Science.gov

Sample records for jackknifing

  1. 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…

  2. Jackknife and bootstrap inferential procedures for censored survival data

    NASA Astrophysics Data System (ADS)

    Fang, Loh Yue; Arasan, Jayanthi; Midi, Habshah; Bakar, Mohd Rizam Abu

    2015-10-01

    Confidence interval is an estimate of a certain parameter. Classical construction of confidence interval based on asymptotic normality (Wald) often produces misleading inferences when dealing with censored data especially in small samples. Alternative techniques allow us to construct the confidence interval estimation without relying on this assumption. In this paper, we compare the performances of the jackknife and several bootstraps confidence interval estimates for the parameters of a log logistic model with censored data and covariate. We investigate their performances at two nominal error probability levels and several levels of censoring proportion. Conclusions were then drawn based on the results of the coverage probability study.

  3. A Comparison of Interval Estimation of Coefficient Alpha Using the Feldt and the Jackknife Procedures.

    ERIC Educational Resources Information Center

    Pandey, Tej N.; Hubert, Lawrence J.

    This investigation had two major purposes. The first was to explore the use of an inferential technique called Tukey's Jackknife in establishing a confidence interval about cooefficient alpha reliability. The second purpose was to study the robustness of the Feldt and the jackknife procedures when the data fails to satisfy usual normality…

  4. Use of the Jackknife Statistic To Establish the External Validity of Discriminant Analysis Results.

    ERIC Educational Resources Information Center

    Daniel, Larry G.

    That the jackknifing technique is superior to traditional techniques for assessing the external validity of statistical results of discriminant analysis is defended. Traditional approaches assessed include: (1) the empirical method, in which the discriminant function coefficients (DFCs) obtained in a given analysis are applied to predict group…

  5. How Comparable Are the Jackknife and Bootstrap Results: An Investigation for a Case of Canonical Correlation Analysis.

    ERIC Educational Resources Information Center

    Fan, Xitao; Wang, Lin

    The jackknife and bootstrap methods are becoming more popular in research. Although the two approaches have similar goals and employ similar strategies, information is lacking with regard to the comparability of their results. This study systematically investigated the issue for a canonical correlation analysis, using data from four random samples…

  6. 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…

  7. The many structural faces of calmodulin: a multitasking molecular jackknife.

    PubMed

    Kursula, Petri

    2014-10-01

    Calmodulin (CaM) is a highly conserved protein and a crucial calcium sensor in eukaryotes. CaM is a regulator of hundreds of diverse target proteins. A wealth of studies has been carried out on the structure of CaM, both in the unliganded form and in complexes with target proteins and peptides. The outcome of these studies points toward a high propensity to attain various conformational states, depending on the binding partner. The purpose of this review is to provide examples of different conformations of CaM trapped in the crystal state. In addition, comparisons are made to corresponding studies in solution. The different CaM conformations in crystal structures are also compared based on the positions of the metal ions bound to their EF hands, in terms of distances, angles, and pseudo-torsion angles. Possible caveats and artifacts in CaM crystal structures are discussed, as well as the possibilities of trapping biologically relevant CaM conformations in the crystal state. PMID:25005783

  8. Delta and Jackknife Estimators with Low Bias for Functions of Binomial and

    E-print Network

    Sidorov, Nikita

    and research report quality in nutrition practice- related research, crash-prediction models for multilane microbial community, longline hook selectivity for red tilefish Bran- chiostegus japonicus in the East China

  9. 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...

  10. 16 CFR 1632.1 - Definitions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...and the mattress core, upholstered furniture which does not contain a detachable mattress such as chaise lounges, drop-arm love seats, press-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa...

  11. 16 CFR 1632.1 - Definitions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...and the mattress core, upholstered furniture which does not contain a detachable mattress such as chaise lounges, drop-arm love seats, press-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa...

  12. 16 CFR 1632.1 - Definitions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...and the mattress core, upholstered furniture which does not contain a detachable mattress such as chaise lounges, drop-arm love seats, press-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa...

  13. 16 CFR 1632.1 - Definitions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...and the mattress core, upholstered furniture which does not contain a detachable mattress such as chaise lounges, drop-arm love seats, press-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa...

  14. 16 CFR 1632.1 - Definitions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...and the mattress core, upholstered furniture which does not contain a detachable mattress such as chaise lounges, drop-arm love seats, press-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa...

  15. Royal Statistical Society J. R. Statist. Soc. B (2006)

    E-print Network

    Maryland at College Park, University of

    2006-01-01

    a jackknife method of MSE estimation in an empirical Bayes framework, using log- normal models in which important in survey applications, particularly in those fields of official statistics where legislative

  16. An Empirical Investigation of Sampling Errors in Educational Survey Research.

    ERIC Educational Resources Information Center

    Ross, Kenneth N.

    1979-01-01

    It is shown that using formulae for the estimation of sampling errors based on simple random sampling, when a design actually involves cluster sampling, can lead to serious underestimation of error. Jackknife and balanced repeated replication are recommended as techniques for dealing with this problem. (Author/CTM)

  17. Statistical Inference for Regression Models with Covariate Measurement Error and Auxiliary Information

    PubMed Central

    You, Jinhong; Zhou, Haibo

    2011-01-01

    We consider statistical inference on a regression model in which some covariables are measured with errors together with an auxiliary variable. The proposed estimation for the regression coefficients is based on some estimating equations. This new method alleates some drawbacks of previously proposed estimations. This includes the requirment of undersmoothing the regressor functions over the auxiliary variable, the restriction on other covariables which can be observed exactly, among others. The large sample properties of the proposed estimator are established. We further propose a jackknife estimation, which consists of deleting one estimating equation (instead of one obervation) at a time. We show that the jackknife estimator of the regression coefficients and the estimating equations based estimator are asymptotically equivalent. Simulations show that the jackknife estimator has smaller biases when sample size is small or moderate. In addition, the jackknife estimation can also provide a consistent estimator of the asymptotic covariance matrix, which is robust to the heteroscedasticity. We illustrate these methods by applying them to a real data set from marketing science. PMID:22199460

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant Vessels § 160.043-4 Construction and workmanship. (a...be of hard brass, not less than 0.048 inch in diameter. Middle and end pins shall be of hard brass not less than...

  19. [The evolution of the sequences of the internal spacer of nuclear ribosomal DNA for American species in the genus Nicotiana].

    PubMed

    Komarnyts'ky?, S I; Komarnyts'ky?, I K; Cox, A; Parokonny?, A S

    1998-01-01

    Phylogenetic relationships of 46 Nicotiana species were estimated from the sequences of internal transcribed spacer region of nuclear ribosomal DNA. Phylogenetic tree, built by parsimony method, was highly concordant with the conclusions of morphological and cytogenetical investigations. The reliability of dendrogram obtained was assessed by both bootstrap and jackknife analyses. PMID:9879106

  20. Statistical Inference for Regression Models with Covariate Measurement Error and Auxiliary Information.

    PubMed

    You, Jinhong; Zhou, Haibo

    2009-01-01

    We consider statistical inference on a regression model in which some covariables are measured with errors together with an auxiliary variable. The proposed estimation for the regression coefficients is based on some estimating equations. This new method alleates some drawbacks of previously proposed estimations. This includes the requirment of undersmoothing the regressor functions over the auxiliary variable, the restriction on other covariables which can be observed exactly, among others. The large sample properties of the proposed estimator are established. We further propose a jackknife estimation, which consists of deleting one estimating equation (instead of one obervation) at a time. We show that the jackknife estimator of the regression coefficients and the estimating equations based estimator are asymptotically equivalent. Simulations show that the jackknife estimator has smaller biases when sample size is small or moderate. In addition, the jackknife estimation can also provide a consistent estimator of the asymptotic covariance matrix, which is robust to the heteroscedasticity. We illustrate these methods by applying them to a real data set from marketing science. PMID:22199460

  1. International Journal of Medical Microbiology 298 (2008) 245252 Differentiation of fecal Escherichia coli from poultry and free-living birds

    E-print Network

    Mazumder, Asit

    2008-01-01

    analysis with the jack-knife algorithm of (GTG)5-PCR DNA fingerprints revealed that 95%, 94.1%, 93.2%, 84; Genotyping; (GTG)5-PCR; DNA fingerprinting Introduction Fecal pollution from non-point sources Escherichia coli from poultry and free-living birds by (GTG)5-PCR genomic fingerprinting Bidyut R. Mohapatraa

  2. 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…

  3. 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…

  4. 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…

  5. Captain M. A. Ainslie (1869-1951): his observations and telescopes

    NASA Astrophysics Data System (ADS)

    Mobberley, M. P.

    2010-02-01

    The astronomical career of one of the BAA's most enthusiastic planetary observers, who contributed observations in the first five decades of the twentieth century, is described. In addition, his pioneering observation of the occultation of a star by Saturn's rings in 1917 is examined and the full story of his unique 'Jack-Knife telescope', designed by Horace Dall, is given.

  6. Possession, Transportation, and Use of Firearms by Older Youth in 4-H Shooting Sports Programs

    ERIC Educational Resources Information Center

    White, David J.; Williver, S. Todd

    2014-01-01

    Thirty years ago we would think nothing of driving to school with a jackknife in our pocket or rifle in the gun rack. Since then, the practices of possessing, transporting, and using firearms have been limited by laws, rules, and public perception. Despite restrictions on youth, the Youth Handgun Safety Act does afford 4-H shooting sports members…

  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. 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

  9. Predicting protein secondary structure and solvent accessibility with an improved multiple linear regression method.

    PubMed

    Qin, Sanbo; He, Yun; Pan, Xian-Ming

    2005-11-15

    We have improved the multiple linear regression (MLR) algorithm for protein secondary structure prediction by combining it with the evolutionary information provided by multiple sequence alignment of PSI-BLAST. On the CB513 dataset, the three states average overall per-residue accuracy, Q(3), reached 76.4%, while segment overlap accuracy, SOV99, reached 73.2%, using a rigorous jackknife procedure and the strictest reduction of eight states DSSP definition to three states. This represents an improvement of approximately 5% on overall per-residue accuracy compared with previous work. The relative solvent accessibility prediction also benefited from this combination of methods. The system achieved 77.7% average jackknifed accuracy for two states prediction based on a 25% relative solvent accessibility mode, with a Mathews' correlation coefficient of 0.548. The improved MLR secondary structure and relative solvent accessibility prediction server is available at http://spg.biosci.tsinghua.edu.cn/. PMID:16152601

  10. Inferring Phylogenetic Networks from Gene Order Data

    PubMed Central

    Morozov, Alexey Anatolievich; Galachyants, Yuri Pavlovich; Likhoshway, Yelena Valentinovna

    2013-01-01

    Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary), sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm). Binary encoding can also be useful, but only when the methods mentioned above cannot be used. PMID:24069602

  11. 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.

  12. Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

    USGS Publications Warehouse

    McNew, Lance B.; Handel, Colleen M.

    2015-01-01

    Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results indicate that neglecting the effects of site covariates on species detection probabilities may lead to significant bias in estimation of species richness, as well as the inferred relationships between community size and environmental covariates.

