Sample records for jackknifing

  1. Jackknifing Disattenuated Correlations

    ERIC Educational Resources Information Center

    Rogers, W. Todd

    1976-01-01

    The utility of the jackknife for constructing confidence intervals and testing hypotheses about the disattenuated correlation is evaluated for small samples. Results of computer simulations support the claim that the jackknife can be used to construct confidence intervals but has limited utility for testing hypotheses about the disattenuated…

  2. ESTIMATING SPECIES RICHNESS USING THE JACKKNIFE PROCEDURE

    EPA Science Inventory

    An exact expression is given for the jackknife estimate of the number of species in a community and its variance when one uses quadrat sampling procedures. The jackknife estimate is a function of the number of species that occur in one and only one quadrat. The variance of the nu...

  3. The Infinitesimal Jackknife with Exploratory Factor Analysis

    ERIC Educational Resources Information Center

    Zhang, Guangjian; Preacher, Kristopher J.; Jennrich, Robert I.

    2012-01-01

    The infinitesimal jackknife, a nonparametric method for estimating standard errors, has been used to obtain standard error estimates in covariance structure analysis. In this article, we adapt it for obtaining standard errors for rotated factor loadings and factor correlations in exploratory factor analysis with sample correlation matrices. Both…

  4. overview Randomisation tests Cross-validation Jackknife Bootstrap Conclusion Introduction to resampling methods

    E-print Network

    Rossi, Vivien

    overview Randomisation tests Cross-validation Jackknife Bootstrap Conclusion Introduction resampling #12;overview Randomisation tests Cross-validation Jackknife Bootstrap Conclusion objectives of the course 1 to present resampling technics randomization tests cross-validation jackknife bootstrap 2

  5. A SAS Macro for Jackknifing the Results of Discriminant Analyses.

    ERIC Educational Resources Information Center

    Chant, David; Dalgleish, Lenard I.

    1992-01-01

    A Statistical Analysis System (SAS) macro procedure for performing a jackknife analysis on structure coefficients in discriminant analysis is described together with issues and caveats about its use in multivariate methods. An example of use of the SAS macro is provided. (SLD)

  6. Nonparametric Estimation of Standard Errors in Covariance Analysis Using the Infinitesimal Jackknife

    ERIC Educational Resources Information Center

    Jennrich, Robert I.

    2008-01-01

    The infinitesimal jackknife provides a simple general method for estimating standard errors in covariance structure analysis. Beyond its simplicity and generality what makes the infinitesimal jackknife method attractive is that essentially no assumptions are required to produce consistent standard error estimates, not even the requirement that the…

  7. Exhausted jackknife validation exemplified by prediction of temperature optimum in enzymatic reaction of cellulases.

    PubMed

    Yan, Shaomin; Wu, Guang

    2012-02-01

    This was the continuation of our previous study along the same line with more focus on technical details because the data are usually divided into two datasets, one for model development and the other for model validation during the development of predictive model. The widely used validation method is the delete-1 jackknife validation. However, no systematical studies were conducted to determine whether the jackknife validation with different deletions works better because the number of validations with different deletions increases in a factorial fashion. Therefore it is only small dataset that can be used for such an exhausted study. Cellulase is an enzyme playing an important role in modern industry, and many parameters related to cellulase in enzymatic reactions were poorly documented. With increased interests in cellulases in bio-fuel industry, the prediction of parameters in enzymatic reactions is listed on agenda. In this study, two aims were defined (a) which amino acid property works better to predict the temperature optimum and (b) with which deletion the jackknife validation works. The results showed that the amino acid distribution probability works better in predicting the optimum temperature of catalytic reaction by cellulase, and the delete-4, more precisely one-fifth deletion, jackknife validation works better. PMID:22207587

  8. A jackknife and voting classifier approach to feature selection and classification.

    PubMed

    Taylor, Sandra L; Kim, Kyoungmi

    2011-01-01

    With technological advances now allowing measurement of thousands of genes, proteins and metabolites, researchers are using this information to develop diagnostic and prognostic tests and discern the biological pathways underlying diseases. Often, an investigator's objective is to develop a classification rule to predict group membership of unknown samples based on a small set of features and that could ultimately be used in a clinical setting. While common classification methods such as random forest and support vector machines are effective at separating groups, they do not directly translate into a clinically-applicable classification rule based on a small number of features.We present a simple feature selection and classification method for biomarker detection that is intuitively understandable and can be directly extended for application to a clinical setting. We first use a jackknife procedure to identify important features and then, for classification, we use voting classifiers which are simple and easy to implement. We compared our method to random forest and support vector machines using three benchmark cancer 'omics datasets with different characteristics. We found our jackknife procedure and voting classifier to perform comparably to these two methods in terms of accuracy. Further, the jackknife procedure yielded stable feature sets. Voting classifiers in combination with a robust feature selection method such as our jackknife procedure offer an effective, simple and intuitive approach to feature selection and classification with a clear extension to clinical applications. PMID:21584263

  9. SECOND ORDER COMPARISON OF DIFFERENT BOOTSTRAP AND JACKKNIFE METHODS IN REGRESSION

    E-print Network

    Chatterjee, Snigdhansu

    SECOND ORDER COMPARISON OF DIFFERENT BOOTSTRAP AND JACKKNIFE METHODS IN REGRESSION Arup Bose of the Uncorrelated Weights Bootstrap; which is a generalisation of the paired bootstrap; over other resampling techniques is established under very general conditions. #12; 1 Introduction Consider the linear regression

  10. Determinants of health expenditure growth of the OECD countries: jackknife resampling plan estimates.

    PubMed

    Okunade, Albert A; Karakus, Mustafa C; Okeke, Charles

    2004-08-01

    Due to the lack of internal consistency across unit root and cointegration test methods for short time-series data, past research findings conflict on whether the OECD health expenditure data are stationary. Stationarity reasonably guarantees that the estimated OLS relationship is nonspurious. This paper departs from past investigations that applied asymptotic statistical tests of unit root to insufficient time-series lengths. Instead, data were calibrated in annual growth rates, in 5-year (1968-72, ..., 1993-97) partitions, for maximum likelihood estimation using flexible Box-Cox transformations model and bias-reducing jackknife resampling plan for data expansion. The drivers of OECD health care spending growth are economic and institutional. Findings from the growth convergence theory affirm that health care expenditure growth accords with conditional beta convergence. Statistical significance and optimal functional form models are not unique across the growth period models. Our findings exemplify the benefits of jackknife resampling plan for short data series, and caution researchers against imposing faulty functional forms and applying asymptotic statistical methods to short time-series regressions. Policy implications are discussed. PMID:15648560

  11. Use of the Multinomial Jackknife and Bootstrap in Generalized Nonlinear Canonical Correlation Analysis. Research Report 87-4.

    ERIC Educational Resources Information Center

    van der Burg, Eeke; de Leeuw, Jan

    The estimation of mean and standard errors of the eigenvalues and category quantifications in generalized non-linear canonical correlation analysis (OVERALS) is discussed. Starting points are the delta method equations. The jackknife and bootstrap methods are compared for providing finite difference approximations to the derivatives. Examining the…

  12. A Leisurely Look at the Bootstrap, the Jackknife, and Cross-Validation

    Microsoft Academic Search

    Bradley Efron; Gail Gong

    1983-01-01

    This is an invited expository article for The American Statistician. It reviews the nonparametric estimation of statistical error, mainly the bias and standard error of an estimator, or the error rate of a prediction rule. The presentation is written at a relaxed mathematical level, omitting most proofs, regularity conditions, and technical details.

  13. Jackknife instrumental variables estimation: replication and extension of angrist, imbens and krueger (1999)

    Microsoft Academic Search

    Anton Nakov

    2010-01-01

    I replicate most of the results in Angrist, Imbens, and Krueger (Journal of Applied Econometrics 1999; 14: 57-67), point to a possible error in and re-estimate Model 3, and analyze some simple extensions. The programming code, data, and results are available at

  14. Statistical Inference on Associated Fertility Life Parameters Using Jackknife Technique: Computational Aspects

    Microsoft Academic Search

    Aline de H. N. Maia; Alfredo J. B. Luiz; Clayton Campanhola

    2000-01-01

    Knowledge of population growth potential is crucial for studying population dynamics and for establishing management tactics for pest control. Estimation of population growth can be achieved with fertility life tables because they synthesize data on reproduction and mortality of a population. The five main parameters associated with a fertility life table are as follows: (1) the net reproductive rate (Ro),

  15. Cross-Validation, the Jackknife, and the Bootstrap: Excess Error Estimation in Forward Logistic Regression

    Microsoft Academic Search

    Gail Gong

    1986-01-01

    Given a prediction rule based on a set of patients, what is the probability of incorrectly predicting the outcome of a new patient? Call this probability the true error. An optimistic estimate is the apparent error, or the proportion of incorrect predictions on the original set of patients, and it is the goal of this article to study estimates of

  16. A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

    Microsoft Academic Search

    Jerrold I. Davis; Dennis W. Stevenson; Gitte Petersen; Ole Seberg; Lisa M. Campbell; John V. Freudenstein; Douglas H. Goldman; Christopher R. Hardy; Fabian A. Michelangeli; Mark P. Simmons; Chelsea D. Specht; Francisco Vergara-Silva; María Gandolfo

    2004-01-01

    A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid

  17. 46 CFR 160.043-4 - Construction and workmanship.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener...Vessels § 160.043-4 Construction and workmanship. (a)...

  18. 46 CFR 160.043-4 - Construction and workmanship.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener...Vessels § 160.043-4 Construction and workmanship. (a)...

  19. Second order accurate variance estimation in poststratified two-stage sampling 

    E-print Network

    Kim, Kyong Ryun

    2007-09-17

    We proposed new variance estimators for the poststratified estimator of the population total in two-stage sampling. The linearization or Taylor series variance estimator and the jackknife linearization variance estimator are popular...

  20. 29 CFR 1918.54 - Rigging gear.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...54 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED...provided, the guys shall be so placed as to produce a minimum stress and not permit the boom to jackknife. (c) Boom...

  1. 29 CFR 1918.54 - Rigging gear.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...54 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED...provided, the guys shall be so placed as to produce a minimum stress and not permit the boom to jackknife. (c) Boom...

  2. 29 CFR 1918.54 - Rigging gear.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...54 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED...provided, the guys shall be so placed as to produce a minimum stress and not permit the boom to jackknife. (c) Boom...

  3. 29 CFR 1918.54 - Rigging gear.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...54 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED...provided, the guys shall be so placed as to produce a minimum stress and not permit the boom to jackknife. (c) Boom...

  4. 29 CFR 1918.54 - Rigging gear.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...54 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED...provided, the guys shall be so placed as to produce a minimum stress and not permit the boom to jackknife. (c) Boom...

  5. Second order accurate variance estimation in poststratified two-stage sampling

    E-print Network

    Kim, Kyong Ryun

    2007-09-17

    We proposed new variance estimators for the poststratified estimator of the population total in two-stage sampling. The linearization or Taylor series variance estimator and the jackknife linearization variance estimator are popular...

  6. Resampling time series using missing values techniques

    Microsoft Academic Search

    Andrés M. Alonso; Daniel Peña; Juan Romo

    2003-01-01

    Several techniques for resampling dependent data have already been proposed. In this paper we use missing values techniques\\u000a to modify the moving blocks jackknife and bootstrap. More specifically, we consider the blocks of deleted observations in\\u000a the blockwise jackknife as missing data which are recovered by missing values estimates incorporating the observation dependence\\u000a structure. Thus, we estimate the variance of

  7. September 28, 2010 QUEEN'S UNIVERSITY AT KINGSTON

    E-print Network

    Offin, Dan

    . Modular forms are analytic functions which play a central role in modern number theory. We describe:30 p.m. Place: Jeffery 115 Speaker: Wesley Burr, Queen's University Title: The Jackknife: An Introduction Abstract Attached Wednesday, September 29 Curves Seminar Time: 3:30 p.m. ­ 5:00 p.m. Place

  8. Geographic variation in the G matrices of wild populations of the barn swallow

    Microsoft Academic Search

    D A Roff; T Mousseau; A P Møller; F de Lope; N Saino

    2004-01-01

    In this paper, we present an analysis of genetic variation in three wild populations of the barn swallow, Hirundo rustica. We estimated the P, E, and G matrices for six linear morphological measurements and tested for variation among populations using the Flury hierarchical method and the jackknife followed by MANOVA method. Because of nonpositive-definite matrices, we had to employ ‘bending’

  9. Amphibians in a human-dominated landscape: the community structure is related to habitat features and isolation

    Microsoft Academic Search

    Gentile Francesco Ficetola; Fiorenza De Bernardi

    2004-01-01

    We studied amphibian populations in a human-dominated landscape, in Northern Italy, to evaluate the effects of patch quality and isolation on each species distribution and community structure. We used logistic and linear multiple regression to relate amphibian presence during the breeding season in 84 wetlands to wetland features and isolation. Jackknife procedure was used to evaluate predictive capability of the

  10. Amphibians in a human-dominated landscape: the community structure is related to habitat features and isolation

    Microsoft Academic Search

    Gentile Francesco Ficetola; Fiorenza De Bernardi

    We studied amphibian populations in a human-dominated landscape, in Northern Italy, to evaluate the effects of patch quality and isolation on each species distribution and community structure. We used logistic and linear multiple regression to relate am- phibian presence during the breeding season in 84 wetlands to wetland features and isolation. Jackknife procedure was used to evaluate predictive capability of

  11. A Simulation Comparison Study for Estimating the Process Capability Index C

    Microsoft Academic Search

    Shu-Fei Wu

    Process capability indices had been widely used to evaluate the process performance. The process capability index C? pm proposed by Chan et al. (2) does take into account of the proximity of the process mean to the target value T for asymmetric tolerance. For point estimation of this index, a Jackknife method is presented to reduce bias. Five interval esti-

  12. PER UNIT COSTS TO OWN AND OPERATE FARM MACHINERY

    Microsoft Academic Search

    Aaron J. Beaton; Kevin C. Dhuyvetter; Terry L. Kastens

    2003-01-01

    Entropy and jackknife estimation procedures were used to find that custom rates are 20.3% lower than the true cost to own and operate machinery for an average size Kansas farm. A method was then developed to estimate a farms total machinery costs with which to benchmark machinery costs.

  13. Bootstrapping an Econometric Model: Some Empirical Results

    Microsoft Academic Search

    David A. Freedman; Stephen C. Peters

    1984-01-01

    The bootstrap, like the jackknife, is a technique for estimating standard errors. The idea is to use Monte Carlo simulation, based on a nonparametric estimate of the underlying error distribution. The bootstrap will be applied to an econometric model describing the demand for capital, labor, energy, and materials. The model is fitted by three-stage least squares. In sharp contrast with

  14. BIOINFORMATICS APPLICATIONS NOTE Vol. 20 no. 12 2004, pages 19771979

    E-print Network

    and Cell Biology, Iowa State University, Ames, IA 50011, USA. masked progressive alignment. The NJ trees/bth180 LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference Carolyn of an alignment in a revealing way. Lumber- Jack creates non-random jackknifed alignments by progress- ively

  15. Variance Estimation Using Replication Methods in Structural Equation Modeling with Complex Sample Data

    ERIC Educational Resources Information Center

    Stapleton, Laura M.

    2008-01-01

    This article discusses replication sampling variance estimation techniques that are often applied in analyses using data from complex sampling designs: jackknife repeated replication, balanced repeated replication, and bootstrapping. These techniques are used with traditional analyses such as regression, but are currently not used with structural…

  16. A Demonstration of a Systematic Item-Reduction Approach Using Structural Equation Modeling

    ERIC Educational Resources Information Center

    Larwin, Karen; Harvey, Milton

    2012-01-01

    Establishing model parsimony is an important component of structural equation modeling (SEM). Unfortunately, little attention has been given to developing systematic procedures to accomplish this goal. To this end, the current study introduces an innovative application of the jackknife approach first presented in Rensvold and Cheung (1999). Unlike…

  17. This is page viii Printer: Opaque this

    E-print Network

    Asmussen, Søren

    . . . . . . . . . . . . . . . . . 118 8 Perfect Sampling . . . . . . . . . . . . . . . . . . . . . 120 V Variance-Reduction Methods 126 by Expectations 77 5 Sectioning, Jackknifing, and Bootstrapping . . . . . . . 80 6 Variance/Bias Trade-Off Issues Formulas for the Bias and Variance . . . . . . . . . . . 102 3 Variance Estimation for Stationary Processes

  18. an introduction to Principal Component Analysis

    E-print Network

    Masci, Frank

    an introduction to Principal Component Analysis (PCA) #12;abstract Principal component analysis is the Wishart distribution else utilize a bootstrap approximation #12;usage of PCA: Probability distribution for and then analytic expressions exist* for else bootstrap and jackknife approximations exist *see references, esp

  19. The truck backer-upper: an example of self-learning in neural networks

    Microsoft Academic Search

    Derrick Nguyen; Bernard Widrow

    1989-01-01

    Neural networks can be used to solve highly nonlinear control problems. A two-layer neural network containing 26 adaptive neural elements has learned to back up a computer-simulated trailer truck to a loading dock, even when initially jackknifed. It is not yet known how to design a controller to perform this steering task. Nevertheless, the neural net was able to learn

  20. Resampling Methods Revisited: Advancing the Understanding and Applications in Educational Research

    ERIC Educational Resources Information Center

    Bai, Haiyan; Pan, Wei

    2008-01-01

    Resampling methods including randomization test, cross-validation, the jackknife and the bootstrap are widely employed in the research areas of natural science, engineering and medicine, but they lack appreciation in educational research. The purpose of the present review is to revisit and highlight the key principles and developments of…

  1. Tractor-Semitrailer Dynamics: Design of the Fifth Wheel

    Microsoft Academic Search

    WILLIAM E. TOBLER; ALLAN I. KRAUTER

    1972-01-01

    The nonlinear equations of motion are derived for a tractor-semitrailer truck where both the itractor and the semitrailer yaw, pitch, roll, and translate. Special emphasis is placed on the constraints imposed by the fifth wheel on the vehicle motion. In particular, the effects of two proposed fifth wheel design changes on the jackknifing behavior of a vehicle in a turning,

  2. Steering and independent braking control for tractor-semitrailer vehicles in automated highway systems

    Microsoft Academic Search

    Chieh Chen; Masayoshi Tomizuka

    1995-01-01

    A steering and independent braking control for a tractor-semitrailer vehicle is proposed to achieve lane following in automated highway systems. Independent braking force of the semitrailer is utilized to stabilize the trailer yaw motion and thus to prevent the potential occurrence of jack-knifing. The control algorithm is designed by the input\\/output linearization and the adaptive backstepping design methodologies

  3. Resampling methods for evaluating classification accuracy of wildlife habitat models

    Microsoft Academic Search

    David L. Verbyla; John A. Litvaitis

    1989-01-01

    Predictive models of wildlife-habitat relationships often have been developed without being tested The apparent classification accuracy of such models can be optimistically biased and misleading. Data resampling methods exist that yield a more realistic estimate of model classification accuracy These methods are simple and require no new sample data. We illustrate these methods (cross-validation, jackknife resampling, and bootstrap resampling) with

  4. Growth estimation of mangrove cockle Anadara tuberculosa (Mollusca: Bivalvia): application and evaluation of length-based methods.

    PubMed

    Flores, Luis A

    2011-03-01

    Growth is one of the key processes in the dynamic of exploited resources, since it provides part of the information required for structured population models. Growth of mangrove cockle, Anadara tuberculosa was estimated through length-based methods (ELEFAN I y NSLCA) and using diverse shell length intervals (SLI). The variability of L(infinity), k and phi prime (phi') estimates and the effect of each sample were quantified by jackknife techniques. Results showed the same L(infinity) estimates from ELEFAN I and NSLCA across each SLI used, and all L(infinity) were within the expected range. On the contrary, k estimates differed between methods. Jackknife estimations uncovered the tendency of ELEFAN I to overestimate k with increases in SLI, and allowed the identification of differences in uncertainty (PE and CV) between both methods. The average values of phi' derived from NSCLA1.5 and length-age sources were similar and corresponded to ranges reported by other authors. Estimates of L(infinity), k and (phi' from NSCLA1.5 were 85.97 mm, 0.124/year and 2.953 with jackknife and 86.36mm de L(infinity), 0.110/year de k and 2.914 de phi' without jackknife, respectively. Based on the observed evidence and according to the biology of the species, NSCLA is suggested to be used with jackknife and a SLI of 1.5 mm as an ad hoc approach to estimate the growth parameters of mangrove cockle. PMID:21513195

  5. Sampling effort and estimates of species richness based on prepositioned area electrofisher samples

    USGS Publications Warehouse

    Bowen, Z.H.; Freeman, Mary C.

    1998-01-01

    Estimates of species richness based on electrofishing data are commonly used to describe the structure of fish communities. One electrofishing method for sampling riverine fishes that has become popular in the last decade is the prepositioned area electrofisher (PAE). We investigated the relationship between sampling effort and fish species richness at seven sites in the Tallapoosa River system, USA based on 1,400 PAE samples collected during 1994 and 1995. First, we estimated species richness at each site using the first-order jackknife and compared observed values for species richness and jackknife estimates of species richness to estimates based on historical collection data. Second, we used a permutation procedure and nonlinear regression to examine rates of species accumulation. Third, we used regression to predict the number of PAE samples required to collect the jackknife estimate of species richness at each site during 1994 and 1995. We found that jackknife estimates of species richness generally were less than or equal to estimates based on historical collection data. The relationship between PAE electrofishing effort and species richness in the Tallapoosa River was described by a positive asymptotic curve as found in other studies using different electrofishing gears in wadable streams. Results from nonlinear regression analyses indicted that rates of species accumulation were variable among sites and between years. Across sites and years, predictions of sampling effort required to collect jackknife estimates of species richness suggested that doubling sampling effort (to 200 PAEs) would typically increase observed species richness by not more than six species. However, sampling effort beyond about 60 PAE samples typically increased observed species richness by < 10%. We recommend using historical collection data in conjunction with a preliminary sample size of at least 70 PAE samples to evaluate estimates of species richness in medium-sized rivers. Seventy PAE samples should provide enough information to describe the relationship between sampling effort and species richness and thus facilitate evaluation of a sampling effort.

  6. Life Table and Consumption Capacity of Corn Earworm, Helicoverpa armigera, Fed Asparagus, Asparagus officinalis

    PubMed Central

    Jha, Ratna Kumar; Tuan, Shu-Jen; Chi, Hsin; Tang, Li-Cheng

    2014-01-01

    The life table and consumption rate of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) reared on asparagus, Asparagus officinalis L. (Asparagales: Asparagaceae) were studied under laboratory conditions to assess their interaction. Development, survival, fecundity, and consumption data were analyzed by the age-stage, two-sex life table. This study indicated that asparagus is a natural host of H. armigera. However, the poor nutritional content in asparagus foliage and the poor fitness of H. armigera that fed on asparagus indicated that asparagus is a suboptimal host in comparison to hybrid sweet corn. The uncertainty associated with life table parameters was estimated by using jackknife and bootstrap techniques, and the results were compared for statistical inference. The intrinsic rate of increase (r), finite rate of increase (?), net reproductive rate (R0), and mean generation time (T) were estimated by the jackknife technique to be 0.0780 day-1, 1.0811 day-1, 67.4 offspring, and 54.8 days, respectively, while those estimated by the bootstrap technique were 0.0752 day-1, 1.0781 day-1, 68.0 offspring, and 55.3 days, respectively. The net consumption rate of H. armigera, as estimated by the jackknife and bootstrap technique, was 1183.02 and 1132.9 mg per individual, respectively. The frequency distribution of sample means obtained by the jackknife technique failed the normality test, while the bootstrap results fit the normal distribution well. By contrast, the relationship between the mean fecundity and the net reproductive rate, as estimated by the bootstrap technique, was slightly inconsistent with the relationship found by mathematical proof. The application of the jackknife and bootstrap techniques in estimating population parameters requires further examination. PMID:25373181

  7. Life table and consumption capacity of corn earworm, Helicoverpa armigera, fed asparagus, Asparagus officinalis.

    PubMed

    Jha, Ratna Kumar; Tuan, Shu-Jen; Chi, Hsin; Tang, Li-Cheng

    2014-01-01

    The life table and consumption rate of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) reared on asparagus, Asparagus officinalis L. (Asparagales: Asparagaceae) were studied under laboratory conditions to assess their interaction. Development, survival, fecundity, and consumption data were analyzed by the age-stage, twosex life table. This study indicated that asparagus is a natural host of H. armigera. However, the poor nutritional content in asparagus foliage and the poor fitness of H. armigera that fed on asparagus indicated that asparagus is a suboptimal host in comparison to hybrid sweet corn. The uncertainty associated with life table parameters was estimated by using jackknife and bootstrap techniques, and the results were compared for statistical inference. The intrinsic rate of increase (r), finite rate of increase (?), net reproductive rate (R0), and mean generation time (T) were estimated by the jackknife technique to be 0.0780 day(-1), 1.0811 day(-1), 67.4 offspring, and 54.8 days, respectively, while those estimated by the bootstrap technique were 0.0752 day(-1), 1.0781 day(-1), 68.0 offspring, and 55.3 days, respectively. The net consumption rate of H. armigera, as estimated by the jackknife and bootstrap technique, was 1183.02 and 1132.9 mg per individual, respectively. The frequency distribution of sample means obtained by the jackknife technique failed the normality test, while the bootstrap results fit the normal distribution well. By contrast, the relationship between the mean fecundity and the net reproductive rate, as estimated by the bootstrap technique, was slightly inconsistent with the relationship found by mathematical proof. The application of the jackknife and bootstrap techniques in estimating population parameters requires further examination. PMID:25373181

  8. First season QUaD CMB temperature and polarization power spectra

    E-print Network

    QUaD Collaboration; P. Ade; J. Bock; M. Bowden; M. L. Brown; G. Cahill; J. E. Carlstrom; P. G. Castro; S. Church; T. Culverhouse; R. Friedman; K. Ganga; W. K. Gear; J. Hinderks; J. Kovac; A. E. Lange; E. Leitch; S. J. Melhuish; J. A. Murphy; A. Orlando; R. Schwarz; C. O'Sullivan; L. Piccirillo; C. Pryke; N. Rajguru; B. Rusholme; A. N. Taylor; K. L. Thompson; E. Y. S. Wu; M. Zemcov

    2007-05-16

    QUaD is a bolometric CMB polarimeter sited at the South Pole, operating at frequencies of 100 and 150 GHz. In this paper we report preliminary results from the first season of operation (austral winter 2005). All six CMB power spectra are presented derived as cross spectra between the 100 and 150 GHz maps using 67 days of observation in a low foreground region of approximately 60 square degrees. This data is a small fraction of the data acquired to date. The measured spectra are consistent with the LCDM cosmological model. We perform jackknife tests which indicate that the observed signal has negligible contamination from instrumental systematics. In addition by using a frequency jackknife we find no evidence for foreground contamination.

  9. New methodology of influential point detection in regression model building for the prediction of metabolic clearance rate of glucose

    Microsoft Academic Search

    Milan Meloun; Martin Hill; Jana Vrbikova ´; Sona Stanicka ´; Jan Skrha

    2004-01-01

    Identifying outliers and high-leverage points is a fun- damental step in the least-squares regression model building process. The examination of data quality involves the detection of influential points, outliers and high-leverages, which cause many problems in regression analysis. On the basis of a statistical anal- ysis of the residuals (classical, normalized, standard- ized, jackknife, predicted and recursive) and diagonal elements

  10. Estimation of the size of a closed population when capture probabilities vary among animals

    USGS Publications Warehouse

    Burnham, K.P.; Overton, W.S.

    1978-01-01

    A model which allows capture probabilities to vary by individuals is introduced for multiple recapture studies n closed populations. The set of individual capture probabilities is modelled as a random sample from an arbitrary probability distribution over the unit interval. We show that the capture frequencies are a sufficient statistic. A nonparametric estimator of population size is developed based on the generalized jackknife; this estimator is found to be a linear combination of the capture frequencies. Finally, tests of underlying assumptions are presented.

  11. Resampling Methods: Concepts, Applications, and Justification

    NSDL National Science Digital Library

    Yu, Chong Hu

    Created by Chong Hu Yu for Cisco Systems, this journal article is a summary of resampling methods such as the jackknife, bootstrap, and permutation tests. It summarizes the tests, describes various software to perform the tests, and has a list of references. The author provides an introduction, resampling methods, software for, the rationale of supporting, criticisms of resampling, a conclusion and references. This is a expansive resource which goes very in-depth into the study of resampling methods.

  12. Calibration of Littoral Diatoms to Water Chemistry in Standing Fresh Waters (Flanders, Lower Belgium): Inference Models for Historical Sediment Assemblages

    Microsoft Academic Search

    Luc Denys

    2006-01-01

    Relationships between littoral surface-sediment diatom assemblages and ambient limnological conditions were examined in 186\\u000a lentic fresh waters throughout lower Belgium (Flanders). Most of these waters were small, unstratified, alkaline and rich\\u000a in nutrients. Using weighted-averaging techniques, robust and accurate transfer functions were developed for median pH-values\\u000a ranging from 3.4 to 9.3 and dissolved inorganic carbon concentrations from ?1 (jackknifed r

  13. Angiosperm phylogeny inferred from 18S rDNA, rbcL , and atpB sequences

    Microsoft Academic Search

    DOUGLAS E SOLTIS; PAMELA S SOLTIS; MARK W CHASE; MARK E MORT; DIRK C ALBACH; MICHAEL ZANIS; VINCENT SAVOLAINEN; WILLIAM H HAHN; SARA B HOOT; MICHAEL F FAY; MICHAEL AXTELL; SUSAN M SWENSEN; LINDA M PRINCE; W JOHN KRESS; KEVIN C NIXON; JAMES S FARRIS

    2000-01-01

    A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades.

  14. Computer-intensive methods in statistical analysis

    Microsoft Academic Search

    D. N. Politis

    1998-01-01

    As far back as the late 1970s, the impact of affordable, high-speed computers on the theory and practice of modern statistics was recognized by Efron (1979, 1982). As a result, the bootstrap and other computer-intensive statistical methods (such as subsampling and the jackknife) have been developed extensively since that time and now constitute very powerful (and intuitive) tools to do

  15. Sample size effects in multivariate fitting of correlated data

    E-print Network

    D. Toussaint; W. Freeman

    2008-08-24

    A common problem in analysis of experiments or in lattice QCD simulations is fitting a parameterized model to the average over a number of samples of correlated data values. If the number of samples is not infinite, estimates of the variance of the parameters ("error bars") and of the goodness of fit are affected. We illustrate these problems with numerical simulations, and calculate approximate corrections to the variance of the parameters for estimates made in the standard way from derivatives of the parameters' probability distribution as well as from jackknife and bootstrap estimates.

  16. The accurate location of the injection-induced microearthquakes in German Continental Deep Drilling Program

    NASA Astrophysics Data System (ADS)

    Tu, Yi-Min; Chen, Yun-Tai

    2002-11-01

    From August 21, 2000 to October 20, 2000 a fluid injection-induced seismicity experiment has been carried out in the KTB (German Continental Deep Drilling Program). The KTB seismic network recorded more than 2 700 events. Among them 237 events were of high signal-to-noise ratio, and were processed and accurately located. When the events were located, non KTB events were weeded out by Wadati’s method. The standard deviation, mean and median were obtained by Jackknife’s technique, and finally the events were accurately located by Geiger’s method so that the mean error is about 0.1 km. No earthquakes with focal depth greater than 9.3 km, which is nearly at the bottom of the hole, were detected. One of the explanation is that at such depths the stress levels may not close to the rock’s frictional strength so that failure could not be induced by the relatively small perturbation in pore pressure. Or at these depths there may be no permeable, well-oriented faults. This depth may be in close proximity to the bottom of the hole to the brittle-ductile transition, even in this relatively stable interior of the interaplate. This phenomenon is explained by the experimental results and geothermal data from the superdeep borehole.

  17. Estimation of bioconcentration factors of nonionic organic compounds in fish by molecular connectivity indices and polarity correction factors.

    PubMed

    Lu, X; Tao, S; Hu, H; Dawson, R W

    2000-11-01

    A bioconcentration factor (BCF) estimation model for a wide range of nonionic organic compounds was developed on the basis of molecular connectivity indices and polarity correction factors. The nonlinear topological modeling using polarity correction factors resulted in the best BCF estimation quality for all of the 239 compounds studied, with a mean absolute estimation error of 0.478 log units. Residual analysis indicated that the estimation errors came from many sources including BCF measurement, test species, and selection of descriptors. Statistical robustness of the developed model was validated by modified jackknifed tests where random deletion of a set of compounds and specific deletion of a class of compounds were both performed. Comparison between the MCI-based (molecular connectivity indices) model and a Kow-based (octanol/water partition coefficient) model revealed that the BCF estimation based on topological parameters was as good as that achieved by Kow. PMID:11057696

  18. Robust estimation of population size when capture probabilities vary among animals

    USGS Publications Warehouse

    Burnham, K.P.; Overton, W.S.

    1979-01-01

    A model is given for multiple recapture studies on closed populations which allows capture probabilities to vary among individuals. The capture probability of each individual is assumed to be constant over time. Based on this model we give a nonparametric estimation procedure for population size. The estimator involves selecting one of a sequence of estimator which are each linear combinations of the capture frequencies. The individual estimators are derived from the generalized jackknife method. We also give a goodness of fit test for the model's assumption that individual capture probabilities do not change during the study. The robustness of the estimation procedure is investigated with a simulation study. By virtue of this study, and the theoretical nature of the estimator, it is judged to be robust to moderate variations in individual capture probabilities which may occur in commonly used short-term livetrapping studies.

  19. Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2.

    PubMed

    Sterckx, Yann G J; Volkov, Alexander N; Vranken, Wim F; Kragelj, Jaka; Jensen, Malene Ringkjøbing; Buts, Lieven; Garcia-Pino, Abel; Jové, Thomas; Van Melderen, Laurence; Blackledge, Martin; van Nuland, Nico A J; Loris, Remy

    2014-06-10

    Antitoxins from prokaryotic type II toxin-antitoxin modules are characterized by a high degree of intrinsic disorder. The description of such highly flexible proteins is challenging because they cannot be represented by a single structure. Here, we present a combination of SAXS and NMR data to describe the conformational ensemble of the PaaA2 antitoxin from the human pathogen E. coli O157. The method encompasses the use of SAXS data to filter ensembles out of a pool of conformers generated by a custom NMR structure calculation protocol and the subsequent refinement by a block jackknife procedure. The final ensemble obtained through the method is validated by an established residual dipolar coupling analysis. We show that the conformational ensemble of PaaA2 is highly compact and that the protein exists in solution as two preformed helices, connected by a flexible linker, that probably act as molecular recognition elements for toxin inhibition. PMID:24768114

  20. Statistical modelling of tropical cyclone tracks: a comparison of models for the variance of trajectories

    E-print Network

    Hall, T; Hall, Tim; Jewson, Stephen

    2005-01-01

    We describe results from the second stage of a project to build a statistical model for hurricane tracks. In the first stage we modelled the unconditional mean track. We now attempt to model the unconditional variance of fluctuations around the mean. The variance models we describe use a semi-parametric nearest neighbours approach in which the optimal averaging length-scale is estimated using a jack-knife out-of-sample fitting procedure. We test three different models. These models consider the variance structure of the deviations from the unconditional mean track to be isotropic, anisotropic but uncorrelated, and anisotropic and correlated, respectively. The results show that, of these models, the anisotropic correlated model gives the best predictions of the distribution of future positions of hurricanes.

