular Methods for Typing of Streptococcus agalactiae with Special Emphasis on the Development and Validation of a Multi-Locus Variable Number of Tandem Repeats Assay (MLVA)


    Radtke, Andreas


    Molekylære metoder for typing av Streptococcus agalactiae med særlig vektlegging av utvikling og validering av et multi-locus variable number of tandem repeats assay (MLVA) Sammendraget: Streptococcus agalactiae eller gruppe B streptokokker (GBS) forårsaker livsfarlige infeksjoner hos nyfødte, gravide eller voksne med kroniske sykdommer. Den forårsaker også jurbetennelse i storfe. Typing av GBS gir innblikk i bakteriens epidemiologi og dens fylogenetiske slektskap. Ulike deler av bakterie...

  2. Novel axolotl cardiac function analysis method using magnetic resonance imaging.

    Directory of Open Access Journals (Sweden)

    Pedro Gomes Sanches

    Full Text Available The salamander axolotl is capable of complete regeneration of amputated heart tissue. However, non-invasive imaging tools for assessing its cardiac function were so far not employed. In this study, cardiac magnetic resonance imaging is introduced as a non-invasive technique to image heart function of axolotls. Three axolotls were imaged with magnetic resonance imaging using a retrospectively gated Fast Low Angle Shot cine sequence. Within one scanning session the axolotl heart was imaged three times in all planes, consecutively. Heart rate, ejection fraction, stroke volume and cardiac output were calculated using three techniques: (1 combined long-axis, (2 short-axis series, and (3 ultrasound (control for heart rate only. All values are presented as mean ± standard deviation. Heart rate (beats per minute among different animals was 32.2±6.0 (long axis, 30.4±5.5 (short axis and 32.7±4.9 (ultrasound and statistically similar regardless of the imaging method (p > 0.05. Ejection fraction (% was 59.6±10.8 (long axis and 48.1±11.3 (short axis and it differed significantly (p = 0.019. Stroke volume (μl/beat was 133.7±33.7 (long axis and 93.2±31.2 (short axis, also differed significantly (p = 0.015. Calculations were consistent among the animals and over three repeated measurements. The heart rate varied depending on depth of anaesthesia. We described a new method for defining and imaging the anatomical planes of the axolotl heart and propose one of our techniques (long axis analysis may prove useful in defining cardiac function in regenerating axolotl hearts.

  3. Large Diversity of Porcine Yersinia enterocolitica 4/O:3 in Eight European Countries Assessed by Multiple-Locus Variable-Number Tandem-Repeat Analysis. (United States)

    Alakurtti, Sini; Keto-Timonen, Riikka; Virtanen, Sonja; Martínez, Pilar Ortiz; Laukkanen-Ninios, Riikka; Korkeala, Hannu


    A total of 253 multiple-locus variable-number tandem-repeat analysis (MLVA) types among 634 isolates were discovered while studying the genetic diversity of porcine Yersinia enterocolitica 4/O:3 isolates from eight different European countries. Six variable-number tandem-repeat (VNTR) loci V2A, V4, V5, V6, V7, and V9 were used to study the isolates from 82 farms in Belgium (n = 93, 7 farms), England (n = 41, 8 farms), Estonia (n = 106, 12 farms), Finland (n = 70, 13 farms), Italy (n = 111, 20 farms), Latvia (n = 66, 3 farms), Russia (n = 60, 10 farms), and Spain (n = 87, 9 farms). Cluster analysis revealed mainly country-specific clusters, and only one MLVA type consisting of two isolates was found from two countries: Russia and Italy. Also, farm-specific clusters were discovered, but same MLVA types could also be found from different farms. Analysis of multiple isolates originating either from the same tonsils (n = 4) or from the same farm, but 6 months apart, revealed both identical and different MLVA types. MLVA showed a very good discriminatory ability with a Simpson's discriminatory index (DI) of 0.989. DIs for VNTR loci V2A, V4, V5, V6, V7, and V9 were 0.916, 0.791, 0.901, 0.877, 0.912, and 0.785, respectively, when studying all isolates together, but variation was evident between isolates originating from different countries. Locus V4 in the Spanish isolates and locus V9 in the Latvian isolates did not differentiate (DI 0.000), and locus V9 in the English isolates showed very low discriminatory power (DI 0.049). The porcine Y. enterocolitica 4/O:3 isolates were diverse, but the variation in DI demonstrates that the well discriminating loci V2A, V5, V6, and V7 should be included in MLVA protocol when maximal discriminatory power is needed.

  4. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)



    Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

  5. Repeat migration and disappointment. (United States)

    Grant, E K; Vanderkamp, J


    This article investigates the determinants of repeat migration among the 44 regions of Canada, using information from a large micro-database which spans the period 1968 to 1971. The explanation of repeat migration probabilities is a difficult task, and this attempt is only partly successful. May of the explanatory variables are not significant, and the overall explanatory power of the equations is not high. In the area of personal characteristics, the variables related to age, sex, and marital status are generally significant and with expected signs. The distance variable has a strongly positive effect on onward move probabilities. Variables related to prior migration experience have an important impact that differs between return and onward probabilities. In particular, the occurrence of prior moves has a striking effect on the probability of onward migration. The variable representing disappointment, or relative success of the initial move, plays a significant role in explaining repeat migration probabilities. The disappointment variable represents the ratio of actural versus expected wage income in the year after the initial move, and its effect on both repeat migration probabilities is always negative and almost always highly significant. The repeat probabilities diminish after a year's stay in the destination region, but disappointment in the most recent year still has a bearing on the delayed repeat probabilities. While the quantitative impact of the disappointment variable is not large, it is difficult to draw comparisons since similar estimates are not available elsewhere.

  6. Analysis of thermal power calibration method

    International Nuclear Information System (INIS)

    Zagar, T.; Ravnik, M.; Persic, A.