  13. MMOD: an R library for the calculation of population differentiation statistics.

    PubMed

    Winter, David J

    2012-11-01

    MMOD is a library for the R programming language that allows the calculation of the population differentiation measures D(est), G?(ST) and ?'(ST). R provides a powerful environment in which to conduct and record population genetic analyses but, at present, no R libraries provide functions for the calculation of these statistics from standard population genetic files. In addition to the calculation of differentiation measures, mmod can produce parametric bootstrap and jackknife samples of data sets for further analysis. By integrating with and complimenting the existing libraries adegenet and pegas, mmod extends the power of R as a population genetic platform. PMID:22883857

  14. Phylogeny and Rates of Molecular Evolution in the Aphelocoma Jays (Corvidae)

    E-print Network

    Peterson, A. Townsend

    1992-01-01

    , in the United States and Mexico (Table 1, Fig. 1). I attempted to obtain samples of 20 individuals at each site to maximize tree stability (Archie et al. 1989): Scrub Jay samples averaged 19.2 (range 13-27) indi- viduals; Gray-breasted Jay samples averaged... analyzed subsets of the data in two ways. I either assumed species to be monophyletic and analyzed each separately, or I used representative populations from each of the subspecies groups. All trees were checked for stability using a jackknife...

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

    NASA Astrophysics Data System (ADS)

    Verbyla, David L.; Litvaitis, John A.

    1989-11-01

    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 computer simulation to demonstrate the increase in precision of the estimate. The bootstrap method is then applied to field data as a technique for model comparison We recommend that biologists use some resampling procedure to evaluate wildlife habitat models prior to field evaluation.

  16. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    PubMed Central

    Shahrudin, Shahriza

    2015-01-01

    This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs) which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM-) LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity. PMID:25802839

  17. Reweighting estimators for Cox regression with missing covariate data: analysis of insulin resistance and risk of stroke in the Northern Manhattan Study.

    PubMed

    Xu, Qiang; Paik, Myunghee Cho; Rundek, Tatjana; Elkind, Mitchell S V; Sacco, Ralph L

    2011-12-10

    Incomplete covariates often obscure analysis results from a Cox regression. In an analysis of the Northern Manhattan Study (NOMAS) to determine the influence of insulin resistance on the incidence of stroke in nondiabetic individuals, insulin level is unknown for 34.1% of the subjects. The available data suggest that the missingness mechanism depends on outcome variables, which may generate biases in estimating the parameters of interest if only using the complete observations. This article aimed to introduce practical strategies to analyze the NOMAS data and present sensitivity analyses by using the reweighting method in standard statistical packages. When the data set structure is in counting process style, the reweighting estimates can be obtained by built-in procedures with variance estimated by the jackknife method. Simulation results indicate that the jackknife variance estimate provides reasonable coverage probability in moderate sample sizes. We subsequently conducted sensitivity analyses for the NOMAS data, showing that the risk estimates are robust to a variety of missingness mechanisms. At the end of this article, we present the core SAS and R programs used in the analysis. PMID:21965165

  18. Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome.

    PubMed

    Chen, Wei; Tran, Hong; Liang, Zhiyong; Lin, Hao; Zhang, Liqing

    2015-01-01

    Knowledge of the distribution of N(6)-methyladenosine (m(6)A) is invaluable for understanding RNA biological functions. However, limitation in experimental methods impedes the progress towards the identification of m(6)A site. As a complement of experimental methods, a support vector machine based-method is proposed to identify m(6)A sites in Saccharomyces cerevisiae genome. In this model, RNA sequences are encoded by their nucleotide chemical property and accumulated nucleotide frequency information. It is observed in the jackknife test that the accuracy achieved by the proposed model in identifying the m(6)A site was 78.15%. For the convenience of experimental scientists, a web-server for the proposed model is provided at http://lin.uestc.edu.cn/server/m6Apred.php. PMID:26343792

  19. 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

  20. Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome

    PubMed Central

    Chen, Wei; Tran, Hong; Liang, Zhiyong; Lin, Hao; Zhang, Liqing

    2015-01-01

    Knowledge of the distribution of N6-methyladenosine (m6A) is invaluable for understanding RNA biological functions. However, limitation in experimental methods impedes the progress towards the identification of m6A site. As a complement of experimental methods, a support vector machine based-method is proposed to identify m6A sites in Saccharomyces cerevisiae genome. In this model, RNA sequences are encoded by their nucleotide chemical property and accumulated nucleotide frequency information. It is observed in the jackknife test that the accuracy achieved by the proposed model in identifying the m6A site was 78.15%. For the convenience of experimental scientists, a web-server for the proposed model is provided at http://lin.uestc.edu.cn/server/m6Apred.php. PMID:26343792

  1. Post-processing for spectral coherence of magnetoencephalogram background activity: application to Alzheimer's disease.

    PubMed

    Escudero, Javier; Anastasiou, Athanasios; Fernández, Alberto

    2014-01-01

    Estimating the connectivity between magnetoencephalogram (MEG) signals provides an excellent opportunity to analyze whole brain functional integration across a spectrum of conditions from health to disease. For this purpose, spectral coherence has been used widely as an easy-to-interpret metric of signal coupling. However, a number of systematic effects may influence the estimations of spectral coherence and subsequent inferences about brain activity. In this pilot study, we focus on the potentially confounding effects of the field spread and the on-going dynamic temporal variability inherent in the signals. We propose two simple post-processing approaches to account for these: 1) a jack-knife procedure to account for the variance in the estimation of spectral coherence; and 2) a detrending technique to reduce its dependence on sensor proximity. We illustrate the effect of these techniques in the estimation of MEG spectral coherence in the ? band for 36 patients with Alzheimer's disease and 26 control subjects. PMID:25571447

  2. 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.

  3. 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

  4. Quantitative analysis of mebendazole polymorphs in pharmaceutical raw materials using near-infrared spectroscopy.

    PubMed

    da Silva, Vitor H; Gonçalves, Jacqueline L; Vasconcelos, Fernanda V C; Pimentel, M Fernanda; Pereira, Claudete F

    2015-11-10

    This work evaluates the feasibility of using NIR spectroscopy for quantification of three polymorphs of mebendazole (MBZ) in pharmaceutical raw materials. Thirty ternary mixtures of polymorphic forms of MBZ were prepared, varying the content of forms A and C from 0 to 100% (w/w), and for form B from 0 to 30% (w/w). Reflectance NIR spectra were used to develop partial least square (PLS) regression models using all spectral variables and the variables with significant regression coefficients selected by the Jack-Knife algorithm (PLS/JK). MBZ polymorphs were quantified with RMSEP values of 2.37% w/w, 1.23% w/w and 1.48% w/w for polymorphs A, B and C, respectively. This is an easy, fast and feasible method for monitoring the quality of raw pharmaceutical materials of MBZ according to polymorph purity. PMID:26320077

  5. Ontogeny of the barley plant as related to mutation expression and detection of pollen mutations

    SciTech Connect

    Hodgdon, A.L.; Marcus, A.H.; Arenaz, P.; Rosichan, J.L.; Bogyo, T.P.; Nilan, R.A.

    1980-05-29

    Clustering of mutant pollen grains in a population of normal pollen due to premeiotic mutational events complicates translating mutation frequencies into rates. Embryo ontogeny in barley will be described and used to illustrate the formation of such mutant clusters. The nature of the statistics for mutation frequency will be described from a study of the reversion frequencies of various waxy mutants in barley. Computer analysis by a jackknife method of the reversion frequencies of a waxy mutant treated with the mutagen sodium azide showed a significantly higher reversion frequency than untreated material. Problems of the computer analysis suggest a better experimental design for pollen mutation experiments. Preliminary work on computer modeling for pollen development and mutation will be described.

  6. 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

  7. Design-based treatment of unit nonresponse in environmental surveys using calibration weighting.

    PubMed

    Fattorini, Lorenzo; Franceschi, Sara; Maffei, Daniela

    2013-11-01

    Unit nonresponse is often a problem in sample surveys. It arises when the values of the survey variable cannot be recorded for some sampled units. In this paper, the use of nonresponse calibration weighting to treat nonresponse is considered in a complete design-based framework. Nonresponse is viewed as a fixed characteristic of the units. The approach is suitable in environmental and forest surveys when sampled sites cannot be reached by field crews. Approximate expressions of design-based bias and variance of the calibration estimator are derived and design-based consistency is investigated. Choice of auxiliary variables to perform calibration is discussed. Sen-Yates-Grundy, Horvitz-Thompson, and jackknife estimators of the sampling variance are proposed. Analytical and Monte Carlo results demonstrate the validity of the procedure when the relationship between survey and auxiliary variables is similar in respondent and nonrespondent strata. An application to a forest survey performed in Northeastern Italy is considered. PMID:24022794

  8. Multicanonical Simulations Step by Step

    E-print Network

    Bernd A. Berg

    2002-08-09

    The purpose of this article is to provide a starter kit for multicanonical simulations in statistical physics. Fortran code for the $q$-state Potts model in $d=2, 3,...$ dimensions can be downloaded from the Web and this paper describes simulation results, which are in all details reproducible by running prepared programs. To allow for comparison with exact results, the internal energy, the specific heat, the free energy and the entropy are calculated for the $d=2$ Ising ($q=2$) and the $q=10$ Potts model. % in a temperature range from $T=\\infty$ down to sufficiently low % temperatures, such that the groundstates are included in the sampling. Analysis programs, relying on an all-log jackknife technique, which is suitable for handling sums of very large numbers, are introduced to calculate our final estimators.

  9. From Data to Probability Densities without Histograms

    E-print Network

    Bernd A. Berg; Robert C. Harris

    2007-12-22

    When one deals with data drawn from continuous variables, a histogram is often inadequate to display their probability density. It deals inefficiently with statistical noise, and binsizes are free parameters. In contrast to that, the empirical cumulative distribution function (obtained after sorting the data) is parameter free. But it is a step function, so that its differentiation does not give a smooth probability density. Based on Fourier series expansion and Kolmogorov tests, we introduce a simple method, which overcomes this problem. Error bars on the estimated probability density are calculated using a jackknife method. We give several examples and provide computer code reproducing them. You may want to look at the corresponding figures 4 to 9 first.

  10. Second and third season QUaD CMB temperature and polarization power spectra

    E-print Network

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

    2009-02-25

    We report results from the second and third seasons of observation with the QUaD experiment. Angular power spectra of the Cosmic Microwave Background are derived for both temperature and polarization at both 100 GHz and 150 GHz, and as cross frequency spectra. All spectra are subjected to an extensive set of jackknife tests to probe for possible systematic contamination. For the implemented data cuts and processing technique such contamination is undetectable. We analyze the difference map formed between the 100 and 150 GHz bands and find no evidence of foreground contamination in polarization. The spectra are then combined to form a single set of results which are shown to be consistent with the prevailing LCDM model. The sensitivity of the polarization results is considerably better than that of any previous experiment -- for the first time multiple acoustic peaks are detected in the E-mode power spectrum at high significance.

  11. ETAP: An Exoplanetary Transit Analyzer Program

    NASA Astrophysics Data System (ADS)

    Demircan, O.; Bak??, V.

    2015-07-01

    We introduce new software for the modeling of exoplanet transit light curves. The technique is based on the aperture cross correlation between the light changes and the diffraction pattern of the apertures representing the eclipsing binary components (Kopal 1977; Kopal & Demircan 1978), where in the present case the eclipsing component is considered to be a transiting exoplanet. The software finds the best parameters including the fractional radii of the exoplanet and the host star, the inclination and eccentricity of the orbit, the longitude of periastron, limb-darkening coefficients of any degree, and the transit time, yielding the lowest ?2. Parameter uncertainties are calculated with the jackknife method. We compare results for selected exoplanet transit light curves against those available in the literature.

  12. A new brachycladiid species (Digenea) from Gervais' beaked whale Mesoplodon europaeus in north-western Atlantic waters.