  1. Cascaded multiple classifiers for secondary structure prediction.

    PubMed Central

    Ouali, M.; King, R. D.

    2000-01-01

    We describe a new classifier for protein secondary structure prediction that is formed by cascading together different types of classifiers using neural networks and linear discrimination. The new classifier achieves an accuracy of 76.7% (assessed by a rigorous full Jack-knife procedure) on a new nonredundant dataset of 496 nonhomologous sequences (obtained from G.J. Barton and J.A. Cuff). This database was especially designed to train and test protein secondary structure prediction methods, and it uses a more stringent definition of homologous sequence than in previous studies. We show that it is possible to design classifiers that can highly discriminate the three classes (H, E, C) with an accuracy of up to 78% for beta-strands, using only a local window and resampling techniques. This indicates that the importance of long-range interactions for the prediction of beta-strands has been probably previously overestimated. PMID:10892809

  2. Galaxy-Galaxy Lensing in Dark Energy Survey Science Verification Data

    NASA Astrophysics Data System (ADS)

    Jain, Bhuvnesh; Clampitt, Joseph; Sanchez, Carles; Maccrann, Niall; Kwan, Juliana; Dark Energy Survey Collaboration

    2015-04-01

    We present galaxy-galaxy lensing results from 150 square degrees of Dark Energy Survey science verification data. Our lens sample consists of red galaxies which are specifically selected to have a low photometric redshift outlier rate. The lenses cover a wide redshift range 0.2 < z < 0.8, which divided into three bins yields a S/N > 20 lensing measurement for each bin. The result is checked by performing a number of null tests, including various checks on the shear catalog and photometric redshifts. Covariances from jackknife subsamples of the data are validated with a suite of 100 mock surveys. We fit an HOD model that constrains the lens sample's central halo mass, mass-luminosity scatter, and satellite population.

  3. Isotopic and Elemental Composition of Roasted Coffee as a Guide to Authenticity and Origin.

    PubMed

    Carter, James F; Yates, Hans S A; Tinggi, Ujang

    2015-06-24

    This study presents the stable isotopic and elemental compositions of single-origin, roasted coffees available to retail consumers. The ?(13)C, ?(15)N, and ?(18)O compositions were in agreement with those previously reported for green coffee beans. The ?(15)N composition was seen to be related to organic cultivation, reflected in both ?(2)H and ?(18)O compositions. The ?(13)C composition of extracted caffeine differed little from that of the bulk coffee. Stepwise discriminant analysis with jackknife tests, using isotopic and elemental data, provided up to 77% correct classification of regions of production. Samples from Africa and India were readily classified. The wide range in both isotopic and elemental compositions of samples from other regions, specifically Central/South America, resulted in poor discrimination between or within these regions. Simpler X-Y and geo-spatial plots of the isotopic data provided effective visual means to distinguish between coffees from different regions. PMID:26001050

  4. Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study.

    PubMed

    Araújo, Susana; Henriques, Isabel S; Leandro, Sérgio Miguel; Alves, Artur; Pereira, Anabela; Correia, António

    2014-02-01

    Gulls were reported as sources of fecal pollution in coastal environments and potential vectors of human infections. Microbial source tracking (MST) methods were rarely tested to identify this pollution origin. This study was conducted to ascertain the source of water fecal contamination in the Berlenga Island, Portugal. A total of 169 Escherichia coli isolates from human sewage, 423 isolates from gull feces and 334 water isolates were analyzed by BOX-PCR. An average correct classification of 79.3% was achieved. When an 85% similarity cutoff was applied 24% of water isolates were present in gull feces against 2.7% detected in sewage. Jackknifing resulted in 29.3% of water isolates classified as gull, and 10.8% classified as human. Results indicate that gulls constitute a major source of water contamination in the Berlenga Island. This study validated a methodology to differentiate human and gull fecal pollution sources in a real case of a contaminated beach. PMID:24140684

  5. Indian Ocean sea surface temperature and Eritrean highlands rainfall

    NASA Astrophysics Data System (ADS)

    Mebrhatu, Mehari Tesfazgi; Walker, Sue

    Given an improved understanding of Eritrean climate, numerous benefits could be expected in many related activities: better management of agriculture and water resources stemming from more reliable seasonal predictions. In this study the Indian Ocean sea surface temperature was identified out of 11 predictors to be the most influential predictor for the July and August rainfall in the highlands of Eritrea. A statistical model was developed for peak rainy months (July-August, JA) of the study area. The model jack-knife skill test gave the correlation of 0.89 and 0.85 for Asmara and Mendefera stations, which is very high for rainfall prediction. Thus, validation of the model shows that the model can reproduce the measured monthly sum for JA rainfall totals with confidence.

  6. A model recognition approach to the prediction of all-helical membrane protein structure and topology.

    PubMed

    Jones, D T; Taylor, W R; Thornton, J M

    1994-03-15

    This paper describes a new method for the prediction of the secondary structure and topology of integral membrane proteins based on the recognition of topological models. The method employs a set of statistical tables (log likelihoods) complied from well-characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. The statistical tables show definite biases toward certain amino acid species on the inside, middle, and outside of a cellular membrane. Using a set of 83 integral membrane protein sequences taken from a variety of bacterial, plant, and animal species, and a strict jackknifing procedure, where each protein (along with any detectable homologues) is removed from the training set used to calculate the tables before prediction, the method successfully predicted 64 of the 83 topologies, and of the 37 complex multispanning topologies 34 were predicted correctly. PMID:8130217

  7. Statistical inference based on the nonparametric maximum likelihood estimator under double-truncation.

    PubMed

    Emura, Takeshi; Konno, Yoshihiko; Michimae, Hirofumi

    2015-07-01

    Doubly truncated data consist of samples whose observed values fall between the right- and left- truncation limits. With such samples, the distribution function of interest is estimated using the nonparametric maximum likelihood estimator (NPMLE) that is obtained through a self-consistency algorithm. Owing to the complicated asymptotic distribution of the NPMLE, the bootstrap method has been suggested for statistical inference. This paper proposes a closed-form estimator for the asymptotic covariance function of the NPMLE, which is computationally attractive alternative to bootstrapping. Furthermore, we develop various statistical inference procedures, such as confidence interval, goodness-of-fit tests, and confidence bands to demonstrate the usefulness of the proposed covariance estimator. Simulations are performed to compare the proposed method with both the bootstrap and jackknife methods. The methods are illustrated using the childhood cancer dataset. PMID:25001399

  8. Prediction of Cancer Drugs by Chemical-Chemical Interactions

    PubMed Central

    Li, Hai-Peng; Feng, Kai-Yan; Chen, Lei; Zheng, Ming-Yue; Cai, Yu-Dong

    2014-01-01

    Cancer, which is a leading cause of death worldwide, places a big burden on health-care system. In this study, an order-prediction model was built to predict a series of cancer drug indications based on chemical-chemical interactions. According to the confidence scores of their interactions, the order from the most likely cancer to the least one was obtained for each query drug. The 1st order prediction accuracy of the training dataset was 55.93%, evaluated by Jackknife test, while it was 55.56% and 59.09% on a validation test dataset and an independent test dataset, respectively. The proposed method outperformed a popular method based on molecular descriptors. Moreover, it was verified that some drugs were effective to the ‘wrong’ predicted indications, indicating that some ‘wrong’ drug indications were actually correct indications. Encouraged by the promising results, the method may become a useful tool to the prediction of drugs indications. PMID:24498372

  9. Bootstrapped MRMC confidence intervals

    NASA Astrophysics Data System (ADS)

    Samuelson, Frank W.; Wagner, Robert F.

    2005-04-01

    The multiple-reader, multiple-case (MRMC) paradigm of Swets and Pickett (1982) for ROC analysis was expressed as a components of variance model by Dorfman, Berbaum, and Metz (1992) and validated by Roe and Metz (1997) for Type I error rates. Our group proposed an analysis of the MRMC components of variance model using bootstrap (Beiden, Wagner, and Campbell, 2000) experiments instead of jackknife pseudo-values. These approaches have been challenged by some contemporary authors (e.g. Zhou, Obuchowski, and McClish, 2002). The purpose of the present paper is to formally compare the models and to carry out validation tests of their performance. We investigate different approaches to statistical inference, including several types of nonparametric bootstrap confidence intervals and report on validation and simulation experiments of Type I errors.

  10. A new multi-label classifier in identifying the functional types of human membrane proteins.

    PubMed

    Zou, Hong-Liang; Xiao, Xuan

    2015-04-01

    Membrane proteins were found to be involved in various cellular processes performing various important functions, which are mainly associated to their type. Given a membrane protein sequence, how can we identify its type(s)? Particularly, how can we deal with the multi-type problem since one membrane protein may simultaneously belong to two or more different types? To address these problems, which are obviously very important to both basic research and drug development, a new multi-label classifier was developed based on pseudo amino acid composition with multi-label k-nearest neighbor algorithm. The success rate achieved by the new predictor on the benchmark dataset by jackknife test is 73.94%, indicating that the method is promising and the predictor may become a very useful high-throughput tool, or at least play a complementary role to the existing predictors in identifying functional types of membrane proteins. PMID:25433431

  11. Avian community response to small-scale habitat disturbance in Maine

    USGS Publications Warehouse

    Derleth, E.L.; McAuley, D.G.; Dwyer, T.J.

    1989-01-01

    The effects of small clearcuts (1 - 8 ha) on avian communities in the forest of eastern Maine were studied using point counts during spring 1978 - 1981. Surveys were conducted in uncut (control) and clear-cut (treatment) plots in three stand types: conifer, hardwood, and mixed growth. We used a mark-recapture model and its associated jackknife species richness estimator (N), as an indicator of avian community structure. Increases in estimated richness (N) and Shannon - Weaver diversity (H') were noted in the treated hardwood and mixed growth, but not in the conifer stands. Seventeen avian species increased in relative abundance, whereas two species declined. Stand treatment was associated with important changes in bird species composition. Increased habitat patchiness and the creation of forest edge are hypothesized as causes for the greater estimates of richness and diversity.

  12. A limited sampling strategy for tacrolimus in liver transplant patients.

    PubMed

    Zhu, Liqin; Wang, Hao; Rao, Wei; Qu, Wei; Sun, Liying

    2013-06-01

    To develop limited sampling strategy (LSS) equations to estimate area under the curve (AUC0-12) in Chinese adult transplant patients. 26 adult liver transplant patients were included in this study. The blood samples, collected within 12 hours, were analyzed by microparticle enzyme immunoassay. By multiple stepwise linear regression analysis, LSS equations were identified. The predictive performance of these models was validated by the jackknife technique. As a result, the two sampling time point (trough and 4 hours postdose) model accurately predicted AUC0-12. (R2 = 0.949, ICC = 0.976). The two-point LSS equation (AUC0-12 = 7.26 + (2.17·C0) + (8.30·C4)) can be used as a predictable measure of AUC0-12 of tacrolimus in Chinese liver transplant patients. PMID:23547852

  13. On the tail risk of violent conflict and its underestimation

    E-print Network

    Cirillo, Pasquale

    2015-01-01

    We examine all possible statistical pictures of violent conflicts over common era history with a focus on dealing with incompleteness and unreliability of data. We apply methods from extreme value theory on log-transformed data to remove compact support, then, owing to the boundedness of maximum casualties, retransform the data and derive expected means. We find the estimated mean likely to be at least three times larger than the sample mean, meaning severe underestimation of the severity of conflicts from naive observation. We check for robustness by sampling between high and low estimates and jackknifing the data. We study inter-arrival times between tail events and find (first-order) memorylessless of events. The statistical pictures obtained are at variance with the claims about "long peace".

  14. Statistical discrimination of liquid gasoline samples from casework.

    PubMed

    Petraco, Nicholas D K; Gil, Mark; Pizzola, Peter A; Kubic, T A

    2008-09-01

    The intention of this study was to differentiate liquid gasoline samples from casework by utilizing multivariate pattern recognition procedures on data from gas chromatography-mass spectrometry. A supervised learning approach was undertaken to achieve this goal employing the methods of principal component analysis (PCA), canonical variate analysis (CVA), orthogonal canonical variate analysis (OCVA), and linear discriminant analysis. The study revealed that the variability in the sample population was sufficient enough to distinguish all the samples from one another knowing their groups a priori. CVA was able to differentiate all samples in the population using only three dimensions, while OCVA required four dimensions. PCA required 10 dimensions of data in order to predict the correct groupings. These results were all cross-validated using the "jackknife" method to confirm the classification functions and compute estimates of error rates. The results of this initial study have helped to develop procedures for the application of multivariate analysis to fire debris casework. PMID:18643865

  15. PACo: A Novel Procrustes Application to Cophylogenetic Analysis

    PubMed Central

    Balbuena, Juan Antonio; Míguez-Lozano, Raúl; Blasco-Costa, Isabel

    2013-01-01

    We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for congruence between phylogenetic trees, or between phylogenetic distance matrices of associated taxa. Unlike previous tests, PACo evaluates the dependence of one phylogeny upon the other. This makes it especially appropriate to test the classical coevolutionary model that assumes that parasites that spend part of their life in or on their hosts track the phylogeny of their hosts. The new method does not require fully resolved phylogenies and allows for multiple host-parasite associations. PACo produces a Procrustes superimposition plot enabling a graphical assessment of the fit of the parasite phylogeny onto the host phylogeny and a goodness-of-fit statistic, whose significance is established by randomization of the host-parasite association data. The contribution of each individual host-parasite association to the global fit is measured by means of jackknife estimation of their respective squared residuals and confidence intervals associated to each host-parasite link. We carried out different simulations to evaluate the performance of PACo in terms of Type I and Type II errors with respect to two similar published tests. In most instances, PACo performed at least as well as the other tests and showed higher overall statistical power. In addition, the jackknife estimation of squared residuals enabled more elaborate validations about the nature of individual links than the ParaFitLink1 test of the program ParaFit. In order to demonstrate how it can be used in real biological situations, we applied PACo to two published studies using a script written in the public-domain statistical software R. PMID:23580325

  16. Pine Hollow Watershed Project : FY 2000 Projects.

    SciTech Connect

    Sherman County Soil and Water Conservation District

    2001-06-01

    The Pine Hollow Project (1999-010-00) is an on-going watershed restoration effort administered by Sherman County Soil and Water Conservation District and spearheaded by Pine Hollow/Jackknife Watershed Council. The headwaters are located near Shaniko in Wasco County, and the mouth is in Sherman County on the John Day River. Pine Hollow provides more than 20 miles of potential summer steelhead spawning and rearing habitat. The watershed is 92,000 acres. Land use is mostly range, with some dryland grain. There are no water rights on Pine Hollow. Due to shallow soils, the watershed is prone to rapid runoff events which scour out the streambed and the riparian vegetation. This project seeks to improve the quality of upland, riparian and in-stream habitat by restoring the natural hydrologic function of the entire watershed. Project implementation to date has consisted of construction of water/sediment control basins, gradient terraces on croplands, pasture cross-fences, upland water sources, and grass seeding on degraded sites, many of which were crop fields in the early part of the century. The project is expected to continue through about 2007. From March 2000 to June 2001, the Pine Hollow Project built 6 sediment basins, 1 cross-fence, 2 spring developments, 1 well development, 1 solar pump, 50 acres of native range seeding and 1 livestock waterline. FY2000 projects were funded by BPA, Oregon Watershed Enhancement Board, US Fish and Wildlife Service and landowners. In-kind services were provided by Sherman County Soil and Water Conservation District, USDA Natural Resources Conservation Service, USDI Bureau of Land Management, Oregon Department of Fish and Wildlife, Pine Hollow/Jackknife Watershed Council, landowners and Wasco County Soil and Water Conservation District.

  17. Sample Size, Library Composition, and Genotypic Diversity among Natural Populations of Escherichia coli from Different Animals Influence Accuracy of Determining Sources of Fecal Pollution

    PubMed Central

    Johnson, LeeAnn K.; Brown, Mary B.; Carruthers, Ethan A.; Ferguson, John A.; Dombek, Priscilla E.; Sadowsky, Michael J.

    2004-01-01

    A horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique (HFERP) was developed and evaluated as a means to differentiate human from animal sources of Escherichia coli. Box A1R primers and PCR were used to generate 2,466 rep-PCR and 1,531 HFERP DNA fingerprints from E. coli strains isolated from fecal material from known human and 12 animal sources: dogs, cats, horses, deer, geese, ducks, chickens, turkeys, cows, pigs, goats, and sheep. HFERP DNA fingerprinting reduced within-gel grouping of DNA fingerprints and improved alignment of DNA fingerprints between gels, relative to that achieved using rep-PCR DNA fingerprinting. Jackknife analysis of the complete rep-PCR DNA fingerprint library, done using Pearson's product-moment correlation coefficient, indicated that animal and human isolates were assigned to the correct source groups with an 82.2% average rate of correct classification. However, when only unique isolates were examined, isolates from a single animal having a unique DNA fingerprint, Jackknife analysis showed that isolates were assigned to the correct source groups with a 60.5% average rate of correct classification. The percentages of correctly classified isolates were about 15 and 17% greater for rep-PCR and HFERP, respectively, when analyses were done using the curve-based Pearson's product-moment correlation coefficient, rather than the band-based Jaccard algorithm. Rarefaction analysis indicated that, despite the relatively large size of the known-source database, genetic diversity in E. coli was very great and is most likely accounting for our inability to correctly classify many environmental E. coli isolates. Our data indicate that removal of duplicate genotypes within DNA fingerprint libraries, increased database size, proper methods of statistical analysis, and correct alignment of band data within and between gels improve the accuracy of microbial source tracking methods. PMID:15294775

  18. Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys

    USGS Publications Warehouse

    Kery, M.; Royle, J.A.

    2008-01-01

    1. Species richness is the most widely used biodiversity metric, but cannot be observed directly as, typically, some species are overlooked. Imperfect detectability must therefore be accounted for to obtain unbiased species-richness estimates. When richness is assessed at multiple sites, two approaches can be used to estimate species richness: either estimating for each site separately, or pooling all samples. The first approach produces imprecise estimates, while the second loses site-specific information. 2. In contrast, a hierarchical Bayes (HB) multispecies site-occupancy model benefits from the combination of information across sites without losing site-specific information and also yields occupancy estimates for each species. The heart of the model is an estimate of the incompletely observed presence-absence matrix, a centrepiece of biogeography and monitoring studies. We illustrate the model using Swiss breeding bird survey data, and compare its estimates with the widely used jackknife species-richness estimator and raw species counts. 3. Two independent observers each conducted three surveys in 26 1-km(2) quadrats, and detected 27-56 (total 103) species. The average estimated proportion of species detected after three surveys was 0.87 under the HB model. Jackknife estimates were less precise (less repeatable between observers) than raw counts, but HB estimates were as repeatable as raw counts. The combination of information in the HB model thus resulted in species-richness estimates presumably at least as unbiased as previous approaches that correct for detectability, but without costs in precision relative to uncorrected, biased species counts. 4. Total species richness in the entire region sampled was estimated at 113.1 (CI 106-123); species detectability ranged from 0.08 to 0.99, illustrating very heterogeneous species detectability; and species occupancy was 0.06-0.96. Even after six surveys, absolute bias in observed occupancy was estimated at up to 0.40. 5. Synthesis and applications. The HB model for species-richness estimation combines information across sites and enjoys more precise, and presumably less biased, estimates than previous approaches. It also yields estimates of several measures of community size and composition. Covariates for occupancy and detectability can be included. We believe it has considerable potential for monitoring programmes as well as in biogeography and community ecology.

  19. Tracing the pathways of neotropical migratory shorebirds using stable isotopes: a pilot study.

    PubMed

    Farmer, A; Rye, R; Landis, G; Bern, C; Kester, C; Ridley, I

    2003-09-01

    We evaluated the potential use of stable isotopes to establish linkages between the wintering grounds and the breeding grounds of the Pectoral Sandpiper (Calidris melanotos), the White-rumped Sandpiper (Calidris fuscicollis), the Baird's Sandpiper (Calidris bairdii), and other Neotropical migratory shorebird species (e.g., Tringa spp.). These species molt their flight feathers on the wintering grounds and hence their flight feathers carry chemical signatures that are characteristic of their winter habitat. The objective of our pilot study was to assess the feasibility of identifying the winter origin of individual birds by: (1) collecting shorebird flight feathers from several widely separated Argentine sites and analyzing these for a suite of stable isotopes; and 2) analyzing the deuterium and 18O isotope data that were available from precipitation measurement stations in Argentina. Isotopic ratios (delta13C, delta15N and delta34S) of flight feathers were significantly different among three widely separated sites in Argentina during January 2001. In terms of relative importance in separating the sites, delta34S was most important, followed by delta15N, and then delta13C. In the complete discriminant analysis, the classification function correctly predicted group membership in 85% of the cases (jackknifed classification matrix). In a stepwise analysis delta13C was dropped from the solution, and site membership was correctly predicted in 92% of cases (jackknifed matrix). Analysis of precipitation data showed that both deltaD and delta18O were significantly related to both latitude and longitude on a countrywide scale (p < 0.001). Other variables, month, altitude, explained little additional variation in these isotope ratios. Several issues were identified that will likely constrain the degree of accuracy one can expect in predicting the geographic origin of birds from Argentina. There was unexplained variation in isotope ratios within and among the different wing feathers from individual birds. Such variation may indicate that birds are not faithful to a local site during their winter stay in Argentina. There was significant interannual variation in the deltaD and delta18O of precipitation. Hence, specific locations may not have a constant signature for some isotopes. Moreover, the fractionation that occurs in wetlands due to evaporation significantly skews local deltaD and delta18O values, which may undermine the strong large-scale gradients seen in the precipitation data. We are continuing the research with universities in Argentina with a focus on expanding the breadth of feather collection and attempting to resolve the identified issues. PMID:14521278

  20. New method to compute Rcomplete enables maximum likelihood refinement for small datasets.

    PubMed

    Luebben, Jens; Gruene, Tim

    2015-07-21

    The crystallographic reliability index [Formula: see text] is based on a method proposed more than two decades ago. Because its calculation is computationally expensive its use did not spread into the crystallographic community in favor of the cross-validation method known as [Formula: see text]. The importance of [Formula: see text] has grown beyond a pure validation tool. However, its application requires a sufficiently large dataset. In this work we assess the reliability of [Formula: see text] and we compare it with k-fold cross-validation, bootstrapping, and jackknifing. As opposed to proper cross-validation as realized with [Formula: see text], [Formula: see text] relies on a method of reducing bias from the structural model. We compare two different methods reducing model bias and question the widely spread notion that random parameter shifts are required for this purpose. We show that [Formula: see text] has as little statistical bias as [Formula: see text] with the benefit of a much smaller variance. Because the calculation of [Formula: see text] is based on the entire dataset instead of a small subset, it allows the estimation of maximum likelihood parameters even for small datasets. [Formula: see text] enables maximum likelihood-based refinement to be extended to virtually all areas of crystallographic structure determination including high-pressure studies, neutron diffraction studies, and datasets from free electron lasers. PMID:26150515

  1. Crash involvement of large trucks by configuration: a case-control study.

    PubMed Central

    Stein, H S; Jones, I S

    1988-01-01

    For a two-year period, large truck crashes on the interstate system in Washington State were investigated using a case-control method. For each large truck involved in a crash, three trucks were randomly selected for inspection from the traffic stream at the same time and place as the crash but one week later. The effects of truck and driver characteristics on crashes were assessed by comparing their relative frequency among the crash-involved and comparison sample trucks. Double trailer trucks were consistently overinvolved in crashes by a factor of two to three in both single and multiple vehicle crashes. Single unit trucks pulling trailers also were overinvolved. Doubles also had a higher frequency of jackknifing compared to tractor-trailers. The substantial overinvolvement of doubles in crashes was found regardless of driver age, hours of driving, cargo weight, or type of fleet. Younger drivers, long hours of driving, and operating empty trucks were also associated with higher crash involvement. PMID:3354729

  2. Crash involvement of large trucks by configuration: a case-control study.

    PubMed

    Stein, H S; Jones, I S

    1988-05-01

    For a two-year period, large truck crashes on the interstate system in Washington State were investigated using a case-control method. For each large truck involved in a crash, three trucks were randomly selected for inspection from the traffic stream at the same time and place as the crash but one week later. The effects of truck and driver characteristics on crashes were assessed by comparing their relative frequency among the crash-involved and comparison sample trucks. Double trailer trucks were consistently overinvolved in crashes by a factor of two to three in both single and multiple vehicle crashes. Single unit trucks pulling trailers also were overinvolved. Doubles also had a higher frequency of jackknifing compared to tractor-trailers. The substantial overinvolvement of doubles in crashes was found regardless of driver age, hours of driving, cargo weight, or type of fleet. Younger drivers, long hours of driving, and operating empty trucks were also associated with higher crash involvement. PMID:3354729

  3. Limited sampling hampers “big data” estimation of species richness in a tropical biodiversity hotspot

    PubMed Central

    Engemann, Kristine; Enquist, Brian J; Sandel, Brody; Boyle, Brad; Jørgensen, Peter M; Morueta-Holme, Naia; Peet, Robert K; Violle, Cyrille; Svenning, Jens-Christian

    2015-01-01

    Macro-scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as mislead conservation prioritization. In recent years, this has resulted in an increased focus on developing methods to correct for sampling bias. In this study, we use sample-size-correcting methods to examine patterns of tropical plant diversity in Ecuador, one of the most species-rich and climatically heterogeneous biodiversity hotspots. Species richness estimates were calculated based on 205,735 georeferenced specimens of 15,788 species using the Margalef diversity index, the Chao estimator, the second-order Jackknife and Bootstrapping resampling methods, and Hill numbers and rarefaction. Species richness was heavily correlated with sampling effort, and only rarefaction was able to remove this effect, and we recommend this method for estimation of species richness with “big data” collections. PMID:25692000

  4. Heritable changes in regional cortical thickness with age

    PubMed Central

    Chouinard-Decorte, Francois; McKay, D. Reese; Reid, Andrew; Khundrakpam, Budhachandra; Zhao, Lu; Karama, Sherif; Rioux, Pierre; Sprooten, Emma; Knowles, Emma; Kent, Jack W.; Curran, Joanne E.; Göring, Harald H. H.; Dyer, Thomas D.; Olvera, Rene L.; Kochunov, Peter; Duggirala, Ravi; Fox, Peter T.; Almasy, Laura; Blangero, John; Bellec, Pierre; Evans, Alan C.

    2014-01-01

    It is now well established that regional indices of brain structure such as cortical thickness, surface area or grey matter volume exhibit spatially variable patterns of heritability. However, a recent study found these patterns to change with age during development, a result supported by gene expression studies. Changes in heritability have not been investigated in adulthood so far and could have important implications in the study of heritability and genetic correlations in the brain as well as in the discovery of specific genes explaining them. Herein, we tested for genotype by age (G × A) interactions, an extension of genotype by environment interactions, through adulthood and healthy aging in 902 subjects from the Genetics of Brain Structure (GOBS) study. A “jackknife” based method for the analysis of stable cortical thickness clusters (JASC) and scale selection is also introduced. Although additive genetic variance remained constant throughout adulthood, we found evidence for incomplete pleiotropy across age in the cortical thickness of paralimbic and parieto-temporal areas. This suggests that different genetic factors account for cortical thickness heritability at different ages in these regions. PMID:24752552

  5. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

    PubMed Central

    Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

    2014-01-01

    The ?54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the ?54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the ?54 promoters. PMID:25361964

  6. Fast and Accurate Construction of Ultra-Dense Consensus Genetic Maps Using Evolution Strategy Optimization

    PubMed Central

    Mester, David; Ronin, Yefim; Schnable, Patrick; Aluru, Srinivas; Korol, Abraham

    2015-01-01

    Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time. PMID:25867943

  7. Gastrointestinal Parasites of Ecuadorian Mantled Howler Monkeys (Alouatta palliata aequatorialis) Based on Fecal Analysis.

    PubMed

    Helenbrook, William D; Wade, Susan E; Shields, William M; Stehman, Stephen V; Whipps, Christopher M

    2015-06-01

    An analysis of gastrointestinal parasites of Ecuadorian mantled howler monkeys, Alouatta palliata aequatorialis, was conducted based on examination of fecal smears, flotations, and sedimentations. At least 1 type of parasite was detected in 97% of the 96 fecal samples screened across 19 howler monkey groups using these techniques. Samples averaged 3.6 parasite species per individual (±1.4 SD). Parasites included species representing genera of 2 apicomplexans: Cyclospora sp. (18% of individual samples) and Isospora sp. (3%); 6 other protozoa: Balantidium sp. (9%), Blastocystis sp. (60%), Chilomastix sp. (4%), Dientamoeba sp. (3%), Entamoeba species (56%), Iodamoeba sp. (5%); 4 nematodes: Enterobius sp. (3%), Capillaria sp. (78%), Strongyloides spp. (88%) which included 2 morphotypes, Trypanoxyuris sp. (12%); and the platyhelminth Controrchis sp. (15%). A statistically significant positive correlation was found between group size and each of 3 different estimators of parasite species richness adjusted for sampling effort (ICE: r(2) = 0.24, P = 0.05; Chao2: r(2) = 0.25, P = 0.05, and Jackknife: r(2) = 0.31, P = 0.03). Two significant associations between co-infecting parasites were identified. Based on the prevalence data, individuals infected with Balantidium sp. were more likely to also be infected with Isospora sp. (?(2) = 6.02, P = 0.01), while individuals harboring Chilomastix sp. were less likely to have Capillaria sp. present (?(2) = 4.03, P = 0.04). PMID:25686475

  8. AAFreqCoil: a new classifier to distinguish parallel dimeric and trimeric coiled coils.

    PubMed

    Wang, Xiaofeng; Zhou, Yuan; Yan, Renxiang

    2015-06-16

    Coiled coils are characteristic rope-like protein structures, constituted by one or more heptad repeats. Native coiled-coil structures play important roles in various biological processes, while the designed ones are widely employed in medicine and industry. To date, two major oligomeric states (i.e. dimeric and trimeric states) of a coiled-coil structure have been observed, plausibly exerting different biological functions. Therefore, exploration of the relationship between heptad repeat sequences and coiled coil structures is highly important. In this paper, we develop a new method named AAFreqCoil to classify parallel dimeric and trimeric coiled coils. Our method demonstrated its competitive performance when benchmarked based on 10-fold cross validation and jackknife cross validation. Meanwhile, the rules that can explicitly explain the prediction results of the test coiled coil can be extracted from the AAFreqCoil model for a better explanation of user predictions. A web server and stand-alone program implementing the AAFreqCoil algorithm are freely available at . PMID:25918905

  9. Statistical Downscaling of Wintertime Temperatures over South Korea

    NASA Astrophysics Data System (ADS)

    Lee, S. Y.; Kim, K. Y.

    2014-12-01

    Reanalysis data have global coverage and faithfully render large-scale phenomena. On the other hand, regional and small-scale characteristics of atmospheric variability are poorly resolved. In an attempt to improve reanalysis data for regional use, statistical downscaling method is developed based on CSEOF analysis. Low-resolution data are downscaled into a high-resolution data. The developed algorithm is applied to National Center for Environmental Prediction-National Center for Atmospheric Research (NCEP/NCAR) reanalysis data and European Center of Medium range Weather Forecast (ECMWF) ERA-interim reanalysis data to downscale them into a form of Korea Meteorological Administration (KMA) measurements at 60 stations over the Korean Peninsula. The developed downscaling algorithm is evaluated by predicting winter daily temperatures from Nov 17 - Mar 16 for the period of 34 years (1979-2013). For validation of the method, the Jackknife method is used, in which winter daily temperature is predicted over a one-year period not used for training. This procedure is repeated for the entire data period. The mean and variance of the resulting downscaled dataset match well with those of the KMA measurements. Validation results show that correlation increases and error variance decreases significantly at grid points near the KMA stations with and without the seasonal cycle. We will also address the utility of this technique for downscaling model predictions based on future scenarios.

  10. Predicting Discovery Rates of Genomic Features

    PubMed Central

    Gravel, Simon

    2014-01-01

    Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary data can be challenging, because numerous uncertain model assumptions may be involved. Here, we ask whether we can predict “omics” variation across many samples by sequencing only a fraction of them. In the infinite-genome limit, we find that a pilot study sequencing 5% of a population is sufficient to predict the number of genetic variants in the entire population within 6% of the correct value, using an estimator agnostic to demography, selection, or population structure. To reach similar accuracy in a finite genome with millions of polymorphisms, the pilot study would require ?15% of the population. We present computationally efficient jackknife and linear programming methods that exhibit substantially less bias than the state of the art when applied to simulated data and subsampled 1000 Genomes Project data. Extrapolating based on the National Heart, Lung, and Blood Institute Exome Sequencing Project data, we predict that 7.2% of sites in the capture region would be variable in a sample of 50,000 African Americans and 8.8% in a European sample of equal size. Finally, we show how the linear programming method can also predict discovery rates of various genomic features, such as the number of transcription factor binding sites across different cell types. PMID:24637199

  11. Identification of New Candidate Genes and Chemicals Related to Esophageal Cancer Using a Hybrid Interaction Network of Chemicals and Proteins

    PubMed Central

    Liu, Junbao; Li, Li-Peng; He, Yi-Chun; Gao, Ru-Jian; Cai, Yu-Dong; Jiang, Yang

    2015-01-01

    Cancer is a serious disease responsible for many deaths every year in both developed and developing countries. One reason is that the mechanisms underlying most types of cancer are still mysterious, creating a great block for the design of effective treatments. In this study, we attempted to clarify the mechanism underlying esophageal cancer by searching for novel genes and chemicals. To this end, we constructed a hybrid network containing both proteins and chemicals, and generalized an existing computational method previously used to identify disease genes to identify new candidate genes and chemicals simultaneously. Based on jackknife test, our generalized method outperforms or at least performs at the same level as those obtained by a widely used method - the Random Walk with Restart (RWR). The analysis results of the final obtained genes and chemicals demonstrated that they highly shared gene ontology (GO) terms and KEGG pathways with direct and indirect associations with esophageal cancer. In addition, we also discussed the likelihood of selected candidate genes and chemicals being novel genes and chemicals related to esophageal cancer. PMID:26058041

  12. Distinguishing centrarchid genera by use of lateral line scales

    USGS Publications Warehouse

    Roberts, N.M.; Rabeni, C.F.; Stanovick, J.S.

    2007-01-01

    Predator-prey relations involving fishes are often evaluated using scales remaining in gut contents or feces. While several reliable keys help identify North American freshwater fish scales to the family level, none attempt to separate the family Centrarchidae to the genus level. Centrarchidae is of particular concern in the midwestern United States because it contains several popular sport fishes, such as smallmouth bass Micropterus dolomieu, largemouth bass M. salmoides, and rock bass Ambloplites rupestris, as well as less-sought-after species of sunfishes Lepomis spp. and crappies Pomoxis spp. Differentiating sport fish from non-sport fish has important management implications. Morphological characteristics of lateral line scales (n = 1,581) from known centrarchid fishes were analyzed. The variability of measurements within and between genera was examined to select variables that were the most useful in further classifying unknown centrarchid scales. A linear discriminant analysis model was developed using 10 variables. Based on this model, 84.4% of Ambloplites scales, 81.2% of Lepomis scales, and 86.6% of Micropterus scales were classified correctly using a jackknife procedure. ?? Copyright by the American Fisheries Society 2007.