    The methods for determining fuel element burnup have recently become interesting because of activities related to the shipment of highly enriched fuel elements back to the United States for final disposal before 2009. The most common and practical method for determining fuel element burnup in research reactors is reactor calculation. Experience has shown that burnup calculations become complicated and biased with uncertainties if a long period of reactor operation must be reproduced. Besides this, accuracy of calculated burnup is always limited with accuracy of reactor power calibration, since burnup calculation is based on calculated power density distribution, which is usually expressed in terms of power released per fuel element and normalised to the reactor power It is obvious that reactor thermal power calibration is very important for precise fuel element burnup calculation. Calculated fuel element burnup is linearly dependent on the thermal reactor power. The reactor power level may be determined from measured absolute thermal flux distribution across the core in the horizontal and vertical planes. Flux distributions are measured with activation of cadmium covered and bare foils irradiated by the steady reactor power. But it should be realised that this method is time consuming and not accurate. This method is practical only for zero power reactors and is in practice very seldom performed for other reactors (e.g. for TRIGA reactor in Ljubljana absolute thermal flux distribution was not performed since reactor reconstruction in 1991). In case of power reactors and research reactors in which a temperature rise across the core is produced and measured than a heat balance method is the most common and accurate method of determining the power output of the core. The purpose of this paper is to analyse the accuracy of calorimetric reactor power calibration method and to analyse the influence of control rod position on nuclear detector reading for TRIGA reactors

  7. Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea). (United States)

    Sharma, Ranu; Rawat, Vimal; Suresh, C G


    The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species. Around 50% NBS-LRRs reside in macro-syntenic blocks underlining positional conservation along with sequence conservation of NBS-LRR genes in chickpea. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. Four cis -regulatory elements namely WBOX, DRE, CBF, and GCC boxes, that commonly occur in resistance genes, were present in the promoter regions of these genes. Further, the findings will provide a strong background to use candidate disease resistance NBS-encoding genes and identify their specific roles in chickpea.

  8. Typing and Evaluation of the Genetic Relatedness of Listeria monocytogenes Strains Isolated from Food Samples by the Multiple-Locus Variable number Tandem Repeat Analysis (MLVA

    Directory of Open Access Journals (Sweden)

    Behrooz Sadeghi kalani


    Full Text Available Background and Aim:Listeria monocytogenes cause listeriosis and fatal infections in humans. The aim of this study was typing and evaluation of the genetic relatedness of L. monocytogenes strains from food samples using MLVA technique. Materials and Methods: 317 food samples were collected from 2009 to 2013 in Tehran,Iran. After final diagnosis of L. monocytogenes DNA was extracted to perform of MLVA technique, and also PCR products were analyzed by Gene Tools software. The number of tandem repeats was determined by using special equation for each selected locus. Also typing of strains was done. Results: 24 samples of 317 food samples were positive for L. monocytogenes using standard laboratory techniques. A total 13 different types were determined by MLVA technique that type 2 and type 3 were the most abundant types by 6 and 4 strains, respectively. Conclusions: The results of this study showed the presence of L. monocytogenes in dairy products and meat samples, therefore all people, especially pregnant women should observe health tips when using these products. The results of typing showed that L. monocytogenes strains from different sources can have the same origin. MLVA technique is easy with high accuracy and this method can be used in typing and evaluation of the genetic relatedness of L. monocytogenes for determination the source of contamination.

  9. Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Yuan Tong


    Full Text Available Abstract Background Transmembrane receptor kinases play critical roles in both animal and plant signaling pathways regulating growth, development, differentiation, cell death, and pathogenic defense responses. In Arabidopsis thaliana, there are at least 223 Leucine-rich repeat receptor-like kinases (LRR-RLKs, representing one of the largest protein families. Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated. Results As a resource for the in-depth analysis of this important protein family, the complementary DNA sequences (cDNAs of 194 LRR-RLKs were cloned into the GatewayR donor vector pDONR/ZeoR and analyzed by DNA sequencing. Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. The other 37 cDNAs showed gene structures distinct from the predictions of TAIR8, which was mainly caused by alternative splicing of pre-mRNA. Most of the genes have been further cloned into GatewayR destination vectors with GFP or FLAG epitope tags and have been transformed into Arabidopsis for in planta functional analysis. All clones from this study have been submitted to the Arabidopsis Biological Resource Center (ABRC at Ohio State University for full accessibility by the Arabidopsis research community. Conclusions Most of the Arabidopsis LRR-RLK genes have been isolated and the sequence analysis showed a number of alternatively spliced variants. The generated resources, including cDNA entry clones, expression constructs and transgenic plants, will facilitate further functional analysis of the members of this important gene family.

  10. IL1 receptor antagonist gene IL1-RN variable number of tandem repeats polymorphism and cancer risk: a literature review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Ying Zhang

    Full Text Available IL1 receptor antagonist (IL1RA and IL1beta (IL1β, members of the pro-inflammatory cytokine interleukin-1 (IL1 family, play a potential role against infection and in the pathogenesis of cancers. The variable number of tandem repeats (VNTR polymorphism in the second intron of the IL1 receptor antagonist gene (IL1-RN and a polymorphism in exon 5 of IL1B (IL1B+3954C>T, rs1143634 have been suggested in predisposition to cancer risk. However, studies have shown inconsistent results. To validate any association, a meta-analysis was performed with 14,854 cases and 19,337 controls from 71 published case-control studies for IL1-RN VNTR and 33 eligible studies contained 7,847 cases and 8917 controls for IL1B +3954. Odds ratios (ORs with 95% confidence intervals (CIs were calculated from comparisons to assess the strength of the association. There was significant association between the IL1-RN VNTR polymorphism and the risk of cancer for any overall comparison. Furthermore, cancer type stratification analysis revealed that there were significantly increased risks of gastric cancer, bladder cancer and other cancer groups. Infection status analysis indicated that the H. pylori or HBV/HCV infection and IL1-RN VNTR genotypes were independent factors for developing gastric or hepatocellular cancers. In addition, a borderline significant association was observed between IL1B+3954 polymorphism and the increased cancer risk. Although some modest bias could not be eliminated, this meta-analysis suggested that the IL1-RN VNTR polymorphisms may contribute to genetic susceptibility to gastric cancer. More studies are needed to further evaluate the role of the IL1B+3954 polymorphism in the etiology of cancer.

  11. DORIAN, Bayes Method Plant Age Risk Analysis

    International Nuclear Information System (INIS)

    Atwood, C.L.