    PubMed

    Fraija-Fernández, Natalia; Aznar, Francisco J; Raga, Juan A; Gibson, David; Fernández, Mercedes

    2014-09-01

    A new species of the digenean family Brachycladiidae Odhner, 1905 is described from the bile ducts of a Gervais' beaked whale Mesoplodon europaeus Gervais (Ziphiidae) stranded on the North Atlantic coast of Florida. These parasites were assigned to Brachycladium Looss, 1899 and differed from other species of the genus in the relative size of the oral and ventral suckers, the form and size of the eggs and their extremely small body size. A canonical discriminant analysis was used to examine differences between these specimens and the smallest available individuals of B. atlanticum (Abril, Balbuena and Raga, 1991) Gibson, 2005, considered the morphologically closest species. The overall results exhibited significant differences between the two samples and a jack-knife classification showed that 96.2% of the specimens were correctly classified to their group. In view of evidence from morphological data, the specimens from M. europaeus are considered as new to science and are designated as Brachycladium parvulum n. sp. PMID:25119367

  13. Ontogeny of the barley plant as related to mutation expression and detection of pollen mutations

    SciTech Connect

    Hodgdon, A.L.; Marcus, A.H.; Arenaz, P.; Rosichan, J.L.; Bogyo, T.P.; Nilan, R.A.

    1981-01-01

    Clustering of mutant pollen grains in a population of normal pollen due to premeiotic mutational events complicates translating mutation frequencies into rates. Embryo ontogeny in barley will be described and used to illustrate the formation of such mutant clusters. The nature of the statistics for mutation frequency will be described from a study of the reversion frequencies of various waxy mutants in barley. Computer analysis by a ''jackknife'' method of the reversion of a waxy mutant treated with the mutagen sodium azide showed a significantly higher reversion frequency than untreated material. Problems of the computer analysis suggest a better experimental design for pollen mutation experiments. Preliminary work on computer modeling for pollen development and mutation will be described.

  14. Estimating contaminant loads in rivers: An application of adjusted maximum likelihood to type 1 censored data

    USGS Publications Warehouse

    Cohn, T.A.

    2005-01-01

    This paper presents an adjusted maximum likelihood estimator (AMLE) that can be used to estimate fluvial transport of contaminants, like phosphorus, that are subject to censoring because of analytical detection limits. The AMLE is a generalization of the widely accepted minimum variance unbiased estimator (MVUE), and Monte Carlo experiments confirm that it shares essentially all of the MVUE's desirable properties, including high efficiency and negligible bias. In particular, the AMLE exhibits substantially less bias than alternative censored-data estimators such as the MLE (Tobit) or the MLE followed by a jackknife. As with the MLE and the MVUE the AMLE comes close to achieving the theoretical Frechet-Crame??r-Rao bounds on its variance. This paper also presents a statistical framework, applicable to both censored and complete data, for understanding and estimating the components of uncertainty associated with load estimates. This can serve to lower the cost and improve the efficiency of both traditional and real-time water quality monitoring.

  15. Single-pass versus two-pass boat electrofishing for characterizing river fish assemblages: Species richness estimates and sampling distance

    USGS Publications Warehouse

    Meador, M.R.

    2005-01-01

    Determining adequate sampling effort for characterizing fish assemblage structure in nonwadeable rivers remains a critical issue in river biomonitoring. Two-pass boat electrofishing data collected from 500-1,000-m-long river reaches as part of the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program were analyzed to assess the efficacy of single-pass boat electrofishing. True fish species richness was estimated by use of a two-pass removal model and nonparametric jackknife estimation for 157 sampled reaches across the United States. Compared with estimates made with a relatively unbiased nonparametric estimator, estimates of true species richness based on the removal model may be biased, particularly when true species richness is greater than 10. Based on jackknife estimation, the mean percent of estimated true species richness collected in the first electrofishing pass (p??j,s1) for all 157 reaches was 65.5%. The effectiveness of single-pass boat electrofishing may be greatest when the expected species richness is relatively low (>10 species). The second pass produced additional species (1-13) in 89.2% of sampled reaches. Of these additional species, centrarchids were collected in 50.3% of reaches and cyprinids were collected in 45.9% of reaches. Examination of relations between channel width ratio (reach length divided by wetted channel width) and p??j,s1 values provided no clear recommendation for sampling distances based on channel width ratios. Increasing sampling effort through an extension of the sampled reach distance can increase the percent species richness obtained from single-pass boat electrofishing. When single-pass boat electrofishing is used to characterize fish assemblage structure, determination of the sampling distance should take into account such factors as species richness and patchiness, the presence of species with relatively low probabilities of detection, and human alterations to the channel.

  16. Computerized detection and classification of microcalcifications on mammograms

    NASA Astrophysics Data System (ADS)

    Chan, Heang-Ping; Wei, Datong; Lam, Kwok L.; Lo, Shih-Chung B.; Sahiner, Berkman; Helvie, Mark A.; Adler, Dorit D.

    1995-05-01

    We are developing computer-aided diagnosis algorithms to assist radiologists in detection and classification of microcalcifications on mammograms. A digitized mammogram was processed with a difference-image technique and signal segmentation methods to identify suspicious signals. False-positive detections were reduced by using morphological features as well as a convolution neural network. A regional clustering technique was applied to the remaining signals to identify clinically significant clustered microcalcifications. For the development of a malignant/benign classifier, the microcalcifications were extracted from the digital images by computerized segmentation techniques. A number of visibility descriptors and shape descriptors were developed to describe the features of the microcalcifications. Linear discriminant analysis and receiver operating characteristic (ROC) methodology were used to classify the benign and malignant microcalcifications. For detection of microcalcifications, the computer reached a true-positive (TP) rate of 100% at 0.1 false-positive (FP) clusters per image for obvious microcalcifications, a TP rate of 93% at 1 FP clusters per image for average subtle microcalcifications, and a TP rate of 87% at 1.5 FP clusters per image for very subtle microcalcifications. For classification of microcalcifications, preliminary results indicated that an area under the ROC curve (Az) of 0.91 and 0.89 could be achieved during training, and an Az of 0.82 and 0.87 during jackknife testing for obvious and subtle clusters, respectively. When all cases were combined, the Az was 0.87 and 0.84, respectively, for training and jackknife testing.

  17. Application of Spatial and Closed Capture-Recapture Models on Known Population of the Western Derby Eland (Taurotragus derbianus derbianus) in Senegal

    PubMed Central

    J?nek, Tomáš; J?nková Vymyslická, Pavla; Hozdecká, Kate?ina; Hejcmanová, Pavla

    2015-01-01

    Camera trapping with capture-recapture analyses has provided estimates of the abundances of elusive species over the last two decades. Closed capture-recapture models (CR) based on the recognition of individuals and incorporating natural heterogeneity in capture probabilities are considered robust tools; however, closure assumption is often questionable and the use of an Mh jackknife estimator may fail in estimations of real abundance when the heterogeneity is high and data is sparse. A novel, spatially explicit capture-recapture (SECR) approach based on the location-specific capture histories of individuals overcomes the limitations of closed models. We applied both methods on a closed population of 16 critically endangered Western Derby elands in the fenced 1,060-ha Fathala reserve, Senegal. We analyzed the data from 30 cameras operating during a 66-day sampling period deployed in two densities in grid and line arrays. We captured and identified all 16 individuals in 962 trap-days. Abundances were estimated in the programs CAPTURE (models M0, Mh and Mh Chao) and R, package secr (basic Null and Finite mixture models), and compared with the true population size. We specified 66 days as a threshold in which SECR provides an accurate estimate in all trapping designs within the 7-times divergent density from 0.004 to 0.028 camera trap/ha. Both SECR models showed uniform tendency to overestimate abundance when sampling lasted shorter with no major differences between their outputs. Unlike the closed models, SECR performed well in the line patterns, which indicates promising potential for linear sampling of properly defined habitats of non-territorial and identifiable herbivores in dense wooded savanna conditions. The CR models provided reliable estimates in the grid and we confirmed the advantage of Mh Chao estimator over Mh jackknife when data appeared sparse. We also demonstrated the pooling of trapping occasions with an increase in the capture probabilities, avoiding violation of results. PMID:26334997

  18. 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

  19. Would species richness estimators change the observed species area relationship?

    NASA Astrophysics Data System (ADS)

    Borges, Paulo A. V.; Hortal, Joaquín; Gabriel, Rosalina; Homem, Nídia

    2009-01-01

    We evaluate whether the description of the species area relationship (SAR) can be improved by using richness estimates instead of observed richness values. To do this, we use three independent datasets gathered with standardized survey methods from the native laurisilva forest of the Azorean archipelago, encompassing different distributional extent and biological groups: soil epigean arthropods at eight forest fragments in Terceira Island, canopy arthropods inhabiting Juniperus brevifolia at 16 forest fragments of six different islands, and bryophytes of seven forest fragments from Terceira and Pico islands. Species richness values were estimated for each forest fragment using seven non-parametric estimators (ACE, ICE, Chao1, Chao2, Jackknife1, Jackknife2 and Bootstrap; five in the case of bryophytes). These estimates were fitted to classical log-log species-area curves and the intercept, slope and goodness of fit of these curves were compared with those obtained from the observed species richness values to determine if significant differences appear in these parameters. We hypothesized that the intercepts would be higher in the estimated data sets compared with the observed data, as estimated richness values are typically higher than observed values. We found partial support for the hypothesis - intercepts of the SAR obtained from estimated richness values were significantly higher in the case of epigean arthropods and bryophyte datasets. In contrast, the slope and goodness of fit obtained with estimated values were not significantly different from those obtained from observed species richness in all groups, although a few small differences appeared. We conclude that, although little is gained using these estimators if data come from standardized surveys, their estimations could be used to analyze macroecological relationships with non-standardized observed data, provided that survey incompleteness and/or unevenness are also taken into account.

  20. 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.

  1. Absence of significant cross-correlation between WMAP and SDSS

    NASA Astrophysics Data System (ADS)

    López-Corredoira, M.; Sylos Labini, F.; Betancort-Rijo, J.

    2010-04-01

    Aims: Several authors have claimed to detect a significant cross-correlation between microwave WMAP anisotropies and the SDSS galaxy distribution. We repeat these analyses to determine the different cross-correlation uncertainties caused by re-sampling errors and field-to-field fluctuations. The first type of error concerns overlapping sky regions, while the second type concerns non-overlapping sky regions. Methods: To measure the re-sampling errors, we use bootstrap and jack-knife techniques. For the field-to-field fluctuations, we use three methods: 1) evaluation of the dispersion in the cross-correlation when correlating separated regions of WMAP with the original region of SDSS; 2) use of mock Monte Carlo WMAP maps; 3) a new method (developed in this article), which measures the error as a function of the integral of the product of the self-correlations for each map. Results: The average cross-correlation for b > 30 deg is significantly stronger than the re-sampling errors - both the jack-knife and bootstrap techniques provide similar results - but it is of the order of the field-to-field fluctuations. This is confirmed by the cross-correlation between anisotropies and galaxies in more than the half of the sample being null within re-sampling errors. Conclusions: Re-sampling methods underestimate the errors. Field-to-field fluctuations dominate the detected signals. The ratio of signal to re-sampling errors is larger than unity in a way that strongly depends on the selected sky region. We therefore conclude that there is no evidence yet of a significant detection of the integrated Sachs-Wolfe (ISW) effect. Hence, the value of ?_? ? 0.8 obtained by the authors who assumed they were observing the ISW effect would appear to have originated from noise analysis.

  2. Combined otolith morphology and morphometry for assessing taxonomy and diversity in fossil and extant killifish (Aphanius, Prolebias).