  13. Cuticular hydrocarbons, isoenzymes and behavior of three populations of Anopheles darlingi from Brazil.

    PubMed

    Rosa-Freitas, M G; Broomfield, G; Priestman, A; Milligan, P J; Momen, H; Molyneux, D H

    1992-12-01

    Three populations of Anopheles darlingi were studied for cuticular hydrocarbons, isoenzymes and patterns of peak biting activity. Differences were found in specimens from Costa Marques, a malaria endemic area; Dourado, a site with a very exophilic population and Juturnaíba, located near the type locality. Twelve hour collections from sunset to sunrise showed that An. darlingi from Costa Marques had a bimodal biting activity profile with a major peak at sunset and a minor peak at sunrise. At Dourado, the pattern was trimodal, with peaks at both morning and evening periods of twilight and near midnight. The Juturnaíba population showed a slight increase in activity near 2000 and 0100 h. Nei's genetic distances, determined by isoenzyme electrophoresis between pairs of populations, were low (D < or = 0.049). Using discriminant analysis for the cuticular hydrocarbons, 92.4% of the specimens from Costa Marques, 91.2% of the specimens from Dourado and 61.3% from Juturnaíba were correctly identified. Cuticular hydrocarbon and isoenzyme results matched very well: the smaller the Nei's distance, the more misidentifications occurred in the jackknife estimator used in the cuticular hydrocarbon analysis. This is the first report of cuticular hydrocarbon analysis in combination with isoenzymes to investigate neotropical anopheline species. PMID:1474380

  14. Trends in indices of daily precipitation extremes in Catalonia (NE Spain), 1951-2003

    NASA Astrophysics Data System (ADS)

    Turco, M.; Llasat, M. C.

    2011-12-01

    The aim of this paper is to quantitatively characterize the climatology of daily precipitation indices in Catalonia (northeastern Iberian Peninsula) from 1951 to 2003. This work has been performed analyzing a subset of the ETCCDI (Expert Team on Climate Change Detection and Indices) precipitation indices calculated from a new interpolated dataset of daily precipitation, namely SPAIN02, regular at 0.2° horizontal resolution (around 20 km) and from two high-quality stations: the Ebro and Fabra observatories. Using a jack-knife technique, we have found that the sampling error of the SPAIN02 regional averaged is relatively low. The trend analysis has been implemented using a Circular Block Bootstrap procedure applicable to non-normal distributions and autocorrelated series. A running trend analysis has been applied to analyze the trend persistence. No general trends at a regional scale are observed, considering the annual or the seasonal regional averaged series of all the indices for all the time windows considered. Only the consecutive dry days index (CDD) at annual scale shows a locally coherent spatial trend pattern; around 30% of the Catalonia area has experienced an increase of around 2-3 days decade-1. The Ebro and Fabra observatories show a similar CDD trend, mainly due to the summer contribution. Besides this, a significant decrease in total precipitation (around -10 mm decade-1) and in the index "highest precipitation amount in five-day period" (RX5DAY, around -5 mm decade-1), have been found in summer for the Ebro observatory.

  15. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.

    PubMed

    Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

    2014-12-01

    The ?(54) promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the ?(54) promoters. Here, a predictor called 'iPro54-PseKNC' was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called 'pseudo k-tuple nucleotide composition', which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the ?(54) promoters. PMID:25361964

  16. Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology.

    PubMed

    Schulze, Anja; Cutler, Edward B; Giribet, Gonzalo

    2007-01-01

    The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree. PMID:16919974

  17. Different effects of ER? and TROP2 expression in Chinese patients with early-stage colon cancer.

    PubMed

    Fang, Yu-Jing; Wang, Guo-Qiang; Lu, Zhen-Hai; Zhang, Lin; Li, Ji-Bin; Wu, Xiao-Jun; Ding, Pei-Rong; Ou, Qing-Jian; Zhang, Mei-Fang; Jiang, Wu; Pan, Zhi-Zhong; Wan, De-Sen

    2012-12-01

    Estrogen receptor beta (ER?) and TROP2 expressed in colon carcinoma and might play an important role there. We explored the relationship of ER? and TROP2 expression with the prognosis of early-stage colon cancer. ER? and TROP2 levels were assessed by immunohistochemistry in normal mucosa and tumoral tissues from 220 Chinese patients with T(3)N(0)M(0) (stage IIa) and T(4)N(0)M(0) (stage IIb) colon cancer in the Cancer Center, Sun Yat-sen University, who underwent curative surgical resection between 1995 and 2003. The Cox proportional hazards regression model was applied to analyze the overall survival (OS) data, and the ROC curve, Kaplan-Meier estimate, log rank test, and Jackknife method were used to show the effect of ER? and TROP2 expression at different stages of cancer. The 5-year survival rates were not significantly different between the patients with stage IIa and stage IIb colon cancer (83 vs. 80 %, respectively). The high expression of ER? was related to decreasing OS in stage IIa and stage IIb colon cancer, while the high expression of TROP2 was related to decreasing OS in stage IIb colon cancer. The expression of ER? and TROP2 has tumor-suppressive and tumor-promoting effect in stage IIa and stage IIb colon cancer, respectively. PMID:23055188

  18. The large-scale three-point correlation function of SDSS luminous red galaxies

    NASA Astrophysics Data System (ADS)

    Marin Perucci, Felipe A.

    We present new measurements of the redshift-space three-point correlation function (3PCF) of Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey (SDSS). Using the largest dataset to date, the Data Release 7 (DR7) LRGs, and an improved binning scheme compared to previous measurements, we measure the LRG 3PCF on large scales up to ˜ 90 h-1 Mpc, from the mildly non-linear to quasi-linear regimes. Comparing the LRG correlations to the dark matter two- and three-point correlation functions, obtained from N-body simulations we infer linear and nonlinear bias parameters. As expected, LRGs are highly biased tracers of large scale structure, with a linear bias b1 ˜ 2; the LRGs also have a large positive non-linear bias parameter, in agreement with predictions of galaxy population models. The use of the 3PCF to estimate biasing helps to also make estimates of the cosmological parameter sigma8, as well as to infer best-fit parameters of the Halo Occupation Distribution parameters for LRGs. We also use a large suite of public mock catalogs to characterize the error covariance matrix for the 3PCF and compare the variance among simulation results with jackknife error estimates.

  19. North American Tropical Cyclone Landfall and SST: A Statistical Model Study

    NASA Technical Reports Server (NTRS)

    Hall, Timothy; Yonekura, Emmi

    2013-01-01

    A statistical-stochastic model of the complete life cycle of North Atlantic (NA) tropical cyclones (TCs) is used to examine the relationship between climate and landfall rates along the North American Atlantic and Gulf Coasts. The model draws on archived data of TCs throughout the North Atlantic to estimate landfall rates at high geographic resolution as a function of the ENSO state and one of two different measures of sea surface temperature (SST): 1) SST averaged over the NA subtropics and the hurricane season and 2) this SST relative to the seasonal global subtropical mean SST (termed relSST). Here, the authors focus on SST by holding ENSO to a neutral state. Jackknife uncertainty tests are employed to test the significance of SST and relSST landfall relationships. There are more TC and major hurricane landfalls overall in warm years than cold, using either SST or relSST, primarily due to a basinwide increase in the number of storms. The signal along the coast, however, is complex. Some regions have large and significant sensitivity (e.g., an approximate doubling of annual major hurricane landfall probability on Texas from -2 to +2 standard deviations in relSST), while other regions have no significant sensitivity (e.g., the U.S. mid-Atlantic and Northeast coasts). This geographic structure is due to both shifts in the regions of primary TC genesis and shifts in TC propagation.

  20. First Results from the Q/U Imaging ExperimenT (QUIET)

    NASA Astrophysics Data System (ADS)

    Zwart, Jonathan; Quiet Collaboration

    2011-04-01

    The Q/U Imaging ExperimenT (QUIET) is a large-angular-scale telescope designed to measure the polarization of the cosmic microwave background from the Atacama Desert, Chile and to place direct, competitive limits on the tensor-to-scalar ratio (which parameterizes primordial inflationary B modes) using solely polarization information. We have used QUIET to observe ~ 1000 sq. deg. of low-foreground sky at 43 (Q band) and 95 GHz (W band) between October 2008 and December 2010, collecting some 10000 hours of data in that time. The integrity of the Q-band data analysis has been verified with an extensive suite of jackknife tests for nullity, and by comparing results from two independent (and blind) analysis pipelines. I shall give an overview of QUIET and present the first power-spectrum results from the Q-band data set, including the E-mode power spectrum, a limit on the tensor-to-scalar ratio, and the detection of polarized Galactic synchroton emission away from the Galactic plane.

  1. Identification of pathogenic fungi with an optoelectronic nose.

    PubMed

    Zhang, Yinan; Askim, Jon R; Zhong, Wenxuan; Orlean, Peter; Suslick, Kenneth S

    2014-04-21

    Human fungal infections have gained recent notoriety following contamination of pharmaceuticals in the compounding process. Such invasive infections are a more serious global problem, especially for immunocompromised patients. While superficial fungal infections are common and generally curable, invasive fungal infections are often life-threatening and much harder to diagnose and treat. Despite the increasing awareness of the situation's severity, currently available fungal diagnostic methods cannot always meet diagnostic needs, especially for invasive fungal infections. Volatile organic compounds produced by fungi provide an alternative diagnostic approach for identification of fungal strains. We report here an optoelectronic nose based on a disposable colorimetric sensor array capable of rapid differentiation and identification of pathogenic fungi based on their metabolic profiles of emitted volatiles. The sensor arrays were tested with 12 human pathogenic fungal strains grown on standard agar medium. Array responses were monitored with an ordinary flatbed scanner. All fungal strains gave unique composite responses within 3 hours and were correctly clustered using hierarchical cluster analysis. A standard jackknifed linear discriminant analysis gave a classification accuracy of 94% for 155 trials. Tensor discriminant analysis, which takes better advantage of the high dimensionality of the sensor array data, gave a classification accuracy of 98.1%. The sensor array is also able to observe metabolic changes in growth patterns upon the addition of fungicides, and this provides a facile screening tool for determining fungicide efficacy for various fungal strains in real time. PMID:24570999

  2. In-silico prediction of gas chromatographic retention indices of some terpenols.

    PubMed

    Fatemi, Mohammad H; Malekzadeh, Hanieh

    2012-08-01

    A quantitative structure-retention relationship study based on multiple linear regression technique was carried out to investigate the gas chromatographic retention indices (RIs) of some terpenols on the HP 5 ms fused silica column. A collection of 75 terpene alcohols was chosen as dataset. The data were divided into two groups; a training set and a prediction set consist of 60 and 15 molecules, respectively. The best-selected descriptors that appear in the models are; the Randic index order 1, Kier shape index order 2, total charge weighted partial negatively charged surface area, and fractional atomic charge weighted partial positive surface area. These descriptors can encode different features of molecules that are responsible for their steric, electronic, and lipophilicity interactions. The best-obtained model had statistics of R(2)(t) = 0.959 and R(2)(p) = 0.952. The reliability of the model was evaluated by using the leave-many-out cross-validation method (Q(2) = 0.957 and SPRESS = 46.427) as well as by y-scrambling and jackknife test. Furthermore, the chemical applicability domains of these models were determined via leverage approach. The simple developed four-parameter linear model can predict the gas chromatographic RIs of terpenols. PMID:22821703

  3. Prediction of drugs target groups based on ChEBI ontology.

    PubMed

    Gao, Yu-Fei; Chen, Lei; Huang, Guo-Hua; Zhang, Tao; Feng, Kai-Yan; Li, Hai-Peng; Jiang, Yang

    2013-01-01

    Most drugs have beneficial as well as adverse effects and exert their biological functions by adjusting and altering the functions of their target proteins. Thus, knowledge of drugs target proteins is essential for the improvement of therapeutic effects and mitigation of undesirable side effects. In the study, we proposed a novel prediction method based on drug/compound ontology information extracted from ChEBI to identify drugs target groups from which the kind of functions of a drug may be deduced. By collecting data in KEGG, a benchmark dataset consisting of 876 drugs, categorized into four target groups, was constructed. To evaluate the method more thoroughly, the benchmark dataset was divided into a training dataset and an independent test dataset. It is observed by jackknife test that the overall prediction accuracy on the training dataset was 83.12%, while it was 87.50% on the test dataset-the predictor exhibited an excellent generalization. The good performance of the method indicates that the ontology information of the drugs contains rich information about their target groups, and the study may become an inspiration to solve the problems of this sort and bridge the gap between ChEBI ontology and drugs target groups. PMID:24350241

  4. Dissociable executive functions in behavioral variant frontotemporal and Alzheimer dementias

    PubMed Central

    Feigenbaum, Dana; Rankin, Katherine P.; Smith, Glenn E.; Boxer, Adam L.; Wood, Kristie; Hanna, Sherrie M.; Miller, Bruce L.; Kramer, Joel H.

    2013-01-01

    Objective: The objective of this study was to determine which aspects of executive functions are most affected in behavioral variant frontotemporal dementia (bvFTD) and best differentiate this syndrome from Alzheimer disease (AD). Methods: We compared executive functions in 22 patients diagnosed with bvFTD, 26 with AD, and 31 neurologically healthy controls using a conceptually driven and comprehensive battery of executive function tests, the NIH EXAMINER battery (http://examiner.ucsf.edu). Results: The bvFTD and the AD patients were similarly impaired compared with controls on tests of working memory, category fluency, and attention, but the patients with bvFTD showed significantly more severe impairments than the patients with AD on tests of letter fluency, antisaccade accuracy, social decision-making, and social behavior. Discriminant function analysis with jackknifed cross-validation classified the bvFTD and AD patient groups with 73% accuracy. Conclusions: Executive function assessment can support bvFTD diagnosis when measures are carefully selected to emphasize frontally specific functions. PMID:23658382

  5. Neural bases of atypical emotional face processing in autism: A meta-analysis of fMRI studies.

    PubMed

    Aoki, Yuta; Cortese, Samuele; Tansella, Michele

    2014-09-29

    Objectives. We aim to outline the neural correlates of atypical emotional face processing in individuals with ASD. Methods. A comprehensive literature search was conducted through electronic databases to identify functional magnetic resonance imaging (fMRI) studies of whole brain analysis with emotional-face processing tasks in individuals with ASD. The Signed Differential Mapping with random effects model was used to conduct meta-analyses. Identified fMRI studies were further divided into sub-groups based on contrast ("emotional-face vs. non-emotional-face" or "emotional-face vs. non-face") to confirm the results of a meta-analysis of the whole studies. Results. Thirteen studies with 226 individuals with ASD and 251 typically developing people were identified. We found ASD-related hyperactivation in subcortical structures, including bilateral thalamus, bilateral caudate, and right precuneus, and ASD-related hypoactivation in the hypothalamus during emotional-face processing. Sub-analyses with more homogeneous contrasts preserved the findings of the main analysis such as hyperactivation in sub-cortical structure. Jackknife analyses showed that hyperactivation of the left caudate was the most robust finding. Conclusions. Abnormalities in the subcortical structures, such as amygdala, hypothalamus and basal ganglia, are associated with atypical emotional-face processing in individuals with ASD. PMID:25264291

  6. Protein location prediction using atomic composition and global features of the amino acid sequence

    SciTech Connect

    Cherian, Betsy Sheena, E-mail: betsy.skb@gmail.com [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India); Nair, Achuthsankar S. [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)] [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)

    2010-01-22

    Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectively used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.

  7. Increased binding of 5-HT1A receptors in a dissociative amnesic patient after the recovery process.

    PubMed

    Kitamura, Soichiro; Yasuno, Fumihiko; Inoue, Makoto; Kosaka, Jun; Kiuchi, Kuniaki; Matsuoka, Kiwamu; Kishimoto, Toshifumi; Suhara, Tetsuya

    2014-10-30

    Dissociative amnesia is characterized by an inability to retrieve information already saved in memories. 5-HT has some role in neural regulatory control and may be related to the recovery from dissociative amnesia. To examine the role of 5-HT1A receptors in the recovery from dissociative amnesia, we performed two positron emission tomography (PET) scans on a 30-year-old patient of dissociative amnesia using [(11)C]WAY-100635, the first at amnesic state, and the second at the time he had recovered. Exploratory voxel-based analysis (VBA) was performed using SPM software. 5-HT1A BPND images were compared between the patient at amnesic and recovery states and healthy subjects (14 males, mean age 29.8 ± 6.45) with Jack-knife analysis. 5-HT1A receptor bindings of the patient at the recovery state were significantly higher than those of healthy subjects in the right superior and middle frontal cortex, left inferior frontal and orbitofrontal cortex and bilateral inferior temporal cortex. The increase in BPND values of recovery state was beyond 10% of those of amnesia state in these regions except in the right superior frontal cortex. We considered that neural regulatory control by the increase of 5-HT1A receptors in cortical regions played a role in the recovery from dissociative amnesia. PMID:25052950

  8. Predicting subcellular location of proteins using integrated-algorithm method.

    PubMed

    Cai, Yu-Dong; Lu, Lin; Chen, Lei; He, Jian-Feng

    2010-08-01

    Protein's subcellular location, which indicates where a protein resides in a cell, is an important characteristic of protein. Correctly assigning proteins to their subcellular locations would be of great help to the prediction of proteins' function, genome annotation, and drug design. Yet, in spite of great technical advance in the past decades, it is still time-consuming and laborious to experimentally determine protein subcellular locations on a high throughput scale. Hence, four integrated-algorithm methods were developed to fulfill such high throughput prediction in this article. Two data sets taken from the literature (Chou and Elrod, Protein Eng 12:107-118, 1999) were used as training set and test set, which consisted of 2,391 and 2,598 proteins, respectively. Amino acid composition was applied to represent the protein sequences. The jackknife cross-validation was used to test the training set. The final best integrated-algorithm predictor was constructed by integrating 10 algorithms in Weka (a software tool for tackling data mining tasks, http://www.cs.waikato.ac.nz/ml/weka/ ) based on an mRMR (Minimum Redundancy Maximum Relevance, http://research.janelia.org/peng/proj/mRMR/ ) method. It can achieve correct rate of 77.83 and 80.56% for the training set and test set, respectively, which is better than all of the 60 algorithms collected in Weka. This predicting software is available upon request. PMID:19662505

  9. Quality assessment of High Angular Resolution Diffusion Imaging data using bootstrap on Q-ball reconstruction

    PubMed Central

    Cohen-Adad, J.; Descoteaux, M.; Wald, L.L.

    2011-01-01

    Purpose To develop a bootstrap method to assess the quality of High Angular Resolution Diffusion Imaging (HARDI) data using Q-Ball imaging (QBI) reconstruction. Materials and Methods HARDI data were re-shuffled using regular bootstrap with jackknife sampling. For each bootstrap dataset, the diffusion orientation distribution function (ODF) was estimated voxel-wise using QBI reconstruction based on spherical harmonics functions. The reproducibility of the ODF was assessed using the Jensen-Shannon divergence (JSD) and the angular confidence interval was derived for the first and the second ODF maxima. The sensitivity of the bootstrap method was evaluated on a human subject by adding synthetic noise to the data, by acquiring a map of image signal-to-noise ratio (SNR) and by varying the echo time and the b-value. Results The JSD was directly linked to the image SNR. The impact of echo times and b-values was reflected by both the JSD and the angular confidence interval, proving the usefulness of the bootstrap method to evaluate specific features of HARDI data. Conclusion The bootstrap method can effectively assess the quality of HARDI data and can be used to evaluate new hardware and pulse sequences, perform multi-fiber probabilistic tractography, and provide reliability metrics to support clinical studies. PMID:21509879

  10. Prediction of space sickness in astronauts from preflight fluid, electrolyte, and cardiovascular variables and Weightless Environmental Training Facility (WETF) training

    NASA Technical Reports Server (NTRS)

    Simanonok, K.; Mosely, E.; Charles, J.

    1992-01-01

    Nine preflight variables related to fluid, electrolyte, and cardiovascular status from 64 first-time Shuttle crewmembers were differentially weighted by discrimination analysis to predict the incidence and severity of each crewmember's space sickness as rated by NASA flight surgeons. The nine variables are serum uric acid, red cell count, environmental temperature at the launch site, serum phosphate, urine osmolality, serum thyroxine, sitting systolic blood pressure, calculated blood volume, and serum chloride. Using two methods of cross-validation on the original samples (jackknife and a stratefied random subsample), these variables enable the prediction of space sickness incidence (NONE or SICK) with 80 percent sickness and space severity (NONE, MILD, MODERATE, of SEVERE) with 59 percent success by one method of cross-validation and 67 percent by another method. Addition of a tenth variable, hours spent in the Weightlessness Environment Training Facility (WETF) did not improve the prediction of space sickness incidences but did improve the prediction of space sickness severity to 66 percent success by the first method of cross-validation of original samples and to 71 percent by the second method. Results to date suggest the presence of predisposing physiologic factors to space sickness that implicate fluid shift etiology. The data also suggest that prior exposure to fluid shift during WETF training may produce some circulatory pre-adaption to fluid shifts in weightlessness that results in a reduction of space sickness severity.

  11. Stock structure of Lake Baikal omul as determined by whole-body morphology

    USGS Publications Warehouse

    Bronte, Charles R.; Fleischer, G.W.; Maistrenko, S.G.; Pronin, N.M.

    1999-01-01

    In Lake Baikal, three morphotypes of omul Coregonus autumnalis migratorius are recognized; the littoral, pelagic, and deep-water forms. Morphotype assignment is difficult, and similar to that encountered in pelagic and deep-water coregonines in the Laurentian Great Lakes. Principal component analysis revealed separation of all three morphotypes based on caudal peduncle length and depth, length and depth of the body between the dorsal and anal fin, and distance between the pectoral and pelvic fins. Strong negative loadings were associated with head measurements. Omul of the same morphotype captured at different locations were classified to location of capture using step-wise discriminant function analysis. Jackknife correct classifications ranged from 43 to 78% for littoral omul from five locations, and 45-86% for pelagic omul from four locations. Patterns of local misclassification of littoral omul suggested that the sub-population structure, hence stock affinity, may be influenced by movements and intermixing of individuals among areas that are joined bathymetrically. Pelagic omul were more distinguishable by site and may support a previous hypothesis of a spawning based rather than a foraging-based sub-population structure. Omul morphotypes may reflect adaptations to both ecological and local environmental conditions, and may have a genetic basis.

  12. Gravitational Lens Time Delays: A Statistical Assessment of Lens Model Dependences and Implications for the Global Hubble Constant

    E-print Network

    Masamune Oguri

    2007-01-23

    Time delays between lensed multiple images have been known to provide an interesting probe of the Hubble constant, but such application is often limited by degeneracies with the shape of lens potentials. We propose a new statistical approach to examine the dependence of time delays on the complexity of lens potentials, such as higher-order perturbations, non-isothermality, and substructures. Specifically, we introduce a reduced time delay and explore its behavior as a function of the image configuration that is characterized by the asymmetry and opening angle of the image pair. In particular we derive a realistic conditional probability distribution. We find that the probability distribution is sensitive to the image configuration such that more asymmetric and/or smaller opening angle image pairs are more easily affected by perturbations on the primary lens potential. On average time delays of double lenses are less scattered than those of quadruple lenses. Furthermore, the realistic conditional distribution allows a new statistical method to constrain the Hubble constant. We find that 16 published time delay quasars constrain the Hubble constant to be H_0=70+/-6 km/s/Mpc, where the value and its error are estimated using jackknife resampling. After including rough estimates of the sizes of important systematic errors, we find H_0=68+/-6(stat.)+/-8(syst.) km/s/Mpc. The reasonable agreement with other estimates indicates the usefulness of our new approach as a cosmological and astrophysical probe, particularly in the era of large-scale synoptic surveys. (Abridged)

  13. [Diversity of vegetation during its recovery from a catastrophic flood of the Medium Paraná River (Argentina)].

    PubMed

    Franceschi, Eduardo A; Torres, Patricia S; Lewis, Juan P

    2010-06-01

    River floodplains have a high biological diversity that is intensely influenced by vegetation dynamics, changes in space and time scales, and the river's hydrological regime. The vegetation composition of the medium and lower Paraná River has been analyzed previously, with different approaches and criteria that cannot be compared. The aim of this study is to analyze the diversity of the herbaceous vegetation over long time spans, from its regeneration after a catastrophic flood to its recovery, in the North and South sites of the flooding valley of the Medium Paraná River. The first sampling of a pioneer community was performed after the 1982-83 catastrophic flood, and included the surveillance of two plots in two successive recovery stages. Floristic composition and cover-abundance of all species were recorded per plot. Floristic richness, using jackknife, Shannon and Hurlbert diversity and Simpson dominance curves were calculated for each site and for each survey, using EcoSim (software). Floristic richness was higher in the North of Medium Paraná, while dominance was higher in the South. Diversity indexes did not varied significantly and resulted in relatively stable values, because its components compensate each other. PMID:20527470

  14. Retrorectal dermoid cyst manifested as an extrasphincteric perianal fistula - case report.

    PubMed

    Karagjozov, A; Milev, I; Antovic, S; Kadri, E

    2014-01-01

    Retrorectal tumors are very rare but well defined pathological entities in the literature. Also, an extrasphincteric fistula is a very rare form of perianal fistula which makes our case a very unusual and rare one, especially by the fact that it was successfully treated with the first operation and without protective stoma formation. The patient was first treated in hospital for a retrorectal abscess that had spontaneously ruptured in the postanal space. Because of the constant drainage of the suppurative content from the postanal opening in the following months, MRI and fistulography were performed, registering cystic formation in the retrorectal space with fistulous communication with the rectum above and completely separate from the sphincter mechanism. After that the patient was admitted for definitive treatment. The operation was performed with the patient in a prone jack-knife position. Complete excision of the cyst with the fistulous communication was performed and the rectum was sutured in two layers with separate slowly absorbable sutures. The wound was laid open and the patient was discharged on the 5th post operative day. After about ten months the defecation is normal, the wound is sealed and there are no signs of inflammation and secretion locally. PMID:25560513

  15. MEASUREMENT OF COSMIC MICROWAVE BACKGROUND POLARIZATION POWER SPECTRA FROM TWO YEARS OF BICEP DATA

    SciTech Connect

    Chiang, H. C.; Barkats, D.; Bock, J. J.; Hristov, V. V.; Jones, W. C.; Kovac, J. M.; Lange, A. E.; Mason, P. V.; Matsumura, T. [Department of Physics, California Institute of Technology, Pasadena, CA 91125 (United States); Ade, P. A. R. [Department of Physics and Astronomy, University of Wales, Cardiff, CF24 3YB, Wales (United Kingdom); Battle, J. O.; Dowell, C. D.; Nguyen, H. T. [Jet Propulsion Laboratory, Pasadena, CA 91109 (United States); Bierman, E. M.; Keating, B. G. [Department of Physics, University of California at San Diego, La Jolla, CA 92093 (United States); Duband, L. [SBT, Commissariat a l'Energie Atomique, Grenoble (France); Hivon, E. F. [Institut d'Astrophysique de Paris, Paris (France); Holzapfel, W. L. [Department of Physics, University of California at Berkeley, Berkeley, CA 94720 (United States); Kuo, C. L. [Stanford University, Palo Alto, CA 94305 (United States); Leitch, E. M. [University of Chicago, Chicago, IL 60637 (United States)

    2010-03-10

    Background Imaging of Cosmic Extragalactic Polarization (BICEP) is a bolometric polarimeter designed to measure the inflationary B-mode polarization of the cosmic microwave background (CMB) at degree angular scales. During three seasons of observing at the South Pole (2006 through 2008), BICEP mapped {approx}2% of the sky chosen to be uniquely clean of polarized foreground emission. Here, we present initial results derived from a subset of the data acquired during the first two years. We present maps of temperature, Stokes Q and U, E and B modes, and associated angular power spectra. We demonstrate that the polarization data are self-consistent by performing a series of jackknife tests. We study potential systematic errors in detail and show that they are sub-dominant to the statistical errors. We measure the E-mode angular power spectrum with high precision at 21 <= l <= 335, detecting for the first time the peak expected at l {approx} 140. The measured E-mode spectrum is consistent with expectations from a LAMBDACDM model, and the B-mode spectrum is consistent with zero. The tensor-to-scalar ratio derived from the B-mode spectrum is r = 0.02{sup +0.31}{sub -0.26}, or r < 0.72 at 95% confidence, the first meaningful constraint on the inflationary gravitational wave background to come directly from CMB B-mode polarization.

  16. Parallel Worldline Numerics: Implementation and Error Analysis

    E-print Network

    Dan Mazur; Jeremy S. Heyl

    2014-07-28

    We give an overview of the worldline numerics technique, and discuss the parallel CUDA implementation of a worldline numerics algorithm. In the worldline numerics technique, we wish to generate an ensemble of representative closed-loop particle trajectories, and use these to compute an approximate average value for Wilson loops. We show how this can be done with a specific emphasis on cylindrically symmetric magnetic fields. The fine-grained, massive parallelism provided by the GPU architecture results in considerable speedup in computing Wilson loop averages. Furthermore, we give a brief overview of uncertainty analysis in the worldline numerics method. There are uncertainties from discretizing each loop, and from using a statistical ensemble of representative loops. The former can be minimized so that the latter dominates. However, determining the statistical uncertainties is complicated by two subtleties. Firstly, the distributions generated by the worldline ensembles are highly non-Gaussian, and so the standard error in the mean is not a good measure of the statistical uncertainty. Secondly, because the same ensemble of worldlines is used to compute the Wilson loops at different values of $T$ and $x_\\mathrm{ cm}$, the uncertainties associated with each computed value of the integrand are strongly correlated. We recommend a form of jackknife analysis which deals with both of these problems.

  17. A novel computational method to predict transcription factor DNA binding preference.

    PubMed

    Qian, Ziliang; Cai, Yu-Dong; Li, Yixue

    2006-09-29

    Transcription factor binds to sequence specific sites in regulatory region to control nearby gene's expression. It is termed as the major regulator of transcription. However, identifying DNA binding preference of transcription factors systematically is still a challenge. By using the nearest neighbor algorithm, a novel computational approach was developed to predict transcription factor DNA binding preference based on the gene ontology [M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, G. Sherlock, Gene Ontology: tool for the unification of biology, Nat. Genet. 25 (2000) 25-29.] and 0/1 encoding system of nucleotide. The overall success rate of Jackknife cross-validation test for our predictor reaches 76.6%, which indicates the DNA binding preference is closely correlated with its biological functions and computational method developed in this contribution could be a powerful tool to investigate transcription factor DNA binding preference, especially for those novel transcription factors with little prior knowledge on its DNA binding preference. PMID:16899225

  18. Potential geographical distributions of the fruit flies Ceratitis capitata, Ceratitis cosyra, and Ceratitis rosa in China.

    PubMed

    Li, Baini; Ma, Jun; Hu, Xuenan; Liu, Haijun; Zhang, Runjie

    2009-10-01

    There have been relatively few attempts to model the distributions of the fruit flies Ceratitis capitata (Wiedemann), Ceratitis cosyra (Walker), and Ceratitis rosa Karsch in China, but the geographic distributions of these species are of considerable concern in terms of biosecurity. In this study, two different modeling methods (genetic algorithm for rule-set prediction [GARP] and maximum entropy species distribution modeling [Maxent]) were used to predict the potential distributions of these three fly species in China, by using distribution records and a set of environmental predictor variables. The results showed that Maxent performed well, compared with modeling by GARP, at each test threshold. For all three species, the results predicted by Maxent agreed with the observed distributions in Africa and in other parts of the world. In China, C. capitata seems to have the highest number of favorable habitat areas, relative to C. cosyra and C. rosa, i.e., Yunnan, Guizhou, Guangxi, Guangdong, Hainan, Fujian, Sichuan and Chongqing, whereas C. cosyra has the smallest range of suitable areas, i.e., Yunnan, some parts of Hainan and Sichuan. The suitable areas for C. rosa are mainly restricted to Yunnan, Hainan, southern Guangdong, and a few areas of Sichuan. The indications are that on the whole, Southwest and South China are the areas with the highest risk for establishment from these three fly species. Jackknife tests reveal that environmental variables associated with temperature have the strongest influence on the potential distributions of all three species relative to other variables. PMID:19886442

  19. Optimizing viewing procedures of breast tomosynthesis image volumes using eye tracking combined with a free response human observer study

    NASA Astrophysics Data System (ADS)

    Lång, Kristina; Zackrisson, Sophia; Holmqvist, Kenneth; Nystrom, Marcus; Andersson, Ingvar; Förnvik, Daniel; Tingberg, Anders; Timberg, Pontus

    2011-03-01

    The purpose of this study was to evaluate four different viewing procedures as part of improving viewing conditions of breast tomosynthesis (BT) image volumes. The procedures consisted of free scroll volume browsing, and a combination of initial cine loops at three different frame rates (9, 14 and 25 fps) terminated upon request followed by free scroll volume browsing. Fifty-five normal BT image volumes in MLO view were collected. In these, simulated lesions (20 masses and 20 clusters of microcalcifications) were randomly inserted, creating four unique image sets for each procedure. Four readers interpreted the cases in a random order. Their task was to locate a lesion, mark and assign a five level confidence scale. The diagnostic accuracy was analyzed using Jackknife Free Receiver Operating Characteristics (JAFROC). Time efficiency and visual search behavior were also investigated using eye tracking. The results indicate that there was no statistically significant difference in JAFROC FOM between the different viewing procedures, however the medium cine loop speed seemed to be the preferred viewing procedure in terms of total analyze time and dwell time.

  20. Can horizontally oriented breast tomosynthesis image volumes or the use of a systematic search strategy improve interpretation? An eye tracking and free response human observer study

    NASA Astrophysics Data System (ADS)

    Lång, Kristina; Zackrisson, Sophia; Holmqvist, Kenneth; Nyström, Marcus; Andersson, Ingvar; Förnvik, Daniel; Tingberg, Anders; Timberg, Pontus

    2011-03-01

    Our aim was to evaluate if there is a benefit in diagnostic accuracy and efficiency of viewing breast tomosynthesis (BT) image volumes presented horizontally oriented, but also to evaluate the use of a systematic search strategy where the breast is divided, and analyzed consecutively, into two sections. These image presentations were compared to regular vertical image presentation. All methods were investigated using viewing procedures consisting of free scroll volume browsing, and a combination of initial cine loops at three different frame rates (9, 14, 25 fps) terminated upon request followed by free scroll volume browsing if needed. Fifty-five normal BT image volumes in MLO view were collected. In these, simulated lesions (20 masses and 20 clusters of microcalcifications) were randomly inserted, creating four unique image sets for each procedure. Four readers interpreted the cases in a random order. Their task was to locate the lesions, mark and assign a five level confidence scale. The diagnostic accuracy was analyzed using Jackknife Free Receiver Operating Characteristics (JAFROC). Time efficiency and visual search behavior were also investigated using eye tracking. Results indicate there was no statistically significant difference in JAFROC FOM between the different image presentations, although visual search was more time efficient when viewing horizontally oriented image volumes in medium cine loops.