    1 - Description of program or function: DORIAN is an integrated package for performing Bayesian aging analysis of reliability data; e.g. for identifying trends in component failure rates and/or outage durations as a function of time. The user must specify several alternative hypothesized 'aging models' (i.e., possible trends) along prior probabilities indicating the subject probability that each trend is actually the correct one. DORIAN then uses component failure and/or repair data over time to update these prior probabilities and develop a posterior probability for each aging model, representing the probability that each model is the correct one in light of the observed data rather than a priori. Mean, median, and 5. and 95. percentile trends are also compiled from the posterior probabilities. 2 - Method of solution: DORIAN carries out a Bayesian analysis of failure data and a prior distribution on a time-dependent failure rate to obtain a posterior distribution on the failure rate. The form of the time-dependent failure rate is arbitrary, because DORIAN approximates the form by a step-function, constant within specified time intervals. Similarly, the parameters may have any prior distribution, because DORIAN uses a discrete distribution to approximate this. Likewise, the database file produced by DORIAN approximates the entire range of possible failure rates or outage durations developed by means of a discrete probability distribution containing no more than 20 distinct values with their probabilities. 3 - Restrictions on the complexity of the problem: Prior distribution is discrete with up to 25 values. Up to 60 times are accommodated in the discrete time history

  12. An Analysis of the SURF Method

    Directory of Open Access Journals (Sweden)

    Edouard Oyallon


    Full Text Available The SURF method (Speeded Up Robust Features is a fast and robust algorithm for local, similarity invariant representation and comparison of images. Similarly to many other local descriptor-based approaches, interest points of a given image are defined as salient features from a scale-invariant representation. Such a multiple-scale analysis is provided by the convolution of the initial image with discrete kernels at several scales (box filters. The second step consists in building orientation invariant descriptors, by using local gradient statistics (intensity and orientation. The main interest of the SURF approach lies in its fast computation of operators using box filters, thus enabling real-time applications such as tracking and object recognition. The SURF framework described in this paper is based on the PhD thesis of H. Bay [ETH Zurich, 2009], and more specifically on the paper co-written by H. Bay, A. Ess, T. Tuytelaars and L. Van Gool [Computer Vision and Image Understanding, 110 (2008, pp. 346–359]. An implementation is proposed and used to illustrate the approach for image matching. A short comparison with a state-of-the-art approach is also presented, the SIFT algorithm of D. Lowe [International Journal of Computer Vision, 60 (2004, pp. 91–110], with which SURF shares a lot in common.

  13. Analysis methods used by the geochemistry department

    International Nuclear Information System (INIS)

    Berthollet, P.


    This note presents various analytical techniques which are respectively used for the dosing of uranium in soils (fluorescence method, chromatographic method), for the dosing of uranium in natural waters (ion exchange method, evaporation method), and for the dosing of uranium in plants. Principles, equipment and products, reactant preparation, operation mode, sample preparation and measurements, expression of results and calculations) are indicated for each of these methods

  14. Consistency analysis of Keratograph and traditional methods to evaluate tear film function

    Directory of Open Access Journals (Sweden)

    Pei-Yang Shen


    Full Text Available AIM: To investigate repeatability and accuracy of a latest Keratograph for evaluating the tear film stability and to compare its measurements with that of traditional examination methods. METHODS: The results of noninvasive tear film break-up time(NI-BUTincluding the first tear film break-up time(BUT-fand the average tear film break-up time(BUT-avewere measured by Keratograph. The repeatability of the measurements was evaluated by coefficient of variation(CVand intraclass correlation coefficient(ICC. Wilcoxon Signed-Rank test was used to compare NI-BUT with fluorescein tear film break-up time(FBUTto confirm the correlation between NI-BUT and FBUT, Schirmer I test values. Bland-Altman analysis was used to evaluate consistency. RESULTS: The study recruited 48 subjects(48 eyes(mean age 38.7±15.2 years. The CV and ICC of BUT-f were respectively 12.6% and 0.95, those of BUT-ave were 9.8% and 0.96. The value of BUT-f was lower than that of FBUT. The difference had statistical significance(6.16±2.46s vs 7.46±1.92s, PPCONCLUSION: Keratograph can provide NI-BUT data that has a better repeatability and reliability, which has great application prospects in diagnosis and treatment of dry eye and refractive corneal surgery.

  15. Instrumental neutron activation analysis - a routine method

    International Nuclear Information System (INIS)

    Bruin, M. de.


    This thesis describes the way in which at IRI instrumental neutron activation analysis (INAA) has been developed into an automated system for routine analysis. The basis of this work are 20 publications describing the development of INAA since 1968. (Auth.)

  16. Basic methods of linear functional analysis

    CERN Document Server

    Pryce, John D


    Introduction to the themes of mathematical analysis, geared toward advanced undergraduate and graduate students. Topics include operators, function spaces, Hilbert spaces, and elementary Fourier analysis. Numerous exercises and worked examples.1973 edition.

  17. Specific multilocus variable-number tandem-repeat analysis genotypes of Mycoplasma pneumoniae are associated with diseases severity and macrolide susceptibility.

    Directory of Open Access Journals (Sweden)

    Jiuxin Qu

    Full Text Available Clinical relevance of multilocus variable-number tandem-repeat (VNTR analysis (MLVA in patients with community-acquired pneumonia (CAP by Mycoplasma pneumoniae (M. pneumoniae is unknown. A multi-center, prospective study was conducted from November 2010 to April 2012. Nine hundred and fifty-four CAP patients were consecutively enrolled. M. pneumoniae clinical isolates were obtained from throat swabs. MLVA typing was applied to all isolates. Comparison of pneumonia severity index (PSI and clinical features among patients infected with different MLVA types of M. pneumoniae were conducted. One hundred and thirty-six patients were positive with M. pneumoniae culture. The clinical isolates were clustered into 18 MLVA types. One hundred and fourteen (88.3% isolates were resistant to macrolide, covering major MLVA types. The macrolide non-resistant rate of M. pneumoniae isolates with Mpn13-14-15-16 profile of 3-5-6-2 was significantly higher than that of other types (p ≤ 0.001. Patients infected with types U (5-4-5-7-2 and J (3-4-5-7-2 had significantly higher PSI scores (p<0.001 and longer total duration of cough (p = 0.011. Therefore it seems that there is a correlation between certain MLVA types and clinical severity of disease and the presence of macrolide resistance.