    PubMed

    Reichenbacher, Bettina; Sienknecht, Ulrike; Küchenhoff, Helmut; Fenske, Nora

    2007-10-01

    Systematic assignment of fossil otoliths is virtually always based on studies of otolith morphology and subsequent comparisons with otoliths from collections and/or literature. Although this usually represents a practical method, comparisons and subsequent evaluation may be biased by subjective criteria used in the individual descriptions. Quantitative morphometric studies focusing on variations in the otolith morphology of extant fishes have been conducted in fisheries research, mostly based on Fourier shape analysis and related methods. However, with regard to fossil otoliths, these approaches are generally not suitable, mainly due to preservation-related problems. Here we present a new approach for quantifying otolith variation between species and populations of killifish (cyprinodontiforms) in the genera Aphanius Nardo and daggerProlebias Sauvage that can be used with both extant and fossil otoliths. Our new approach includes the definition of 10 variables from linear and angle measurements of an otolith and statistical analyses. Best results were obtained by presorting the otoliths into three groups based on sulcus shape (straight, bent, S-shaped). In this case, canonical discriminant analysis (CDA) with jackknifed cross-validation yielded an overall species classification success of 86-96%. The three groups based on sulcus shape separate according to zoogeographic patterns (i.e., Mediterranean Aphanius, Arabian Aphanius, European daggerProlebias) and probably reflect phylogenetic lineages. Application of CDA to compare otolith variation between populations resulted in an overall classification success (jackknifed) of 33-83%. High levels of variation were observed for Aphanius dispar and daggerProlebias malzi, but not for A. fasciatus and daggerP. weileri. We suggest that otolith variation between populations results predominantly from geographic separation. Combination of qualitative characters (sulcus morphology) with quantitative approaches (otolith morphometry) presents a new approach for obtaining a better understanding of the taxonomy, diversity, and zoogeography of both fossil and extant killifishes. Moreover, the method may also be suitable for assessing taxonomy and diversity in other species-rich groups like the atheriniforms and many perciforms because these groups display otolith Bauplans that are similar to those seen in killifishes. PMID:17674357

  3. Spectral estimation for geophysical time-series with inconvenient gaps

    NASA Astrophysics Data System (ADS)

    Smith-Boughner, L. T.; Constable, C. G.

    2012-09-01

    The power of spectral estimation as a tool for studying geophysical processes is often limited by short records or breaks in available time-series. Direct spectral estimation using multitaper techniques designed to reduce variance and minimize leakage can help alleviate the first problem. For records with gaps, systematic interpolation or averaging of multitaper spectra derived from record fragments may prove adequate in some cases, but can be cumbersome to implement. Alternatively, multitapers can be modified for use in direct spectral estimation with intermittently sampled data. However, their performance has not been adequately studied. We investigate reliability and resolution of techniques that adapt prolate and minimum bias (MB) multitapers to accommodate the longest breaks in sampling, comparing the tapering functions (referred to as PRG or MBG tapers) with the standard prolate and MB tapers used for complete data series, and with the section-averaging approach. Using a synthetic data set, we test both jackknife and bootstrap methods to calculate confidence intervals for PRG and MBG multitaper spectral estimates and find the jackknife is both more accurate and faster to compute. To implement these techniques for a variety of data sets, we provide an algorithm that allows the user to balance judicious interpolation against the use of suitably adapted tapers, providing empirical measures of both bias and frequency resolution for candidate sets of tapers. These techniques are tested on diverse geophysical data sets: a record of change in the length of day, a model of the external dipole part of the geomagnetic field produced by the magnetospheric ring current, and a 12 Myr long irregularly sampled relative geomagnetic palaeointensity record with pernicious gaps. We conclude that both PRG and MBG tapers generally perform as well as, or better than, an optimized form of the commonly used section averaging approach. The greatest improvements seem to occur when the gap structure creates data segments of very unequal lengths. Ease of computation and more robust behaviour can make MBG tapers a better choice than PRG except when very fine-scale frequency resolution is required. These techniques could readily be applied for cross-spectral and transfer function estimation and are a useful addition to the geophysical toolbox.

  4. 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.

  5. Estimation of ROC curve with complex survey data.

    PubMed

    Yao, Wenliang; Li, Zhaohai; Graubard, Barry I

    2015-04-15

    The receiver operating characteristic (ROC) curve can be utilized to evaluate the performance of diagnostic tests. The area under the ROC curve (AUC) is a widely used summary index for comparing multiple ROC curves. Both parametric and nonparametric methods have been developed to estimate and compare the AUCs. However, these methods are usually only applicable to data collected from simple random samples and not surveys and epidemiologic studies that use complex sample designs such as stratified and/or multistage cluster sampling with sample weighting. Such complex samples can inflate variances from intra-cluster correlation and alter the expectations of test statistics because of the use of sample weights that account for differential sampling rates. In this paper, we modify the nonparametric method to incorporate sampling weights to estimate the AUC and employ leaving-one-out jackknife methods along with the balanced repeated replication method to account for the effects of the complex sampling in the variance estimation of our proposed estimators of the AUC. The finite sample properties of our methods are evaluated using simulations, and our methods are illustrated by comparing the estimated AUC for predicting overweight/obesity using different measures of body weight and adiposity among sampled children and adults in the US Hispanic Health and Nutrition Examination Survey. PMID:25546290

  6. Fusing face-verification algorithms and humans.

    PubMed

    O'Toole, Alice J; Abdi, Hervé; Jiang, Fang; Phillips, P Jonathon

    2007-10-01

    It has been demonstrated recently that state-of-the-art face-recognition algorithms can surpass human accuracy at matching faces over changes in illumination. The ranking of algorithms and humans by accuracy, however, does not provide information about whether algorithms and humans perform the task comparably or whether algorithms and humans can be fused to improve performance. In this paper, we fused humans and algorithms using partial least square regression (PLSR). In the first experiment, we applied PLSR to face-pair similarity scores generated by seven algorithms participating in the Face Recognition Grand Challenge. The PLSR produced an optimal weighting of the similarity scores, which we tested for generality with a jackknife procedure. Fusing the algorithms' similarity scores using the optimal weights produced a twofold reduction of error rate over the most accurate algorithm. Next, human-subject-generated similarity scores were added to the PLSR analysis. Fusing humans and algorithms increased the performance to near-perfect classification accuracy. These results are discussed in terms of maximizing face-verification accuracy with hybrid systems consisting of multiple algorithms and humans. PMID:17926698

  7. 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

  8. Additional Value of Diffusion-weighted MRI to Gd-EOB-DTPA-enhanced Hepatic MRI for the Detection of Liver Metastasis: the Difference Depending on the Experience of the Radiologists.

    PubMed

    Fukumoto, Wataru; Nakamura, Yuko; Higaki, Toru; Tatsugami, Fuminari; Iida, Makoto; Awai, Kazuo

    2015-06-01

    This retrospective study was to investigate whether adding diffusion-weighted imaging (DWI) to Gd-EOB-DTPA-enhanced MRI (EOB-MRI) improved the detection of liver metastasis in radiology resident and board-certified radiologist groups. It was approved by our institutional review board. We selected 18 patients with 35 liver metastases and 12 patients without liver tumors. Five board-certified radiologists and 5 radiology residents participated in the observer performance study. Each observer first interpreted T1- and T2-weighted-, plain-, arterial phase-, and hepatobiliary phase images and specified the location of the liver metastases. The software subsequently displayed the DWI images simultaneously and all participants repeated the reading. We used Jackknife alternative free-response receiver operating characteristic (JAFROC) analysis to compare the observer performance in detecting liver metastases. The mean values for the area under the curve (AUC) for EOB-MRI without and with DWI were 0.78 ± 0.13 [standard deviation: SD] and 0.87 ± 0.09, respectively, for the radiology residents, and the difference was statistically significant (p = 0.045). For the board- certified radiologists these values were 0.92 ± 0.02 and 0.96 ± 0.01, respectively, and the difference was not statistically significant (p = 0.092). EOB-MRI with DWI significantly improved the performance of radiology residents in the identification of liver metastases. PMID:26211220

  9. iTIS-PseKNC: Identification of Translation Initiation Site in human genes using pseudo k-tuple nucleotides composition.

    PubMed

    Kabir, Muhammad; Iqbal, Muhammad; Ahmad, Saeed; Hayat, Maqsood

    2015-11-01

    Translation is an essential genetic process for understanding the mechanism of gene expression. Due to the large number of protein sequences generated in the post-genomic era, conventional methods are unable to identify Translation Initiation Site (TIS) in human genes timely and accurately. It is thus highly desirable to develop an automatic and accurate computational model for identification of TIS. Considerable improvements have been achieved in developing computational models; however, development of accurate and reliable automated systems for TIS identification in human genes is still a challenging task. In this connection, we propose iTIS-PseKNC, a novel protocol for identification of TIS. Three protein sequence representation methods including dinucleotide composition, pseudo-dinucleotide composition and Trinucleotide composition have been used in order to extract numerical descriptors. Support Vector Machine (SVM), K-nearest neighbor and Probabilistic Neural Network are assessed for their performance using the constructed descriptors. The proposed model iTIS-PseKNC has achieved 99.40% accuracy using jackknife test. The experimental results validated the superior performance of iTIS-PseKNC over the existing methods reported in the literature. It is highly anticipated that the iTIS-PseKNC predictor will be useful for basic research studies. PMID:26433457

  10. The projack: a resampling approach to correct for ranking bias in high-throughput studies.

    PubMed

    Zhou, Yi-Hui; Wright, Fred A

    2016-01-01

    The problem of ranked inference arises in a number of settings, for which the investigator wishes to perform parameter inference after ordering a set of [Formula: see text] statistics. In contrast to inference for a single hypothesis, the ranking procedure introduces considerable bias, a problem known as the "winner's curse" in genetic association. We introduce the projack (for Prediction by Re- Ordered Jackknife and Cross-Validation, [Formula: see text]-fold). The projack is a resampling-based procedure that provides low-bias estimates of the expected ranked effect size parameter for a set of possibly correlated [Formula: see text] statistics. The approach is flexible, and has wide applicability to high-dimensional datasets, including those arising from genomics platforms. Initially, motivated for the setting where original data are available for resampling, the projack can be extended to the situation where only the vector of [Formula: see text] values is available. We illustrate the projack for correction of the winner's curse in genetic association, although it can be used much more generally. PMID:26040912

  11. [Comparison of detectability of liquid crystal displays (LCDs) and film using phantoms of small adenocarcinomas as abnormalities].

    PubMed

    Mochizuki, Yasuo; Abe, Shinji; Monma, Masahiko; Yamaguchi, Kojirou; Adachi, Toshiki

    2011-01-01

    Following the trend of the digitalization of the modalities used for diagnostic imaging, the devices for such imaging have increasingly included monitors. The present study was undertaken to evaluate the usefulness of soft-copy (liquid crystal display; LCD) images of phantoms of small adenocarcinomas using receiver operating characteristic (ROC) analysis of two different display systems: LCD and hard copy (film). A two-tailed paired t-test and the jackknife method (parametric methods) were performed, and no significant differences were found in the area under the ROC curve (AUC) for the pulmonary fields, lungs, ribs, or mediastinum between the film and LCD display systems, and the detectability did not differ between the film and LCD monitors. A Mann-Whitney U test, which is a non-parametric method that applies to the analysis of a small sample, also showed no significant differences in the AUC. The results of this study suggest that LCDs can replace hard-copy film as a display system if the signals. PMID:21532242

  12. 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.