  1. Fuzzy Logic-based Recognition of Gait Changes due to Trip-related Falls.

    PubMed

    Hassan, Rafiul; Begg, Rezaul; Taylor, Simon

    2005-01-01

    The main aim of this paper is to explore application of fuzzy rules for automated recognition of gait changes due to falling behaviour. Minimum foot clearance (MFC) during continuous walking on a treadmill was recorded on 10 healthy elderly and 10 elderly with reported balance problem and tripping falls. MFC histogram characteristic features were used as inputs to the set of fuzzy rules; the features were extracted based on estimating the clusters in the data. Each of the clusters found corresponded to a new fuzzy rule, which were then applied to associate the input space to an output region. Gradient descent method was used to optimise the rule parameters. Both cross-validation and Jack-knife (leave-one-out) techniques were utilized for training the models and subsequently, testing the performance of the optimized fuzzy model. Receiver operating characteristics (ROC) plots, as well as accuracy rates were used to evaluate the performance of the developed model. Test results indicated up to a maximum of 95% accuracy in discriminating the healthy and balance-impaired gait patterns. These results suggest good potentials for fuzzy logic to use as gait diagnostics. PMID:17281360

  2. Multivariate seismic calibration for the Novaya Zemlya test site. Report No. 2, 27 June 1991-22 June 1992

    SciTech Connect

    Fisk, M.D.; Gray, H.L.; Alewine, R.W.; McCartor, G.D.

    1992-09-30

    Within the last year, Soviet yield data have been acquired by DARPA for over 40 underground nuclear explosions at the Novaya Zemlya Test Site between 1964 and 1990. These yields are compared to previous estimates by other authors, based on observed seismic magnitudes and magnitude-log yield relations transported from other test sites. Several discrepancies in the yield data are noted. Seismic magnitude data, based on NORSAR Lg and P coda, Grafenberg Lg, and a world-wide m sub b, have been published by Ringdal and Fyen (1991) for 18 of these events. A similar set of Soviet network magnitudes have been published by Israelsson (1992). Using these data, estimates of the multivariate calibration parameters of the magnitude-log yield relations are computed. An outlier test is applied to the residuals to the lines of best fit. One of the two smallest events is identified as an outlier for every multivariate magnitude combination. A classical confidence interval is presented to estimate future yields, based on estimates of the unknown multivariate calibration parameters. A test of TTBT compliance and a definition of the F-number, based on the confidence interval, are also provided. F-number estimates are obtained for various magnitude combinations by jackknifing. The reliability of the results is discussed, in light of the fact that the data are tightly clustered for 16 of the 18 events.

  3. Driver assistance system for passive multi-trailer vehicles with haptic steering limitations on the leading unit.

    PubMed

    Morales, Jesús; Mandow, Anthony; Martínez, Jorge L; Reina, Antonio J; García-Cerezo, Alfonso

    2013-01-01

    Driving vehicles with one or more passive trailers has difficulties in both forward and backward motion due to inter-unit collisions, jackknife, and lack of visibility. Consequently, advanced driver assistance systems (ADAS) for multi-trailer combinations can be beneficial to accident avoidance as well as to driver comfort. The ADAS proposed in this paper aims to prevent unsafe steering commands by means of a haptic handwheel. Furthermore, when driving in reverse, the steering-wheel and pedals can be used as if the vehicle was driven from the back of the last trailer with visual aid from a rear-view camera. This solution, which can be implemented in drive-by-wire vehicles with hitch angle sensors, profits from two methods previously developed by the authors: safe steering by applying a curvature limitation to the leading unit, and a virtual tractor concept for backward motion that includes the complex case of set-point propagation through on-axle hitches. The paper addresses system requirements and provides implementation details to tele-operate two different off- and on-axle combinations of a tracked mobile robot pulling and pushing two dissimilar trailers. PMID:23552102

  4. A multi-label classifier for prediction membrane protein functional types in animal.

    PubMed

    Zou, Hong-Liang

    2014-11-01

    Membrane protein is an important composition of cell membrane. Given a membrane protein sequence, how can we identify its type(s) is very important because the type keeps a close correlation with its functions. According to previous studies, membrane protein can be divided into the following eight types: single-pass type I, single-pass type II, single-pass type III, single-pass type IV, multipass, lipid-anchor, GPI-anchor, peripheral membrane protein. With the avalanche of newly found protein sequences in the post-genomic age, it is urgent to develop an automatic and effective computational method to rapid and reliable prediction of the types of membrane proteins. At present, most of the existing methods were based on the assumption that one membrane protein only belongs to one type. Actually, a membrane protein may simultaneously exist at two or more different functional types. In this study, a new method by hybridizing the pseudo amino acid composition with multi-label algorithm called LIFT (multi-label learning with label-specific features) was proposed to predict the functional types both singleplex and multiplex animal membrane proteins. Experimental result on a stringent benchmark dataset of membrane proteins by jackknife test show that the absolute-true obtained was 0.6342, indicating that our approach is quite promising. It may become a useful high-through tool, or at least play a complementary role to the existing predictors in identifying functional types of membrane proteins. PMID:25107302

  5. iMem-Seq: A Multi-label Learning Classifier for Predicting Membrane Proteins Types.

    PubMed

    Xiao, Xuan; Zou, Hong-Liang; Lin, Wei-Zhong

    2015-08-01

    Predicting membrane protein type is a challenging problem, particularly when the query proteins may simultaneously have two or more different types. Most of the existing methods can only be used to deal with the single-label proteins. Actually, multiple-label proteins should not be ignored because they usually bear some special functions worthy of in-depth studies. By introducing the "multi-labeled learning" and hybridizing evolution information through Grey-PSSM, a novel predictor called iMem-Seq is developed that can be used to deal with the systems containing both single and multiple types of membrane proteins. As a demonstration, the jackknife cross-validation was performed with iMem-Seq on a benchmark dataset of membrane proteins classified into the eight types, where some proteins belong to two or there types, but none has ?25 % pairwise sequence identity to any other in a same subset. It was demonstrated via the rigorous cross-validations that the new predictor remarkably outperformed all its counterparts. As a user-friendly web-server, iMem-Seq is freely accessible to the public at the website http://www.jci-bioinfo.cn/iMem-Seq . PMID:25796484

  6. Pharmacodynamic analysis of analgesic clinical trials: nonlinear mixed-effects logistic models.

    PubMed

    Liu, C Y; Sambol, N C

    1999-05-01

    In the development of an analgesic product, placebo-controlled clinical trials in patients with defined pain are used to study the dose-time-response relationship of the drug. In such trials, the response is usually an ordered categorical variable with longitudinal and subject-specific repeated measurements. The primary causal variables are time and analgesic concentration. The response may be informative right-hand censored because remedication with a known analgesic may be given if a patient has inadequate pain relief. Mixed-effects logistic models are used to estimate the probabilities of having certain pain relief or pain severity scores. A jackknife method is proposed to estimate the standard errors of parameter estimates. Posterior estimates of these probabilities, or of the scores themselves, allow the evaluation of efficacy for an analgesic. In this evaluation, therapeutic as well as statistical significance is assessed. Two case studies, one focusing on pain relief and the other on pain severity, are used to demonstrate the approach. The level of baseline pain appears to be a determinant of the pattern of response. PMID:10379692

  7. Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States

    SciTech Connect

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom (Scripps); (Maryland-MED); (WU-MED); (LBNL)

    2010-09-13

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a 'jackknife model' in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.

  8. Detecting dissimulation: profiles of simulated malingerers, traumatic brain-injury patients, and normal controls on a revised version of Hiscock and Hiscock's Forced-Choice Memory Test.

    PubMed

    Slick, D; Hopp, G; Strauss, E; Hunter, M; Pinch, D

    1994-06-01

    A computer-administered memory test was given to normal subjects instructed to feign brain damage, normal controls, and traumatic brain-injured (TBI) patients with complaints of memory dysfunction. The test, a revised version of an instrument developed by Hiscock and Hiscock (1989) employed forced, two-choice recognition of previously presented five-digit numbers. Two levels of item difficulty and three retention intervals were used. Control and TBI subjects performed at near ceiling level on easy items and items with short retention intervals. Feigning subjects performed worse than TBI and control subjects at all levels of item difficulty and all retention intervals. Subjects groups were maximally distinguishable from one another by performance on difficult items and items with the longest retention interval. All TBI patients performed at or above chance level. Only 15% of the feigning subjects performed below chance level on any section of the test. Jack-knifed discriminant function analysis correctly classified 83% of all subjects into their respective groups. Although evaluation of patient performance relative to chance probability is useful for indicating the presence of extremely exaggerated memory deficits, criteria derived from sample distributions of group scores were superior for evaluation of motivation in less obvious cases. The Victoria Revision may be useful for detecting true memory deficit as well as dissimulation. PMID:7929714

  9. Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes.

    PubMed

    Qin, Wenli; Li, Yizhou; Li, Juan; Yu, Lezheng; Wu, Di; Jing, Runyu; Pu, Xuemei; Guo, Yanzhi; Li, Menglong

    2012-02-01

    Signal peptides play a crucial role in various biological processes, such as localization of cell surface receptors, translocation of secreted proteins and cell-cell communication. However, the amino acid mutation in signal peptides, also called non-synonymous single nucleotide polymorphisms (nsSNPs or SAPs) may lead to the loss of their functions. In the present study, a computational method was proposed for predicting deleterious nsSNPs in signal peptides based on random forest (RF) by incorporating position specific scoring matrix (PSSM) profile, SignalP score and physicochemical properties. These features were optimized by the maximum relevance minimum redundancy (mRMR) method. Then, a cost matrix was used to minimize the effect of the imbalanced data classification problem that usually occurred in nsSNPs prediction. The method achieved an overall accuracy of 84.5% and the area under the ROC curve (AUC) of 0.822 by Jackknife test, when the optimal subset included 10 features. Furthermore, on the same dataset, we compared our predictor with other existing methods, including R-score-based method and D-score-based methods, and the result of our method was superior to those of the two methods. The satisfactory performance suggests that our method is effective in predicting the deleterious nsSNPs in signal peptides. PMID:22277674

  10. New methodology of influential point detection in regression model building for the prediction of metabolic clearance rate of glucose.

    PubMed

    Meloun, Milan; Hill, Martin; Militký, Jirí; Vrbíková, Jana; Stanická, Sona; Skrha, Jan

    2004-03-01

    Identifying outliers and high-leverage points is a fundamental step in the least-squares regression model building process. The examination of data quality involves the detection of influential points, outliers and high-leverages, which cause many problems in regression analysis. On the basis of a statistical analysis of the residuals (classical, normalized, standardized, jackknife, predicted and recursive) and diagonal elements of a projection matrix, diagnostic plots for influential points indication are formed. The identification of outliers and high leverage points are combined with graphs for the identification of influence type based on the likelihood distance. The powerful procedure for the computation of influential points characteristics written in S-Plus is demonstrated on the model predicting the metabolic clearance rate of glucose (MCRg) that represents the ratio of the amount of glucose supplied to maintain blood glucose levels during the euglycemic clamp and the blood glucose concentration from common laboratory and anthropometric indices. MCRg reflects insulin sensitivity filtering-off the effect of blood glucose. The prediction of clamp parameters should enable us to avoid the demanding clamp examination, which is connected with a higher load and risk for patients. PMID:15080566

  11. Intercalibration of hydroacoustic and mark-recapture methods for assessing the spawning population size of a threatened fish species.

    PubMed

    Rakowitz, G; Kubecka, J; Fesl, C; Keckeis, H

    2009-10-01

    Hydroacoustic counting and a three-year mark-recapture study with passive integrated transponders (PIT tags) were used to estimate the size of a spawning population of nase Chondrostoma nasus, a threatened potamodromous cyprinid that undertakes annual spawning migrations into a tributary of the Danube River. In 2005, the estimates of the size of the spawning population from the hydroacoustic counts (N = 2234, 95% CL 1929-2538) and from the Jolly-Seber model (N = 1198, 95% CL 461-5842) corresponded well. Estimates from the jackknife-estimator based on the hydroacoustic counts yielded slightly higher values (N = 2783, 95% CL 2529-3037), but were still in the same order of magnitude as those from the hydroacoustic and mark-recapture approach. At low run-size, hydroacoustic counting was more time consuming and technically demanding than mark-recapture studies. At the same time, it was non-invasive, provided real-time data on a fine temporal scale, and estimates showed less variability than the Jolly-Seber model. Mark-recapture of fish in spawning streams involved substantial disturbance at a sensitive stage of the life cycle. Hence, hydroacoustics is highly suited for population estimates of threatened potamodromous fishes, where interference needs to be minimized. PMID:20738619

  12. Statistical analysis of galaxy surveys - IV. An objective way to quantify the impact of superstructures on galaxy clustering statistics

    NASA Astrophysics Data System (ADS)

    Norberg, P.; Gaztañaga, E.; Baugh, C. M.; Croton, D. J.

    2011-12-01

    For galaxy clustering to provide robust constraints on cosmological parameters and galaxy formation models, it is essential to make reliable estimates of the errors on clustering measurements. We present a new technique, based on a spatial jackknife (JK) resampling, which provides an objective way to estimate errors on clustering statistics. Our approach allows us to set the appropriate size for the JK subsamples. The method also provides a means to assess the impact of individual regions on the measured clustering, and thereby to establish whether or not a given galaxy catalogue is dominated by one or several large structures, preventing it to be considered as a ‘fair sample’. We apply this methodology to the two- and three-point correlation functions measured from a volume-limited sample of M* galaxies drawn from Data Release 7 of the Sloan Digital Sky Survey (SDSS). The frequency of JK subsample outliers in the data is shown to be consistent with that seen in large N-body simulations of clustering in the cosmological constant plus cold dark matter cosmology. We also present a comparison of the three-point correlation function in SDSS and Two-degree-Field Galaxy Redshift Survey using this approach and find consistent measurements between the two samples.

  13. Number of mammography cases read per year is a strong predictor of sensitivity

    PubMed Central

    Suleiman, Wasfi I.; Lewis, Sarah J.; Georgian-Smith, Dianne; Evanoff, Michael G.; McEntee, Mark F.

    2014-01-01

    Abstract. Early detection of breast cancers affects the 5-year recurrence rates and treatment options for diagnosed patients, and consequently, many countries have instituted nationwide screening programs. This study compared the performance of expert radiologists from Australia and the United States in detection of breast cancer. Forty-one radiologists, 21 from Australia and 20 from the United States, reviewed 30 mammographic cases containing two-view mammograms. Twenty cases had abnormal findings and 10 cases had normal findings. Radiologists were asked to locate malignancies and assign a level of confidence. A jackknife free-response receiver operating characteristic, figure of merit (JAFROC, FOM), inferred receiver operating characteristic, area under curve (ROC, AUC), specificity, sensitivity, and location sensitivity were calculated using Ziltron software and JAFROC v4.1. A Mann-Whitney U test was used to compare the performance of Australian and U.S. radiologists. The results showed that when experience and the number of mammograms read per year were taken into account, the Australian radiologists sampled showed significantly higher sensitivity and location sensitivity (p?0.001). JAFROC (FOM) and inferred ROC (AUC) analysis showed no difference between the overall performance of the two countries. ROC (AUC) and location sensitivity were higher for the Australian radiologists who read the most cases per year.

  14. Diagnostic performance of detecting breast cancer on computed radiographic (CR) mammograms: comparison of hard copy film, 3-megapixel liquid-crystal-display (LCD) monitor and 5-megapixel LCD monitor.

    PubMed

    Yamada, Takayuki; Suzuki, Akihiko; Uchiyama, Nachiko; Ohuchi, Noriaki; Takahashi, Shoki

    2008-11-01

    The purpose was to compare observer performance in the detection of breast cancer using hard-copy film, and 3-megapixel (3-MP) and 5-megapixel (5-MP) liquid crystal display (LCD) monitors in a simulated screening setting. We amassed 100 sample sets, including 32 patients with surgically proven breast cancer (masses present, N = 12; microcalcifications, N = 10; other types, N = 10) and 68 normal controls. All the mammograms were obtained using computed radiography (CR; sampling pitch of 50 mum). Twelve mammographers independently assessed CR mammograms presented in random order for hard-copy and soft-copy reading at minimal 4-week intervals. Observers rated the images on seven-point (1 to 7) and continuous (0 to 100) malignancy scales. Receiver-operating-characteristics analysis was performed, and the average area under the curve (AUC) was calculated for each modality. The jackknife method with the Bonferroni correction was applied to multireader/multicase analysis. The average AUC values for the 3-MP LCD, 5-MP LCD, and hard-copy film were 0.954, 0.947, and 0.956 on the seven-point scale and 0.943, 0.923, and 0.944 on the continuous scale, respectively. There were no significant differences among the three modalities on either scale. Soft-copy reading using 3-MP and 5-MP LCDs is comparable to hard-copy reading for detecting breast cancer. PMID:18491108

  15. Nucleosome positioning based on the sequence word composition.

    PubMed

    Yi, Xian-Fu; He, Zhi-Song; Chou, Kuo-Chen; Kong, Xiang-Yin

    2012-01-01

    The DNA of all eukaryotic organisms is packaged into nucleosomes (a basic repeating unit of chromatin). A nucleosome consists of histone octamer wrapped by core DNA and linker histone H1 associated with linker DNA. It has profound effects on all DNA-dependent processes by affecting sequence accessibility. Understanding the factors that influence nucleosome positioning has great help to the study of genomic control mechanism. Among many determinants, the inherent DNA sequence has been suggested to have a dominant role in nucleosome positioning in vivo. Here, we used the method of minimum redundancy maximum relevance (mRMR) feature selection and the nearest neighbor algorithm (NNA) combined with the incremental feature selection (IFS) method to identify the most important sequence features that either favor or inhibit nucleosome positioning. We analyzed the words of 53,021 nucleosome DNA sequences and 50,299 linker DNA sequences of Saccharomyces cerevisiae. 32 important features were abstracted from 5,460 features, and the overall prediction accuracy through jackknife cross-validation test was 76.5%. Our results support that sequence-dependent DNA flexibility plays an important role in positioning nucleosome core particles and that genome sequence facilitates the rapid nucleosome reassembly instead of nucleosome depletion. Besides, our results suggest that there exist some additional features playing a considerable role in discriminating nucleosome forming and inhibiting sequences. These results confirmed that the underlying DNA sequence plays a major role in nucleosome positioning. PMID:21919856

  16. Use of remote sensing for analysis and estimation of vector-borne disease

    NASA Astrophysics Data System (ADS)

    Rahman, Atiqur

    An epidemiological data of malaria cases were correlated with satellite-based vegetation health (VH) indices to investigate if they can be used as a proxy for monitoring the number of malaria cases. Mosquitoes, which spread malaria in Bangladesh, are very sensitive to environmental conditions, especially to changes in weather. Therefore, VH indices, which characterize weather conditions, were tested as indicators of mosquitoes' activities in the spread of malaria. Satellite data were presented by the following VH indices: Vegetation Condition Index (VCI), Temperature Condition Index (TCI), and Vegetation Health Index (VHI). They were derived from radiances and measured by the Advanced Very High Resolution Radiometer (AVHRR) flown on NOAA afternoon polar orbiting satellites. Assessment of sensitivity of the VH was performed using correlation and regression analysis. Estimation models were validated using of Jackknife Cross-Validation procedure. Results show that the VH indices can be used for detection, and numerical estimate of the number of malaria cases. During the cooler months (January--April) when mosquitoes are less active, the correlation is low and increases considerably during the warm and wet season (April--November), for TCI in early October and for VCI in mid September. All analysis and estimation model developed here are based on data obtained for Bangladesh.

  17. Predicting the potential geographic distribution of cotton mealybug Phenacoccus solenopsis in India based on MAXENT ecological niche model.

    PubMed

    Fand, Babasaheb B; Kumar, Mahesh; Kamble, Ankush L

    2014-09-01

    Mealybug, Phenacoccus solenopsis Tinsley has recently emerged as a serious insect pest of cotton in India. This study demonstrates the use of Maxent algorithm for modeling the potential geographic distribution of P. solenopsis in India with presence-only data. Predictions were made based on the analysis of the relationship between 111 occurrence records for P. solenopsis and the corresponding current and future climate data defined on the study area. The climate data from worldclim database for current (1950-2000) and future (SRES A2 emission scenario for 2050) conditions were used. DIVA-GIS, an open source software for conducting spatial analysis was used for mapping the predictions from Maxent. The algorithm provided reasonable estimates of the species range indicating better discrimination of suitable and unsuitable areas for its occurrence in India under both present and future climatic conditions. The fit for the model as measured by AUC was high, with value of 0.930 for the training data and 0.895 for the test data, indicating the high level of discriminatory power for the Maxent. A Jackknife test for variable importance indicated that mean temperature of coldest quarter with highest gain value was the most important environmental variable determining the potential geographic distribution of P. solenopsis. The approaches used for delineating the ecological niche and prediction of potential geographic distribution are described briefly. Possible applications and limitations of the present modeling approach in future research and as a decision making tool in integrated pest management are discussed. PMID:25204075

  18. Design of a Protein Potential Energy Landscape by Parameter Optimization

    E-print Network

    Julian Lee; Seung-Yeon Kim; Jooyoung Lee

    2003-09-29

    We propose an automated protocol for designing the energy landscape of a protein energy function by optimizing its parameters. The parameters are optimized so that not only the global minimum energy conformation becomes native-like, but also the conformations distinct from the native structure have higher energies than those close to the native one. We successfully apply our protocol to the parameter optimization of the UNRES potential energy, using the training set of betanova, 1fsd, the 36-residue subdomain of chicken villin headpiece (PDB ID 1vii), and the 10-55 residue fragment of staphylococcal protein A (PDB ID 1bdd). The new protocol of the parameter optimization shows better performance than earlier methods where only the difference between the lowest energies of native-like and non-native conformations was adjusted without considering various degrees of native-likeness of the conformations. We also perform jackknife tests on other proteins not included in the training set and obtain promising results. The results suggest that the parameters we obtained using the training set of the four proteins are transferable to other proteins to some extent.

  19. Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach.

    PubMed

    Xu, Ruifeng; Zhou, Jiyun; Liu, Bin; He, Yulan; Zou, Quan; Wang, Xiaolong; Chou, Kuo-Chen

    2015-08-01

    DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well. PMID:25252709

  20. Identification of Essential Proteins Based on Ranking Edge-Weights in Protein-Protein Interaction Networks

    PubMed Central

    Wang, Yan; Sun, Huiyan; Du, Wei; Blanzieri, Enrico; Viero, Gabriella; Xu, Ying; Liang, Yanchun

    2014-01-01

    Essential proteins are those that are indispensable to cellular survival and development. Existing methods for essential protein identification generally rely on knock-out experiments and/or the relative density of their interactions (edges) with other proteins in a Protein-Protein Interaction (PPI) network. Here, we present a computational method, called EW, to first rank protein-protein interactions in terms of their Edge Weights, and then identify sub-PPI-networks consisting of only the highly-ranked edges and predict their proteins as essential proteins. We have applied this method to publicly-available PPI data on Saccharomyces cerevisiae (Yeast) and Escherichia coli (E. coli) for essential protein identification, and demonstrated that EW achieves better performance than the state-of-the-art methods in terms of the precision-recall and Jackknife measures. The highly-ranked protein-protein interactions by our prediction tend to be biologically significant in both the Yeast and E. coli PPI networks. Further analyses on systematically perturbed Yeast and E. coli PPI networks through randomly deleting edges demonstrate that the proposed method is robust and the top-ranked edges tend to be more associated with known essential proteins than the lowly-ranked edges. PMID:25268881

  1. A hybrid orographic plus statistical model for downscaling daily precipitation in Northern California

    USGS Publications Warehouse

    Pandey, G.R.; Cayan, D.R.; Dettinger, M.D.; Georgakakos, K.P.

    2000-01-01

    A hybrid (physical-statistical) scheme is developed to resolve the finescale distribution of daily precipitation over complex terrain. The scheme generates precipitation by combining information from the upper-air conditions and from sparsely distributed station measurements; thus, it proceeds in two steps. First, an initial estimate of the precipitation is made using a simplified orographic precipitation model. It is a steady-state, multilayer, and two-dimensional model following the concepts of Rhea. The model is driven by the 2.5?? ?? 2.5?? gridded National Oceanic and Atmospheric Administration-National Centers for Environmental Prediction upper-air profiles, and its parameters are tuned using the observed precipitation structure of the region. Precipitation is generated assuming a forced lifting of the air parcels as they cross the mountain barrier following a straight trajectory. Second, the precipitation is adjusted using errors between derived precipitation and observations from nearby sites. The study area covers the northern half of California, including coastal mountains, central valley, and the Sierra Nevada. The model is run for a 5-km rendition of terrain for days of January-March over the period of 1988-95. A jackknife analysis demonstrates the validity of the approach. The spatial and temporal distributions of the simulated precipitation field agree well with the observed precipitation. Further, a mapping of model performance indices (correlation coefficients, model bias, root-mean-square error, and threat scores) from an array of stations from the region indicates that the model performs satisfactorily in resolving daily precipitation at 5-km resolution.

  2. Climate change in our backyards: the reshuffling of North America's winter bird communities.

    PubMed

    Princé, Karine; Zuckerberg, Benjamin

    2015-02-01

    Much of the recent changes in North American climate have occurred during the winter months, and as result, overwintering birds represent important sentinels of anthropogenic climate change. While there is mounting evidence that bird populations are responding to a warming climate (e.g., poleward shifts) questions remain as to whether these species-specific responses are resulting in community-wide changes. Here, we test the hypothesis that a changing winter climate should favor the formation of winter bird communities dominated by warm-adapted species. To do this, we quantified changes in community composition using a functional index--the Community Temperature Index (CTI)--which measures the balance between low- and high-temperature dwelling species in a community. Using data from Project FeederWatch, an international citizen science program, we quantified spatiotemporal changes in winter bird communities (n = 38 bird species) across eastern North America and tested the influence of changes in winter minimum temperature over a 22-year period. We implemented a jackknife analysis to identify those species most influential in driving changes at the community level and the population dynamics (e.g., extinction or colonization) responsible for these community changes. Since 1990, we found that the winter bird community structure has changed with communities increasingly composed of warm-adapted species. This reshuffling of winter bird communities was strongest in southerly latitudes and driven primarily by local increases in abundance and regional patterns of colonization by southerly birds. CTI tracked patterns of changing winter temperature at different temporal scales ranging from 1 to 35 years. We conclude that a shifting winter climate has provided an opportunity for smaller, southerly distributed species to colonize new regions and promote the formation of unique winter bird assemblages throughout eastern North America. PMID:25322929

  3. Observer performance for adaptive, image-based denoising and filtered back projection compared to scanner-based iterative reconstruction for lower dose CT enterography

    PubMed Central

    Fletcher, Joel G.; Hara, Amy K.; Fidler, Jeff L.; Silva, Alvin C.; Barlow, John M.; Carter, Rickey E.; Bartley, Adam; Shiung, Maria; Holmes, David R.; Weber, Nicolas K.; Bruining, David H.; Yu, Lifeng; McCollough, Cynthia H.

    2015-01-01

    Purpose The purpose of this study was to compare observer performance for detection of intestinal inflammation for low-dose CT enterography (LD-CTE) using scanner-based iterative reconstruction (IR) vs. vendor-independent, adaptive image-based noise reduction (ANLM) or filtered back projection (FBP). Methods Sixty-two LD-CTE exams were performed. LD-CTE images were reconstructed using IR, ANLM, and FBP. Three readers, blinded to image type, marked intestinal inflammation directly on patient images using a specialized workstation over three sessions, interpreting one image type/patient/session. Reference standard was created by a gastroenterologist and radiologist, who reviewed all available data including dismissal Gastroenterology records, and who marked all inflamed bowel segments on the same workstation. Reader and reference localizations were then compared. Non-inferiority was tested using Jackknife free-response ROC (JAFROC) figures of merit (FOM) for ANLM and FBP compared to IR. Patient-level analyses for the presence or absence of inflammation were also conducted. Results There were 46 inflamed bowel segments in 24/62 patients (CTDIvol interquartile range 6.9–10.1 mGy). JAFROC FOM for ANLM and FBP were 0.84 (95% CI 0.75–0.92) and 0.84 (95% CI 0.75–0.92), and were statistically non-inferior to IR (FOM 0.84; 95% CI 0.76–0.93). Patient-level pooled confidence intervals for sensitivity widely overlapped, as did specificities. Image quality was rated as better with IR and AMLM compared to FBP (p < 0.0001), with no difference in reading times (p = 0.89). Conclusions Vendor-independent adaptive image-based noise reduction and FBP provided observer performance that was non-inferior to scanner-based IR methods. Adaptive image-based noise reduction maintained or improved upon image quality ratings compared to FBP when performing CTE at lower dose levels. PMID:25725794

  4. Limited-sampling strategy models for estimating the pharmacokinetic parameters of 4-methylaminoantipyrine, an active metabolite of dipyrone.

    PubMed

    Suarez-Kurtz, G; Ribeiro, F M; Estrela, R C; Vicente, F L; Struchiner, C J

    2001-11-01

    Bioanalytical data from a bioequivalence study were used to develop limited-sampling strategy (LSS) models for estimating the area under the plasma concentration versus time curve (AUC) and the peak plasma concentration (Cmax) of 4-methylaminoantipyrine (MAA), an active metabolite of dipyrone. Twelve healthy adult male volunteers received single 600 mg oral doses of dipyrone in two formulations at a 7-day interval in a randomized, crossover protocol. Plasma concentrations of MAA (N = 336), measured by HPLC, were used to develop LSS models. Linear regression analysis and a "jack-knife" validation procedure revealed that the AUC(0-infinity) and the Cmax of MAA can be accurately predicted (R2>0.95, bias <1.5%, precision between 3.1 and 8.3%) by LSS models based on two sampling times. Validation tests indicate that the most informative 2-point LSS models developed for one formulation provide good estimates (R2>0.85) of the AUC(0-infinity) or Cmax for the other formulation. LSS models based on three sampling points (1.5, 4 and 24 h), but using different coefficients for AUC(0-infinity) and Cmax, predicted the individual values of both parameters for the enrolled volunteers (R2>0.88, bias = -0.65 and -0.37%, precision = 4.3 and 7.4%) as well as for plasma concentration data sets generated by simulation (R2>0.88, bias = -1.9 and 8.5%, precision = 5.2 and 8.7%). Bioequivalence assessment of the dipyrone formulations based on the 90% confidence interval of log-transformed AUC(0-infinity) and Cmax provided similar results when either the best-estimated or the LSS-derived metrics were used. PMID:11668360

  5. Test–Retest Intervisit Variability of Functional and Structural Parameters in X-Linked Retinoschisis

    PubMed Central

    Jeffrey, Brett G.; Cukras, Catherine A.; Vitale, Susan; Turriff, Amy; Bowles, Kristin; Sieving, Paul A.

    2014-01-01

    Purpose To examine the variability of four outcome measures that could be used to address safety and efficacy in therapeutic trials with X-linked juvenile retinoschisis. Methods Seven men with confirmed mutations in the RS1 gene were evaluated over four visits spanning 6 months. Assessments included visual acuity, full-field electroretinograms (ERG), microperimetric macular sensitivity, and retinal thickness measured by optical coherence tomography (OCT). Eyes were separated into Better or Worse Eye groups based on acuity at baseline. Repeatability coefficients were calculated for each parameter and jackknife resampling used to derive 95% confidence intervals (CIs). Results The threshold for statistically significant change in visual acuity ranged from three to eight letters. For ERG a-wave, an amplitude reduction greater than 56% would be considered significant. For other parameters, variabilities were lower in the Worse Eye group, likely a result of floor effects due to collapse of the schisis pockets and/or retinal atrophy. The criteria for significant change (Better/Worse Eye) for three important parameters were: ERG b/a-wave ratio (0.44/0.23), point wise sensitivity (10.4/7.0 dB), and central retinal thickness (31%/18%). Conclusions The 95% CI range for visual acuity, ERG, retinal sensitivity, and central retinal thickness relative to baseline are described for this cohort of participants with X-linked juvenile retinoschisis (XLRS). Translational Relevance A quantitative understanding of the variability of outcome measures is vital to establishing the safety and efficacy limits for therapeutic trials of XLRS patients. PMID:25346871

  6. Comparative Quantitation of Cytomegalovirus (CMV) DNA in Solid Organ Transplant Recipients with CMV Infection by Using Two High-Throughput Automated Systems

    PubMed Central

    Razonable, Raymund R.; Brown, Robert A.; Espy, Mark J.; Rivero, Antonio; Kremers, Walter; Wilson, Jennie; Groettum, Cynthia; Smith, Thomas F.; Paya, Carlos V.

    2001-01-01

    Cytomegalovirus (CMV) DNA quantitation in clinical specimens is progressively becoming a cornerstone in the diagnosis and management of CMV infection in the immunocompromised host. We evaluated two automated and reproducible PCR tests, the LightCycler (Roche Molecular Biochemicals, Indianapolis, Ind.) and the COBAS AMPLICOR CMV Monitor (Roche Diagnostics, Pleasanton, Calif.), for the detection of CMV DNA in blood samples from transplant recipients with CMV infection as determined by shell vial culture. Following a log transformation analysis, the mean CMV DNA in plasma (PL), whole blood (WB), peripheral blood leukocytes (PBL), and peripheral blood mononuclear cells (PBMC) using the LightCycler was 6.79 copies per ml, 7.23 copies per ml, 6.38 copies per 2 × 106 cells, and 6.27 copies per 2 × 106 cells, respectively. This compares to 7.86 copies per ml, 8.37 copies per ml, 7.59 copies per 2 × 106 cells, and 7.44 copies per 2 × 106 cells, respectively, using COBAS AMPLICOR CMV Monitor. While higher CMV DNA levels were observed for the various blood compartments analyzed using COBAS AMPLICOR CMV Monitor, a high degree of correlation was evident between the two automated systems (jackknife correlation r = PL 0.77 [95% confidence interval (CI); 0.64, 0.90], WB 0.77 [95% CI; 0.62, 0.92], PBL 0.77 [95% CI; 0.67, 0.88], and PBMC 0.81 [95% CI; 0.72, 0.89], all P < 0.001). Therefore, we conclude that either automated diagnostic system is accurate for CMV DNA quantitation. PMID:11724864

  7. Housefly Population Density Correlates with Shigellosis among Children in Mirzapur, Bangladesh: A Time Series Analysis

    PubMed Central

    Farag, Tamer H.; Faruque, Abu S.; Wu, Yukun; Das, Sumon K.; Hossain, Anowar; Ahmed, Shahnawaz; Ahmed, Dilruba; Nasrin, Dilruba; Kotloff, Karen L.; Panchilangam, Sandra; Nataro, James P.; Cohen, Dani; Blackwelder, William C.; Levine, Myron M.