  18. The prognostic role of Leucine-rich repeat-containing G-protein-coupled receptor 5 in gastric cancer: A systematic review with meta-analysis. (United States)

    Huang, Tianchen; Qiu, Xinguang; Xiao, Jianan; Wang, Qingbing; Wang, Yanjun; Zhang, Yong; Bai, Dongxiao


    The prognostic value of Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5) in gastric cancer remains controversial. To further investigate this relationship, we performed meta-analyses to systematically review the association between LGR5 expression and various clinical parameters in gastric cancer patients. Eligible studies from PubMed, Embase, Web of Science, CNKI (Chinese National Knowledge Infrastructure), Wangfang (Database of Chinese Ministry of Science & Technology) and CBM (China Biological Medicine) databases were evaluated to investigate the association of LGR5 expression with overall survival (OS) and clinicopathological features of gastric cancer. LGR5 overexpression was significantly associated with poor OS in patients with gastric cancer (HR 1.66, 95% CI 1.02-2.69). LGR5 overexpression was also significantly associated with TNM stage (TIII/TIV vs TI/TII: OR 5.42, 95% CI 1.02-28.72) and lymph node metastasis (positive vs negative: OR 2.30, 95% CI 1.06-5.0). Our meta-analysis indicates that LGR5 may be a predictive factor for invasion and metastasis, and poor prognosis in patients with gastric cancer. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  19. Genetic diversity of Neisseria meningitidis serogroup C ST-4821 in China based on multiple-locus variable number tandem repeat analysis.

    Directory of Open Access Journals (Sweden)

    Xiaoying Shan

    Full Text Available Neisseria meningitidis sequence type (ST-4821 was first reported in China in 2003, and a new hyper-virulent lineage has been designated as the ST-4821 complex. A large number of N. meningitidis ST-4821 strains have been identified in China since 2003; however, the microevolution characteristics of this complex are unclear. Different combinations of variable number of tandem repeats (VNTR loci were used in multiple-locus VNTR analysis (MLVA to analyze 118 N. meningitidis serogroup C ST-4821 strains isolated from seventeen provinces between 2003 and 2012. Additionally, MLVA with five VNTR loci was performed due to its high discriminatory power. One hundred and eighteen isolates were found to comprise 112 subtypes based on MLVA, and 16 outbreak-associated strains were clustered into one group. These data indicate a high level of diversity for N. meningitidis ST-4821 due to microevolution in the last decade. In addition, the results revealed high similarity between isolates from the same geographic origins, which is helpful when monitoring the spread of N. meningitidis serogroup C ST-4821 and will provide valuable information for the control and prevention of bacterial meningitis in China.

  20. Comparative analysis of transcriptomic responses to repeated-dose exposure to 2-MCPD and 3-MCPD in rat kidney, liver and testis. (United States)

    Buhrke, Thorsten; Schultrich, Katharina; Braeuning, Albert; Lampen, Alfonso


    3-Chloro-1,2-propanediol (3-MCPD) and its isomer 2-chloro-1,3-propanediol (2-MCPD) are heat-induced food contaminants present in oil- and fat-containing foodstuff. Kidney and testes are among the main target organs of 3-MCPD. Almost no data on 2-MCPD toxicity are available. Here, transcriptomic responses following repeated-dose exposure of rats to non-toxic doses of 10 mg/kg body weight per day 2-MCPD or 3-MCPD for 28 days were characterized by microarray analysis of kidney, liver, and testes. 3-MCPD exerted more pronounced effects than 2-MCPD in all organs. The limited overlap between the datasets indicates that 2-MCPD and 3-MCPD do not share the same molecular mechanisms of toxicity. By combining transcriptomic data with datasets on proteomic regulation by 3-MCPD, a comprehensive view on 3-MCPD-induced regulation of glucose utilization and oxidative stress response was developed. Bioinformatic analyses revealed that Nrf2 (nuclear factor (erythroid-derived 2)-like 2) signaling is likely to be involved in mediating the oxidative stress response to 3-MCPD. In summary, this study for the first time presents data on alterations in global gene expression by two important food contaminants, 2-MCPD and 3-MCPD. Data demonstrate profound differences between the effects of the two compounds and substantially broaden our knowledge on molecular details of 3-MCPD-induced disturbance of glucose utilization and redox balance. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome. (United States)

    Rajan-Babu, Indhu-Shree; Lian, Mulias; Cheah, Felicia S H; Chen, Min; Tan, Arnold S C; Prasath, Ethiraj B; Loh, Seong Feei; Chong, Samuel S


    Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification. The assay was optimised and validated on single lymphoblasts isolated from fragile X reference cell lines, and applied to a simulated PGD case and a clinical in vitro fertilisation (IVF)-PGD case. In the simulated PGD case, definitive diagnosis of the expected results was achieved for all 'embryos'. In the clinical IVF-PGD case, delivery of a healthy baby girl was achieved after transfer of an expansion-negative blastocyst. FMR1 TP-PCR reliably detects presence of expansion mutations and obviates reliance on informative normal alleles for determining expansion status in female embryos. Together with multi-marker haplotyping and gender determination, misdiagnosis and diagnostic ambiguity due to allele dropout is minimised, and couple-specific assay customisation can be avoided.

  2. Repeat-aware modeling and correction of short read errors. (United States)

    Yang, Xiao; Aluru, Srinivas; Dorman, Karin S


    High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at " = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors

  3. The Pentapeptide Repeat Proteins


    Vetting, Matthew W.; Hegde, Subray S.; Fajardo, J. Eduardo; Fiser, Andras; Roderick, Steven L.; Takiff, Howard E.; Blanchard, John S.


    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S,T,A,V][D,N][L,F]-[S,T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Myc...

  4. Information System Hazard Analysis: A Method for Identifying Technology-induced Latent Errors for Safety. (United States)

    Weber, Jens H; Mason-Blakley, Fieran; Price, Morgan


    Many health information and communication technologies (ICT) are safety-critical; moreover, reports of technology-induced adverse events related to them are plentiful in the literature. Despite repeated criticism and calls to action, recent data collected by the Institute of Medicine (IOM) and other organization do not indicate significant improvements with respect to the safety of health ICT systems. A large part of the industry still operates on a reactive "break & patch" model; the application of pro-active, systematic hazard analysis methods for engineering ICT that produce "safe by design" products is sparse. This paper applies one such method: Information System Hazard Analysis (ISHA). ISHA adapts and combines hazard analysis techniques from other safety-critical domains and customizes them for ICT. We provide an overview of the steps involved in ISHA and describe.