  13. Swfoldrate: predicting protein folding rates from amino acid sequence with sliding window method.

    PubMed

    Cheng, Xiang; Xiao, Xuan; Wu, Zhi-cheng; Wang, Pu; Lin, Wei-zhong

    2013-01-01

    Protein folding is the process by which a protein processes from its denatured state to its specific biologically active conformation. Understanding the relationship between sequences and the folding rates of proteins remains an important challenge. Most previous methods of predicting protein folding rate require the tertiary structure of a protein as an input. In this study, the long-range and short-range contact in protein were used to derive extended version of the pseudo amino acid composition based on sliding window method. This method is capable of predicting the protein folding rates just from the amino acid sequence without the aid of any structural class information. We systematically studied the contributions of individual features to folding rate prediction. The optimal feature selection procedures are adopted by means of combining the forward feature selection and sequential backward selection method. Using the jackknife cross validation test, the method was demonstrated on the large dataset. The predictor was achieved on the basis of multitudinous physicochemical features and statistical features from protein using nonlinear support vector machine (SVM) regression model, the method obtained an excellent agreement between predicted and experimentally observed folding rates of proteins. The correlation coefficient is 0.9313 and the standard error is 2.2692. The prediction server is freely available at http://www.jci-bioinfo.cn/swfrate/input.jsp. PMID:22933332

  14. Predicting miRNA's target from primary structure by the nearest neighbor algorithm.

    PubMed

    Lin, Kao; Qian, Ziliang; Lu, Lin; Lu, Lingyi; Lai, Lihui; Gu, Jieyi; Zeng, Zhenbing; Li, Haipeng; Cai, Yudong

    2010-11-01

    We used a machine learning method, the nearest neighbor algorithm (NNA), to learn the relationship between miRNAs and their target proteins, generating a predictor which can then judge whether a new miRNA-target pair is true or not. We acquired 198 positive (true) miRNA-target pairs from Tarbase and the literature, and generated 4,888 negative (false) pairs through random combination. A 0/1 system and the frequencies of single nucleotides and di-nucleotides were used to encode miRNAs into vectors while various physicochemical parameters were used to encode the targets. The NNA was then applied, learning from these data to produce a predictor. We implemented minimum redundancy maximum relevance (mRMR) and properties forward selection (PFS) to reduce the redundancy of our encoding system, obtaining 91 most efficient properties. Finally, via the Jackknife cross-validation test, we got a positive accuracy of 69.2% and an overall accuracy of 96.0% with all the 253 properties. Besides, we got a positive accuracy of 83.8% and an overall accuracy of 97.2% with the 91 most efficient properties. A web-server for predictions is also made available at http://app3.biosino.org:8080/miRTP/index.jsp. PMID:20041294

  15. 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.

  16. Predicting cancerlectins by the optimal g-gap dipeptides

    PubMed Central

    Lin, Hao; Liu, Wei-Xin; He, Jiao; Liu, Xin-Hui; Ding, Hui; Chen, Wei

    2015-01-01

    The cancerlectin plays a key role in the process of tumor cell differentiation. Thus, to fully understand the function of cancerlectin is significant because it sheds light on the future direction for the cancer therapy. However, the traditional wet-experimental methods were money- and time-consuming. It is highly desirable to develop an effective and efficient computational tool to identify cancerlectins. In this study, we developed a sequence-based method to discriminate between cancerlectins and non-cancerlectins. The analysis of variance (ANOVA) was used to choose the optimal feature set derived from the g-gap dipeptide composition. The jackknife cross-validated results showed that the proposed method achieved the accuracy of 75.19%, which is superior to other published methods. For the convenience of other researchers, an online web-server CaLecPred was established and can be freely accessed from the website http://lin.uestc.edu.cn/server/CalecPred. We believe that the CaLecPred is a powerful tool to study cancerlectins and to guide the related experimental validations. PMID:26648527

  17. 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

  18. Separation of malignant and benign masses using maximum-likelihood modeling and neural networks

    NASA Astrophysics Data System (ADS)

    Kinnard, Lisa M.; Lo, Shih-Chung B.; Wang, Paul C.; Freedman, Matthew T.; Chouikha, Mohammed F.

    2002-05-01

    This study attempted to accurately segment the masses and distinguish malignant from benign tumors. The masses were segmented using a technique that combines pixel aggregation with maximum likelihood analysis. We found that the segmentation method can delineate the tumor body as well as tumor peripheral regions covering typical mass boundaries and some spiculation patterns. We have developed a Multiple Circular Path Convolution Neural Network (MCPCNN) to analyze a set of mass intensity, shape, and texture features for determination of the tumors as malignant or benign. The features were also fed into a conventional neural network for comparison. We also used values obtained from the maximum likelihood values as inputs into a conventional backpropagation neural network. We have tested these methods on 51 mammograms using a grouped Jackknife experiment incorporated with the ROC method. Tumor sizes ranged from 6mm to 3cm. The conventional neural network whose inputs were image features achieved an Az of 0.66. However the MCPCNN achieved an Az value of 0.71. The conventional neural network whose inputs were maximum likelihood values achieved an Az value of 0.84. In addition, the maximum likelihood segmentation method can identify the mass body and boundary regions, which is essential to the analysis of mammographic masses.

  19. A gene expression pattern in blood for the early detection of Alzheimer's disease.

    PubMed

    Booij, Birgitte Boonstra; Lindahl, Torbjørn; Wetterberg, Peter; Skaane, Nina Voss; Sæbø, Solve; Feten, Guri; Rye, Phil D; Kristiansen, Lena Iren; Hagen, Nina; Jensen, Marianne; Bårdsen, Ken; Winblad, Bengt; Sharma, Praveen; Lönneborg, Anders

    2011-01-01

    A whole genome screen was performed using oligonucleotide microarray analysis on blood from a large clinical cohort of Alzheimer's disease (AD) patients and control subjects as clinical sample. Blood samples for total RNA extraction were collected in PAXgene tubes, and gene expression analysis performed on the AB1700 Whole Genome Survey Microarrays. When comparing the gene expression of 94 AD patients and 94 cognitive healthy controls, a Jackknife gene selection based method and Partial Least Square Regression (PLSR) was used to develop a disease classifier algorithm, which gives a test score indicating the presence (positive) or absence (negative) of AD. This algorithm, based on 1239 probes, was validated in an independent test set of 63 subjects comprising 31 AD patients, 25 age-matched cognitively healthy controls, and 7 young controls. This algorithm correctly predicted the class of 55/63 (accuracy 87%), including 26/31 AD samples (sensitivity 84%) and 29/32 controls (specificity 91%). The positive likelihood ratio was 8.9 and the area under the receiver operating characteristic curve (ROC AUC) was 0.94. Furthermore, the algorithm also discriminated AD from Parkinson's disease in 24/27 patients (accuracy 89%). We have identified and validated a gene expression signature in blood that classifies AD patients and cognitively healthy controls with high accuracy and show that alterations specific for AD can be detected distant from the primary site of the disease. PMID:20930264

  20. 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.

  1. Computer aided morphometry of the neonatal fetal alcohol syndrome face

    NASA Astrophysics Data System (ADS)

    Chik, Lawrence; Sokol, Robert J.; Martier, Susan S.

    1993-09-01

    Facial dysmorphology related to Fetal Alcohol Syndrome (FAS) has been studied from neonatal snapshots with computer-aided imaging tools by looking at facial landmarks and silhouettes. Statistical methods were used to characterize FAS-related midfacial hypoplasia by using standardized landmark coordinates of frontal and profile snapshots. Additional analyses were performed by tracing a segment of the facial silhouettes from the profile snapshots. In spite of inherent distortions due to the coordinate standardization procedure, controlled for race, three significant facial landmark coordinates accounted for 30.6% of the explained variance of FAS. Residualized for race, eight points along the silhouettes were shown to be significant in explaining 45.8% of the outcome variance. Combining the landmark coordinates and silhouettes points, 57% of the outcome variance was explained. Finally, including birthweight with landmark coordinates and silhouettes, 63% of the outcome variance was explained, with a jackknifed sensitivity of 95% (19/20) and a specificity of 92.9% (52/56).

  2. Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plants.

    PubMed Central

    McCauley, D E

    1994-01-01

    The distribution of chloroplast DNA (cp-DNA) length variants was analyzed within and among 10 local populations of Silene alba, a dioecious angiosperm. The populations displayed considerable allele frequency variation, resulting in an estimate of Wright's Fst of 0.67 over a 25 x 25 km portion of the species' range. By contrast, a concurrent analysis of the genetic structure of these same populations based on seven polymorphic allozyme loci yielded an estimate of Fst of 0.13. The two Fst estimates are significantly different from one another when their respective confidence limits are estimated by jackknifing. The results of a breeding study were consistent with maternal inheritance of the cpDNA variants. With maternal inheritance the genetic structure of the cpDNA should reflect seed movement, whereas the genetic structure of the nuclear-encoded allozyme loci should reflect the movement of both seeds and pollen. Comparison of the two markedly different Fst estimates in the context of recent models of the population genetics of organelles suggests that the movement of both seeds and pollen contributes significantly to gene flow. Images PMID:11607493

  3. 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

    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.

  4. Newest mobile drilling rig

    SciTech Connect

    Not Available

    1981-01-01

    The weighing half of what a standard jackknife rig with the same drilling capacities weights this rig cuts transportation costs while reducing transportation time. Also, rig-up and rig-down time is shortened half-a-day each way because of the light structure and the ability to hydraulically raise and lower the substructure and mast. It is powered by three Caterpillar 3412 diesel engines - 600 hp each at 1,800 rpm - delivering 1,500 hp to the drawworks through single-stage torque converters. Chain-type drawworks, set on the trailer flatbed next to the diesel engines instead of on the rig floor, consist of a 25-in. diam by 50-in.-long drum barrel, 50-in. diam by 12-in.-wide brakes, and 1/one quarter/-in. line, capable of a 75,000-lb single line pull. The mast - a 127-ft API-rated, vertical freestanding, telescoping type - is extended and telescoped in the horizontal position before being hydraulically raised. Gross nominal capacity of the mast is 1 million lb, with a rotary load of 715,000 lb and a setback load of 400,000 lb.

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

    SciTech Connect

    Cherian, Betsy Sheena; Nair, Achuthsankar S.

    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.

  6. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  7. Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis.

    PubMed

    Ding, Hui; Feng, Peng-Mian; Chen, Wei; Lin, Hao

    2014-08-01

    The bacteriophage virion proteins play extremely important roles in the fate of host bacterial cells. Accurate identification of bacteriophage virion proteins is very important for understanding their functions and clarifying the lysis mechanism of bacterial cells. In this study, a new sequence-based method was developed to identify phage virion proteins. In the new method, the protein sequences were initially formulated by the g-gap dipeptide compositions. Subsequently, the analysis of variance (ANOVA) with incremental feature selection (IFS) was used to search for the optimal feature set. It was observed that, in jackknife cross-validation, the optimal feature set including 160 optimized features can produce the maximum accuracy of 85.02%. By performing feature analysis, we found that the correlation between two amino acids with one gap was more important than other correlations for phage virion protein prediction and that some of the 1-gap dipeptides were important and mainly contributed to the virion protein prediction. This analysis will provide novel insights into the function of phage virion proteins. On the basis of the proposed method, an online web-server, PVPred, was established and can be freely accessed from the website (http://lin.uestc.edu.cn/server/PVPred). We believe that the PVPred will become a powerful tool to study phage virion proteins and to guide the related experimental validations. PMID:24931825

  8. Cosmic Shear Measurements with DES Science Verification Data

    SciTech Connect

    Becker, M. R.