    2013-01-01

    Background Shigella infections are a public health problem in developing and transitional countries because of high transmissibility, severity of clinical disease, widespread antibiotic resistance and lack of a licensed vaccine. Whereas Shigellae are known to be transmitted primarily by direct fecal-oral contact and less commonly by contaminated food and water, the role of the housefly Musca domestica as a mechanical vector of transmission is less appreciated. We sought to assess the contribution of houseflies to Shigella-associated moderate-to-severe diarrhea (MSD) among children less than five years old in Mirzapur, Bangladesh, a site where shigellosis is hyperendemic, and to model the potential impact of a housefly control intervention. Methods Stool samples from 843 children presenting to Kumudini Hospital during 2009–2010 with new episodes of MSD (diarrhea accompanied by dehydration, dysentery or hospitalization) were analyzed. Housefly density was measured twice weekly in six randomly selected sentinel households. Poisson time series regression was performed and autoregression-adjusted attributable fractions (AFs) were calculated using the Bruzzi method, with standard errors via jackknife procedure. Findings Dramatic springtime peaks in housefly density in 2009 and 2010 were followed one to two months later by peaks of Shigella-associated MSD among toddlers and pre-school children. Poisson time series regression showed that housefly density was associated with Shigella cases at three lags (six weeks) (Incidence Rate Ratio?=?1.39 [95% CI: 1.23 to 1.58] for each log increase in fly count), an association that was not confounded by ambient air temperature. Autocorrelation-adjusted AF calculations showed that a housefly control intervention could have prevented approximately 37% of the Shigella cases over the study period. Interpretation Houseflies may play an important role in the seasonal transmission of Shigella in some developing country ecologies. Interventions to control houseflies should be evaluated as possible additions to the public health arsenal to diminish Shigella (and perhaps other causes of) diarrheal infection. PMID:23818998

  8. EMPeror: a tool for visualizing high-throughput microbial community data

    PubMed Central

    2013-01-01

    Background As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. In particular, the Earth Microbiome Project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types. Findings Features of EMPeror include: ability to visualize gradients and categorical data, visualize different principal coordinates axes, present the data in the form of parallel coordinates, show taxa as well as environmental samples, dynamically adjust the size and transparency of the spheres representing the communities on a per-category basis, dynamically scale the axes according to the fraction of variance each explains, show, hide or recolor points according to arbitrary metadata including that compliant with the MIxS family of standards developed by the Genomic Standards Consortium, display jackknifed-resampled data to assess statistical confidence in clustering, perform coordinate comparisons (useful for procrustes analysis plots), and greatly reduce loading times and overall memory footprint compared with existing approaches. Additionally, ease of sharing, given EMPeror’s small output file size, enables agile collaboration by allowing users to embed these visualizations via emails or web pages without the need for extra plugins. Conclusions Here we present EMPeror, an open source and web browser enabled tool with a versatile command line interface that allows researchers to perform rapid exploratory investigations of 3D visualizations of microbial community data, such as the widely used principal coordinates plots. EMPeror includes a rich set of controllers to modify features as a function of the metadata. By being specifically tailored to the requirements of microbial ecologists, EMPeror thus increases the speed with which insight can be gained from large microbiome datasets. PMID:24280061

  9. Virus-ECC-mPLoc: a multi-label predictor for predicting the subcellular localization of virus proteins with both single and multiple sites based on a general form of Chou's pseudo amino acid composition.

    PubMed

    Wang, Xiao; Li, Guo-Zheng; Lu, Wen-Cong

    2013-03-01

    Protein subcellular localization aims at predicting the location of a protein within a cell using computational methods. Knowledge of subcellular localization of viral proteins in a host cell or virus-infected cell is important because it is closely related to their destructive tendencies and consequences. Prediction of viral protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods specialized for viral proteins are only used to deal with the single-location proteins. To better reflect the characteristics of multiplex proteins, a new predictor, called Virus-ECC-mPLoc, has been developed that can be used to deal with the systems containing both singleplex and multiplex proteins by introducing a powerful multi-label learning approach which exploits correlations between subcellular locations and by hybridizing the gene ontology information with the dipeptide composition information. It can be utilized to identify viral proteins among the following six locations: (1) viral capsid, (2) host cell membrane, (3) host endoplasmic reticulum, (4) host cytoplasm, (5) host nucleus, and (6) secreted. Experimental results show that the overall success rates thus obtained by Virus-ECC-mPLoc are 86.9% for jackknife test and 87.2% for independent data set test, which are significantly higher than that by any of the existing predictors. As a user-friendly web-server, Virus-ECCmPLoc is freely accessible to the public at the web-site http://levis.tongji.edu.cn:8080/bioinfo/Virus-ECC-mPLoc/. PMID:22591474

  10. Population pharmacokinetics of caffeine and its metabolites theobromine, paraxanthine and theophylline after inhalation in combination with diacetylmorphine.

    PubMed

    Zandvliet, Anthe S; Huitema, Alwin D R; de Jonge, Milly E; den Hoed, Rob; Sparidans, Rolf W; Hendriks, Vincent M; van den Brink, Wim; van Ree, Jan M; Beijnen, Jos H

    2005-01-01

    The stimulant effect of caffeine, as an additive in diacetylmorphine preparations for study purposes, may interfere with the pharmacodynamic effects of diacetylmorphine. In order to obtain insight into the pharmacology of caffeine after inhalation in heroin users, the pharmacokinetics of caffeine and its dimethylxanthine metabolites were studied. The objectives were to establish the population pharmacokinetics under these exceptional circumstances and to compare the results to published data regarding intravenous and oral administration in healthy volunteers. Diacetylmorphine preparations containing 100 mg of caffeine were used by 10 persons by inhalation. Plasma concentrations of caffeine, theobromine, paraxanthine and theophylline were measured by high performance liquid chromatography. Non-linear mixed effects modelling was used to estimate population pharmacokinetic parameters. The model was evaluated by the jack-knife procedure. Caffeine was rapidly and effectively absorbed after inhalation. Population pharmacokinetics of caffeine and its dimethylxanthine metabolites could adequately and simultaneously be described by a linear multi-compartment model. The volume of distribution for the central compartment was estimated to be 45.7 l and the apparent elimination rate constant of caffeine at 8 hr after inhalation was 0.150 hr(-1) for a typical individual. The bioavailability was approximately 60%. The presented model adequately describes the population pharmacokinetics of caffeine and its dimethylxanthine metabolites after inhalation of the caffeine sublimate of a 100 mg tablet. Validation proved the stability of the model. Pharmacokinetics of caffeine after inhalation and intravenous administration are to a large extent similar. The bioavailability of inhaled caffeine is approximately 60% in experienced smokers. PMID:15667599

  11. [Seasonal evaluation of mammal species richness and abundance in the "Mário Viana" municipal reserve, Mato Grosso, Brasil].

    PubMed

    Rocha, Ednaldo Cândido; Silva, Elias; Martins, Sebastião Venâncio; Barreto, Francisco Cândido Cardoso

    2006-09-01

    We evaluated seasonal species presence and richness, and abundance of medium and large sized mammalian terrestrial fauna in the "Mário Viana" Municipal Biological Reserve, Nova Xavantina, Mato Grosso, Brazil. During 2001, two monthly visits were made to an established transect, 2,820 m in length. Records of 22 mammal species were obtained and individual footprint sequences quantified for seasonal calculation of species richness and relative abundance index (x footprints/km traveled). All 22 species occurred during the rainy season, but only 18 during the dry season. Pseudalopex vetulus (Lund, 1842) (hoary fox), Eira barbara (Linnaeus, 1758) (tayra), Puma concolor (Linnaeus, 1771) (cougar) and Hydrochaeris hydrochaeris (Linnaeus, 1766) (capybara) were only registered during the rainy season. The species diversity estimated using the Jackknife procedure in the dry season (19.83, CI = 2.73) was smaller than in the rainy season (25.67, CI = 3.43). Among the 18 species common in the two seasons, only four presented significantly different abundance indexes: Dasypus novemcinctus Linnaeus, 1758 (nine-banded armadillo), Euphractus sexcinctus (Linnaeus, 1758) (six-banded armadillo), Dasyprocta azarae Lichtenstein, 1823 (Azara's Agouti) and Tapirus terrestris (Linnaeus, 1758) (tapir). On the other hand, Priodontes maximus (Kerr, 1792) (giant armadillo) and Leopardus pardalis (Linnaeus, 1758) (ocelot) had identical abundance index over the two seasons. Distribution of species abundance in the sampled area followed the expected pattern for communities in equilibrium, especially in the rainy season, suggesting that the environment still maintains good characteristics for mammal conservation. The present study shows that the reserve, although only 470 ha in size, plays an important role for conservation of mastofauna of the area as a refuge in an environment full of anthropic influence (mainly cattle breeding in exotic pasture). PMID:18491629

  12. Dose reduction and its influence on diagnostic accuracy and radiation risk in digital mammography: an observer performance study using an anthropomorphic breast phantom

    PubMed Central

    Svahn, Tony; Hemdal, Bengt; Ruschin, Mark; Chakraborty, Dev P; Andersson, Ingvar; Tingberg, Anders; Mattsson, Sören

    2008-01-01

    This study aimed to investigate the effect of dose reduction on diagnostic accuracy and radiation risk in digital mammography. Simulated masses and microcalcifications were positioned in an anthropomorphic breast phantom. Thirty digital images, 14 with lesions, 16 without, were acquired of the phantom using a Mammomat Novation (Siemens, Erlangen, Germany) at each of three dose levels. These corresponded to 100%, 50% and 30% of the normally used average glandular dose (AGD; 1.3 mGy for a standard breast). Eight observers interpreted the 90 unprocessed images in a free-response study and the data was analyzed with the jackknife free-response receiver operating characteristic (JAFROC) method. Observer performance was assessed using the JAFROC figure of merit (FOM). The benefit of radiation risk reduction was estimated based on several risk models. There was no statistically significant difference in performance, as described by the FOM, between the 100% and the 50% dose levels. However, the FOMs for both the 100% and the 50% dose were significantly different from the corresponding quantity for the 30% dose level (F-statistic = 4.95, p-value = 0.01). A dose reduction of 50% would result in 3-9 fewer breast cancer fatalities per 100,000 women undergoing annual screening from the age of 40 to 49 years. The results of the study indicate a possibility of reducing the dose to the breast to half of the dose level currently used. This has to be confirmed in clinical studies and possible differences depending on lesion type should be further examined. PMID:17704316

  13. A phantom-based JAFROC observer study of two CT reconstruction methods: the search for optimisation of lesion detection and effective dose

    NASA Astrophysics Data System (ADS)

    Thompson, John D.; Chakraborty, Dev P.; Szczepura, Katy; Vamvakas, Ioannis; Tootell, Andrew; Manning, David J.; Hogg, Peter

    2015-03-01

    Purpose: To investigate the dose saving potential of iterative reconstruction (IR) in a computed tomography (CT) examination of the thorax. Materials and Methods: An anthropomorphic chest phantom containing various configurations of simulated lesions (5, 8, 10 and 12mm; +100, -630 and -800 Hounsfield Units, HU) was imaged on a modern CT system over a tube current range (20, 40, 60 and 80mA). Images were reconstructed with (IR) and filtered back projection (FBP). An ATOM 701D (CIRS, Norfolk, VA) dosimetry phantom was used to measure organ dose. Effective dose was calculated. Eleven observers (15.11+/-8.75 years of experience) completed a free response study, localizing lesions in 544 single CT image slices. A modified jackknife alternative free-response receiver operating characteristic (JAFROC) analysis was completed to look for a significant effect of two factors: reconstruction method and tube current. Alpha was set at 0.05 to control the Type I error in this study. Results: For modified JAFROC analysis of reconstruction method there was no statistically significant difference in lesion detection performance between FBP and IR when figures-of-merit were averaged over tube current (F(1,10)=0.08, p = 0.789). For tube current analysis, significant differences were revealed between multiple pairs of tube current settings (F(3,10) = 16.96, p<0.001) when averaged over image reconstruction method. Conclusion: The free-response study suggests that lesion detection can be optimized at 40mA in this phantom model, a measured effective dose of 0.97mSv. In high-contrast regions the diagnostic value of IR, compared to FBP, is less clear.

  14. Spatial variation in otolith chemistry of Lutjanus apodus at Turneffe Atoll, Belize

    NASA Astrophysics Data System (ADS)

    Chittaro, P. M.; Usseglio, P.; Fryer, B. J.; Sale, P. F.

    2006-05-01

    Lutjanus apodus (Schoolmaster) were collected from several mangroves and coral reefs at Turneffe Atoll, Belize, in order to investigate whether elemental concentrations from the otolith edge could be used as a means to identify the habitat (mangrove or coral reef) and site (9 mangrove sites and 6 reef sites) from which they were collected. Results of a two factor nested MANOVA (sites nested within habitat) indicated significant differences in elemental concentrations between habitats (i.e., mangrove versus reef) as well as among sites. When separate Linear Discriminant Function Analyses (LDFA) were used to assess whether the spatial variability in otolith chemistry was sufficient to differentiate individuals to their respective habitats or sites, the results indicated that fish were classified (jackknife procedure) with a moderate to poor degree of accuracy (i.e., on average, 67% and 40% of the individuals were correctly classified to the habitat and site from which they were collected, respectively). Using a partial Mantel test we did not find a significant correlation between the differences in otolith elemental concentrations between sites and the distance between sites, while controlling the effect of habitat type (mangrove or reef). This suggests that for mangrove and reef sites at Turneffe Atoll, Belize, the overlap in terms of L. apodus otolith elemental concentrations is too high for investigations of fish movement. Finally, by comparing previously published Haemulon flavolineatum otolith chemistry to that of L. apodus we assessed whether these species showed similar habitat and/or site specific patterns in their otolith chemistry. Although both species were collected from the same sites our results indicated little similarity in their elemental concentrations, thus suggesting that habitat and site elemental signatures are species specific.

  15. A multi-scale study of Orthoptera species richness and human population size controlling for sampling effort

    NASA Astrophysics Data System (ADS)

    Cantarello, Elena; Steck, Claude E.; Fontana, Paolo; Fontaneto, Diego; Marini, Lorenzo; Pautasso, Marco

    2010-03-01

    Recent large-scale studies have shown that biodiversity-rich regions also tend to be densely populated areas. The most obvious explanation is that biodiversity and human beings tend to match the distribution of energy availability, environmental stability and/or habitat heterogeneity. However, the species-people correlation can also be an artefact, as more populated regions could show more species because of a more thorough sampling. Few studies have tested this sampling bias hypothesis. Using a newly collated dataset, we studied whether Orthoptera species richness is related to human population size in Italy’s regions (average area 15,000 km2) and provinces (2,900 km2). As expected, the observed number of species increases significantly with increasing human population size for both grain sizes, although the proportion of variance explained is minimal at the provincial level. However, variations in observed Orthoptera species richness are primarily associated with the available number of records, which is in turn well correlated with human population size (at least at the regional level). Estimated Orthoptera species richness (Chao2 and Jackknife) also increases with human population size both for regions and provinces. Both for regions and provinces, this increase is not significant when controlling for variation in area and number of records. Our study confirms the hypothesis that broad-scale human population-biodiversity correlations can in some cases be artefactual. More systematic sampling of less studied taxa such as invertebrates is necessary to ascertain whether biogeographical patterns persist when sampling effort is kept constant or included in models.

  16. Rainfall variability drives interannual variation in N?O emissions from a humid, subtropical pasture.

    PubMed

    Rowlings, D W; Grace, P R; Scheer, C; Liu, S

    2015-04-15

    Variations in interannual rainfall totals can lead to large uncertainties in annual N2O emission budget estimates from short term field studies. The interannual variation in nitrous oxide (N2O) emissions from a subtropical pasture in Queensland, Australia, was examined using continuous measurements of automated chambers over 2 consecutive years. Nitrous oxide emissions were highest during the summer months and were highly episodic, related more to the size and distribution of rain events than soil water content. Over 48% of the total N2O emitted was lost in just 16% of measurement days. Interannual variation in annual N2O estimates was high, with cumulative emissions increasing with decreasing rainfall. Cumulative emissions averaged 1826.7±199.9 g N2O-N ha(-1) yr(-1) over the two year period, though emissions from 2008 (2148±273 g N2O-N ha(-1) yr(-1)) were 42% higher than 2007 (1504±126 g N2O-N ha(-1) yr(-1)). This increase in annual emissions coincided with almost half of the summer precipitation from 2007 to 2008. Emissions dynamics were chiefly driven by the distribution and size of rain events which varied on a seasonal and annual basis. Sampling frequency effects on cumulative N2O flux estimation were assessed using a jackknife technique to inform future manual sampling campaigns. Test subsets of the daily measured data were generated for the pasture and two adjacent land-uses (rainforest and lychee orchard) by selecting measured flux values at regular time intervals ranging from 1 to 30 days. Errors associated with weekly sampling were up to 34% of the sub-daily mean and were highly biased towards overestimation if strategically sampled following rain events. Sampling time of day also played a critical role. Morning sampling best represented the 24 hour mean in the pasture, whereas sampling at noon proved the most accurate in the shaded rainforest and lychee orchard. PMID:25613765

  17. Microseismicity distribution in the southern Dead Sea basin and its implications on the structure of the basin

    NASA Astrophysics Data System (ADS)

    Braeuer, B.; Asch, Guenter; Hofstetter, R.; Haberland, Ch.; Jaser, D.; El-Kelani, R.; Weber, M.

    2012-03-01

    While the Dead Sea basin has been studied for a long time, the available knowledge about the detailed seismicity distribution in the area, as well as the deeper structure of the basin, is limited. Therefore, within the framework of the international project DESIRE (DEad Sea Integrated REsearch project), a dense temporary local seismological network was operated in the southern Dead Sea area. We use 530 local earthquakes, having all together 26 730 P- and S-arrival times for a simultaneous inversion of 1-D velocity models, station corrections and precise earthquake locations. Jackknife tests suggest an accuracy of the derived hypocentre locations of about 1 km. Thus, the result is the first clear image of the absolute distribution of the microseismicity of the area, especially in depth. The seismicity is concentrated in the upper crust down to 20 km depth while the lower limit of the seismicity is reached at 31 km depth. The seismic events at the eastern boundary fault (EBF) in the southern part of the study area represent the northward transform motion of the Arabian Plate along the Dead Sea Transform. North of the Boqeq fault the seismic activity represents the transfer of the motion in the pull-apart basin from the eastern to the western boundary. We find that from the surface downward the seismic events are tracing the boundary faults of the basin. The western boundary is mapped down to 12 km depth while the EBF reaches about 17 km depth, forming an asymmetric basin. One fifth of the data set is related to a specific cluster in time and space, which occurred in 2007 February at the western border fault. This cluster is aligned vertically, that is, it is perpendicular to the direction of the dominating left-lateral strike-slip movement at the main transform fault.

  18. Early detection of production deficit hot spots in semi-arid environment using FAPAR time series and a probabilistic approach

    NASA Astrophysics Data System (ADS)

    Meroni, M.; Fasbender, D.; Kayitakire, F.; Pini, G.; Rembold, F.; Urbano, F.; Verstraete, M. M.

    2013-12-01

    Timely information on vegetation development at regional scale is needed in arid and semiarid African regions where rainfall variability leads to high inter-annual fluctuations in crop and pasture productivity, as well as to high risk of food crisis in the presence of severe drought events. The present study aims at developing and testing an automatic procedure to estimate the probability of experiencing a seasonal biomass production deficit solely on the basis of historical and near real-time remote sensing observations. The method is based on the extraction of vegetation phenology from SPOT-VEGTATION time series of the Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) and the subsequent computation of seasonally cumulated FAPAR as a proxy for vegetation gross primary production. Within season forecasts of the overall seasonal performance, expressed in terms of probability of experiencing a critical deficit, are based on a statistical approach taking into account two factors: i) the similarity between the current FAPAR profile and past profiles observable in the 15 years FAPAR time series; ii) the uncertainty of past predictions of season outcome as derived using jack-knifing technique. The method is applicable at the regional to continental scale and can be updated regularly during the season (whenever a new satellite observation is made available) to provide a synoptic view of the hot spots of likely production deficit. The specific objective of the procedure described here is to deliver to the food security analyst, as early as possible within the season, only the relevant information (e.g., masking out areas without active vegetation at the time of analysis), expressed through a reliable and easily interpretable measure of impending risk. Evaluation of method performance and examples of application in the Sahel region are discussed.

  19. Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells.

    PubMed

    Shen, Hong-Bin; Chou, Kuo-Chen

    2007-02-15

    Viruses can reproduce their progenies only within a host cell, and their actions depend both on its destructive tendencies toward a specific host cell and on environmental conditions. Therefore, knowledge of the subcellular localization of viral proteins in a host cell or virus-infected cell is very useful for in-depth studying of their functions and mechanisms as well as designing antiviral drugs. An analysis on the Swiss-Prot database (version 50.0, released on May 30, 2006) indicates that only 23.5% of viral protein entries are annotated for their subcellular locations in this regard. As for the gene ontology database, the corresponding percentage is 23.8%. Such a gap calls for the development of high throughput tools for timely annotating the localization of viral proteins within host and virus-infected cells. In this article, a predictor called "Virus-PLoc" has been developed that is featured by fusing many basic classifiers with each engineered according to the K-nearest neighbor rule. The overall jackknife success rate obtained by Virus-PLoc in identifying the subcellular compartments of viral proteins was 80% for a benchmark dataset in which none of proteins has more than 25% sequence identity to any other in a same location site. Virus-PLoc will be freely available as a web-server at http://202.120.37.186/bioinf/virus for the public usage. Furthermore, Virus-PLoc has been used to provide large-scale predictions of all viral protein entries in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The results thus obtained have been deposited in a downloadable file prepared with Microsoft Excel and named "Tab_Virus-PLoc.xls." This file is available at the same website and will be updated twice a year to include the new entries of viral proteins and reflect the continuous development of Virus-PLoc. PMID:17120237

  20. iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins.

    PubMed

    Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

    2013-04-01

    Predicting protein subcellular localization is a challenging problem, particularly when query proteins have multi-label features meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing methods can only be used to deal with the single-label proteins. Actually, multi-label proteins should not be ignored because they usually bear some special function worthy of in-depth studies. By introducing the "multi-label learning" approach, a new predictor, called iLoc-Animal, has been developed that can be used to deal with the systems containing both single- and multi-label animal (metazoan except human) proteins. Meanwhile, to measure the prediction quality of a multi-label system in a rigorous way, five indices were introduced; they are "Absolute-True", "Absolute-False" (or Hamming-Loss"), "Accuracy", "Precision", and "Recall". As a demonstration, the jackknife cross-validation was performed with iLoc-Animal on a benchmark dataset of animal proteins classified into the following 20 location sites: (1) acrosome, (2) cell membrane, (3) centriole, (4) centrosome, (5) cell cortex, (6) cytoplasm, (7) cytoskeleton, (8) endoplasmic reticulum, (9) endosome, (10) extracellular, (11) Golgi apparatus, (12) lysosome, (13) mitochondrion, (14) melanosome, (15) microsome, (16) nucleus, (17) peroxisome, (18) plasma membrane, (19) spindle, and (20) synapse, where many proteins belong to two or more locations. For such a complicated system, the outcomes achieved by iLoc-Animal for all the aforementioned five indices were quite encouraging, indicating that the predictor may become a useful tool in this area. It has not escaped our notice that the multi-label approach and the rigorous measurement metrics can also be used to investigate many other multi-label problems in molecular biology. As a user-friendly web-server, iLoc-Animal is freely accessible to the public at the web-site . PMID:23370050

  1. Comparing halo bias from abundance and clustering

    NASA Astrophysics Data System (ADS)

    Hoffmann, K.; Bel, J.; Gaztañaga, E.

    2015-06-01

    We model the abundance of haloes in the ˜(3 Gpc h-1)3 volume of the MICE Grand Challenge simulation by fitting the universal mass function with an improved Jackknife error covariance estimator that matches theory predictions. We present unifying relations between different fitting models and new predictions for linear (b1) and non-linear (c2 and c3) halo clustering bias. Different mass function fits show strong variations in their performance when including the low mass range (Mh ? 3 × 1012 M? h-1) in the analysis. Together with fits from the literature, we find an overall variation in the amplitudes of around 10 per cent in the low mass and up to 50 per cent in the high mass (galaxy cluster) range (Mh > 1014 M? h-1). These variations propagate into a 10 per cent change in b1 predictions and a 50 per cent change in c2 or c3. Despite these strong variations, we find universal relations between b1 and c2 or c3 for which we provide simple fits. Excluding low-mass haloes, different models fitted with reasonable goodness in this analysis, show per cent level agreement in their b1 predictions, but are systematically 5-10 per cent lower than the bias directly measured with two-point halo-mass clustering. This result confirms previous findings derived from smaller volumes (and smaller masses). Inaccuracies in the bias predictions lead to 5-10 per cent errors in growth measurements. They also affect any halo occupation distribution fitting or (cluster) mass calibration from clustering measurements.

  2. Evaluation of Limiting Climatic Factors and Simulation of a Climatically Suitable Habitat for Chinese Sea Buckthorn

    PubMed Central

    Li, Guoqing; Du, Sheng; Guo, Ke

    2015-01-01

    Chinese sea buckthorn (Hippophae rhamnoides subsp. sinensis) has considerable economic potential and plays an important role in reclamation and soil and water conservation. For scientific cultivation of this species across China, we identified the key climatic factors and explored climatically suitable habitat in order to maximize survival of Chinese sea buckthorn using MaxEnt and GIS tools, based on 98 occurrence records from herbarium and publications and 13 climatic factors from Bioclim, Holdridge life zone and Kria' index variables. Our simulation showed that the MaxEnt model performance was significantly better than random, with an average test AUC value of 0.93 with 10-fold cross validation. A jackknife test and the regularized gain change, which were applied to the training algorithm, showed that precipitation of the driest month (PDM), annual precipitation (AP), coldness index (CI) and annual range of temperature (ART) were the most influential climatic factors in limiting the distribution of Chinese sea buckthorn, which explained 70.1% of the variation. The predicted map showed that the core of climatically suitable habitat was distributed from the southwest to northwest of Gansu, Ningxia, Shaanxi and Shanxi provinces, where the most influential climate variables were PDM of 1.0–7.0 mm, AP of 344.0–1089.0 mm, CI of -47.7–0.0°C, and ART of 26.1–45.0°C. We conclude that the distribution patterns of Chinese sea buckthorn are related to the northwest winter monsoon, the southwest summer monsoon and the southeast summer monsoon systems in China. PMID:26177033

  3. Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi

    PubMed Central

    2009-01-01

    Background Wolbachia (wBm) is an obligate endosymbiotic bacterium of Brugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as B. malayi. As wBm is required for B. malayi development and fertility, targeting wBm is a promising approach. However, the lifecycle of neither B. malayi nor wBm can be maintained in vitro. To facilitate selection of potential drug targets we computationally ranked the wBm genome based on confidence that a particular gene is essential for the survival of the bacterium. Results wBm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG) version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS), was developed to predict each wBm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS), was calculated on the basis of phyletic conservation of genes across Wolbachia's parent order Rickettsiales. Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability of wBm proteins was predicted by alignment to a database of protein targets of known compounds. Conclusion Ranking wBm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes), those highly conserved across Rickettsiales (299 genes), those similar to distant essential genes (8 genes), and those with low confidence of essentiality (253 genes). These data facilitate selection of wBm genes for entry into drug design pipelines. PMID:19943957

  4. Quantifying variability in earthquake rupture models using multidimensional scaling: application to the 2011 Tohoku earthquake

    NASA Astrophysics Data System (ADS)

    Razafindrakoto, Hoby N. T.; Mai, P. Martin; Genton, Marc G.; Zhang, Ling; Thingbaijam, Kiran K. S.

    2015-07-01

    Finite-fault earthquake source inversion is an ill-posed inverse problem leading to non-unique solutions. In addition, various fault parametrizations and input data may have been used by different researchers for the same earthquake. Such variability leads to large intra-event variability in the inferred rupture models. One way to understand this problem is to develop robust metrics to quantify model variability. We propose a Multi Dimensional Scaling (MDS) approach to compare rupture models quantitatively. We consider normalized squared and grey-scale metrics that reflect the variability in the location, intensity and geometry of the source parameters. We test the approach on two-dimensional random fields generated using a von Kármán autocorrelation function and varying its spectral parameters. The spread of points in the MDS solution indicates different levels of model variability. We observe that the normalized squared metric is insensitive to variability of spectral parameters, whereas the grey-scale metric is sensitive to small-scale changes in geometry. From this benchmark, we formulate a similarity scale to rank the rupture models. As case studies, we examine inverted models from the Source Inversion Validation (SIV) exercise and published models of the 2011 Mw 9.0 Tohoku earthquake, allowing us to test our approach for a case with a known reference model and one with an unknown true solution. The normalized squared and grey-scale metrics are respectively sensitive to the overall intensity and the extension of the three classes of slip (very large, large, and low). Additionally, we observe that a three-dimensional MDS configuration is preferable for models with large variability. We also find that the models for the Tohoku earthquake derived from tsunami data and their corresponding predictions cluster with a systematic deviation from other models. We demonstrate the stability of the MDS point-cloud using a number of realizations and jackknife tests, for both the random field and the case studies.

  5. Breast tomosynthesis and digital mammography: a comparison of diagnostic accuracy

    PubMed Central

    Svahn, T M; Chakraborty, D P; Ikeda, D; Zackrisson, S; Do, Y; Mattsson, S; Andersson, I

    2012-01-01

    Objective Our aim was to compare the ability of radiologists to detect breast cancers using one-view breast tomosynthesis (BT) and two-view digital mammography (DM) in an enriched population of diseased patients and benign and/or healthy patients. Methods All participants gave informed consent. The BT and DM examinations were performed with about the same average glandular dose to the breast. The study population comprised patients with subtle signs of malignancy seen on DM and/or ultrasonography. Ground truth was established by pathology, needle biopsy and/or by 1-year follow-up by mammography, which retrospectively resulted in 89 diseased breasts (1 breast per patient) with 95 malignant lesions and 96 healthy or benign breasts. Two experienced radiologists, who were not participants in the study, determined the locations of the malignant lesions. Five radiologists, experienced in mammography, interpreted the cases independently in a free-response study. The data were analysed by the receiver operating characteristic (ROC) and jackknife alternative free-response ROC (JAFROC) methods, regarding both readers and cases as random effects. Results The diagnostic accuracy of BT was significantly better than that of DM (JAFROC: p=0.0031, ROC: p=0.0415). The average sensitivity of BT was higher than that of DM (?90% vs ?79%; 95% confidence interval of difference: 0.036, 0.108) while the average false-positive fraction was not significantly different (95% confidence interval of difference: ?0.117, 0.010). Conclusion The diagnostic accuracy of BT was superior to DM in an enriched population. PMID:22674710

  6. Polynesian ant (Hymenoptera: Formicidae) species richness and distribution: a regional survey

    NASA Astrophysics Data System (ADS)

    Morrison, Lloyd W.

    1997-11-01

    Thirteen Polynesian islands, including five true atolls, an uplifted atoll, and seven high volcanic islands of varying ages, were surveyed for ants by hand collecting techniques. Ten of the thirteen islands had been surveyed previously, and more and species were found in the present survey than were known from all earlier surveys combined, with two exception (Ducie Atoll and Easter Island). This represents the first report of the Argentine ant, Linepithema humile Mayr, from Easter Island. L. humile is a very successful pest species which has only recently invaded Easter Island, and is now very abundant and widespread, occurring at 16 of the 17 sample sites scattered across the island. The introduction of this species is almost certainly responsible for the apparent decline in species richness on Easter Island. In general, more species were present on high islands than atolls of a similar size, and elevation was significant while log (area) and latitude were not in a multiple linear regression with ant species number as the dependent variable. Not enough time was spent on the islands to survey their ant faunas completely, and extrapolations from species effort curves and jackknife estimators of earlier, thorough surverys for ants in the society Islands suggest that only about 50% of the total species were collected in the present survey, at least on the high islands. My collections were probably more complete on the atolls. The increase in species numbers from the present survey relative to known species richnesses (particularly when a large fraction of the species actually present were probably not included in the present survey) supports the hypothesis that remote Polynesian islands are not as depauperate in terms of ant species numbers as previously thought.

  7. Demographic history and rare allele sharing among human populations.

    PubMed

    Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D

    2011-07-19

    High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ?1,000 sequenced chromosomes per population, whereas ?2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

  8. Absolute and relative locations of earthquakes at Mount St. Helens, Washington, using continuous data: implications for magmatic processes: Chapter 4 in A volcano rekindled: the renewed eruption of Mount St. Helens, 2004-2006

    USGS Publications Warehouse

    Thelen, Weston A.; Crosson, Robert S.; Creager, Kenneth C.

    2008-01-01

    This study uses a combination of absolute and relative locations from earthquake multiplets to investigate the seismicity associated with the eruptive sequence at Mount St. Helens between September 23, 2004, and November 20, 2004. Multiplets, a prominent feature of seismicity during this time period, occurred as volcano-tectonic, hybrid, and low-frequency earthquakes spanning a large range of magnitudes and lifespans. Absolute locations were improved through the use of a new one-dimensional velocity model with excellent shallow constraints on P-wave velocities. We used jackknife tests to minimize possible biases in absolute and relative locations resulting from station outages and changing station configurations. In this paper, we show that earthquake hypocenters shallowed before the October 1 explosion along a north-dipping structure under the 1980-86 dome. Relative relocations of multiplets during the initial seismic unrest and ensuing eruption showed rather small source volumes before the October 1 explosion and larger tabular source volumes after October 5. All multiplets possess absolute locations very close to each other. However, the highly dissimilar waveforms displayed by each of the multiplets analyzed suggest that different sources and mechanisms were present within a very small source volume. We suggest that multiplets were related to pressurization of the conduit system that produced a stationary source that was highly stable over long time periods. On the basis of their response to explosions occurring in October 2004, earthquakes not associated with multiplets also appeared to be pressure dependent. The pressure source for these earthquakes appeared, however, to be different from the pressure source of the multiplets.

  9. Detection of calcification clusters in digital breast tomosynthesis slices at different dose levels utilizing a SRSAR reconstruction and JAFROC

    NASA Astrophysics Data System (ADS)

    Timberg, P.; Dustler, M.; Petersson, H.; Tingberg, A.; Zackrisson, S.

    2015-03-01

    Purpose: To investigate detection performance for calcification clusters in reconstructed digital breast tomosynthesis (DBT) slices at different dose levels using a Super Resolution and Statistical Artifact Reduction (SRSAR) reconstruction method. Method: Simulated calcifications with irregular profile (0.2 mm diameter) where combined to form clusters that were added to projection images (1-3 per abnormal image) acquired on a DBT system (Mammomat Inspiration, Siemens). The projection images were dose reduced by software to form 35 abnormal cases and 25 normal cases as if acquired at 100%, 75% and 50% dose level (AGD of approximately 1.6 mGy for a 53 mm standard breast, measured according to EUREF v0.15). A standard FBP and a SRSAR reconstruction method (utilizing IRIS (iterative reconstruction filters), and outlier detection using Maximum-Intensity Projections and Average-Intensity Projections) were used to reconstruct single central slices to be used in a Free-response task (60 images per observer and dose level). Six observers participated and their task was to detect the clusters and assign confidence rating in randomly presented images from the whole image set (balanced by dose level). Each trial was separated by one weeks to reduce possible memory bias. The outcome was analyzed for statistical differences using Jackknifed Alternative Free-response Receiver Operating Characteristics. Results: The results indicate that it is possible reduce the dose by 50% with SRSAR without jeopardizing cluster detection. Conclusions: The detection performance for clusters can be maintained at a lower dose level by using SRSAR reconstruction.

  10. Development and Validation of Limited-Sampling Strategies for Predicting Amoxicillin Pharmacokinetic and Pharmacodynamic Parameters

    PubMed Central

    Suarez-Kurtz, Guilherme; Ribeiro, Frederico Mota; Vicente, Flávio L.; Struchiner, Claudio J.