  5. Applying homotopy analysis method for solving differential-difference equation

    International Nuclear Information System (INIS)

    Wang Zhen; Zou Li; Zhang Hongqing


    In this Letter, we apply the homotopy analysis method to solving the differential-difference equations. A simple but typical example is applied to illustrate the validity and the great potential of the generalized homotopy analysis method in solving differential-difference equation. Comparisons are made between the results of the proposed method and exact solutions. The results show that the homotopy analysis method is an attractive method in solving the differential-difference equations

  6. Analysis of future nuclear power plants competitiveness with stochastic methods

    International Nuclear Information System (INIS)

    Feretic, D.; Tomsic, Z.


    operation and maintenance cost , variable maintenance and operational cost (no fuel), load factor, plant efficiency, years of credit repayment, years of plant life time. The input data for the analysis are given within best estimated or optimistically predicted ranges with a probability distribution of each within range. By applying the STATS computer which by using the Monte Carlo method selects randomly value of a parameter in predicted range and performs a calculation of required output. By repeating this process several thousand times a distribution of output values is obtained and also corresponding most probable value. The Probabilistic Analysis is performed in three steps: The analysis determines the expected range of uncertainty for key design and economic variables that make the greatest impact on the levelized cost of electricity; Developing a probability distribution for each key input variable; Monte Carlo analysis generates a probability distribution for each key performance and cost parameter using developed probability distributions. The results of analysis showed that under given assumptions future competitive nuclear power plant specific investment cost would be not considerably different from presently expected values. It amounts to a value between 1700 USD/kW and 1900 USD/kW depending if the nuclear plant is compared with gas plants working jointly with wind power units or without such units. The results show that economic competitiveness of future nuclear units relative to its main competitors will probably be not difficult to achieve.(author)

  7. Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes. (United States)

    Sun, Jiangmei; Li, Leiting; Wang, Peng; Zhang, Shaoling; Wu, Juyou


    Leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest gene family of receptor-like protein kinases (RLKs) and actively participates in regulating the growth, development, signal transduction, immunity, and stress responses of plants. However, the patterns of LRR-RLK gene family evolution in the five main Rosaceae species for which genome sequences are available have not yet been reported. In this study, we performed a comprehensive analysis of LRR-RLK genes for five Rosaceae species: Fragaria vesca (strawberry), Malus domestica (apple), Pyrus bretschneideri (Chinese white pear), Prunus mume (mei), and Prunus persica (peach), which contained 201, 244, 427, 267, and 258 LRR-RLK genes, respectively. All LRR-RLK genes were further grouped into 23 subfamilies based on the hidden Markov models approach. RLK-Pelle_LRR-XII-1, RLK-Pelle_LRR-XI-1, and RLK-Pelle_LRR-III were the three largest subfamilies. Synteny analysis indicated that there were 236 tandem duplicated genes in the five Rosaceae species, among which subfamilies XII-1 (82 genes) and XI-1 (80 genes) comprised 68.6%. Our results indicate that tandem duplication made a large contribution to the expansion of the subfamilies. The gene expression, tissue-specific expression, and subcellular localization data revealed that LRR-RLK genes were differentially expressed in various organs and tissues, and the largest subfamily XI-1 was highly expressed in all five Rosaceae species, suggesting that LRR-RLKs play important roles in each stage of plant growth and development. Taken together, our results provide an overview of the LRR-RLK family in Rosaceae genomes and the basis for further functional studies.

  8. Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database (United States)

    Iakhiaeva, Elena; Howard, Susan T.; Brown Elliott, Barbara A.; McNulty, Steven; Newman, Kristopher L.; Falkinham, Joseph O.; Williams, Myra; Kwait, Rebecca; Lande, Leah; Vasireddy, Ravikiran; Turenne, Christine


    “Mycobacterium avium subsp. hominissuis” is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilm M. avium isolates underwent molecular identification. Testing for IS901 was done to separate M. avium subsp. avium from M. avium subsp. hominissuis. VNTR types were defined using VNTR loci, and subtyping was performed using 3′ hsp65 and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes of M. avium subsp. hominissuis (IS901 negative) were identified among 416 isolates of M. avium from 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3′ hsp65 sequence code (sequevar). A total of 44 isolates belonging to four M. avium subsp. hominissuis VNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901 PCR primers. By sequencing, all 44 amplicons were not IS901 but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis of M. avium subsp. hominissuis isolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates of M. avium subsp. avium were identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan. PMID:26739155

  9. Effect of exposure to evening light on sleep initiation in the elderly: a longitudinal analysis for repeated measurements in home settings. (United States)

    Obayashi, Kenji; Saeki, Keigo; Iwamoto, Junko; Okamoto, Nozomi; Tomioka, Kimiko; Nezu, Satoko; Ikada, Yoshito; Kurumatani, Norio


    Epidemiologic data have demonstrated associations of sleep-onset insomnia with a variety of diseases, including depression, dementia, diabetes and cardiovascular diseases. Sleep initiation is controlled by the suprachiasmatic nucleus of the hypothalamus and endogenous melatonin, both of which are influenced by environmental light. Exposure to evening light is hypothesized to cause circadian phase delay and melatonin suppression before bedtime, resulting in circadian misalignment and sleep-onset insomnia; however, whether exposure to evening light disturbs sleep initiation in home settings remains unclear. In this longitudinal analysis of 192 elderly individuals (mean age: 69.9 years), we measured evening light exposure and sleep-onset latency for 4 days using a wrist actigraph incorporating a light meter and an accelerometer. Mixed-effect linear regression analysis for repeated measurements was used to evaluate the effect of evening light exposure on subsequent sleep-onset latency. The median intensity of evening light exposure and the median sleep-onset latency were 27.3 lux (interquartile range, 17.9-43.4) and 17 min (interquartile range, 7-33), respectively. Univariate models showed significant associations between sleep-onset latency and age, gender, daytime physical activity, in-bed time, day length and average intensity of evening and nighttime light exposures. In a multivariate model, log-transformed average intensity of evening light exposure was significantly associated with log-transformed sleep-onset latency independent of the former potential confounding factors (regression coefficient, 0.133; 95% CI, 0.020-0.247; p = 0.021). Day length and nighttime light exposure were also significantly associated with log-transformed sleep-onset latency (p = 0.001 and p < 0.001, respectively). In conclusion, exposure to evening light in home setting prolongs subsequent sleep-onset latency in the elderly.