    2015-07-20

    We present measurements of weak gravitational lensing cosmic shear two-point statistics using Dark Energy Survey Science Verification data. We demonstrate that our results are robust to the choice of shear measurement pipeline, either ngmix or im3shape, and robust to the choice of two-point statistic, including both real and Fourier-space statistics. Our results pass a suite of null tests including tests for B-mode contamination and direct tests for any dependence of the two-point functions on a set of 16 observing conditions and galaxy properties, such as seeing, airmass, galaxy color, galaxy magnitude, etc. We use a large suite of simulations to compute the covariance matrix of the cosmic shear measurements and assign statistical significance to our null tests. We find that our covariance matrix is consistent with the halo model prediction, indicating that it has the appropriate level of halo sample variance. We also compare the same jackknife procedure applied to the data and the simulations in order to search for additional sources of noise not captured by the simulations. We find no statistically significant extra sources of noise in the data. The overall detection significance with tomography for our highest source density catalog is 9.7?. Cosmological constraints from the measurements in this work are presented in a companion paper (DES et al. 2015).

  9. BICEP2/Keck Array V: Measurements of B-mode Polarization at Degree Angular Scales and 150 GHz by the Keck Array

    NASA Astrophysics Data System (ADS)

    BICEP2 and Keck Array Collaborations; Ade, P. A. R.; Ahmed, Z.; Aikin, R. W.; Alexander, K. D.; Barkats, D.; Benton, S. J.; Bischoff, C. A.; Bock, J. J.; Brevik, J. A.; Buder, I.; Bullock, E.; Buza, V.; Connors, J.; Crill, B. P.; Dowell, C. D.; Dvorkin, C.; Duband, L.; Filippini, J. P.; Fliescher, S.; Golwala, S. R.; Halpern, M.; Harrison, S.; Hasselfield, M.; Hildebrandt, S. R.; Hilton, G. C.; Hristov, V. V.; Hui, H.; Irwin, K. D.; Karkare, K. S.; Kaufman, J. P.; Keating, B. G.; Kefeli, S.; Kernasovskiy, S. A.; Kovac, J. M.; Kuo, C. L.; Leitch, E. M.; Lueker, M.; Mason, P.; Megerian, K. G.; Netterfield, C. B.; Nguyen, H. T.; O'Brient, R.; Ogburn, R. W., IV; Orlando, A.; Pryke, C.; Reintsema, C. D.; Richter, S.; Schwarz, R.; Sheehy, C. D.; Staniszewski, Z. K.; Sudiwala, R. V.; Teply, G. P.; Thompson, K. L.; Tolan, J. E.; Turner, A. D.; Vieregg, A. G.; Weber, A. C.; Willmert, J.; Wong, C. L.; Yoon, K. W.

    2015-10-01

    The Keck Array is a system of cosmic microwave background polarimeters, each similar to the Bicep2 experiment. In this paper we report results from the 2012 to 2013 observing seasons, during which the Keck Array consisted of five receivers all operating in the same (150 GHz) frequency band and observing field as Bicep2. We again find an excess of B-mode power over the lensed-?CDM expectation of >5? in the range 30 < ? < 150 and confirm that this is not due to systematics using jackknife tests and simulations based on detailed calibration measurements. In map difference and spectral difference tests these new data are shown to be consistent with Bicep2. Finally, we combine the maps from the two experiments to produce final Q and U maps which have a depth of 57 nK deg (3.4 ?K arcmin) over an effective area of 400 deg2 for an equivalent survey weight of 250,000 ?K-2. The final BB band powers have noise uncertainty a factor of 2.3 times better than the previous results, and a significance of detection of excess power of >6?.

  10. The prediction of protein structural class using averaged chemical shifts.

    PubMed

    Lin, Hao; Ding, Chen; Song, Qiang; Yang, Ping; Ding, Hui; Deng, Ke-Jun; Chen, Wei

    2012-01-01

    Knowledge of protein structural class can provide important information about its folding patterns. Many approaches have been developed for the prediction of protein structural classes. However, the information used by these approaches is primarily based on amino acid sequences. In this study, a novel method is presented to predict protein structural classes by use of chemical shift (CS) information derived from nuclear magnetic resonance spectra. Firstly, 399 non-homologue (about 15% identity) proteins were constructed to investigate the distribution of averaged CS values of six nuclei ((13)CO, (13)C?, (13)C?, (1)HN, (1)H? and (15)N) in three protein structural classes. Subsequently, support vector machine was proposed to predict three protein structural classes by using averaged CS information of six nuclei. Overall accuracy of jackknife cross-validation achieves 87.0%. Finally, the feature selection technique is applied to exclude redundant information and find out an optimized feature set. Results show that the overall accuracy increased to 88.0% by using the averaged CSs of (13)CO, (1)H? and (15)N. The proposed approach outperformed other state-of-the-art methods in terms of predictive accuracy in particular for low-similarity protein data. We expect that our proposed approach will be an excellent alternative to traditional methods for protein structural class prediction. PMID:22545995

  11. Hypothesis tests for hydrologic alteration

    NASA Astrophysics Data System (ADS)

    Kroll, Charles N.; Croteau, Kelly E.; Vogel, Richard M.

    2015-11-01

    Hydrologic systems can be altered by anthropogenic and climatic influences. While there are a number of statistical frameworks for describing and evaluating the extent of hydrologic alteration, here we present a new framework for assessing whether statistically significant hydrologic alteration has occurred, or whether the shift in the hydrologic regime is consistent with the natural variability of the system. Four hypothesis tests based on shifts of flow duration curves (FDCs) are developed and tested using three different experimental designs based on different strategies for resampling of annual FDCs. The four hypothesis tests examined are the Kolmogorov-Smirnov (KS), Kuiper (K), confidence interval (CI), and ecosurplus and ecodeficit (Eco). Here 117 streamflow sites that have potentially undergone hydrologic alteration due to reservoir construction are examined. 20 years of pre-reservoir record is used to develop the critical value of the test statistic for type I errors of 5% and 10%, while 10 years of post-alteration record is used to examine the power of each test. The best experimental design, based on calculating the mean annual FDC from an exhaustive jackknife resampling regime, provided a larger number of unique values of each test statistic and properly reproduced type I errors. Of the four tests, the CI test consistently had the highest power, while the K test had the second highest power; KS and Eco always had the lowest power. The power of the CI test appeared related to the storage ratio of the reservoir, a rough measure of the hydrologic alteration of the system.

  12. Predicting cancerlectins by the optimal g-gap dipeptides.

    PubMed

    Lin, Hao; Liu, Wei-Xin; He, Jiao; Liu, Xin-Hui; Ding, Hui; Chen, Wei

    2015-01-01

    The cancerlectin plays a key role in the process of tumor cell differentiation. Thus, to fully understand the function of cancerlectin is significant because it sheds light on the future direction for the cancer therapy. However, the traditional wet-experimental methods were money- and time-consuming. It is highly desirable to develop an effective and efficient computational tool to identify cancerlectins. In this study, we developed a sequence-based method to discriminate between cancerlectins and non-cancerlectins. The analysis of variance (ANOVA) was used to choose the optimal feature set derived from the g-gap dipeptide composition. The jackknife cross-validated results showed that the proposed method achieved the accuracy of 75.19%, which is superior to other published methods. For the convenience of other researchers, an online web-server CaLecPred was established and can be freely accessed from the website http://lin.uestc.edu.cn/server/CalecPred. We believe that the CaLecPred is a powerful tool to study cancerlectins and to guide the related experimental validations. PMID:26648527

  13. Driver Assistance System for Passive Multi-Trailer Vehicles with Haptic Steering Limitations on the Leading Unit

    PubMed Central

    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

  14. Identifying the Subfamilies of Voltage-Gated Potassium Channels Using Feature Selection Technique

    PubMed Central

    Liu, Wei-Xin; Deng, En-Ze; Chen, Wei; Lin, Hao

    2014-01-01

    Voltage-gated K+ channel (VKC) plays important roles in biology procession, especially in nervous system. Different subfamilies of VKCs have different biological functions. Thus, knowing VKCs’ subfamilies has become a meaningful job because it can guide the direction for the disease diagnosis and drug design. However, the traditional wet-experimental methods were costly and time-consuming. It is highly desirable to develop an effective and powerful computational tool for identifying different subfamilies of VKCs. In this study, a predictor, called iVKC-OTC, has been developed by incorporating the optimized tripeptide composition (OTC) generated by feature selection technique into the general form of pseudo-amino acid composition to identify six subfamilies of VKCs. One of the remarkable advantages of introducing the optimized tripeptide composition is being able to avoid the notorious dimension disaster or over fitting problems in statistical predictions. It was observed on a benchmark dataset, by using a jackknife test, that the overall accuracy achieved by iVKC-OTC reaches to 96.77% in identifying the six subfamilies of VKCs, indicating that the new predictor is promising or at least may become a complementary tool to the existing methods in this area. It has not escaped our notice that the optimized tripeptide composition can also be used to investigate other protein classification problems. PMID:25054318

  15. Prediction of Protein Structural Class Based on Gapped-Dipeptides and a Recursive Feature Selection Approach.

    PubMed

    Liu, Taigang; Qin, Yufang; Wang, Yongjie; Wang, Chunhua

    2015-01-01

    The prior knowledge of protein structural class may offer useful clues on understanding its functionality as well as its tertiary structure. Though various significant efforts have been made to find a fast and effective computational approach to address this problem, it is still a challenging topic in the field of bioinformatics. The position-specific score matrix (PSSM) profile has been shown to provide a useful source of information for improving the prediction performance of protein structural class. However, this information has not been adequately explored. To this end, in this study, we present a feature extraction technique which is based on gapped-dipeptides composition computed directly from PSSM. Then, a careful feature selection technique is performed based on support vector machine-recursive feature elimination (SVM-RFE). These optimal features are selected to construct a final predictor. The results of jackknife tests on four working datasets show that our method obtains satisfactory prediction accuracies by extracting features solely based on PSSM and could serve as a very promising tool to predict protein structural class. PMID:26712737

  16. Control System Design of Multitrailer Using Neurocontrollers with Recessive Gene Structure by Step-up GA Training

    NASA Astrophysics Data System (ADS)

    Kiyuna, Ayaki; Kinjo, Hiroshi; Kurata, Koji; Yamamoto, Tetsuhiko

    In a previous study, we proposed a step-up training method for the multitrailer truck control system using neurocontrollers (NCs) evolved by a genetic algorithm (GA) and showed its efficiency. However, the method does not enable the training of NCs for a five-trailer connected truck system. In this paper, we present a new version of the step-up training method that enables the training of NCs for a five-trailer connected truck system. The proposed method is as follows: First, NCs are trained only to avoid the “jackknife phenomenon". Second, NCs are trained for minimizing squared errors starting from easy initial configurations. Finally, NCs are trained for minimizing the squared errors starting from more difficult initial configurations. The difficulty of training steps increases gradually. To improve training performance, we applied a recessive gene model to network weight coding and genetic operations. In this study, we applied the recessive gene model to the classic exclusive-or (XOR) training problem and showed its convergence performance. The GA training of NCs with the recessive gene model maintains diversity in the population and avoids evolutionary stagnation. Simulation shows that NCs with the recessive gene model and the proposed step-up training method are useful in the controller design of the multitrailer system.

  17. OligoPred: a web-server for predicting homo-oligomeric proteins by incorporating discrete wavelet transform into Chou's pseudo amino acid composition.