    2001-01-01

    Amoxicillin plasma concentrations (n = 1,152) obtained from 48 healthy subjects in two bioequivalence studies were used to develop limited-sampling strategy (LSS) models for estimating the area under the concentration-time curve (AUC), the maximum concentration of drug in plasma (Cmax), and the time interval of concentration above MIC susceptibility breakpoints in plasma (T>MIC). Each subject received 500-mg amoxicillin, as reference and test capsules or suspensions, and plasma concentrations were measured by a validated microbiological assay. Linear regression analysis and a “jack-knife” procedure revealed that three-point LSS models accurately estimated (R2, 0.92; precision, <5.8%) the AUC from 0 h to infinity (AUC0-?) of amoxicillin for the four formulations tested. Validation tests indicated that a three-point LSS model (1, 2, and 5 h) developed for the reference capsule formulation predicts the following accurately (R2, 0.94 to 0.99): (i) the individual AUC0-? for the test capsule formulation in the same subjects, (ii) the individual AUC0-? for both reference and test suspensions in 24 other subjects, and (iii) the average AUC0-? following single oral doses (250 to 1,000 mg) of various amoxicillin formulations in 11 previously published studies. A linear regression equation was derived, using the same sampling time points of the LSS model for the AUC0-?, but using different coefficients and intercept, for estimating Cmax. Bioequivalence assessments based on LSS-derived AUC0-?'s and Cmax's provided results similar to those obtained using the original values for these parameters. Finally, two-point LSS models (R2 = 0.86 to 0.95) were developed for T>MICs of 0.25 or 2.0 ?g/ml, which are representative of microorganisms susceptible and resistant to amoxicillin. PMID:11600352

  11. Experience in reading digital images may decrease observer accuracy in mammography

    NASA Astrophysics Data System (ADS)

    Rawashdeh, Mohammad A.; Lewis, Sarah J.; Lee, Warwick; Mello-Thoms, Claudia; Reed, Warren M.; McEntee, Mark; Tapia, Kriscia; Brennan, Patrick C.

    2015-03-01

    Rationale and Objectives: To identify parameters linked to higher levels of performance in screening mammography. In particular we explored whether experience in reading digital cases enhances radiologists' performance. Methods: A total of 60 cases were presented to the readers, of which 20 contained cancers and 40 showed no abnormality. Each case comprised of four images and 129 breast readers participated in the study. Each reader was asked to identify and locate any malignancies using a 1-5 confidence scale. All images were displayed using 5MP monitors, supported by radiology workstations with full image manipulation capabilities. A jack-knife free-response receiver operating characteristic, figure of merit (JAFROC, FOM) methodology was employed to assess reader performance. Details were obtained from each reader regarding their experience, qualifications and breast reading activities. Spearman and Mann Whitney U techniques were used for statistical analysis. Results: Higher performance was positively related to numbers of years professionally qualified (r= 0.18; P<0.05), number of years reading breast images (r= 0.24; P<0.01), number of mammography images read per year (r= 0.28; P<0.001) and number of hours reading mammographic images per week (r= 0.19; P<0.04). Unexpectedly, higher performance was inversely linked to previous experience with digital images (r= - 0.17; p<0.05) and further analysis, demonstrated that this finding was due to changes in specificity. Conclusion: This study suggests suggestion that readers with experience in digital images reporting may exhibit a reduced ability to correctly identify normal appearances requires further investigation. Higher performance is linked to number of cases read per year.

  12. A comparison of ROC inferred from FROC and conventional ROC

    NASA Astrophysics Data System (ADS)

    McEntee, Mark F.; Littlefair, Stephen; Pietrzyk, Mariusz W.

    2014-03-01

    This study aims to determine whether receiver operating characteristic (ROC) scores inferred from free-response receiver operating characteristic (FROC) were equivalent to conventional ROC scores for the same readers and cases. Forty-five examining radiologists of the American Board of Radiology independently reviewed 47 PA chest radiographs under at least two conditions. Thirty-seven cases had abnormal findings and 10 cases had normal findings. Half the readers were asked to first locate any visualized lung nodules, mark them and assign a level of confidence [the FROC mark-rating pair] and second give an overall to the entire image on the same scale [the ROC score]. The second half of readers gave the ROC rating first followed by the FROC mark-rating pairs. A normal image was represented with number 1 and malignant lesions with numbers 2-5. A jackknife free-response receiver operating characteristic (JAFROC), and inferred ROC (infROC) was calculated from the mark-rating pairs using JAFROC V4.1 software. ROC based on the overall rating of the image calculated using DBM MRMC software, which was also used to compare infROC and ROC AUCs treating the methods as modalities. Pearson's correlations coefficient and linear regression were used to examine their relationship using SPSS, version 21.0; (SPSS, Chicago, IL). The results of this study showed no significant difference between the ROC and Inferred ROC AUCs (p?0.25). While Pearson's correlation coefficient was 0.7 (p?0.01). Inter-reader correlation calculated from Obuchowski- Rockette covariance's ranged from 0.43-0.86 while intra-reader agreement was greater than previously reported ranging from 0.68-0.82.

  13. The role of body size in individual-based foraging strategies of a top marine predator.

    PubMed

    Weise, Michael J; Harvey, James T; Costa, Daniel P

    2010-04-01

    Body size is an important determinant of the diving and foraging ability in air-breathing marine vertebrate predators. Satellite-linked dive recorders were used during 2003-2004 to investigate the foraging behavior of 22 male California sea lions (Zalophus californianus, a large, sexually dimorphic otariid) and to evaluate the extent to which body size explained variation among individuals and foraging strategies. Multivariate analyses were used to reduce the number of behavioral variables used to characterize foraging strategies (principal component analysis, PCA), to identify individually based foraging strategies in multidimensional space (hierarchical cluster analysis), and to classify each individual into a cluster or foraging strategy (discriminant analysis). Approximately 81.1% of the variation in diving behavior among individuals was explained by three factors: diving patterns (PC1), foraging effort (PC2), and behavior at the surface (PC3). Individuals were classified into three distinct groups based on their diving behavior (shallow, mixed depth, and deeper divers), and jackknife resampling of the data resulted in correct group assignment 86% of the time. Body size as an independent variable was positively related to dive duration and time spent ashore and negatively related to time at sea, and it was a key parameter in PC2 used to classify the three distinct clusters. Differences among individual-based foraging strategies probably were driven by differences in body size, which enabled larger animals to dive deeper and forage more efficiently by targeting different and perhaps larger prey items. The occurrence of foraging specializations within a species and age class has implications for quantitative modeling of population-level predator-prey interactions and ecosystem structure. PMID:20462115

  14. Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties.

    PubMed

    Huang, Tao; Wang, Ping; Ye, Zhi-Qiang; Xu, Heng; He, Zhisong; Feng, Kai-Yan; Hu, Lele; Cui, Weiren; Wang, Kai; Dong, Xiao; Xie, Lu; Kong, Xiangyin; Cai, Yu-Dong; Li, Yixue

    2010-01-01

    Non-synonymous SNPs (nsSNPs), also known as Single Amino acid Polymorphisms (SAPs) account for the majority of human inherited diseases. It is important to distinguish the deleterious SAPs from neutral ones. Most traditional computational methods to classify SAPs are based on sequential or structural features. However, these features cannot fully explain the association between a SAP and the observed pathophysiological phenotype. We believe the better rationale for deleterious SAP prediction should be: If a SAP lies in the protein with important functions and it can change the protein sequence and structure severely, it is more likely related to disease. So we established a method to predict deleterious SAPs based on both protein interaction network and traditional hybrid properties. Each SAP is represented by 472 features that include sequential features, structural features and network features. Maximum Relevance Minimum Redundancy (mRMR) method and Incremental Feature Selection (IFS) were applied to obtain the optimal feature set and the prediction model was Nearest Neighbor Algorithm (NNA). In jackknife cross-validation, 83.27% of SAPs were correctly predicted when the optimized 263 features were used. The optimized predictor with 263 features was also tested in an independent dataset and the accuracy was still 80.00%. In contrast, SIFT, a widely used predictor of deleterious SAPs based on sequential features, has a prediction accuracy of 71.05% on the same dataset. In our study, network features were found to be most important for accurate prediction and can significantly improve the prediction performance. Our results suggest that the protein interaction context could provide important clues to help better illustrate SAP's functional association. This research will facilitate the post genome-wide association studies. PMID:20689580

  15. Phylogenetic studies favour the unification of Pennisetum, Cenchrus and Odontelytrum (Poaceae): a combined nuclear, plastid and morphological analysis, and nomenclatural combinations in Cenchrus

    PubMed Central

    Chemisquy, M. Amelia; Giussani, Liliana M.; Scataglini, María A.; Kellogg, Elizabeth A.; Morrone, Osvaldo

    2010-01-01

    Backgrounds and Aims Twenty-five genera having sterile inflorescence branches were recognized as the bristle clade within the x = 9 Paniceae (Panicoideae). Within the bristle clade, taxonomic circumscription of Cenchrus (20–25 species), Pennisetum (80–140) and the monotypic Odontelytrum is still unclear. Several criteria have been applied to characterize Cenchrus and Pennisetum, but none of these has proved satisfactory as the diagnostic characters, such as fusion of bristles in the inflorescences, show continuous variation. Methods A phylogenetic analysis based on morphological, plastid (trnL-F, ndhF) and nuclear (knotted) data is presented for a representative species sampling of the genera. All analyses were conducted under parsimony, using heuristic searches with TBR branch swapping. Branch support was assessed with parsimony jackknifing. Key Results Based on plastid and morphological data, Pennisetum, Cenchrus and Odontelytrum were supported as a monophyletic group: the PCO clade. Only one section of Pennisetum (Brevivalvula) was supported as monophyletic. The position of P. lanatum differed among data partitions, although the combined plastid and morphology and nuclear analyses showed this species to be a member of the PCO clade. The basic chromosome number x = 9 was found to be plesiomorphic, and x = 5, 7, 8, 10 and 17 were derived states. The nuclear phylogenetic analysis revealed a reticulate pattern of relationships among Pennisetum and Cenchrus, suggesting that there are at least three different genomes. Because apomixis can be transferred among species through hybridization, its history most likely reflects crossing relationships, rather than multiple independent appearances. Conclusions Due to the consistency between the present results and different phylogenetic hypotheses (including morphological, developmental and multilocus approaches), and the high support found for the PCO clade, also including the type species of the three genera, we propose unification of Pennisetum, Cenchrus and Odontelytrum. Species of Pennisetum and Odontelytrum are here transferred into Cenchrus, which has priority. Sixty-six new combinations are made here. PMID:20570830

  16. A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes.

    PubMed

    Chen, Lei; Lu, Jing; Zhang, Ning; Huang, Tao; Cai, Yu-Dong

    2014-04-01

    In the Anatomical Therapeutic Chemical (ATC) classification system, therapeutic drugs are divided into 14 main classes according to the organ or system on which they act and their chemical, pharmacological and therapeutic properties. This system, recommended by the World Health Organization (WHO), provides a global standard for classifying medical substances and serves as a tool for international drug utilization research to improve quality of drug use. In view of this, it is necessary to develop effective computational prediction methods to identify the ATC-class of a given drug, which thereby could facilitate further analysis of this system. In this study, we initiated an attempt to develop a prediction method and to gain insights from it by utilizing ontology information of drug compounds. Since only about one-fourth of drugs in the ATC classification system have ontology information, a hybrid prediction method combining the ontology information, chemical interaction information and chemical structure information of drug compounds was proposed for the prediction of drug ATC-classes. As a result, by using the Jackknife test, the 1st prediction accuracies for identifying the 14 main ATC-classes in the training dataset, the internal validation dataset and the external validation dataset were 75.90%, 75.70% and 66.36%, respectively. Analysis of some samples with false-positive predictions in the internal and external validation datasets indicated that some of them may even have a relationship with the false-positive predicted ATC-class, suggesting novel uses of these drugs. It was conceivable that the proposed method could be used as an efficient tool to identify ATC-classes of novel drugs or to discover novel uses of known drugs. PMID:24492783

  17. Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.

    PubMed

    Hayat, Maqsood; Khan, Asifullah

    2011-02-21

    Membrane proteins are vital type of proteins that serve as channels, receptors, and energy transducers in a cell. Prediction of membrane protein types is an important research area in bioinformatics. Knowledge of membrane protein types provides some valuable information for predicting novel example of the membrane protein types. However, classification of membrane protein types can be both time consuming and susceptible to errors due to the inherent similarity of membrane protein types. In this paper, neural networks based membrane protein type prediction system is proposed. Composite protein sequence representation (CPSR) is used to extract the features of a protein sequence, which includes seven feature sets; amino acid composition, sequence length, 2 gram exchange group frequency, hydrophobic group, electronic group, sum of hydrophobicity, and R-group. Principal component analysis is then employed to reduce the dimensionality of the feature vector. The probabilistic neural network (PNN), generalized regression neural network, and support vector machine (SVM) are used as classifiers. A high success rate of 86.01% is obtained using SVM for the jackknife test. In case of independent dataset test, PNN yields the highest accuracy of 95.73%. These classifiers exhibit improved performance using other performance measures such as sensitivity, specificity, Mathew's correlation coefficient, and F-measure. The experimental results show that the prediction performance of the proposed scheme for classifying membrane protein types is the best reported, so far. This performance improvement may largely be credited to the learning capabilities of neural networks and the composite feature extraction strategy, which exploits seven different properties of protein sequences. The proposed Mem-Predictor can be accessed at http://111.68.99.218/Mem-Predictor. PMID:21110985

  18. MR Imaging in Patients with Suspected Liver Metastases: Value of Liver-Specific Contrast Agent Gadoxetic Acid

    PubMed Central

    Lee, Kyung Hee; Park, Ji Hoon; Kim, Jung Hoon; Park, Hee Sun; Yu, Mi Hye; Yoon, Jeong-Hee; Han, Joon Koo; Choi, Byung Ihn

    2013-01-01

    Objective To compare the diagnostic performance of gadoxetic acid-enhanced magnetic resonance (MR) imaging with that of triple-phase multidetector-row computed tomography (MDCT) in the detection of liver metastasis. Materials and Methods Our institutional review board approved this retrospective study and waived informed consent. The study population consisted of 51 patients with hepatic metastases and 62 patients with benign hepatic lesions, who underwent triple-phase MDCT and gadoxetic acid-enhanced MRI within one month. Two radiologists independently and randomly reviewed MDCT and MRI images regarding the presence and probability of liver metastasis. In order to determine additional value of hepatobiliary-phase (HBP), the dynamic-MRI set alone and combined dynamic-and-HBP set were evaluated, respectively. The standard of reference was a combination of pathology diagnosis and follow-up imaging. For each reader, diagnostic accuracy was compared using the jackknife alternative free-response receiver-operating-characteristic (JAFROC). Results For both readers, average JAFROC figure-of-merit (FOM) was significantly higher on the MR image sets than on the MDCT images: average FOM was 0.582 on the MDCT, 0.788 on the dynamic-MRI set and 0.847 on the combined HBP set, respectively (p < 0.0001). The differences were more prominent for small (? 1 cm) lesions: average FOM values were 0.433 on MDCT, 0.711 on the dynamic-MRI set and 0.828 on the combined HBP set, respectively (p < 0.0001). Sensitivity increased significantly with the addition of HBP in gadoxetic acid-enhanced MR imaging (p < 0.0001). Conclusion Gadoxetic acid-enhanced MRI shows a better performance than triple-phase MDCT for the detection of hepatic metastasis, especially for small (? 1 cm) lesions. PMID:24265564

  19. Development of Pneumatic Aerodynamic Devices to Improve the Performance, Economics, and Safety of Heavy Vehicles

    SciTech Connect

    Robert J. Englar

    2000-06-19

    Under contract to the DOE Office of Heavy Vehicle Technologies, the Georgia Tech Research Institute (GTRI) is developing and evaluating pneumatic (blown) aerodynamic devices to improve the performance, economics, stability and safety of operation of Heavy Vehicles. The objective of this program is to apply the pneumatic aerodynamic aircraft technology previously developed and flight-tested by GTRI personnel to the design of an efficient blown tractor-trailer configuration. Recent experimental results obtained by GTRI using blowing have shown drag reductions of 35% on a streamlined automobile wind-tunnel model. Also measured were lift or down-load increases of 100-150% and the ability to control aerodynamic moments about all 3 axes without any moving control surfaces. Similar drag reductions yielded by blowing on bluff afterbody trailers in current US trucking fleet operations are anticipated to reduce yearly fuel consumption by more than 1.2 billion gallons, while even further reduction is possible using pneumatic lift to reduce tire rolling resistance. Conversely, increased drag and down force generated instantaneously by blowing can greatly increase braking characteristics and control in wet/icy weather due to effective ''weight'' increases on the tires. Safety is also enhanced by controlling side loads and moments caused on these Heavy Vehicles by winds, gusts and other vehicles passing. This may also help to eliminate the jack-knifing problem if caused by extreme wind side loads on the trailer. Lastly, reduction of the turbulent wake behind the trailer can reduce splash and spray patterns and rough air being experienced by following vehicles. To be presented by GTRI in this paper will be results developed during the early portion of this effort, including a preliminary systems study, CFD prediction of the blown flowfields, and design of the baseline conventional tractor-trailer model and the pneumatic wind-tunnel model.

  20. Dose dependence of mass and microcalcification detection in digital mammography: Free response human observer studies

    SciTech Connect

    Ruschin, Mark; Timberg, Pontus; Ba ring th, Magnus; Hemdal, Bengt; Svahn, Tony; Saunders, Rob S.; Samei, Ehsan; Andersson, Ingvar; Mattsson, Soeren; Chakraborty, Dev P.; Tingberg, Anders [Department of Medical Radiation Physics, Lund University, Malmoe University Hospital, SE-205 02, Malmoe (Sweden); Department of Medical Physics and Biomedical Engineering, Sahlgrenska University Hospital, SE-413 45, Goeteborg (Sweden); Department of Medical Radiation Physics, Lund University, Malmoe University Hospital, SE-205 02 Malmoe, (Sweden); Duke Advanced Imaging Laboratories, Department of Radiology, Duke University Medical Center, Durham, North Carolina 27710 (United States); Department of Diagnostic Radiology, Lund University, Malmoe University Hospital, SE-205 02, Malmoe (Sweden); Department of Medical Radiation Physics, Lund University, Malmoe University Hospital, SE-205 02, Malmoe (Sweden); Imaging Research, Department of Radiology, University of Pittsburgh, 3520 5th Ave, Suite 300, Pittsburgh, Pennsylvania 15261 (United States); Department of Medical Radiation Physics, Lund University, Malmoe University Hospital, SE-205 02, Malmoe (Sweden)

    2007-02-15

    The purpose of this study was to evaluate the effect of dose reduction in digital mammography on the detection of two lesion types--malignant masses and clusters of microcalcifications. Two free-response observer studies were performed--one for each lesion type. Ninety screening images were retrospectively selected; each image was originally acquired under automatic exposure conditions, corresponding to an average glandular dose of 1.3 mGy for a standard breast (50 mm compressed breast thickness with 50% glandularity). For each study, one to three simulated lesions were added to each of 40 images (abnormals) while 50 were kept without lesions (normals). Two levels of simulated system noise were added to the images yielding two new image sets, corresponding to simulated dose levels of 50% and 30% of the original images (100%). The manufacturer's standard display processing was subsequently applied to all images. Four radiologists experienced in mammography evaluated the images by searching for lesions and marking and assigning confidence levels to suspicious regions. The search data were analyzed using jackknife free-response (JAFROC) methodology. For the detection of masses, the mean figure-of-merit (FOM) averaged over all readers was 0.74, 0.71, and 0.68 corresponding to dose levels of 100%, 50%, and 30%, respectively. These values were not statistically different from each other (F=1.67, p=0.19) but showed a decreasing trend. In contrast, in the microcalcification study the mean FOM was 0.93, 0.67, and 0.38 for the same dose levels and these values were all significantly different from each other (F=109.84, p<0.0001). The results indicate that lowering the present dose level by a factor of two compromised the detection of microcalcifications but had a weaker effect on mass detection.

  1. Evaluation of diets for the development and reproduction of Franklinothrips orizabensis (Thysanoptera: Aeolothripidae).

    PubMed

    Hoddle, M S; Jones, J; Oishi, K; Morgan, D; Robinson, L

    2001-08-01

    The suitability of ten diets for the development and reproduction of Franklinothrips orizabensis Johansen, the key natural enemy of Scirtothrips perseae Nakahara, a pest of California grown avocados, was determined in the laboratory. The experimental diets evaluated were: (i) irradiated Ephestia kuehniella Zeller eggs; (ii) irradiated E. kuehniella eggs and avocado pollen; (iii) Tetranychus pacificus McGregor eggs; (iv) T. pacificus eggs and avocado pollen; (v) irradiated E. kuehniella eggs and T. pacificus eggs; (vi) irradiated E. kuehniella eggs, T. pacificus eggs and avocado pollen; (vii) Scirtothrips perseae; (viii) Heliothrips haemorrhoidalis (Bouchè); (ix) avocado pollen; and (x) a young avocado leaf. Franklinothrips orizabensis larvae were unable to develop to adulthood on diets 9 and 10. The remaining eight diets supported complete development of F. orizabensis, but only diets 1, 2, 5, 6, 7 and 8 produced fecund females. On diet 5, F. orizabensis exhibited high larval to adult survivorship (90%), mated females exhibited highest daily and lifetime fecundity, and the progeny of mated females were female biased (53%). Analysis of jackknife estimates of net reproduction (Ro), intrinsic rate of increase (rm), and finite rate of increase (lambda) were all significantly greater for F. orizabensis reared on irradiated E. kuehniella eggs and T. pacificus eggs (i.e. diet 5) than corresponding values for other diets on which female F. orizabensis were able to complete development and reproduce. Incorporation of avocado pollen into diets had an adverse effect on demographic statistics for F. orizabensis, and low quality diets resulted in male biased sex ratios for this predator. PMID:11587623

  2. Developmental and reproductive biology of Scirtothrips perseae (Thysanoptera: Thripidae): a new avocado pest in California.

    PubMed

    Hoddle, M S

    2002-08-01

    The developmental and reproductive biology of a new avocado pest, Scirtothrips perseae Nakahara, was determined in the laboratory at five constant temperatures, 15, 20, 25, 27.5 and 30 degrees C. At 20 degrees C, S. perseae exhibited greatest larval to adult survivorship (41%), and mated females produced a greater proportion of female offspring at this temperature when compared to 15, 25, 27.5 and 30 degrees C. Average lifetime fecundity and preoviposition period was greatest at 15 degrees C at 39.6 eggs per female and 17.6 days, respectively. Jackknifed estimates of net reproduction (Ro), capacity for increase (rc), intrinsic rate of increase (rm), and finite rate of increase (lambda) were all significantly greater at 20 degrees C than corresponding values at 15, 25 and 27.5 degrees C. Population doubling time (Td) was significantly lower at 20 degrees C, indicating S. perseae populations can double 33-71% faster at this temperature in comparison to 15, 25 and 27.5 degrees C. Mean adult longevity decreased with increasing temperature, from a maximum of 52.4 days at 15 degrees C to a minimum of 2.4 days at 30 degrees C. Developmental rates increased linearly with increasing temperatures for eggs and rates were non-linear for development of first and second instar larvae, propupae, pupae, and for egg to adult development. Linear regression and fitting of the modified Logan model to developmental rate data for egg to adult development estimated that 344.8 day degrees were required above a minimum threshold of 6.9 degrees C to complete development. An upper developmental threshold was estimated at 37.6 degrees C with an optimal temperature of 30.5 degrees C for egg to adult development. Unmated females produced only male offspring confirming arrhenotoky in S. perseae. PMID:12191435

  3. Prediction of protein structure classes using hybrid space of multi-profile Bayes and bi-gram probability feature spaces.

    PubMed

    Hayat, Maqsood; Tahir, Muhammad; Khan, Sher Afzal

    2014-04-01

    Proteins are the executants of biological functions in living organisms. Comprehension of protein structure is a challenging problem in the era of proteomics, computational biology, and bioinformatics because of its pivotal role in protein folding patterns. Owing to the large exploration of protein sequences in protein databanks and intricacy of protein structures, experimental and theoretical methods are insufficient for prediction of protein structure classes. Therefore, it is highly desirable to develop an accurate, reliable, and high throughput computational model to predict protein structure classes correctly from polygenetic sequences. In this regard, we propose a promising model employing hybrid descriptor space in conjunction with optimized evidence-theoretic K-nearest neighbor algorithm. Hybrid space is the composition of two descriptor spaces including Multi-profile Bayes and bi-gram probability. In order to enhance the generalization power of the classifier, we have selected high discriminative descriptors from the hybrid space using particle swarm optimization, a well-known evolutionary feature selection technique. Performance evaluation of the proposed model is performed using the jackknife test on three low similarity benchmark datasets including 25PDB, 1189, and 640. The success rates of the proposed model are 87.0%, 86.6%, and 88.4%, respectively on the three benchmark datasets. The comparative analysis exhibits that our proposed model has yielded promising results compared to the existing methods in the literature. In addition, our proposed prediction system might be helpful in future research particularly in cases where the major focus of research is on low similarity datasets. PMID:24384128

  4. MSLoc-DT: a new method for predicting the protein subcellular location of multispecies based on decision templates.

    PubMed

    Zhang, Shao-Wu; Liu, Yan-Fang; Yu, Yong; Zhang, Ting-He; Fan, Xiao-Nan

    2014-03-15

    Revealing the subcellular location of newly discovered protein sequences can bring insight to their function and guide research at the cellular level. The rapidly increasing number of sequences entering the genome databanks has called for the development of automated analysis methods. Currently, most existing methods used to predict protein subcellular locations cover only one, or a very limited number of species. Therefore, it is necessary to develop reliable and effective computational approaches to further improve the performance of protein subcellular prediction and, at the same time, cover more species. The current study reports the development of a novel predictor called MSLoc-DT to predict the protein subcellular locations of human, animal, plant, bacteria, virus, fungi, and archaea by introducing a novel feature extraction approach termed Amino Acid Index Distribution (AAID) and then fusing gene ontology information, sequential evolutionary information, and sequence statistical information through four different modes of pseudo amino acid composition (PseAAC) with a decision template rule. Using the jackknife test, MSLoc-DT can achieve 86.5, 98.3, 90.3, 98.5, 95.9, 98.1, and 99.3% overall accuracy for human, animal, plant, bacteria, virus, fungi, and archaea, respectively, on seven stringent benchmark datasets. Compared with other predictors (e.g., Gpos-PLoc, Gneg-PLoc, Virus-PLoc, Plant-PLoc, Plant-mPLoc, ProLoc-Go, Hum-PLoc, GOASVM) on the gram-positive, gram-negative, virus, plant, eukaryotic, and human datasets, the new MSLoc-DT predictor is much more effective and robust. Although the MSLoc-DT predictor is designed to predict the single location of proteins, our method can be extended to multiple locations of proteins by introducing multilabel machine learning approaches, such as the support vector machine and deep learning, as substitutes for the K-nearest neighbor (KNN) method. As a user-friendly web server, MSLoc-DT is freely accessible at http://bioinfo.ibp.ac.cn/MSLOC_DT/index.html. PMID:24361712

  5. Casimir interactions between magnetic flux tubes in a dense lattice

    NASA Astrophysics Data System (ADS)

    Mazur, Dan; Heyl, Jeremy S.

    2015-03-01

    We use the worldline numerics technique to study a cylindrically symmetric model of magnetic flux tubes in a dense lattice and the nonlocal Casimir forces acting between regions of magnetic flux. Within a superconductor the magnetic field is constrained within magnetic flux tubes and if the background magnetic field is on the order the quantum critical field strength, Bk=m/2 e =4.4 ×1013 Gauss, the magnetic field is likely to vary rapidly on the scales where QED effects are important. In this paper, we construct a cylindrically symmetric toy model of a flux tube lattice in which the nonlocal influence of QED on neighboring flux tubes is taken into account. We compute the effective action densities using the worldline numerics technique. The numerics predict a greater effective energy density in the region of the flux tube, but a smaller energy density in the regions between the flux tubes compared to a locally constant-field approximation. We also compute the interaction energy between a flux tube and its neighbors as the lattice spacing is reduced from infinity. Because our flux tubes exhibit compact support, this energy is entirely nonlocal and predicted to be zero in local approximations such as the derivative expansion. This Casimir-Polder energy can take positive or negative values depending on the distance between the flux tubes, and it may cause the flux tubes in neutron stars to form bunches. In addition to the above results we also discuss two important subtleties of determining the statistical uncertainties within the worldline numerics technique. Firstly, the distributions generated by the worldline ensembles are highly non-Gaussian, and so the standard error in the mean is not a good measure of the statistical uncertainty. Secondly, because the same ensemble of worldlines is used to compute the Wilson loops at different values of T and xcm, the uncertainties associated with each computed value of the integrand are strongly correlated. We recommend a form of jackknife analysis which deals with both of these problems.

  6. Measuring agreement between ratings interpretations and binary clinical interpretations of images: a simulation study of methods for quantifying the clinical relevance of an observer performance paradigm

    PubMed Central

    Chakraborty, Dev P.

    2012-01-01

    Laboratory receiver operating characteristic (ROC) studies, that are often used to evaluate medical imaging systems, differ from “live” clinical interpretations in several respects which could compromise their clinical relevance. The aim was to develop methodology for quantifying the clinical relevance of a laboratory ROC study. A simulator was developed to generate ROC ratings data and binary clinical interpretations classified as correct or incorrect for a common set of images interpreted under clinical and laboratory conditions. The area under the trapezoidal ROC curve was used as the laboratory figure-of-merit and the fraction of correct clinical decisions as the clinical figure-of-merit. Conventional agreement measures (Pearson, Spearman, Kendall and kappa) between the bootstrap-induced fluctuations of the two figures-of-merit were estimated. A jackknife pseudovalue transformation applied to the figures-of-merit was also investigated as a way to capture agreement existing at the individual image level that could be lost at the figure-of-merit level. It is shown that the pseudovalues define a relevance ROC curve the area under which (rAUC) measures the ability of the laboratory figure-of-merit based pseudovalues to correctly classify incorrect vs. correct clinical interpretations, and is a measure of the clinical relevance of an ROC study. The conventional measures and rAUC were compared under varying simulator conditions. It was found that design details of the ROC study, namely the number of bins, the difficulty level of the images, the ratio of disease-present to disease-absent images, and the unavoidable difference between laboratory and clinical performance levels, can seriously underestimate the agreement as indicated by conventional agreement measures, even for perfectly correlated data, while rAUC showed high agreement and was relatively immune to these details. At the same time rAUC was sensitive to factors such as intrinsic correlation between the laboratory and clinical decision variables and differences in reporting thresholds that are expected to influence agreement both at the individual image level and at the figure-of-merit level. Suggestions are made for how to conduct relevance ROC studies aimed at assessing agreement between laboratory and clinical interpretations. PMID:22516804

  7. Computer-aided detection of clustered microcalcifications in multiscale bilateral filtering regularized reconstructed digital breast tomosynthesis volume

    PubMed Central

    Samala, Ravi K.; Chan, Heang-Ping; Lu, Yao; Hadjiiski, Lubomir; Wei, Jun; Sahiner, Berkman; Helvie, Mark A.

    2014-01-01

    Purpose: Develop a computer-aided detection (CADe) system for clustered microcalcifications in digital breast tomosynthesis (DBT) volume enhanced with multiscale bilateral filtering (MSBF) regularization. Methods: With Institutional Review Board approval and written informed consent, two-view DBT of 154 breasts, of which 116 had biopsy-proven microcalcification (MC) clusters and 38 were free of MCs, was imaged with a General Electric GEN2 prototype DBT system. The DBT volumes were reconstructed with MSBF-regularized simultaneous algebraic reconstruction technique (SART) that was designed to enhance MCs and reduce background noise while preserving the quality of other tissue structures. The contrast-to-noise ratio (CNR) of MCs was further improved with enhancement-modulated calcification response (EMCR) preprocessing, which combined multiscale Hessian response to enhance MCs by shape and bandpass filtering to remove the low-frequency structured background. MC candidates were then located in the EMCR volume using iterative thresholding and segmented by adaptive region growing. Two sets of potential MC objects, cluster centroid objects and MC seed objects, were generated and the CNR of each object was calculated. The number of candidates in each set was controlled based on the breast volume. Dynamic clustering around the centroid objects grouped the MC candidates to form clusters. Adaptive criteria were designed to reduce false positive (FP) clusters based on the size, CNR values and the number of MCs in the cluster, cluster shape, and cluster based maximum intensity projection. Free-response receiver operating characteristic (FROC) and jackknife alternative FROC (JAFROC) analyses were used to assess the performance and compare with that of a previous study. Results: Unpaired two-tailed t-test showed a significant increase (p < 0.0001) in the ratio of CNRs for MCs with and without MSBF regularization compared to similar ratios for FPs. For view-based detection, a sensitivity of 85% was achieved at an FP rate of 2.16 per DBT volume. For case-based detection, a sensitivity of 85% was achieved at an FP rate of 0.85 per DBT volume. JAFROC analysis showed a significant improvement in the performance of the current CADe system compared to that of our previous system (p = 0.003). Conclusions: MBSF regularized SART reconstruction enhances MCs. The enhancement in the signals, in combination with properly designed adaptive threshold criteria, effective MC feature analysis, and false positive reduction techniques, leads to a significant improvement in the detection of clustered MCs in DBT. PMID:24506622

  8. Atlantic Tropical Cyclone Monitoring with AMSU-A: Estimation of Maximum Sustained Wind Speeds

    NASA Technical Reports Server (NTRS)

    Spencer, Roy W.; Braswell, William D.

    2001-01-01

    The first Advanced Microwave Sounding Unit temperature sounder (AMSU-A) was launched on the NOAA-15 satellite on 13 May 1998. The AMSU-A's higher spatial and radiometric resolutions provide more useful information on the strength of the middle- and upper-tropospheric warm cores associated with tropical cyclones than have previous microwave temperature sounders. The gradient wind relationship suggests that the temperature gradient near the core of tropical cyclones increases nonlinearly with wind speed. The gradient wind equation is recast to include AMSU-A-derived variables, Stepwise regression is used to determine which of these variables is most closely related to maximum sustained winds (V(sub max)). The satellite variables investigated include the radially averaged gradients at two spatial resolutions of AMSU-A channels 1-10 T(sub b) data (delta(sub r)T(sub B)), the squares of these gradients, a channel-15-based scattering index (SI(sub 89)), and area-averaged T(sub B). Calculations of T(sub B) and delta(sub r)T(sub B) from mesoscale model simulations of Andrew reveal the effects of the AMSU spatial sampling on the cyclone warm core presentation. Stepwise regression of 66 AMSU-A terms against National Hurricane Center V(sub max) estimates from the 1998 and 1999 Atlantic hurricane season confirms the existence of a nonlinear relationship between wind speed and radially averaged temperature gradients near the cyclone warm core. Of six regression terms, four are dominated by temperature information, and two are interpreted as correcting for hydrometeor contamination. Jackknifed regressions were performed to estimate the algorithm performance on independent data. For the 82 cases that had in situ measurements of V(sub max), the average error standard deviation was 4.7 m/s. For 108 cases without in situ wind data, the average error standard deviation was 7.5 m/s Operational considerations, including the detection of weak cyclones and false alarm reduction, are also discussed.

  9. Atlantic Tropical Cyclone Monitoring with AMSU-A: Estimation of Maximum Sustained Wind Speeds

    NASA Technical Reports Server (NTRS)

    Spencer, Roy; Braswell, William D.; Goodman, H. Michael (Technical Monitor)

    2001-01-01

    The first Advanced Microwave Sounding Unit temperature sounder (AMSU-A) was launched on the NOAA-15 satellite on 13 May 1998. The AMSU-A's higher spatial and radiometric resolutions provide more useful information on the strength of the middle and upper tropospheric warm cores associated with tropical cyclones than have previous microwave temperature sounders. The gradient wind relationship suggests that the temperature gradient near the core of tropical cyclones increases nonlinearly with wind speed. We recast the gradient wind equation to include AMSU-A derived variables. Stepwise regression is used to determine which of these variables is most closely related to maximum sustained winds (V(sub max)). The satellite variables investigated include the radially averaged gradients at two spatial resolutions of AMSU-A channels 1 through 10 T(sub b) data (delta(sub r)T(sub b)), the squares of these gradients, a channel 15 based scattering index (SI-89), and area averaged T(sub b). Calculations of Tb and delta(sub r)T(sub b) from mesoscale model simulations of Andrew reveal the effects of the AMSU spatial sampling on the cyclone warm core presentation. Stepwise regression of 66 AMSU-A terms against National Hurricane Center (NHC) V(sub max) estimates from the 1998 and 1999 Atlantic hurricane season confirms the existence of a nonlinear relationship between wind speed and radially averaged temperature gradients near the cyclone warm core. Of six regression terms, four are dominated by temperature information, and two are interpreted as correcting for hydrometeor contamination. Jackknifed regressions were performed to estimate the algorithm performance on independent data. For the 82 cases that had in situ measurements of V(sub max), the average error standard deviation was 4.7 m/s. For 108 cases without in situ wind data, the average error standard deviation was 7.5 m/s. Operational considerations, including the detection of weak cyclones and false alarm reduction are also discussed.