  10. 2. Methods of elemental analysis of materials

    International Nuclear Information System (INIS)

    Musilek, L.


    The principles of activation analysis are outlined including the preparation of samples and reference materials, the choice of suitable activation sources, interfering effects, detection of radiation emitted and analysis of mixtures of emitters, and the potential of activation analysis in various fields of science and technology. The principles of X-ray fluorescence analysis and the associated instrumentation are also dealt with, and examples of applications are given. Described are also the physical nature of the Moessbauer effect, Moessbauer sources and spectrometers, and the applicability of this effect in physical research and in the investigation of iron-containing materials. (Z.S.). 1 tab., 20 figs., 90 refs

  11. Extension and Validation of UNDEX Analysis Methods

    National Research Council Canada - National Science Library

    Donahue, L


    .... Adaptive grid schemes for underwater shock and bubble analysis, hydrostatic pressure and airwater/seafloor boundaries, underwater explosion profiles, and fluid-backed shapes were also implemented...

  12. A novel magnet based 3D printed marker wand as basis for repeated in-shoe multi segment foot analysis: a proof of concept. (United States)

    Eerdekens, Maarten; Staes, Filip; Pilkington, Thomas; Deschamps, Kevin


    Application of in-shoe multi-segment foot kinematic analyses currently faces a number of challenges, including: (i) the difficulty to apply regular markers onto the skin, (ii) the necessity for an adequate shoe which fits various foot morphologies and (iii) the need for adequate repeatability throughout a repeated measure condition. The aim of this study therefore was to design novel magnet based 3D printed markers for repeated in-shoe measurements while using accordingly adapted modified shoes for a specific multi-segment foot model. Multi-segment foot kinematics of ten participants were recorded and kinematics of hindfoot, midfoot and forefoot were calculated. Dynamic trials were conducted to check for intra and inter-session repeatability when combining novel markers and modified shoes in a repeated measures design. Intraclass correlation coefficients were calculated to determine reliability. Both repeatability and reliability were proven to be good to excellent with maximum joint angle deviations of 1.11° for intra-session variability and 1.29° for same-day inter-session variability respectively and ICC values of >0.91. The novel markers can be reliably used in future research settings using in-shoe multi-segment foot kinematic analyses with multiple shod conditions.

  13. Repeated Causal Decision Making (United States)

    Hagmayer, York; Meder, Bjorn


    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

  14. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  15. Response matrix method for large LMFBR analysis

    International Nuclear Information System (INIS)

    King, M.J.


    The feasibility of using response matrix techniques for computational models of large LMFBRs is examined. Since finite-difference methods based on diffusion theory have generally found a place in fast-reactor codes, a brief review of their general matrix foundation is given first in order to contrast it to the general strategy of response matrix methods. Then, in order to present the general method of response matrix technique, two illustrative examples are given. Matrix algorithms arising in the application to large LMFBRs are discussed, and the potential of the response matrix method is explored for a variety of computational problems. Principal properties of the matrices involved are derived with a view to application of numerical methods of solution. The Jacobi iterative method as applied to the current-balance eigenvalue problem is discussed

  16. Climate Action Benefits: Methods of Analysis (United States)

    This page provides detailed information on the methods used in the CIRA analyses, including the overall framework, temperature projections, precipitation projections, sea level rise projections, uncertainty, and limitations.

  17. Numerical analysis in electromagnetics the TLM method

    CERN Document Server

    Saguet, Pierre


    The aim of this book is to give a broad overview of the TLM (Transmission Line Matrix) method, which is one of the "time-domain numerical methods". These methods are reputed for their significant reliance on computer resources. However, they have the advantage of being highly general.The TLM method has acquired a reputation for being a powerful and effective tool by numerous teams and still benefits today from significant theoretical developments. In particular, in recent years, its ability to simulate various situations with excellent precision, including complex materials, has been

  18. Methods for Mediation Analysis with Missing Data (United States)

    Zhang, Zhiyong; Wang, Lijuan


    Despite wide applications of both mediation models and missing data techniques, formal discussion of mediation analysis with missing data is still rare. We introduce and compare four approaches to dealing with missing data in mediation analysis including list wise deletion, pairwise deletion, multiple imputation (MI), and a two-stage maximum…

  19. Development of analysis methods for seismically isolated nuclear structures

    International Nuclear Information System (INIS)

    Yoo, Bong; Lee, Jae-Han; Koo, Gyeng-Hoi


    KAERI's contributions to the project entitled Development of Analysis Methods for Seismically Isolated Nuclear Structures under IAEA CRP of the intercomparison of analysis methods for predicting the behaviour of seismically isolated nuclear structures during 1996-1999 in effort to develop the numerical analysis methods and to compare the analysis results with the benchmark test results of seismic isolation bearings and isolated nuclear structures provided by participating countries are briefly described. Certain progress in the analysis procedures for isolation bearings and isolated nuclear structures has been made throughout the IAEA CRPs and the analysis methods developed can be improved for future nuclear facility applications. (author)

  20. Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method

    DEFF Research Database (Denmark)

    Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels


    The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models the probabi......The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models...... the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace...... method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous...

  1. Methods of stability analysis in nonlinear mechanics

    International Nuclear Information System (INIS)

    Warnock, R.L.; Ruth, R.D.; Gabella, W.; Ecklund, K.


    We review our recent work on methods to study stability in nonlinear mechanics, especially for the problems of particle accelerators, and compare our ideals to those of other authors. We emphasize methods that (1) show promise as practical design tools, (2) are effective when the nonlinearity is large, and (3) have a strong theoretical basis. 24 refs., 2 figs., 2 tabs

  2. Nuclear analysis methods in monitoring occupational health

    International Nuclear Information System (INIS)

    Clayton, E.