    PubMed

    Qiu, Jian-Ding; Suo, Sheng-Bao; Sun, Xing-Yu; Shi, Shao-Ping; Liang, Ru-Ping

    2011-09-01

    In vivo, some proteins exist as monomers (single polypeptide chains) and others as oligomers. Not like monomers, oligomers are composed of two or more chains (subunits) that are associated with each other through non-covalent interactions and, occasionally, through disulfide bonds. These proteins are the structural components of various biological functions, including cooperative effects, allosteric mechanisms and ion-channel gating. However, with the dramatic increase in the number of protein sequences submitted to the public data bank, it is important for both basic research and drug discovery research to acquire the possible knowledge about homo-oligomeric attributes of their interested proteins in a timely manner. In this paper, a high-throughput method, combined support vector machines with discrete wavelet transform, has been developed to predict the protein homo-oligomers. The total accuracy obtained by the re-substitution test, jackknife test and independent dataset test are 99.94%, 96.17% and 96.18%, respectively, showing that the proposed method of extracting feature from the protein sequences is effective and feasible for predicting homo-oligomers. The online service is available at http://bioinfo.ncu.edu.cn/Services.aspx. PMID:21802968

  18. CUPSAT: prediction of protein stability upon point mutations.

    PubMed

    Parthiban, Vijaya; Gromiha, M Michael; Schomburg, Dietmar

    2006-07-01

    CUPSAT (Cologne University Protein Stability Analysis Tool) is a web tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations). This program uses structural environment specific atom potentials and torsion angle potentials to predict DeltaDeltaG, the difference in free energy of unfolding between wild-type and mutant proteins. It requires the protein structure in Protein Data Bank format and the location of the residue to be mutated. The output consists information about mutation site, its structural features (solvent accessibility, secondary structure and torsion angles), and comprehensive information about changes in protein stability for 19 possible substitutions of a specific amino acid mutation. Additionally, it also analyses the ability of the mutated amino acids to adapt the observed torsion angles. Results were tested on 1538 mutations from thermal denaturation and 1603 mutations from chemical denaturation experiments. Several validation tests (split-sample, jack-knife and k-fold) were carried out to ensure the reliability, accuracy and transferability of the prediction method that gives >80% prediction accuracy for most of these validation tests. Thus, the program serves as a valuable tool for the analysis of protein design and stability. The tool is accessible from the link http://cupsat.uni-koeln.de. PMID:16845001

  19. Charmed and strange pseudoscalar meson decay constants from HISQ simulations

    NASA Astrophysics Data System (ADS)

    Bazavov, A.; Bernard, C.; Bouchard, C.; DeTar, C.; Du, D.; El-Khadra, A.; Foley, J.; Freeland, E.; Gamiz, E.; Gottlieb, S.; Heller, U. M.; Kim, J.; Komijani, J.; Kronfeld, A.; Laiho, J.; Levkova, L.; Mackenzie, P. B.; Neil, E.; Simone, J.; Sugar, R.; Toussaint, D.; Van de Water, R. S.; Zhou, R.

    We update our determinations of $f_{D^+}$, $f_{D_s}$, $f_K$, and quark mass ratios from simulations with four flavors of HISQ dynamical quarks. The availability of ensembles with light quarks near their physical mass means that we can extract physical results with only small corrections for valence- and sea-quark mass mistunings instead of a chiral extrapolation. The adjusted valence-quark masses and lattice spacings may be determined from an ensemble-by-ensemble analysis, and the results for the quark mass ratios then extrapolated to the continuum limit. Our central values of the charmed meson decay constants, however, come from an alternative analysis, which uses staggered chiral perturbation theory for the heavy-light mesons, and allows us to incorporate data at unphysical quark masses where statistical errors are often smaller. A jackknife analysis propagated through all of these steps takes account of the correlations among all the quantities used in the analysis. Systematic errors from the finite spatial size and EM effects are estimated by varying the parameters in the analysis, and systematic errors from the assumptions in the continuum extrapolation are estimated from the spread of values from different extrapolations.

  20. 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

  1. Protein submitochondrial localization from integrated sequence representation and SVM-based backward feature extraction.

    PubMed

    Li, Liqi; Yu, Sanjiu; Xiao, Weidong; Li, Yongsheng; Hu, Wenjuan; Huang, Lan; Zheng, Xiaoqi; Zhou, Shiwen; Yang, Hua

    2015-01-01

    Mitochondrion, a tiny energy factory, plays an important role in various biological processes of most eukaryotic cells. Mitochondrial defection is associated with a series of human diseases. Knowledge of the submitochondrial locations of proteins can help to reveal the biological functions of novel proteins, and understand the mechanisms underlying various biological processes occurring in the mitochondrion. However, experimental methods to determine protein submitochondrial locations are costly and time consuming. Thus it is essential to develop a fast and reliable computational method to predict protein submitochondrial locations. Here, we proposed a support vector machine (SVM) based approach for predicting protein submitochondrial locations. Information from the position-specific score matrix (PSSM), gene ontology (GO) and the protein feature (PROFEAT) was integrated into the principal features of this model. Then a recursive feature selection scheme was employed to select the optimal features. Finally, an SVM module was used to predict protein submitochondrial locations based on the optimal features. Through the jackknife cross-validation test, our method achieved an accuracy of 99.37% on benchmark dataset M317, and 100% on the other two datasets, M1105 and T86. These results indicate that our method is economic and effective for accurate prediction of the protein submitochondrial location. PMID:25335193

  2. Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

    PubMed Central

    Yang, Ya; Smith, Stephen A.

    2014-01-01

    Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction. PMID:25158799

  3. [Composition of the Araneae (Arachnida) fauna of the provincial Iberá Reserve, Corrientes, Argentina].

    PubMed

    Avalos, Gilberto; Damborsky, Miryam P; Bar, María E; Oscherov, Elena B; Porcel, E

    2009-01-01

    A survey of the spider community composition and diversity was carried out in grasslands and woods in three localities: Colonia Pellegrini, Paraje Galarza and Estancia Rinc6n (Iberá province Reserve). Pit fall traps, leaf litter sifting, foliage beating, hand collecting and sweep nets were used. Shannon's diversity index, evenness, Berger-Parker's dominance index, beta and gamma diversity were calculated, and a checklist of spider fauna was compiled. Species richness was estimated by Chao 1, Chao 2, first and second order Jack-knife. A total of 4,138 spiders grouped into 150 species from 33 families of Araneomorphae and two species from two families of Mygalomorphae were collected. Five species are new records for Argentina and eleven for Corrientes province. Araneidae was the most abundant family (39.8%), followed by Salticidae (10.9%), Anyphaenidae (7.9%), Tetragnathidae (7.4%), and Lycosidae (5.5%). The other families represented less than 5% of the total catch. The web-builder guild had the highest number of specimens and the highest richness index. The abundance, observed richness, Shannon diversity and evenness indexes were highest in Colonia Pellegrini woodland and Paraje Galarza grassland. Alpha diversity represented 89% of the gamma; the remaining 11% corresponded to beta diversity. According to the indexes, between 67% and 97% of the existing spider fauna was represented in the collected specimens from Iberá. PMID:19637711

  4. iCataly-PseAAC: Identification of Enzymes Catalytic Sites Using Sequence Evolution Information with Grey Model GM (2,1).

    PubMed

    Xiao, Xuan; Hui, Meng-Juan; Liu, Zi; Qiu, Wang-Ren

    2015-12-01

    Enzymes play pivotal roles in most of the biological reaction. The catalytic residues of an enzyme are defined as the amino acids which are directly involved in chemical catalysis; the knowledge of these residues is important for understanding enzyme function. Given an enzyme, which residues are the catalytic sites, and which residues are not? This is the first important problem for in-depth understanding the catalytic mechanism and drug development. With the explosive of protein sequences generated during the post-genomic era, it is highly desirable for both basic research and drug design to develop fast and reliable method for identifying the catalytic sites of enzymes according to their sequences. To address this problem, we proposed a new predictor, called iCataly-PseAAC. In the prediction system, the peptide sample was formulated with sequence evolution information via grey system model GM(2,1). It was observed by the rigorous jackknife test and independent dataset test that iCataly-PseAAC was superior to exist predictions though its only use sequence information. As a user-friendly web server, iCataly-PseAAC is freely accessible at http://www.jci-bioinfo.cn/iCataly-PseAAC . A step-by-step guide has been provided on how to use the web server to get the desired results for the convenience of most experimental scientists. PMID:26077845

  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. Patterns of connectivity among populations of a coral reef fish

    NASA Astrophysics Data System (ADS)

    Chittaro, P. M.; Hogan, J. D.

    2013-06-01

    Knowledge of the patterns and scale of connectivity among populations is essential for the effective management of species, but our understanding is still poor for marine species. We used otolith microchemistry of newly settled bicolor damselfish ( Stegastes partitus) in the Mesoamerican Reef System (MRS), Western Caribbean, to investigate patterns of connectivity among populations over 2 years. First, we assessed spatial and temporal variability in trace elemental concentrations from the otolith edge to make a `chemical map' of potential source reef(s) in the region. Significant otolith chemical differences were detected at three spatial scales (within-atoll, between-atolls, and region-wide), such that individuals were classified to locations with moderate (52 % jackknife classification) to high (99 %) accuracy. Most sites at Turneffe Atoll, Belize showed significant temporal variability in otolith concentrations on the scale of 1-2 months. Using a maximum likelihood approach, we estimated the natal source of larvae recruiting to reefs across the MRS by comparing `natal' chemical signatures from the otolith of recruits to the `chemical map' of potential source reef(s). Our results indicated that populations at both Turneffe Atoll and Banco Chinchorro supply a substantial amount of individuals to their own reefs (i.e., self-recruitment) and thus emphasize that marine conservation and management in the MRS region would benefit from localized management efforts as well as international cooperation.

  7. On the value of nuclear and mitochondrial gene sequences for reconstructing the phylogeny of vanilloid orchids (Vanilloideae, Orchidaceae)

    PubMed Central

    Cameron, Kenneth M.

    2009-01-01

    Background and Aims Most molecular phylogenetic studies of Orchidaceae have relied heavily on DNA sequences from the plastid genome. Nuclear and mitochondrial loci have only been superficially examined for their systematic value. Since 40% of the genera within Vanilloideae are achlorophyllous mycoheterotrophs, this is an ideal group of orchids in which to evaluate non-plastid gene sequences. Methods Phylogenetic reconstructions for Vanilloideae were produced using independent and combined data from the nuclear 18S, 5·8S and 26S rDNA genes and the mitochondrial atpA gene and nad1b-c intron. Key Results These new data indicate placements for genera such as Lecanorchis and Galeola, for which plastid gene sequences have been mostly unavailable. Nuclear and mitochondrial parsimony jackknife trees are congruent with each other and previously published trees based solely on plastid data. Because of high rates of sequence divergence among vanilloid orchids, even the short 5·8S rDNA gene provides impressive levels of resolution and support. Conclusions Orchid systematists are encouraged to sequence nuclear and mitochondrial gene regions along with the growing number of plastid loci available. PMID:19251715

  8. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska

    PubMed Central

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-01-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0–10 cm to 10–20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen ( and ). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. PMID:24893754

  9. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    PubMed

    Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  10. 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

  11. 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

  12. 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.

  13. iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition.

    PubMed

    Zuo, Yongchun; Lv, Yang; Wei, Zhuying; Yang, Lei; Li, Guangpeng; Fan, Guoliang

    2015-01-01

    Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design. PMID:26713618

  14. Nonparametric methods for drought severity estimation at ungauged sites

    NASA Astrophysics Data System (ADS)

    Sadri, S.; Burn, D. H.