  10. Subspace Dimensionality: A Tool for Automated QC in Seismic Array Processing

    NASA Astrophysics Data System (ADS)

    Rowe, C. A.; Stead, R. J.; Begnaud, M. L.

    2013-12-01

    Because of the great resolving power of seismic arrays, the application of automated processing to array data is critically important in treaty verification work. A significant problem in array analysis is the inclusion of bad sensor channels in the beamforming process. We are testing an approach to automated, on-the-fly quality control (QC) to aid in the identification of poorly performing sensor channels prior to beam-forming in routine event detection or location processing. The idea stems from methods used for large computer servers, when monitoring traffic at enormous numbers of nodes is impractical on a node-by node basis, so the dimensionality of the node traffic is instead monitoried for anomalies that could represent malware, cyber-attacks or other problems. The technique relies upon the use of subspace dimensionality or principal components of the overall system traffic. The subspace technique is not new to seismology, but its most common application has been limited to comparing waveforms to an a priori collection of templates for detecting highly similar events in a swarm or seismic cluster. In the established template application, a detector functions in a manner analogous to waveform cross-correlation, applying a statistical test to assess the similarity of the incoming data stream to known templates for events of interest. In our approach, we seek not to detect matching signals, but instead, we examine the signal subspace dimensionality in much the same way that the method addresses node traffic anomalies in large computer systems. Signal anomalies recorded on seismic arrays affect the dimensional structure of the array-wide time-series. We have shown previously that this observation is useful in identifying real seismic events, either by looking at the raw signal or derivatives thereof (entropy, kurtosis), but here we explore the effects of malfunctioning channels on the dimension of the data and its derivatives, and how to leverage this effect for identifying bad array elements through a jackknifing process to isolate the anomalous channels, so that an automated analysis system might discard them prior to FK analysis and beamforming on events of interest.

  11. Reproducibility and optimization of in? vivo human diffusion-weighted MRS of the corpus callosum at 3T and 7T.

    PubMed

    Wood, Emily T; Ercan, Ayse Ece; Branzoli, Francesca; Webb, Andrew; Sati, Pascal; Reich, Daniel S; Ronen, Itamar

    2015-08-01

    Diffusion-weighted MRS (DWS) of brain metabolites enables the study of cell-specific alterations in tissue microstructure by probing the diffusion of intracellular metabolites. In particular, the diffusion properties of neuronal N-acetylaspartate (NAA), typically co-measured with N-acetylaspartyl glutamate (NAAG) (NAA?+?NAAG?=?tNAA), have been shown to be sensitive to intraneuronal/axonal damage in pathologies such as stroke and multiple sclerosis. Lacking, so far, are empirical assessments of the reproducibility of DWS measures across time and subjects, as well as a systematic investigation of the optimal acquisition parameters for DWS experiments, both of which are sorely needed for clinical applications of the method. In this study, we acquired comprehensive single-volume DWS datasets of the human corpus callosum at 3T and 7T. We investigated the inter- and intra-subject variability of empirical and modeled diffusion properties of tNAA [Davg (tNAA) and Dmodel (tNAA), respectively]. Subsequently, we used a jackknife-like resampling approach to explore the variance of these properties in partial data subsets reflecting different total scan durations. The coefficients of variation (CV ) and repeatability coefficients (CR ) for Davg (tNAA) and Dmodel (tNAA) were calculated for both 3T and 7T, with overall lower variability in the 7T results. Although this work is limited to the estimation of the diffusion properties in the corpus callosum, we show that a careful choice of diffusion-weighting conditions at both field strengths allows the accurate measurement of tNAA diffusion properties in clinically relevant experimental time. Based on the resampling results, we suggest optimized acquisition schemes of 13-min duration at 3T and 10-min duration at 7T, whilst retaining low variability (CV ???8%) for the tNAA diffusion measures. Power calculations for the estimation of Dmodel (tNAA) and Davg (tNAA) based on the suggested schemes show that less than 21 subjects per group are sufficient for the detection of a 10% effect between two groups in case-control studies. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26084563

  12. Characterization of landslide kinematics with a long range terrestrial laser scan: a methodological approach

    NASA Astrophysics Data System (ADS)

    Travelletti, J.; Oppikofer, T.; Malet, J.-P.; Jaboyedoff, M.

    2009-04-01

    The objective of this work is to present a methodology for analyzing large displacements of landslide with a terrestrial laser scan (TLS) and to characterize the acquisition and computation errors of the displacement fields. Several high resolution TLS observations (0.3 to 4 pt.cm-2) were acquired in representative plots of the Super-Sauze mudslide in 2007 and 2008: the main scarp in the upper part, the medium part exhibiting the highest displacement rates and the toe in the lower part. The TLS equipment is an Optech ILRIS-3D. All the processing has been performed with the Polyworks software. Among the procedures influencing the quality of the derived displacement fields, the alignment of the scans is the most sensitive. The distribution of statistical noise associated to equipment errors follows a normal law and does not significantly influence the quality of the displacement field ( = 0.1 cm, = 1.0 cm). As well, local changes in surface soil moisture do not significantly influence the quality of the displacement field; although the intensity of the signal is drastically decreased (~24% of the maximum intensity), observations on nearly saturated and unsaturated plots still indicate a tolerable error band of = 0.3 cm and = 0.2 cm at a distance of 30 m from the laser scan. To quantify the displacement field from the original point clouds, several approaches can be used: (1) point cloud comparisons (e.g. algorithm looking for the shortest points along a vector), (2) rebuilding of object geometry (TIN model analysis), and (3) difference of DEMs. In order to characterize displacements with an important horizontal component, it is demonstrated that the object recognition method is more efficient to characterize the kinematics on relative smooth topography than point clouds algorithms. To characterize displacement with a more important vertical component, such as the collapse of material from the main scarp of the mudslide, a "jackknife" procedure was used to identify the best interpolation techniques for producing the DEM. A differential DEM analysis allowed to define the volume of the collapse (~23.000 m3) as well as a progressive subsidence of the area downslope. The quality of the alignment is the most sensitive parameter influencing the accuracy of the laser scan observations. A good coverage among the scans and the inclusion of stable parts are necessary to maximize the alignment procedure, but the number of scans to acquire has also to be minimized in a survey planning.

  13. iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints.

    PubMed

    Xiao, Xuan; Min, Jian-Liang; Wang, Pu; Chou, Kuo-Chen

    2013-11-21

    Many crucial functions in life, such as heartbeat, sensory transduction and central nervous system response, are controlled by cell signalings via various ion channels. Therefore, ion channels have become an excellent drug target, and study of ion channel-drug interaction networks is an important topic for drug development. However, it is both time-consuming and costly to determine whether a drug and a protein ion channel are interacting with each other in a cellular network by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (three-dimensional) structure of protein, unfortunately their usage is quite limited because the 3D structures for most protein ion channels are still unknown. With the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop the sequence-based computational method to address this problem. To take up the challenge, we developed a new predictor called iCDI-PseFpt, in which the protein ion-channel sample is formulated by the PseAAC (pseudo amino acid composition) generated with the gray model theory, the drug compound by the 2D molecular fingerprint, and the operation engine is the fuzzy K-nearest neighbor algorithm. The overall success rate achieved by iCDI-PseFpt via the jackknife cross-validation was 87.27%, which is remarkably higher than that by any of the existing predictors in this area. As a user-friendly web-server, iCDI-PseFpt is freely accessible to the public at the website http://www.jci-bioinfo.cn/iCDI-PseFpt/. Furthermore, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated math equations presented in the paper just for its integrity. It has not escaped our notice that the current approach can also be used to study other drug-target interaction networks. PMID:23988798

  14. One year survival of ART and conventional restorations in patients with disability

    PubMed Central

    2014-01-01

    Background Providing restorative treatment for persons with disability may be challenging and has been related to the patient’s ability to cope with the anxiety engendered by treatment and to cooperate fully with the demands of the clinical situation. The aim of the present study was to assess the survival rate of ART restorations compared to conventional restorations in people with disability referred for special care dentistry. Methods Three treatment protocols were distinguished: ART (hand instruments/high-viscosity glass-ionomer); conventional restorative treatment (rotary instrumentation/resin composite) in the clinic (CRT/clinic) and under general anaesthesia (CRT/GA). Patients were referred for restorative care to a special care centre and treated by one of two specialists. Patients and/or their caregivers were provided with written and verbal information regarding the proposed techniques, and selected the type of treatment they were to receive. Treatment was provided as selected but if this option proved clinically unfeasible one of the alternative techniques was subsequently proposed. Evaluation of restoration survival was performed by two independent trained and calibrated examiners using established ART restoration assessment codes at 6 months and 12 months. The Proportional Hazard model with frailty corrections was applied to calculate survival estimates over a one year period. Results 66 patients (13.6?±?7.8 years) with 16 different medical disorders participated. CRT/clinic proved feasible for 5 patients (7.5%), the ART approach for 47 patients (71.2%), and 14 patients received CRT/GA (21.2%). In all, 298 dentine carious lesions were restored in primary and permanent teeth, 182 (ART), 21 (CRT/clinic) and 95 (CRT/GA). The 1-year survival rates and jackknife standard error of ART and CRT restorations were 97.8?±?1.0% and 90.5?±?3.2%, respectively (p?=?0.01). Conclusions These short-term results indicate that ART appears to be an effective treatment protocol for treating patients with disability restoratively, many of whom have difficulty coping with the conventional restorative treatment. Trial registration number Netherlands Trial Registration: NTR 4400 PMID:24885938

  15. Presence-only approach to assess landslide triggering-thickness susceptibility. A test for the Mili catchment (North-Eastern Sicily, Italy)

    NASA Astrophysics Data System (ADS)

    Lombardo, Luigi; Fubelli, Giandomenico; Amato, Gabriele; Bonasera, Mauro; Hochschild, Volker; Rotigliano, Edoardo

    2015-04-01

    This study aims at comparing the performances of a presence only approach, namely Maximum Entropy, in assessing landslide triggering-thickness susceptibility within the Mili catchment, located in the north-eastern Sicily, Italy. This catchment has been recently exposed to three main meteorological extreme events, resulting in the activation of multiple fast landslides, which occurred on the 1st October 2009, 10th March 2010 and 1st March 2011. Differently from the 2009 event, which only marginally hit the catchment, the 2010 and 2011 storms fully involved the area of the Mili catchment. Detailed field data was collected to associate the thickness of mobilised materials at the triggering zone to each mass movement within the catchment. This information has been used to model the landslide susceptibility for two classes of processes clustered into shallow failures for maximum depths of 0.5m and deep ones in case of values equal or greater than 0.5m. As the authors believed that the peculiar geomorphometry of this narrow and steep catchment played a fundamental role in generating two distinct patterns of landslide thicknesses during the initiation phase, a HRDEM was used to extract topographic attributes to express near-triggering geomorphological conditions. On the other hand, medium resolution vegetation indexes derived from ASTER scenes were used as explanatory variables pertaining to a wider spatial neighbourhood, whilst a revised geological map, the land use from CORINE and a tectonic map were used to convey an even wider area connected to the slope instability. The choice of a presence-only approach allowed to effectively discriminate between the two types of landslide thicknesses at the triggering zone, producing outstanding prediction skills associated with relatively low variances across a set of 20 randomly generated replicates. The validation phase produced indeed average AUC values of 0.91 with a standard deviation of 0.03 for both the modelled landslide thicknesses. In addition, the role of each predictor within the whole modelling procedure was assessed by applying Jackknife tests. These analyses focussed on evaluating the variation of AUC values across replicates comparing single variable models with models based on the full set of predictors iteratively deprived of one covariate. As a result, relevant differences among main contributors between the two considered classes were also quantitatively derived and geomorphologically interpreted. This work can be considered as an example for creating specific landslide susceptibility maps to be used in master planning in order to establish proportional countermeasures to different activation mechanisms. Keywords: statistical analysis, shallow landslide, landslide susceptibility, triggering factors, presence-only approach

  16. Computer-aided detection of clustered microcalcifications in multiscale bilateral filtering regularized reconstructed digital breast tomosynthesis volume

    SciTech Connect

    Samala, Ravi K., E-mail: rsamala@umich.edu; Chan, Heang-Ping; Lu, Yao; Hadjiiski, Lubomir; Wei, Jun; Helvie, Mark A. [Department of Radiology, University of Michigan, Ann Arbor, Michigan 48109-5842 (United States)] [Department of Radiology, University of Michigan, Ann Arbor, Michigan 48109-5842 (United States); Sahiner, Berkman [Center for Devices and Radiological Health, U.S. Food and Drug Administration, Maryland 20993 (United States)] [Center for Devices and Radiological Health, U.S. Food and Drug Administration, Maryland 20993 (United States)

    2014-02-15

    Purpose: Develop a computer-aided detection (CADe) system for clustered microcalcifications in digital breast tomosynthesis (DBT) volume enhanced with multiscale bilateral filtering (MSBF) regularization. Methods: With Institutional Review Board approval and written informed consent, two-view DBT of 154 breasts, of which 116 had biopsy-proven microcalcification (MC) clusters and 38 were free of MCs, was imaged with a General Electric GEN2 prototype DBT system. The DBT volumes were reconstructed with MSBF-regularized simultaneous algebraic reconstruction technique (SART) that was designed to enhance MCs and reduce background noise while preserving the quality of other tissue structures. The contrast-to-noise ratio (CNR) of MCs was further improved with enhancement-modulated calcification response (EMCR) preprocessing, which combined multiscale Hessian response to enhance MCs by shape and bandpass filtering to remove the low-frequency structured background. MC candidates were then located in the EMCR volume using iterative thresholding and segmented by adaptive region growing. Two sets of potential MC objects, cluster centroid objects and MC seed objects, were generated and the CNR of each object was calculated. The number of candidates in each set was controlled based on the breast volume. Dynamic clustering around the centroid objects grouped the MC candidates to form clusters. Adaptive criteria were designed to reduce false positive (FP) clusters based on the size, CNR values and the number of MCs in the cluster, cluster shape, and cluster based maximum intensity projection. Free-response receiver operating characteristic (FROC) and jackknife alternative FROC (JAFROC) analyses were used to assess the performance and compare with that of a previous study. Results: Unpaired two-tailedt-test showed a significant increase (p < 0.0001) in the ratio of CNRs for MCs with and without MSBF regularization compared to similar ratios for FPs. For view-based detection, a sensitivity of 85% was achieved at an FP rate of 2.16 per DBT volume. For case-based detection, a sensitivity of 85% was achieved at an FP rate of 0.85 per DBT volume. JAFROC analysis showed a significant improvement in the performance of the current CADe system compared to that of our previous system (p = 0.003). Conclusions: MBSF regularized SART reconstruction enhances MCs. The enhancement in the signals, in combination with properly designed adaptive threshold criteria, effective MC feature analysis, and false positive reduction techniques, leads to a significant improvement in the detection of clustered MCs in DBT.

  17. Observer Performance in the Detection and Classification of Malignant Hepatic Nodules and Masses with CT Image-Space Denoising and Iterative Reconstruction.

    PubMed

    Fletcher, Joel G; Yu, Lifeng; Li, Zhoubo; Manduca, Armando; Blezek, Daniel J; Hough, David M; Venkatesh, Sudhakar K; Brickner, Gregory C; Cernigliaro, Joseph C; Hara, Amy K; Fidler, Jeff L; Lake, David S; Shiung, Maria; Lewis, David; Leng, Shuai; Augustine, Kurt E; Carter, Rickey E; Holmes, David R; McCollough, Cynthia H

    2015-08-01

    Purpose To determine if lower-dose computed tomographic (CT) scans obtained with adaptive image-based noise reduction (adaptive nonlocal means [ANLM]) or iterative reconstruction (sinogram-affirmed iterative reconstruction [SAFIRE]) result in reduced observer performance in the detection of malignant hepatic nodules and masses compared with routine-dose scans obtained with filtered back projection (FBP). Materials and Methods This study was approved by the institutional review board and was compliant with HIPAA. Informed consent was obtained from patients for the retrospective use of medical records for research purposes. CT projection data from 33 abdominal and 27 liver or pancreas CT examinations were collected (median volume CT dose index, 13.8 and 24.0 mGy, respectively). Hepatic malignancy was defined by progression or regression or with histopathologic findings. Lower-dose data were created by using a validated noise insertion method (10.4 mGy for abdominal CT and 14.6 mGy for liver or pancreas CT) and images reconstructed with FBP, ANLM, and SAFIRE. Four readers evaluated routine-dose FBP images and all lower-dose images, circumscribing liver lesions and selecting diagnosis. The jackknife free-response receiver operating characteristic figure of merit (FOM) was calculated on a per-malignant nodule or per-mass basis. Noninferiority was defined by the lower limit of the 95% confidence interval (CI) of the difference between lower-dose and routine-dose FOMs being less than -0.10. Results Twenty-nine patients had 62 malignant hepatic nodules and masses. Estimated FOM differences between lower-dose FBP and lower-dose ANLM versus routine-dose FBP were noninferior (difference: -0.041 [95% CI: -0.090, 0.009] and -0.003 [95% CI: -0.052, 0.047], respectively). In patients with dedicated liver scans, lower-dose ANLM images were noninferior (difference: +0.015 [95% CI: -0.077, 0.106]), whereas lower-dose FBP images were not (difference -0.049 [95% CI: -0.140, 0.043]). In 37 patients with SAFIRE reconstructions, the three lower-dose alternatives were found to be noninferior to the routine-dose FBP. Conclusion At moderate levels of dose reduction, lower-dose FBP images without ANLM or SAFIRE were noninferior to routine-dose images for abdominal CT but not for liver or pancreas CT. (©) RSNA, 2015 Online supplemental material is available for this article. PMID:26020436

  18. A stable pattern of EEG spectral coherence distinguishes children with autism from neuro-typical controls - a large case control study

    PubMed Central

    2012-01-01

    Background The autism rate has recently increased to 1 in 100 children. Genetic studies demonstrate poorly understood complexity. Environmental factors apparently also play a role. Magnetic resonance imaging (MRI) studies demonstrate increased brain sizes and altered connectivity. Electroencephalogram (EEG) coherence studies confirm connectivity changes. However, genetic-, MRI- and/or EEG-based diagnostic tests are not yet available. The varied study results likely reflect methodological and population differences, small samples and, for EEG, lack of attention to group-specific artifact. Methods Of the 1,304 subjects who participated in this study, with ages ranging from 1 to 18 years old and assessed with comparable EEG studies, 463 children were diagnosed with autism spectrum disorder (ASD); 571 children were neuro-typical controls (C). After artifact management, principal components analysis (PCA) identified EEG spectral coherence factors with corresponding loading patterns. The 2- to 12-year-old subsample consisted of 430 ASD- and 554 C-group subjects (n = 984). Discriminant function analysis (DFA) determined the spectral coherence factors' discrimination success for the two groups. Loading patterns on the DFA-selected coherence factors described ASD-specific coherence differences when compared to controls. Results Total sample PCA of coherence data identified 40 factors which explained 50.8% of the total population variance. For the 2- to 12-year-olds, the 40 factors showed highly significant group differences (P < 0.0001). Ten randomly generated split half replications demonstrated high-average classification success (C, 88.5%; ASD, 86.0%). Still higher success was obtained in the more restricted age sub-samples using the jackknifing technique: 2- to 4-year-olds (C, 90.6%; ASD, 98.1%); 4- to 6-year-olds (C, 90.9%; ASD 99.1%); and 6- to 12-year-olds (C, 98.7%; ASD, 93.9%). Coherence loadings demonstrated reduced short-distance and reduced, as well as increased, long-distance coherences for the ASD-groups, when compared to the controls. Average spectral loading per factor was wide (10.1 Hz). Conclusions Classification success suggests a stable coherence loading pattern that differentiates ASD- from C-group subjects. This might constitute an EEG coherence-based phenotype of childhood autism. The predominantly reduced short-distance coherences may indicate poor local network function. The increased long-distance coherences may represent compensatory processes or reduced neural pruning. The wide average spectral range of factor loadings may suggest over-damped neural networks. PMID:22730909

  19. Using Chironomid-Based Transfer Function and Stable Isotopes for Reconstructing Past Climate in South Eastern Australia

    NASA Astrophysics Data System (ADS)

    Chang, J.; Shulmeister, J.; Woodward, C.

    2014-12-01

    A transfer-function based on chironomids was created to reconstruct past summer temperatures from a training set comprised of 33 south eastern Australian lakes. Statistical analyses show that mean February temperature (MFT) is the most robust and independent variable explaining chironomid species variability. The best MFT transfer function was a partial least squares (PLS) model with a coefficient of determination (r2Jackknifed) of 0.69, a root mean squared error of prediction (RMSEP) of 2.33?C, and maximum bias of 2.15°C. The transfer function was tested by applying it to a Late Glacial to Holocene record from Blue Lake, New South Wales using published data. The reconstruction displays an overall pattern very similar to the Milankovitch driven summer insolation curve for 30°S and to the chironomid based summer temperature reconstruction from Eagle Tarn, Tasmania (Rees and Cwynar 2010) suggesting that the model is robust. The transfer function was also applied to reconstruct the Last Glacial Maxium (LGM) summer temperature from Welsby Lagoon, North Stradbroke Island (Queensland). Preliminary results show a c. 4.2~8.6?C of cooling in summer temperatures during the LGM from south east Australia. Stable oxygen and deuterium isotope composition (?18O and ?D) of the chitnous subfossil head capsules from Australian chironomids were also measured to explore the opportunity developing them as an independent temperature proxy. This is the first application of this technique in the Southern Hemisphere. The modern range of chironomid ?18O values were measured based on the same 33 lakes sampled for the transfer function. For these lakes, head capsules of single genera were picked to avoid complications from 'vital effects'. The relationship of chironomid ?18O to modern lake temperatures has been investigated. Deuterium (?D) on the head capsules has been measured concurrently and the relationship to climate and environment will be explored based on the latest available results. References Rees A.B.H, and Cwynar, L.C. (2010) Evidence for early postglacial warming in Mount Field National Park, Tasmania. Quaternary Science Reviews29, 443-454.

  20. Population attributable fractions of farm vector tick (Rhipicephalus appendiculatus) presence on Theileria parva infection seroprevalence under endemic instability.

    PubMed

    Gachohi, J M; Kitala, P M; Ngumi, P N; Skilton, R A; Bett, B

    2013-02-01

    The primary objective of this study was to assess the impact of Rhipicephalus appendiculatus tick presence (exposure variable) on Theileria parva infection seroprevalence (outcome variable) in a group of cattle belonging to a farm using population attributable fractions (PAF). The analyses were based on a representative sample of 80 traditional smallholder mixed farms. The farms were selected by first stratifying the population administratively and implementing a multistage random sampling in Mbeere district in Kenya. The PAFs were estimated using the stratified, Bruzzi, and sequential partitioned PAF approaches. A secondary objective was, thus, to evaluate the impact of the approaches on the PAF estimates. The stratified and Bruzzi approaches estimated proportion of T. parva infection cases directly attributable to the exposure after controlling for confounding by agro-ecological zone (AEZ). The sequential partitioned PAF approach estimated a PAF associated with exposure after adjusting for any effect that the AEZ may have had by influencing the prevalence of the exposure. All analyses were carried out at the farm level where a farm was classified as infested if the tick was found on cattle on a farm, and infected if at least one animal on a farm was positive for T. parva antibodies. Variance estimation for PAFs was implemented using 'delete-a-group' jackknife re-sampling method. The stratified PAF (26.7% [95% CI: 9.0%, 44.4%]) and Bruzzi PAF (26.4% [95% CI: 9.6%, 43.2%]) were consistent in estimating a relatively low impact of farm vector tick presence with a relatively high level of uncertainty. The partitioned PAF (15.5% [95% CI: 1.5%, 29.6%]) suggested that part of the impacts estimated using the stratified PAF and Bruzzi approaches was driven by AEZ effects. Overall, the results suggested that under endemic instability in Mbeere district, (1) presence of R. appendiculatus was not a good indicator of T. parva infection occurrence on a farm; (2) ecological variation could play a role in determining infection impacts. This study provides a preliminary basis for evaluating the potential value and utility of estimating PAFs for variables amenable to control in tick-borne diseases (TBDs) epidemiological studies. PMID:22964105

  1. Geographic assignment of seabirds to their origin: combining morphologic, genetic, and biogeochemical analyses.

    PubMed

    Gómez-Díaz, Elena; González-Solis, Jacob

    2007-07-01

    Longline fisheries, oil spills, and offshore wind farms are some of the major threats increasing seabird mortality at sea, but the impact of these threats on specific populations has been difficult to determine so far. We tested the use of molecular markers, morphometric measures, and stable isotope (delta15N and delta13C) and trace element concentrations in the first primary feather (grown at the end of the breeding period) to assign the geographic origin of Calonectris shearwaters. Overall, we sampled birds from three taxa: 13 Mediterranean Cory's Shearwater (Calonectris diomedea diomedea) breeding sites, 10 Atlantic Cory's Shearwater (Calonectris diomedea borealis) breeding sites, and one Cape Verde Shearwater (C. edwardsii) breeding site. Assignment rates were investigated at three spatial scales: breeding colony, breeding archipelago, and taxa levels. Genetic analyses based on the mitochondrial control region (198 birds from 21 breeding colonies) correctly assigned 100% of birds to the three main taxa but failed in detecting geographic structuring at lower scales. Discriminant analyses based on trace elements composition achieved the best rate of correct assignment to colony (77.5%). Body measurements or stable isotopes mainly succeeded in assigning individuals among taxa (87.9% and 89.9%, respectively) but failed at the colony level (27.1% and 38.0%, respectively). Combining all three approaches (morphometrics, isotopes, and trace elements on 186 birds from 15 breeding colonies) substantially improved correct classifications (86.0%, 90.7%, and 100% among colonies, archipelagos, and taxa, respectively). Validations using two independent data sets and jackknife cross-validation confirmed the robustness of the combined approach in the colony assignment (62.5%, 58.8%, and 69.8% for each validation test, respectively). A preliminary application of the discriminant model based on stable isotope delta15N and delta13C values and trace elements (219 birds from 17 breeding sites) showed that 41 Cory's Shearwaters caught by western Mediterranean long-liners came mainly from breeding colonies in Menorca (48.8%), Ibiza (14.6%), and Crete (31.7%). Our findings show that combining analyses of trace elements and stable isotopes on feathers can achieve high rates of correct geographic assignment of birds in the marine environment, opening new prospects for the study of seabird mortality at sea. PMID:17708223

  2. Pulmonary Nodule Detection in Patients with a Primary Malignancy Using Hybrid PET/MRI: Is There Value in Adding Contrast-Enhanced MR Imaging?

    PubMed Central

    Lee, Kyung Hee; Park, Chang Min; Lee, Sang Min; Lee, Jeong Min; Cho, Jeong Yeon; Paeng, Jin Chul; Ahn, Su Yeon; Goo, Jin Mo

    2015-01-01

    Purpose To investigate the added value of post-contrast VIBE (volumetric-interpolated breath-hold examination) to PET/MR imaging for pulmonary nodule detection in patients with primary malignancies. Materials and Methods This retrospective institutional review board–approved study, with waiver of informed consent, included 51 consecutive patients who underwent 18F-fluorodeoxyglucose (FDG) PET/MR followed by PET/CT for cancer staging. In all patients, the thorax was examined with pre-and post-contrast VIBE MR with simultaneous PET acquisition. Two readers blinded to the patients’ data independently recorded their level of suspicion for pulmonary nodules based on PET, pre-contrast VIBE, and fused PET/MR images (first session), and reassessed them 4-weeks later after addition of post-contrast VIBE (second session). Jackknife alternative free-response receiver-operating-characteristic (JAFROC) analysis was performed, with PET/CT as the reference standard. Results A total of 151 pulmonary nodules (44 FDG-avid, 107 non-FDG-avid nodules) were detected on PET/CT, including 62 nodules?5mm in diameter and 89 nodules<5mm. In the first session, the average nodule detection rate was 53.3% for all nodules, 97.7% for FDG-avid, 35.0% for non-FDG-avid nodules, 87.9% for nodules?5mm and 29.2% for nodules<5mm. In the second session, the average detection rate was 53.3% for all nodules, 97.7% for FDG-avid, 35.0% for non-FDG-avid nodules, 85.5% for nodules?5mm and 30.9% for nodules<5mm. The average JAFROC figure-of-merit was 0.837 in the first session and 0.848 in the second session. There were no significant differences in detection performance between sessions (P=0.48). Conclusion The addition of post-contrast VIBE to hybrid PET/MR imaging provided no additional value in the detection of pulmonary nodules. PMID:26065695

  3. Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

    PubMed Central

    2015-01-01

    Background DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/. PMID:25708928

  4. The relative roles of types of extracurricular activity on smoking and drinking initiation among tweens

    PubMed Central

    Adachi-Mejia, Anna M.; Gibson Chambers, Jennifer J.; Li, Zhigang; Sargent, James D.

    2014-01-01

    Objective Youth involvement in extracurricular activities may help prevent smoking and drinking initiation. However, the relative roles of types of extracurricular activity on these risks are unclear. Therefore, we examined the association between substance use and participation in team sports with a coach, other sports without a coach, music, school clubs, and other clubs in a nationally representative sample of US tweens. Methods We conducted telephone surveys with 6,522 U.S. students (ages 10-14) in 2003. We asked participants if they had ever tried smoking or drinking and about their participation in extracurricular activities. We used sample weighting to produce response estimates that were representative of the population of adolescents aged 10-14 years at the time of data collection. Logistic regression models that adjusted for appropriate sampling weights using Jackknife variance estimation tested associations with trying smoking and drinking, controlling for sociodemographics, child and parent characteristics, friend/sibling/parent substance use, and media use. Results A little over half of the students reported participating in team sports with a coach (55.5%) and without a coach (55.4%) a few times per week or more. Most had minimal to no participation in school clubs (74.2%), however most reported being involved in other clubs (85.8%). A little less than half participated in music, choir, dance, and/or band lessons. Over half of participants involved in religious activity did those activities a few times per week or more. In the multiple regression analysis, team sport participation with a coach was the only extracurricular activity associated with lower risk of trying smoking (adjusted OR = 0.68, 95% C.I. 0.49, 0.96) compared to none or minimal participation. Participating in other clubs was the only extracurricular activity associated with lower risk of trying drinking (adjusted OR = 0.56, 95% C.I. 0.32, 0.99) compared to none or minimal participation. Conclusions Type of extracurricular involvement may be associated with risk of youth smoking and drinking initiation. Future research should seek to better understand the underlying reasons behind these differences. PMID:24767780

  5. Effect of CAD on Radiologists’ Detection of Lung Nodules on Thoracic CT Scans: Analysis of an Observer Performance Study by Nodule Size

    PubMed Central

    Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Cascade, Philip N.; Kazerooni, Ella A.; Chughtai, Aamer R.; Poopat, Chad; Song, Thomas; Frank, Luba; Stojanovska, Jadranka; Attili, Anil

    2009-01-01

    Rationale and Objectives To retrospectively investigate the effect of a computer aided detection (CAD) system on radiologists’ performance for detecting small pulmonary nodules in CT examinations, with a panel of expert radiologists serving as the reference standard. Materials and Methods Institutional review board approval was obtained. Our data set contained 52 CT examinations collected by the Lung Image Database Consortium, and 33 from our institution. All CTs were read by multiple expert thoracic radiologists to identify the reference standard for detection. Six other thoracic radiologists read the CT examinations first without, and then with CAD. Performance was evaluated using free-response receiver operating characteristics (FROC) and the jackknife FROC analysis methods (JAFROC) for nodules above different diameter thresholds. Results 241 nodules, ranging in size from 3.0 to 18.6 mm (mean 5.3 mm) were identified as the reference standard. At diameter thresholds of 3, 4, 5, and 6 mm, the CAD system had a sensitivity of 54%, 64%, 68%, and 76%, respectively, with an average of 5.6 false-positives (FPs) per scan. Without CAD, the average figures-of-merit (FOMs) for the six radiologists, obtained from JAFROC analysis, were 0.661, 0.729, 0.793 and 0.838 for the same nodule diameter thresholds, respectively. With CAD, the corresponding average FOMs improved to 0.705, 0.763, 0.810 and 0.862, respectively. The improvement achieved statistical significance for nodules at the 3 and 4 mm thresholds (p=0.002 and 0.020, respectively), and did not achieve significance at 5 and 6 mm (p=0.18 and 0.13, respectively). At a nodule diameter threshold of 3 mm, the radiologists’ average sensitivity and FP rate were 0.56 and 0.67, respectively, without CAD, and 0.67 and 0.78 with CAD. Conclusion CAD improves thoracic radiologists’ performance for detecting pulmonary nodules under 5 mm on CT examinations, which are often overlooked by visual inspection alone. PMID:19896069

  6. Drought in the Netherlands Regional frequency analysis versus time series simulation

    NASA Astrophysics Data System (ADS)

    Beersma, Jules J.; Buishand, T. Adri

    2007-12-01

    SummaryThe distribution of the annual maximum precipitation deficit is studied for six districts within the Netherlands. Gumbel probability plots of this precipitation deficit show a common extraordinary curvature in the upper tail. A regional frequency analysis yields a regional growth curve that can be approximated by a spline consisting of two linear segments on the standard Gumbel scale and a smooth transition between them. Alternatively, the application of a time series model based on nearest-neighbour resampling is explored. To reproduce the persistence structure a 4-month memory term is needed in the resampling model. Using this memory term there is an enhanced positive correlation between past and future precipitation deficits during extremely dry summers, which seems to be responsible for the curvature in the precipitation deficit distributions. This term, however, also leads to a considerable increase of the standard error of large quantile estimates. Much attention is given to the use of the bootstrap and the jackknife to determine the standard errors of quantile estimates based on nearest-neighbour resampling. A simulation experiment with a first-order autoregressive time series model shows that these standard errors can be biased, in particular for the bootstrap. The relative standard errors of quantile estimates are large in the area of large curvature of the Gumbel probability plots. This holds both for nearest-neighbour resampling and regional frequency analysis. When the two methods are used for extrapolation, nearest-neighbour resampling clearly outperforms the regional frequency analysis. The latter then shows a strong increase in the relative standard error of quantile estimates with increasing return period due to the large uncertainty of the parameters in the spline approximation to the regional growth curve. Using nearest-neighbour resampling and the bootstrap, confidence intervals are constructed for the return periods of the largest observed precipitation deficit for each of the six districts. Although these confidence intervals are quite wide, they are on average a factor of two narrower than the interval expected from the size of the sample only.