    With the increasing industrialisation of the world has come an increase in exposure to hazardous chemicals. Their effect on the body depends upon the concentration of the element in the work environment; its chemical form; the possible different routes of intake; and the individual's biological response to the chemical. Nuclear techniques of analysis such as neutron activation analysis (NAA) and proton induced X-ray emission analysis (PIXE), have played an important role in understanding the effects hazardous chemicals can have on occupationally exposed workers. In this review, examples of their application, mainly in monitoring exposure to heavy metals is discussed

  3. The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China

    Directory of Open Access Journals (Sweden)

    Yang Li


    Full Text Available This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%. By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP, and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%. By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.

  4. Computational methods for corpus annotation and analysis

    CERN Document Server

    Lu, Xiaofei


    This book reviews computational tools for lexical, syntactic, semantic, pragmatic and discourse analysis, with instructions on how to obtain, install and use each tool. Covers studies using Natural Language Processing, and offers ideas for better integration.

  5. Progress in spatial analysis methods and applications

    CERN Document Server

    Páez, Antonio; Buliung, Ron N; Dall'erba, Sandy


    This book brings together developments in spatial analysis techniques, including spatial statistics, econometrics, and spatial visualization, and applications to fields such as regional studies, transportation and land use, population and health.

  6. Analysis of queues methods and applications

    CERN Document Server

    Gautam, Natarajan


    Introduction Analysis of Queues: Where, What, and How?Systems Analysis: Key ResultsQueueing Fundamentals and Notations Psychology in Queueing Reference Notes Exercises Exponential Interarrival and Service Times: Closed-Form Expressions Solving Balance Equations via Arc CutsSolving Balance Equations Using Generating Functions Solving Balance Equations Using Reversibility Reference Notes ExercisesExponential Interarrival and Service Times: Numerical Techniques and Approximations Multidimensional Birth and Death ChainsMultidimensional Markov Chains Finite-State Markov ChainsReference Notes Exerci

  7. Analysis of Non Local Image Denoising Methods (United States)

    Pardo, Álvaro

    Image denoising is probably one of the most studied problems in the image processing community. Recently a new paradigm on non local denoising was introduced. The Non Local Means method proposed by Buades, Morel and Coll attracted the attention of other researches who proposed improvements and modifications to their proposal. In this work we analyze those methods trying to understand their properties while connecting them to segmentation based on spectral graph properties. We also propose some improvements to automatically estimate the parameters used on these methods.

  8. Analysis of the sweeped actuator line method


    Nathan Jörn; Masson Christian; Dufresne Louis; Churchfield Matthew


    The actuator line method made it possible to describe the near wake of a wind turbine more accurately than with the actuator disk method. Whereas the actuator line generates the helicoidal vortex system shed from the tip blades, the actuator disk method sheds a vortex sheet from the edge of the rotor plane. But with the actuator line come also temporal and spatial constraints, such as the need for a much smaller time step than with actuator disk. While the latter one only has to obey the Cour...

  9. Contributions to robust methods of creep analysis

    International Nuclear Information System (INIS)

    Penny, B.K.


    Robust methods for the predictions of deformations and lifetimes of components operating in the creep range are presented. The ingredients used for this are well-tried numerical techniques combined with the concepts of continuum damage and so-called reference stresses. The methods described are derived in order to obtain the maximum benefit during the early stages of design where broad assessments of the influences of material choice, loadings and geometry need to be made quickly and with economical use of computers. It is also intended that the same methods will be of value during operation if estimates of damage or if exercises in life extension or inspection timing are required. (orig.)

  10. Impact of the 2008 global financial crisis on the health of Canadians: repeated cross-sectional analysis of the Canadian Community Health Survey, 2007-2013. (United States)

    Nour, Sabrina; Labonté, Ronald; Bancej, Christina


    Despite a clear impact on the Canadian economy, little is known about the subsequent health impacts of the 2008 global financial crisis (GFC) in this country. This study fills this gap in knowledge by conducting a repeated cross-sectional analysis of the Canadian Community Health Survey (CCHS). Data from 7 cycles (2007-2013) of the CCHS were combined to form a large data set representative of the Canadian working-age population (15-64 years) residing in 1 of 10 provinces. A logistic regression model was used to determine whether exposure to various periods of the GFC resulted in increased odds of reporting poor mental health. Exposure was categorised into 4 periods based on political and economic indicators, as follows: precrisis period (baseline), initial crisis period, stimulus period and austerity period. Other outcomes investigated included: anxiety disorders (AD), mood disorders (MD), poor physical health and health-related behaviours (heavy alcohol drinking (HAD) and decreased fruit/vegetable consumption (FVC)). A significant increased odds of reporting poor mental health was observed during the austerity period compared with the precrisis period (OR=1.26 (1.16 to 1.32)); findings remain significant when adjusted for sex, marital status and education. Exposure to the austerity period was also significantly associated with increased odds of reporting AD, MD, HAD and decreased odds of FVC. No significant associations were observed for the poor self-perceived physical health variable. Statistically significant associations were observed between several negative health outcomes and the austerity period when compared with the precrisis period. Austerity has been linked to worsening health in other studies and represents an example of how the policy response can have greater detrimental impact on health than the financial crisis itself. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to

  11. Application of x-ray fluorescence (XRF) absolute analysis method for silica refractories

    International Nuclear Information System (INIS)

    Asakura, Hideo; Yamada, Yasujiro; Kansai, Kouhei; Tomatsu, Ichirou; Murata, Mamoru


    X-ray fluorescence (XRF) analysis is a rapid and precise quantitative analytical method for the determination of major and trace elements in many industries and academics. XRF analytical values are relative due to the use of the calibration curves calculated from measuring the reference standard materials such as Japanese Refractory Reference Materials (JRRM) series with certified values determined by wet chemical analysis. The development of the XRF analytical method from relative to absolute analysis will help much to determine the absolute values of samples from the fields where reference standard samples have not been prepared, and thus can be applied widely in many industries. The implement of the absolute XRF analysis for silica refractories requires high purity reagents and/or reference standard solution for the binary basic calibration curve, and theoretical matrix correction coefficients for the multi-components silica refractories analysis. The reproducibility and repeatability of this method for Al 2 O 3 5 mass% sample were 0.009 and 0.006 mass% in Al 2 O 3 and showed better values that those of ICP-AES recognized as an absolute method in JIS R 2212-2, which yielded 0.028 and 0.031 mass%, respectively. The XRF absolute analysis for JRRM 200 series, 201a and 205a does not show a bias but coincides with their certified values. (author)

  12. A method of uranium isotopes concentration analysis

    International Nuclear Information System (INIS)

    Lin Yuangen; Jiang Meng; Wu Changli; Duan Zhanyuan; Guo Chunying


    A basic method of uranium isotopes concentration is described in this paper. The iteration method is used to calculate the relative efficiency curve, by analyzing the characteristic γ energy spectrum of 235 U, 232 U and the daughter nuclide of 238 U, then the relative activity can be calculated, at last the uranium isotopes concentration can be worked out, and the result is validated by the experimentation. (authors)

  13. Comparative analysis of accelerogram processing methods

    International Nuclear Information System (INIS)

    Goula, X.; Mohammadioun, B.


    The work described here inafter is a short development of an on-going research project, concerning high-quality processing of strong-motion recordings of earthquakes. Several processing procedures have been tested, applied to synthetic signals simulating ground-motion designed for this purpose. The methods of correction operating in the time domain are seen to be strongly dependent upon the sampling rate. Two methods of low-frequency filtering followed by an integration of accelerations yielded satisfactory results [fr

  14. General method of quantitative spectrographic analysis

    International Nuclear Information System (INIS)

    Capdevila, C.; Roca, M.


    A spectrographic method was developed to determine 23 elements in a wide range of concentrations; the method can be applied to metallic or refractory samples. Previous melting with lithium tetraborate and germanium oxide is done in order to avoid the influence of matrix composition and crystalline structure. Germanium oxide is also employed as internal standard. The resulting beads ar mixed with graphite powder (1:1) and excited in a 10 amperes direct current arc. (Author) 12 refs

  15. AVIS: analysis method for document coherence

    International Nuclear Information System (INIS)

    Henry, J.Y.; Elsensohn, O.


    The present document intends to give a short insight into AVIS, a method which permits to verify the quality of technical documents. The paper includes the presentation of the applied approach based on the K.O.D. method, the definition of quality criteria of a technical document, as well as a description of the means of valuating these criteria. (authors). 9 refs., 2 figs

  16. Analysis of methods for quantitative renography

    International Nuclear Information System (INIS)

    Archambaud, F.; Maksud, P.; Prigent, A.; Perrin-Fayolle, O.


    This article reviews the main methods using renography to estimate renal perfusion indices and to quantify differential and global renal function. The review addresses the pathophysiological significance of estimated parameters according to the underlying models and the choice of the radiopharmaceutical. The dependence of these parameters on the region of interest characteristics and on the methods of background and attenuation corrections are surveyed. Some current recommendations are proposed. (authors). 66 refs., 8 figs

  17. Establishment of analytical methods for analysis of pesticides and organic chlorides by hplc

    International Nuclear Information System (INIS)

    Ghaffar, A.; Mashiatullah, A.; Javed, T.


    Methods for the analysis of organic chlorides and pesticides like dichlorophenol (DCP), DDT, Chlorpyrifos, Cypermethrin, Melathion, Diazinon and Pendimathalin by HPLC equipped with UV detector were established. The methods were optimized by applying different wavelengths and by changing the composition of mobile phase and flow rates. A series of analysis were performed to optimize the solvent composition, flow rate and wave length for analysis. The standard solutions with different concentration were prepared and run on HPLC. The calibration curves constructed from the peak area versus concentrations were linear (r = 0. 99). Efficiency of the developed methods was tested by taking known quantities of compounds in sample media by spiking separate portions of samples and repeating the analysis. The accuracy of the established methods was checked by interference and spiking the samples with the standard solution. The sample was analyzed and spiked with equal volume of standard solution. The calculated and actual analyzed concentrations were compared for the accuracy of method. The recoveries of samples ranged between 96-98 %, which prove the accuracy of the established methods. (orig./A.B.)

  18. Non-radioactive detection of trinucleotide repeat size variability. (United States)

    Tomé, Stéphanie; Nicole, Annie; Gomes-Pereira, Mario; Gourdon, Genevieve


    Many human diseases are associated with the abnormal expansion of unstable trinucleotide repeat sequences. The mechanisms of trinucleotide repeat size mutation have not been fully dissected, and their understanding must be grounded on the detailed analysis of repeat size distributions in human tissues and animal models. Small-pool PCR (SP-PCR) is a robust, highly sensitive and efficient PCR-based approach to assess the levels of repeat size variation, providing both quantitative and qualitative data. The method relies on the amplification of a very low number of DNA molecules, through sucessive dilution of a stock genomic DNA solution. Radioactive Southern blot hybridization is sensitive enough to detect SP-PCR products derived from single template molecules, separated by agarose gel electrophoresis and transferred onto DNA membranes. We describe a variation of the detection method that uses digoxigenin-labelled locked nucleic acid probes. This protocol keeps the sensitivity of the original method, while eliminating the health risks associated with the manipulation of radiolabelled probes, and the burden associated with their regulation, manipulation and waste disposal.

  19. Electromagnetic modeling method for eddy current signal analysis

    International Nuclear Information System (INIS)

    Lee, D. H.; Jung, H. K.; Cheong, Y. M.; Lee, Y. S.; Huh, H.; Yang, D. J.


    An electromagnetic modeling method for eddy current signal analysis is necessary before an experiment is performed. Electromagnetic modeling methods consists of the analytical method and the numerical method. Also, the numerical methods can be divided by Finite Element Method(FEM), Boundary Element Method(BEM) and Volume Integral Method(VIM). Each modeling method has some merits and demerits. Therefore, the suitable modeling method can be chosen by considering the characteristics of each modeling. This report explains the principle and application of each modeling method and shows the comparison modeling programs

  20. The ethnographic method and its relationship with the domain analysis

    Directory of Open Access Journals (Sweden)

    Manuel Alejandro Romero Quesada


    Full Text Available This paper analyzes the theoretical and conceptual relationship of the ethnographic method with domain analysis. A documentary analysis was performed, exploring the categories of domain analysis and ethnographic method.It was obtained as a result: the analysis of the points of contact between domain analysis and the ethnographic method from an epistemological, methodological and procedural terms. It is concluded that the ethnographic method is an important research tool to scan the turbulent socio-cultural scenarios that occur within discursive communities that constitute the domains of knowledge.