  7. Estimation of parameters of dose volume models and their confidence limits

    NASA Astrophysics Data System (ADS)

    van Luijk, P.; Delvigne, T. C.; Schilstra, C.; Schippers, J. M.

    2003-07-01

    Predictions of the normal-tissue complication probability (NTCP) for the ranking of treatment plans are based on fits of dose-volume models to clinical and/or experimental data. In the literature several different fit methods are used. In this work frequently used methods and techniques to fit NTCP models to dose response data for establishing dose-volume effects, are discussed. The techniques are tested for their usability with dose-volume data and NTCP models. Different methods to estimate the confidence intervals of the model parameters are part of this study. From a critical-volume (CV) model with biologically realistic parameters a primary dataset was generated, serving as the reference for this study and describable by the NTCP model. The CV model was fitted to this dataset. From the resulting parameters and the CV model, 1000 secondary datasets were generated by Monte Carlo simulation. All secondary datasets were fitted to obtain 1000 parameter sets of the CV model. Thus the 'real' spread in fit results due to statistical spreading in the data is obtained and has been compared with estimates of the confidence intervals obtained by different methods applied to the primary dataset. The confidence limits of the parameters of one dataset were estimated using the methods, employing the covariance matrix, the jackknife method and directly from the likelihood landscape. These results were compared with the spread of the parameters, obtained from the secondary parameter sets. For the estimation of confidence intervals on NTCP predictions, three methods were tested. Firstly, propagation of errors using the covariance matrix was used. Secondly, the meaning of the width of a bundle of curves that resulted from parameters that were within the one standard deviation region in the likelihood space was investigated. Thirdly, many parameter sets and their likelihood were used to create a likelihood-weighted probability distribution of the NTCP. It is concluded that for the type of dose response data used here, only a full likelihood analysis will produce reliable results. The often-used approximations, such as the usage of the covariance matrix, produce inconsistent confidence limits on both the parameter sets and the resulting NTCP values.

  8. Regionalization analysis of low flow for drought risk assessment in Tuscany (Italy)

    NASA Astrophysics Data System (ADS)

    Rossi, Giuseppe; Caporali, Enrica

    2010-05-01

    The estimates of river low flow characteristics play an important role in engineering practice for water resources design and management and their definition is necessary for several purposes, including water supply planning, river basin management, hydropower development and environmental flow characterization. Another important field and thorny task in which they are utilized is in identifying the occurrence, the extent and the magnitude of a drought,. The beginning and the persistency of droughts can be recognized with meteorological indices. With indices derived from low flow it is possible to recognize the hydrological droughts that affect mainly the water supply systems. Low flow characteristics are estimated from observed streamflow data, identifying some duration curves, percentiles characteristics and some indices. Nevertheless the lack of observed streamflow data is a diffuse problem in the real world. For sites where data are not available, alternative techniques are necessary to infer this information. The regional regression approach is one of the more used. It consists in inferring data in ungauged stations using hydrological and statistical regionalization methods. The methods are based on catchment and climatic variables and data from other catchments where stream flow data are recorded. The analysis of low flow indices is carried out on the discharge data from 1st January 1949 to 31st December 2008 of 65 consistent hydrometric stations located in Tuscany Region, in Central Italy. The area is subdivided into different regions using the L-moments method applied to the 7-day annual minimum and to the Q70 annual series. The division into subregions is tested using discordancy and heterogeneity statistics. Different subdivision are tested: a unique region, a subdivision into three different subregions and a subdivision in five subregions. The second subdivision is based on previous studies on rainfall extreme values. The last starts from the previous subdivisions and introduces some hydrological features. Once the catchment area is identified for every river cross-section where a gauge station is installed, a suitable set of catchment physiographic and climatic characteristics is defined and a physiographical space-based method is used to relate the duration and percentile indices of low flow to the investigated territory characteristics. The new space is built as a linear combination of the catchment physiographic and climatic characteristics. Different interpolation techniques, either deterministic or geostatistical, such as Inverse Distance, Thiessen polygon methods and Kriging, are applied. Uncertainties measurements are implemented using jack-knife and bootstrap methods. Different error measurement (mean square error, mean relative error…) are also assessed to compare the results, to quantify the accuracy of the different techniques and to define the most suitable procedure for drought risk assessment.

  9. Modelling and mapping the local distribution of representative species on the Le Danois Bank, El Cachucho Marine Protected Area (Cantabrian Sea)

    NASA Astrophysics Data System (ADS)

    García-Alegre, Ana; Sánchez, Francisco; Gómez-Ballesteros, María; Hinz, Hilmar; Serrano, Alberto; Parra, Santiago

    2014-08-01

    The management and protection of potentially vulnerable species and habitats require the availability of detailed spatial data. However, such data are often not readily available in particular areas that are challenging for sampling by traditional sampling techniques, for example seamounts. Within this study habitat modelling techniques were used to create predictive maps of six species of conservation concern for the Le Danois Bank (El Cachucho Marine Protected Area in the South of the Bay of Biscay). The study used data from ECOMARG multidisciplinary surveys that aimed to create a representative picture of the physical and biological composition of the area. Classical fishing gear (otter trawl and beam trawl) was used to sample benthic communities that inhabit sedimentary areas, and non-destructive visual sampling techniques (ROV and photogrammetric sled) were used to determine the presence of epibenthic macrofauna in complex and vulnerable habitats. Multibeam echosounder data, high-resolution seismic profiles (TOPAS system) and geological data from box-corer were used to characterize the benthic terrain. ArcGIS software was used to produce high-resolution maps (75×75 m2) of such variables in the entire area. The Maximum Entropy (MAXENT) technique was used to process these data and create Habitat Suitability maps for six species of special conservation interest. The model used seven environmental variables (depth, rugosity, aspect, slope, Bathymetric Position Index (BPI) in fine and broad scale and morphosedimentary characteristics) to identify the most suitable habitats for such species and indicates which environmental factors determine their distribution. The six species models performed highly significantly better than random (p<0.0001; Mann-Whitney test) when Area Under the Curve (AUC) values were tested. This indicates that the environmental variables chosen are relevant to distinguish the distribution of these species. The Jackknife test estimated depth to be the key factor structuring their distribution, followed by the seabed morpho-sedimentary characteristics and rugosity variables. Three of the species studied (Asconema setubalense, Callogorgia verticillata and Helicolenus dactylopterus) were found to have small suitable areas as a result of being restrictive species related to the environmental characteristics of the top of the bank. The other species (Pheronema carpenteri, Phycis blennoides and Trachyscorpia cristulata), which were species less restrictive to the environmental variables used, had highly suitable areas of distribution. The study provides high-resolution maps of species that characterize the habitat of two communities included in OSPAR and NATURA networks, whose distributions corroborate the adequate protection of this area by the management measures applied at present.

  10. A DEEP SEARCH FOR EXTENDED RADIO CONTINUUM EMISSION FROM DWARF SPHEROIDAL GALAXIES: IMPLICATIONS FOR PARTICLE DARK MATTER

    SciTech Connect

    Spekkens, Kristine [Department of Physics, Royal Military College of Canada, P.O. Box 17000, Station Forces, Kingston, Ontario K7K 7B4 (Canada); Mason, Brian S. [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903-2475 (United States); Aguirre, James E. [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Nhan, Bang, E-mail: kristine.spekkens@rmc.ca [Department of Astrophysical and Planetary Sciences, University of Colorado, 391 UCB, Boulder, CO 80309 (United States)

    2013-08-10

    We present deep radio observations of four nearby dwarf spheroidal (dSph) galaxies, designed to detect extended synchrotron emission resulting from weakly interacting massive particle (WIMP) dark matter annihilations in their halos. Models by Colafrancesco et al. (CPU07) predict the existence of angularly large, smoothly distributed radio halos in such systems, which stem from electron and positron annihilation products spiraling in a turbulent magnetic field. We map a total of 40.5 deg{sup 2} around the Draco, Ursa Major II, Coma Berenices, and Willman 1 dSphs with the Green Bank Telescope (GBT) at 1.4 GHz to detect this annihilation signature, greatly reducing discrete-source confusion using the NVSS catalog. We achieve a sensitivity of {sigma}{sub sub} {approx}< 7 mJy beam{sup -1} in our discrete source-subtracted maps, implying that the NVSS is highly effective at removing background sources from GBT maps. For Draco we obtained approximately concurrent Very Large Array observations to quantify the variability of the discrete source background, and find it to have a negligible effect on our results. We construct radial surface brightness profiles from each of the subtracted maps, and jackknife the data to quantify the significance of the features therein. At the {approx}10' resolution of our observations, foregrounds contribute a standard deviation of 1.8 mJy beam{sup -1} {<=} {sigma}{sub ast} {<=} 5.7 mJy beam{sup -1} to our high-latitude maps, with the emission in Draco and Coma dominated by foregrounds. On the other hand, we find no significant emission in the Ursa Major II and Willman 1 fields, and explore the implications of non-detections in these fields for particle dark matter using the fiducial models of CPU07. For a WIMP mass M{sub {chi}} = 100 GeV annihilating into b b-bar final states and B = 1 {mu}G, upper limits on the annihilation cross-section for Ursa Major II and Willman I are log (({sigma}v){sub {chi}}, cm{sup 3} s{sup -1}) {approx}< -25 for the preferred set of charged particle propagation parameters adopted by CPU07; this is comparable to that inferred at {gamma}-ray energies from the two-year Fermi Large Area Telescope data. We discuss three avenues for improving the constraints on ({sigma}v){sub {chi}} presented here, and conclude that deep radio observations of dSphs are highly complementary to indirect WIMP searches at higher energies.

  11. IMPROVED MEASUREMENTS OF THE TEMPERATURE AND POLARIZATION OF THE COSMIC MICROWAVE BACKGROUND FROM QUaD

    SciTech Connect

    Brown, M. L. [Cavendish Astrophysics, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 OHE (United Kingdom); Ade, P.; Bowden, M.; Gear, W. K.; Gupta, S.; Orlando, A. [School of Physics and Astronomy, Cardiff University, Queen's Buildings, The Parade, Cardiff CF24 3AA (United Kingdom); Bock, J.; Leitch, E. [Jet Propulsion Laboratory, 4800 Oak Grove Dr., Pasadena, CA 91109 (United States); Cahill, G.; Murphy, J. A. [Department of Experimental Physics, National University of Ireland Maynooth, Maynooth, Co. Kildare, Republic of Ireland (Ireland); Castro, P. G.; Memari, Y. [Institute for Astronomy, University of Edinburgh, Royal Observatory, Blackford Hill, Edinburgh EH9 3HJ (United Kingdom); Church, S.; Hinderks, J. [Kavli Institute for Particle Astrophysics and Cosmology and Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, CA 94305 (United States); Culverhouse, T.; Friedman, R. B. [Kavli Institute for Cosmological Physics, Department of Astronomy and Astrophysics, Enrico Fermi Institute, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 (United States); Ganga, K. [APC/Universite Paris 7-Denis Diderot/CNRS, Batiment Condorcet, 10, rue Alice Domon et Leonie Duquet, 75205 Paris Cedex 13 (France); Kovac, J.; Lange, A. E. [California Institute of Technology, Pasadena, CA 91125 (United States); Melhuish, S. J. [School of Physics and Astronomy, University of Manchester, Manchester M13 9PL (United Kingdom)

    2009-11-01

    We present an improved analysis of the final data set from the QUaD experiment. Using an improved technique to remove ground contamination, we double the effective sky area and hence increase the precision of our cosmic microwave background (CMB) power spectrum measurements by approx30% versus that previously reported. In addition, we have improved our modeling of the instrument beams and have reduced our absolute calibration uncertainty from 5% to 3.5% in temperature. The robustness of our results is confirmed through extensive jackknife tests, and by way of the agreement that we find between our two fully independent analysis pipelines. For the standard six-parameter LAMBDACDM model, the addition of QUaD data marginally improves the constraints on a number of cosmological parameters over those obtained from the WMAP experiment alone. The impact of QUaD data is significantly greater for a model extended to include either a running in the scalar spectral index, or a possible tensor component, or both. Adding both the QUaD data and the results from the Arcminute Cosmology Bolometer Array Receiver experiment, the uncertainty in the spectral index running is reduced by approx25% compared to WMAP alone, while the upper limit on the tensor-to-scalar ratio is reduced from r < 0.48 to r < 0.33 (95% c.l.). This is the strongest limit on tensors to date from the CMB alone. We also use our polarization measurements to place constraints on parity-violating interactions to the surface of last scattering, constraining the energy scale of Lorentz violating interactions to <1.5 x 10{sup -43} GeV (68% c.l.). Finally, we place a robust upper limit on the strength of the lensing B-mode signal. Assuming a single flat band power between l = 200 and l = 2000, we constrain the amplitude of B-modes to be <0.57 muK{sup 2} (95% c.l.).

  12. Disaggregation of legacy soil data using area to point kriging for mapping soil organic carbon at the regional scale

    PubMed Central

    Kerry, Ruth; Goovaerts, Pierre; Rawlins, Barry G.; Marchant, Ben P.

    2015-01-01

    Legacy data in the form of soil maps, which often have typical property measurements associated with each polygon, can be an important source of information for digital soil mapping (DSM). Methods of disaggregating such information and using it for quantitative estimation of soil properties by methods such as regression kriging (RK) are needed. Several disaggregation processes have been investigated; preferred methods include those which include consideration of scorpan factors and those which are mass preserving (pycnophylactic) making transitions between different scales of investigation more theoretically sound. Area to point kriging (AtoP kriging) is pycnophylactic and here we investigate its merits for disaggregating legacy data from soil polygon maps. Area to point regression kriging (AtoP RK) which incorporates ancillary data into the disaggre-gation process was also applied. The AtoP kriging and AtoP RK approaches do not involve collection of new soil measurements and are compared with disaggregation by simple rasterization. Of the disaggregation methods investigated, AtoP RK gave the most accurate predictions of soil organic carbon (SOC) concentrations (smaller mean absolute errors (MAEs) of cross-validation) for disaggregation of soil polygon data across the whole of Northern Ireland. Legacy soil polygon data disaggregated by AtoP kriging and simple rasterization were used in a RK framework for estimating soil organic carbon (SOC) concentrations across the whole of Northern Ireland, using soil sample data from the Tellus survey of Northern Ireland and with other covariates (altitude and airborne radiometric potassium). This allowed direct comparison with previous analysis of the Tellus survey data. Incorporating the legacy data, whether from simple rasterization of the polygons or AtoP kriging, substantially reduced the MAEs of RK compared with previous analyses of the Tellus data. However, using legacy data disaggregated by AtoP kriging in RK resulted in a greater reduction in MAEs. A jack-knife procedure was also performed to determine a suitable number of additional soil samples that would need to be collected for RK of SOC for the whole of Northern Ireland depending on the availability of ancillary data. We recommend i) if only legacy soil polygon map data are available, they should be disaggregated using AtoP kriging, ii) if ancillary data are also available legacy data should be disaggregated using AtoP RK and iii) if new soil measurements are available in addition to ancillary and legacy soil map data, the legacy soil map data should be first disaggregated using AtoP kriging and these data used along with ancillary data as the fixed effects for RK of the new soil measurements. PMID:25729090

  13. Developing Pedotransfer Functions for Saline and Saline-Alkali Soils

    NASA Astrophysics Data System (ADS)

    Ramezani, Meysam; Ghanbarian-Alavijeh, Behzad; Liaghat, Abdolmajid

    2010-05-01

    Soil moisture curve is one of the soil hydraulic properities which its direct measurement is time consuming and expensive. Therefore, indirect methods such as developing pedotransfer functions have been used to predict this characteristic from soil readily available or easily measurable data. In this study, multiple linear regression method was used to develop point pedotransfer functions (PTFs) for saline and saline-alkali soils of Iran. For this purpose, 68 soil samples which their EC values were greater than 4 ds/m, and more than half of them had ESP values greater than 15% were selected. Using Jackknife method, the random splitting of data into the development and validation subsets was repeated 10 times. A ratio of 3:1 was used to split data into development and validation sets in each replication. In the SPSS software, parameters such as geometric standard deviation (?g), geometric mean diameter (dg), sodium adsorption ratio (SAR), electrical conductivity (EC), carbonate calcium (CaCO3), bulk density (BD), organic matter (OM), and clay and silt content were applied as the independent variables, and volumetric water content was determined at matric potentials of -10, -33, -100 , -300, -500, -1000, -1500 kPa. The derived PTFs were compared with the H3 model of Rosetta software for 10 splits of validation data set. Comparison of the mean RMSE and R2 values showed that the developed PTFs resulted in more accurate estimation than the Rosetta software at matric potentials of -100 , -300, -500, -1000, -1500 kPa. Whereas, Rosetta model resulted in slightly better estimation than derived PTFs at matric potentials of -10, -33 kPa. For the PTFs developed in this study, the RMSE and R2 values ranged from 0.12 to 0.35 (cm3.cm-3) and 0.64 to 0.83, respectively. While for the Rosetta model, RMSE and R2 values ranged from 0.22 to 0.33 (cm3.cm-3) and 0.37 to 0.74, respectively.

  14. The Bolocam Lockman Hole millimeter-wave galaxy survey

    NASA Astrophysics Data System (ADS)

    Laurent, G. T.

    2006-06-01

    This work presents results of a new deep (s 1.1mm ~= 1.4 mJy beam -1 ) 1.1 mm submillimeter galaxy survey using Bolocam, a millimeter-wavelength bolometer array camera designed for mapping large fields at fast scan rates, without chopping. A map, galaxy candidate list, and derived number counts are presented. The data were reduced using a custom software pipeline to remove correlated sky and instrument noise via a principal component analysis. Extensive simulations and jackknife tests were performed to confirm the robustness of our source candidates and estimate the effects of false detections, bias, and completeness. In total, 17 source candidates were detected at a significance > 3.0 s, with six expected false detections. From both our observed number counts and a fluctuation analysis, we estimate the underlying differential number count distribution of submillimeter galaxies and find it to be in general agreement with previous surveys. This work also presents 350 mm photometry of all 17 galaxy candidates detected in the Lockman Hole survey. Nine of the Bolocam galaxy candidates were detected at 350 mm and two new candidates were serendipitously detected at 350 mm (bringing the total in the literature detected in this way to three). Five of the galaxies have published spectroscopic redshifts, enabling investigation of the implied temperature ranges and a comparison of photometric redshift techniques. Because l = 350 mm lies near the spectral energy distribution peak for z [approximate] 2.5 thermally emitting galaxies, luminosities can be measured without extrapolating to the peak from detection wavelengths of l >= 850 mm. Characteristically, the galaxy luminosities lie in the range 1.0--1.2 × 10 13 [Special characters omitted.] , with dust temperatures in the range of 40 K to 70 K, depending on the choice of spectral index and wavelength of unit optical depth. The implied dust masses are 3--5 × 10 8 [Special characters omitted.] . We find that the far-infrared to radio relation for star-forming ULIRGs systematically overpredicts the radio luminosities and overestimates redshifts on the order of D z [approximate] 1, whereas redshifts based on either on submillimeter data alone or the 1.6 mm stellar bump and PAH features are more accurate.

  15. Detection of B-mode polarization at degree angular scales by BICEP2.

    PubMed

    Ade, P A R; Aikin, R W; Barkats, D; Benton, S J; Bischoff, C A; Bock, J J; Brevik, J A; Buder, I; Bullock, E; Dowell, C D; Duband, L; Filippini, J P; Fliescher, S; Golwala, S R; Halpern, M; Hasselfield, M; Hildebrandt, S R; Hilton, G C; Hristov, V V; Irwin, K D; Karkare, K S; Kaufman, J P; Keating, B G; Kernasovskiy, S A; Kovac, J M; Kuo, C L; Leitch, E M; Lueker, M; Mason, P; Netterfield, C B; Nguyen, H T; O'Brient, R; Ogburn, R W; Orlando, A; Pryke, C; Reintsema, C D; Richter, S; Schwarz, R; Sheehy, C D; Staniszewski, Z K; Sudiwala, R V; Teply, G P; Tolan, J E; Turner, A D; Vieregg, A G; Wong, C L; Yoon, K W

    2014-06-20

    We report results from the BICEP2 experiment, a cosmic microwave background (CMB) polarimeter specifically designed to search for the signal of inflationary gravitational waves in the B-mode power spectrum around ??80. The telescope comprised a 26 cm aperture all-cold refracting optical system equipped with a focal plane of 512 antenna coupled transition edge sensor 150 GHz bolometers each with temperature sensitivity of ?300???K(CMB)?s. BICEP2 observed from the South Pole for three seasons from 2010 to 2012. A low-foreground region of sky with an effective area of 380 square deg was observed to a depth of 87 nK deg in Stokes Q and U. In this paper we describe the observations, data reduction, maps, simulations, and results. We find an excess of B-mode power over the base lensed-?CDM expectation in the range 30 < ? < 150, inconsistent with the null hypothesis at a significance of >5?. Through jackknife tests and simulations based on detailed calibration measurements we show that systematic contamination is much smaller than the observed excess. Cross correlating against WMAP 23 GHz maps we find that Galactic synchrotron makes a negligible contribution to the observed signal. We also examine a number of available models of polarized dust emission and find that at their default parameter values they predict power ?(5-10)× smaller than the observed excess signal (with no significant cross-correlation with our maps). However, these models are not sufficiently constrained by external public data to exclude the possibility of dust emission bright enough to explain the entire excess signal. Cross correlating BICEP2 against 100 GHz maps from the BICEP1 experiment, the excess signal is confirmed with 3? significance and its spectral index is found to be consistent with that of the CMB, disfavoring dust at 1.7?. The observed B-mode power spectrum is well fit by a lensed-?CDM+tensor theoretical model with tensor-to-scalar ratio r = 0.20_(-0.05)(+0.07), with r = 0 disfavored at 7.0?. Accounting for the contribution of foreground, dust will shift this value downward by an amount which will be better constrained with upcoming data sets. PMID:24996078

  16. Sampling times for monitoring tacrolimus in stable adult liver transplant recipients.

    PubMed

    Dansirikul, Chantaratsamon; Staatz, Christine E; Duffull, Stephen B; Taylor, Paul J; Lynch, Stephen V; Tett, Susan E

    2004-12-01

    The aim of this study was to determine the most informative sampling time(s) providing a precise prediction of tacrolimus area under the concentration-time curve (AUC). Fifty-four concentration-time profiles of tacrolimus from 31 adult liver transplant recipients were analyzed. Each profile contained 5 tacrolimus whole-blood concentrations (predose and 1, 2, 4, and 6 or 8 hours postdose), measured using liquid chromatography-tandem mass spectrometry. The concentration at 6 hours was interpolated for each profile, and 54 values of AUC(0-6) were calculated using the trapezoidal rule. The best sampling times were then determined using limited sampling strategies and sensitivity analysis. Linear mixed-effects modeling was performed to estimate regression coefficients of equations incorporating each concentration-time point (C0, C1, C2, C4, interpolated C5, and interpolated C6) as a predictor of AUC(0-6). Predictive performance was evaluated by assessment of the mean error (ME) and root mean square error (RMSE). Limited sampling strategy (LSS) equations with C2, C4, and C5 provided similar results for prediction of AUC(0-6) (R2 = 0.869, 0.844, and 0.832, respectively). These 3 time points were superior to C0 in the prediction of AUC. The ME was similar for all time points; the RMSE was smallest for C2, C4, and C5. The highest sensitivity index was determined to be 4.9 hours postdose at steady state, suggesting that this time point provides the most information about the AUC(0-12). The results from limited sampling strategies and sensitivity analysis supported the use of a single blood sample at 5 hours postdose as a predictor of both AUC(0-6) and AUC(0-12). A jackknife procedure was used to evaluate the predictive performance of the model, and this demonstrated that collecting a sample at 5 hours after dosing could be considered as the optimal sampling time for predicting AUC(0-6). PMID:15570182

  17. Computer-aided mass detection in mammography: False positive reduction via gray-scale invariant ranklet texture features

    SciTech Connect

    Masotti, Matteo; Lanconelli, Nico; Campanini, Renato [Department of Physics, University of Bologna, Viale Berti-Pichat 6/2, 40127, Bologna (Italy)

    2009-02-15

    In this work, gray-scale invariant ranklet texture features are proposed for false positive reduction (FPR) in computer-aided detection (CAD) of breast masses. Two main considerations are at the basis of this proposal. First, false positive (FP) marks surviving our previous CAD system seem to be characterized by specific texture properties that can be used to discriminate them from masses. Second, our previous CAD system achieves invariance to linear/nonlinear monotonic gray-scale transformations by encoding regions of interest into ranklet images through the ranklet transform, an image transformation similar to the wavelet transform, yet dealing with pixels' ranks rather than with their gray-scale values. Therefore, the new FPR approach proposed herein defines a set of texture features which are calculated directly from the ranklet images corresponding to the regions of interest surviving our previous CAD system, hence, ranklet texture features; then, a support vector machine (SVM) classifier is used for discrimination. As a result of this approach, texture-based information is used to discriminate FP marks surviving our previous CAD system; at the same time, invariance to linear/nonlinear monotonic gray-scale transformations of the new CAD system is guaranteed, as ranklet texture features are calculated from ranklet images that have this property themselves by construction. To emphasize the gray-scale invariance of both the previous and new CAD systems, training and testing are carried out without any in-between parameters' adjustment on mammograms having different gray-scale dynamics; in particular, training is carried out on analog digitized mammograms taken from a publicly available digital database, whereas testing is performed on full-field digital mammograms taken from an in-house database. Free-response receiver operating characteristic (FROC) curve analysis of the two CAD systems demonstrates that the new approach achieves a higher reduction of FP marks when compared to the previous one. Specifically, at 60%, 65%, and 70% per-mammogram sensitivity, the new CAD system achieves 0.50, 0.68, and 0.92 FP marks per mammogram, whereas at 70%, 75%, and 80% per-case sensitivity it achieves 0.37, 0.48, and 0.71 FP marks per mammogram, respectively. Conversely, at the same sensitivities, the previous CAD system reached 0.71, 0.87, and 1.15 FP marks per mammogram, and 0.57, 0.73, and 0.92 FPs per mammogram. Also, statistical significance of the difference between the two per-mammogram and per-case FROC curves is demonstrated by the p-value<0.001 returned by jackknife FROC analysis performed on the two CAD systems.

  18. School-age effects of the newborn individualized developmental care and assessment program for preterm infants with intrauterine growth restriction: preliminary findings

    PubMed Central

    2013-01-01

    Background The experience in the newborn intensive care nursery results in premature infants’ neurobehavioral and neurophysiological dysfunction and poorer brain structure. Preterms with severe intrauterine growth restriction are doubly jeopardized given their compromised brains. The Newborn Individualized Developmental Care and Assessment Program improved outcome at early school-age for preterms with appropriate intrauterine growth. It also showed effectiveness to nine months for preterms with intrauterine growth restriction. The current study tested effectiveness into school-age for preterms with intrauterine growth restriction regarding executive function (EF), electrophysiology (EEG) and neurostructure (MRI). Methods Twenty-three 9-year-old former growth-restricted preterms, randomized at birth to standard care (14 controls) or to the Newborn Individualized Developmental Care and Assessment Program (9 experimentals) were assessed with standardized measures of cognition, achievement, executive function, electroencephalography, and magnetic resonance imaging. The participating children were comparable to those lost to follow-up, and the controls to the experimentals, in terms of newborn background health and demographics. All outcome measures were corrected for mother’s intelligence. Analysis techniques included two-group analysis of variance and stepwise discriminate analysis for the outcome measures, Wilks’ lambda and jackknifed classification to ascertain two-group classification success per and across domains; canonical correlation analysis to explore relationships among neuropsychological, electrophysiological and neurostructural domains at school-age, and from the newborn period to school-age. Results Controls and experimentals were comparable in age at testing, anthropometric and health parameters, and in cognitive and achievement scores. Experimentals scored better in executive function, spectral coherence, and cerebellar volumes. Furthermore, executive function, spectral coherence and brain structural measures discriminated controls from experimentals. Executive function correlated with coherence and brain structure measures, and with newborn-period neurobehavioral assessment. Conclusion The intervention in the intensive care nursery improved executive function as well as spectral coherence between occipital and frontal as well as parietal regions. The experimentals’ cerebella were significantly larger than the controls’. These results, while preliminary, point to the possibility of long-term brain improvement even of intrauterine growth compromised preterms if individualized intervention begins with admission to the NICU and extends throughout transition home. Larger sample replications are required in order to confirm these results. Clinical trial registration The study is registered as a clinical trial. The trial registration number is NCT00914108. PMID:23421857

  19. Modeling deformation associated with the 2004-2008 dome-building eruption of Mount St. Helens

    NASA Astrophysics Data System (ADS)

    Lisowski, M.; Battaglia, M.

    2011-12-01

    We estimate deformation sources active during and after the 2004-2008 dome-building eruption of Mount St. Helens (MSH) by inverting campaign and continuous GPS (CGPS) measured deformation between 2000 and 2011. All data are corrected for background deformation using a tectonic model that includes block rotation and uniform strain accumulation. The campaign GPS surveys characterize the deformation over a large area, and the CGPS data allow estimates of time-dependent changes in the rate of deformation. Only one CGPS station, JRO1, was operating near MSH prior to the start of unrest on September 23, 2004. Most other CGPS stations, installed by the Plate Boundary Observatory and Cascade Volcano Observatory, were operating by mid-October, 2004. The inward displacement of JRO1 started with the seismic unrest on September 23, 2004, and continued at a rate of 0.5 mm/day until the last phreatic explosion on October 5, 2004 (note there was another explosion in March 2005). The deformation then decayed exponentially until activity ceased in January, 2008. The rate of decay was estimated using a number of clean CGPS time series, and then it was fixed to estimate amplitudes for all CGPS station displacements. The inward and downward movements (deflation) observed at all stations during the eruption (2004-2008) were best-fit by a prolate spheroid with geometric aspect ratio 0.19 ± 0.6, a depth of 7.4 ± 1.7 km, and a cavity volume decrease of 0.028 ± 0.005 cubic km. This source is practically vertical (dip angle: 84 ± 5; strike angle 298 ± 84) and is located beneath the dome. All errors are 95% bounds and have been estimated using jackknife. The post-eruption deformation (2008 - present) is characterized by deflation in the near field (within 2 km from the dome) and inflation in the far field. The near-field deflation signal is best fit by a very shallow sill-like source (~0.18 ± 0.05 km below the crater floor) with a radius of 0.5 ± 0.3 km and a cavity volume decrease of 0.010 ± 0.001 cubic km. The best-fitting source for the far-field inflation is a prolate spheroid of geometric aspect ratio 0.12 ± 0.2, a depth of 7.3 ± 0.6 km, and a cavity volume increase of 0.006 ± 0.001 cubic km. The source dips slightly to the north (dip angle: 75 ± 4; strike angle 357 ± 8). Both sources are located beneath the dome. These results suggest that the same deep magma source has been active beneath the volcano for the past 7 years. This source fed the dome eruption and is now slowly being filled. The shallow source controlling the near-field, post-eruption deformation is probably due to the cooling and contraction of the lava dome within the crater.

  20. Optimized multiple quantum MAS lineshape simulations in solid state NMR

    NASA Astrophysics Data System (ADS)

    Brouwer, William J.; Davis, Michael C.; Mueller, Karl T.

    2009-10-01

    The majority of nuclei available for study in solid state Nuclear Magnetic Resonance have half-integer spin I>1/2, with corresponding electric quadrupole moment. As such, they may couple with a surrounding electric field gradient. This effect introduces anisotropic line broadening to spectra, arising from distinct chemical species within polycrystalline solids. In Multiple Quantum Magic Angle Spinning (MQMAS) experiments, a second frequency dimension is created, devoid of quadrupolar anisotropy. As a result, the center of gravity of peaks in the high resolution dimension is a function of isotropic second order quadrupole and chemical shift alone. However, for complex materials, these parameters take on a stochastic nature due in turn to structural and chemical disorder. Lineshapes may still overlap in the isotropic dimension, complicating the task of assignment and interpretation. A distributed computational approach is presented here which permits simulation of the two-dimensional MQMAS spectrum, generated by random variates from model distributions of isotropic chemical and quadrupole shifts. Owing to the non-convex nature of the residual sum of squares (RSS) function between experimental and simulated spectra, simulated annealing is used to optimize the simulation parameters. In this manner, local chemical environments for disordered materials may be characterized, and via a re-sampling approach, error estimates for parameters produced. Program summaryProgram title: mqmasOPT Catalogue identifier: AEEC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3650 No. of bytes in distributed program, including test data, etc.: 73 853 Distribution format: tar.gz Programming language: C, OCTAVE Computer: UNIX/Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron. References:S.K. Zaremba, Annali di Matematica Pura ed Applicata 73 (1966) 293. H. Niederreiter, Random Number Generation and Quasi-Monte Carlo Methods, SIAM, 1992. T. Fox, D. Hinkley, K. Larntz, Technometrics 22 (1980) 29.

  1. Implementing the national AIGA flash flood warning system in France

    NASA Astrophysics Data System (ADS)

    Organde, Didier; Javelle, Pierre; Demargne, Julie; Arnaud, Patrick; Caseri, Angelica; Fine, Jean-Alain; de Saint Aubin, Céline

    2015-04-01

    The French national hydro-meteorological and flood forecasting centre (SCHAPI) aims to implement a national flash flood warning system to improve flood alerts for small-to-medium (up to 1000 km2) ungauged basins. This system is based on the AIGA method, co-developed by IRSTEA these last 10 years. The method, initially set up for the Mediterranean area, is based on a simple event-based hourly hydrologic distributed model run every 15 minutes (Javelle et al. 2014). The hydrologic model ingests operational radar-gauge rainfall grids from Météo-France at a 1-km² resolution to produce discharges for successive outlets along the river network. Discharges are then compared to regionalized flood quantiles of given return periods and warnings (expressed as the range of the return period estimated in real-time) are provided on a river network map. The main interest of the method is to provide forecasters and emergency services with a synthetic view in real time of the ongoing flood situation, information that is especially critical in ungauged flood prone areas. In its enhanced national version, the hourly event-based distributed model is coupled to a continuous daily rainfall-runoff model which provides baseflow and a soil moisture index (for each 1-km² pixel) at the beginning of the hourly simulation. The rainfall-runoff models were calibrated on a selection of 700 French hydrometric stations with Météo-France radar-gauge reanalysis dataset for the 2002-2006 period. To estimate model parameters for ungauged basins, the 2 hydrologic models were regionalised by testing both regressions (using different catchment attributes, such as catchment area, soil type, and climate characteristic) and spatial proximity techniques (transposing parameters from neighbouring donor catchments), as well as different homogeneous hydrological areas. The most valuable regionalisation method was determined for each model through jack-knife cross-validation. The system performance was then evaluated with contingency criteria (e.g., Critical Success Index, Probability Of Detection, Success Ratio) using operational rainfall radar-gauge products from Météo-France for the 2009-2012 period. The regionalised parameters of the distributed model were finally adjusted for each homogeneous hydrological area to optimize the Heidke skill score (HSS) calculated with three levels of warnings (2-, 10- and 50-year flood quantiles). This work is currently being implemented by the SCHAPI to set up an automated national flash flood warning system by 2016. Planned improvements include developing a unique continuous model to be run at a sub-hourly timestep, discharge assimilation, as well as integrating precipitation forecasts while accounting for the main sources of forecast uncertainty. Javelle, P., Demargne, J., Defrance, D., and Arnaud, P. 2014. Evaluating flash flood warnings at ungauged locations using post-event surveys: a case study with the AIGA warning system. Hydrological Sciences Journal, DOI: 10.1080/02626667.2014.923970