    2012-12-01

    The objective in frequency analysis is, given extreme events such as drought severity or duration, to estimate the relationship between that event and the associated return periods at a catchment. Neural networks and other artificial intelligence approaches in function estimation and regression analysis are relatively new techniques in engineering, providing an attractive alternative to traditional statistical models. There are, however, few applications of neural networks and support vector machines in the area of severity quantile estimation for drought frequency analysis. In this paper, we compare three methods for this task: multiple linear regression, radial basis function neural networks, and least squares support vector regression (LS-SVR). The area selected for this study includes 32 catchments in the Canadian Prairies. From each catchment drought severities are extracted and fitted to a Pearson type III distribution, which act as observed values. For each method-duration pair, we use a jackknife algorithm to produce estimated values at each site. The results from these three approaches are compared and analyzed, and it is found that LS-SVR provides the best quantile estimates and extrapolating capacity.

  15. Limited sampling hampers "big data" estimation of species richness in a tropical biodiversity hotspot.

    PubMed

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

    2015-02-01

    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

  16. 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

  17. Effect of CAD on radiologists' detection of lung nodules on thoracic CT scans: observer performance study

    NASA Astrophysics Data System (ADS)

    Sahiner, Berkman; Hadjiiski, Lubomir M.; Chan, Heang-Ping; Shi, Jiazheng; Cascade, Philip N.; Kazerooni, Ella A.; Zhou, Chuan; Wei, Jun; Chughtai, Aamer R.; Poopat, Chad; Song, Thomas; Nojkova, Jadranka S.; Frank, Luba; Attili, Anil

    2007-03-01

    The purpose of this study was to evaluate the effect of computer-aided diagnosis (CAD) on radiologists' performance for the detection of lung nodules on thoracic CT scans. Our computer system was designed using an independent training set of 94 CT scans in our laboratory. The data set for the observer performance study consisted of 48 CT scans. Twenty scans were collected from patient files at the University of Michigan, and 28 scans by the Lung Imaging Database Consortium (LIDC). All scans were read by multiple experienced thoracic radiologists to determine the true nodule locations, defined as any region identified by one or more expert radiologists as containing a nodule larger than 3 mm in diameter. Eighteen CT examinations were nodule-free, while the remaining 30 CT examinations contained a total of 73 nodules having a median size of 5.5 mm (range 3.0-36.4 mm). Four other study radiologists read the CT scans first without and then with CAD, and provided likelihood of nodule ratings for suspicious regions. Two of the study radiologists were fellowship trained in cardiothoracic radiology, and two were cardiothoracic radiology fellows. Freeresponse receiver-operating characteristic (FROC) curves were used to compare the two reading conditions. The computer system had a sensitivity of 79% (58/73) with an average of 4.9 marks per normal scan (88/18). Jackknife alternative FROC (JAFROC) analysis indicated that the improvement with CAD was statistically significant (p=0.03).

  18. An elusive search for regional flood frequency estimates in the River Nile basin

    NASA Astrophysics Data System (ADS)

    Nyeko-Ogiramoi, P.; Willems, P.; Mutua, F. M.; Moges, S. A.

    2012-03-01

    Estimation of peak flow quantiles in ungauged catchments is a challenge often faced by water professionals in many parts of the world. Approaches to address such problem exist but widely used technique such as flood frequency regionalization is often not subjected to performance evaluation. In this study we used the jack-knifing principle to assess the performance of the flood frequency regionalization in the complex and data scarce River Nile basin by examining the error (regionalization error) between locally and regionally estimated peak flow quantiles for different return periods (QT). Agglomerative hierarchical clustering based algorithms were used to search for regions with similar hydrological characteristics taking into account the huge catchment area and strong climatic differences across the area. Hydrological data sets employed were from 180 gauged catchments and several physical characteristics in order to regionalize 365 identified catchments. The GEV distribution, selected using L-moment based approach, was used to construct regional growth curves from which peak flow growth factors (QT/MAF) could be derived and mapped through interpolation. Inside each region, variations in at-site flood frequency distribution were modeled by regression of the mean annual maximum peak flow (MAF) versus catchment area. The results show that the performance of the regionalization is heavily dependent on the historical flow record length and the similarity of the hydrological characteristics inside the regions. The flood frequency regionalization of the River Nile basin can be improved if sufficient flow data of longer record length × 40 become available.

  19. An elusive search for regional flood frequency estimates in the River Nile basin

    NASA Astrophysics Data System (ADS)

    Nyeko-Ogiramoi, P.; Willems, P.; Mutua, F. M.; Moges, S. A.

    2012-09-01

    Estimation of peak flow quantiles in ungauged catchments is a challenge often faced by water professionals in many parts of the world. Approaches to address such problem exist, but widely used techniques such as flood frequency regionalisation is often not subjected to performance evaluation. In this study, the jack-knifing principle is used to assess the performance of the flood frequency regionalisation in the complex and data-scarce River Nile basin by examining the error (regionalisation error) between locally and regionally estimated peak flow quantiles for different return periods (QT). Agglomerative hierarchical clustering based algorithms were used to search for regions with similar hydrological characteristics. Hydrological data employed were from 180 gauged catchments and several physical characteristics in order to regionalise 365 identified catchments. The Generalised Extreme Value (GEV) distribution, selected using L-moment based approach, was used to construct regional growth curves from which peak flow growth factors could be derived and mapped through interpolation. Inside each region, variations in at-site flood frequency distribution were modelled by regression of the mean annual maximum peak flow (MAF) versus catchment area. The results showed that the performance of the regionalisation is heavily dependent on the historical flow record length and the similarity of the hydrological characteristics inside the regions. The flood frequency regionalisation of the River Nile basin can be improved if sufficient flow data of longer record length of at least 40 yr become available.

  20. Does preference influence performance when reading different sizes of cranial computed tomography?

    PubMed Central

    Venjakob, Antje C.; Marnitz, Tim; Gomes, Lavier; Mello-Thoms, Claudia R.

    2014-01-01

    Abstract. Radiology practice is based on the implicit assumption that the preference for a particular presentation mode goes hand in hand with superior performance. The present experiment tests this assumption in what pertains to image size. Forty-three radiologists were asked to identify intracranial hemorrhages on 20 cranial computed tomography scans in two image sizes, 14×14 and 28×28??cm. They were asked to indicate which size they preferred and subsequently rated each size on a continuous scale in terms of how much they liked them. The results show no correlation between the jackknife free-response receiver operating characteristic figure of merit and preference rated on a continuous scale (large image: r=0.14, p=0.38; small images: r=0.14, p=0.39). Similarly, there was no significant correlation between the time a radiologist took to read a case and preference rated on the continuous scale (large image: r=?0.07, p=0.64; small images: r=?0.04, p=0.80). When dividing radiologists into two groups according to their size preference, there was no significant difference in performance between groups with regard to either large or small images. The results suggest that the preference for an image size and performance with regard to it are not related. PMID:26158074

  1. Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach.

    PubMed

    Wang, Xiao-Feng; Chen, Zhen; Wang, Chuan; Yan, Ren-Xiang; Zhang, Ziding; Song, Jiangning

    2011-01-01

    Integral membrane proteins constitute 25-30% of genomes and play crucial roles in many biological processes. However, less than 1% of membrane protein structures are in the Protein Data Bank. In this context, it is important to develop reliable computational methods for predicting the structures of membrane proteins. Here, we present the first application of random forest (RF) for residue-residue contact prediction in transmembrane proteins, which we term as TMhhcp. Rigorous cross-validation tests indicate that the built RF models provide a more favorable prediction performance compared with two state-of-the-art methods, i.e., TMHcon and MEMPACK. Using a strict leave-one-protein-out jackknifing procedure, they were capable of reaching the top L/5 prediction accuracies of 49.5% and 48.8% for two different residue contact definitions, respectively. The predicted residue contacts were further employed to predict interacting helical pairs and achieved the Matthew's correlation coefficients of 0.430 and 0.424, according to two different residue contact definitions, respectively. To facilitate the academic community, the TMhhcp server has been made freely accessible at http://protein.cau.edu.cn/tmhhcp. PMID:22046350

  2. Shrinkage Estimation of the Power Spectrum Covariance Matrix

    E-print Network

    Adrian C. Pope; István Szapudi

    2008-07-22

    We seek to improve estimates of the power spectrum covariance matrix from a limited number of simulations by employing a novel statistical technique known as shrinkage estimation. The shrinkage technique optimally combines an empirical estimate of the covariance with a model (the target) to minimize the total mean squared error compared to the true underlying covariance. We test this technique on N-body simulations and evaluate its performance by estimating cosmological parameters. Using a simple diagonal target, we show that the shrinkage estimator significantly outperforms both the empirical covariance and the target individually when using a small number of simulations. We find that reducing noise in the covariance estimate is essential for properly estimating the values of cosmological parameters as well as their confidence intervals. We extend our method to the jackknife covariance estimator and again find significant improvement, though simulations give better results. Even for thousands of simulations we still find evidence that our method improves estimation of the covariance matrix. Because our method is simple, requires negligible additional numerical effort, and produces superior results, we always advocate shrinkage estimation for the covariance of the power spectrum and other large-scale structure measurements when purely theoretical modeling of the covariance is insufficient.

  3. Estimation of Distribution Overlap of Urn Models

    PubMed Central

    Hampton, Jerrad; Lladser, Manuel E.

    2012-01-01

    A classical problem in statistics is estimating the expected coverage of a sample, which has had applications in gene expression, microbial ecology, optimization, and even numismatics. Here we consider a related extension of this problem to random samples of two discrete distributions. Specifically, we estimate what we call the dissimilarity probability of a sample, i.e., the probability of a draw from one distribution not being observed in draws from another distribution. We show our estimator of dissimilarity to be a -statistic and a uniformly minimum variance unbiased estimator of dissimilarity over the largest appropriate range of . Furthermore, despite the non-Markovian nature of our estimator when applied sequentially over , we show it converges uniformly in probability to the dissimilarity parameter, and we present criteria when it is approximately normally distributed and admits a consistent jackknife estimator of its variance. As proof of concept, we analyze V35 16S rRNA data to discern between various microbial environments. Other potential applications concern any situation where dissimilarity of two discrete distributions may be of interest. For instance, in SELEX experiments, each urn could represent a random RNA pool and each draw a possible solution to a particular binding site problem over that pool. The dissimilarity of these pools is then related to the probability of finding binding site solutions in one pool that are absent in the other. PMID:23139734

  4. 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)

  5. Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method.

    PubMed

    Huang, Wen-Lin; Chen, Hung-Ming; Hwang, Shiow-Fen; Ho, Shinn-Ying

    2007-01-01

    Amphiphilic pseudo-amino acid composition (Am-Pse-AAC) with extra sequence-order information is a useful feature for representing enzymes. This study first utilizes the k-nearest neighbor (k-NN) rule to analyze the distribution of enzymes in the Am-Pse-AAC feature space. This analysis indicates the distributions of multiple classes of enzymes are highly overlapped. To cope with the overlap problem, this study proposes an efficient non-parametric classifier for predicting enzyme subfamily class using an adaptive fuzzy r-nearest neighbor (AFK-NN) method, where k and a fuzzy strength parameter m are adaptively specified. The fuzzy membership values of a query sample Q are dynamically determined according to the position of Q and its weighted distances to the k nearest neighbors. Using the same enzymes of the oxidoreductases family for comparisons, the prediction accuracy of AFK-NN is 76.6%, which is better than those of Support Vector Machine (73.6%), the decision tree method C5.0 (75.4%) and the existing covariant-discriminate algorithm (70.6%) using a jackknife test. To evaluate the generalization ability of AFK-NN, the datasets for all six families of entirely sequenced enzymes are established from the newly updated SWISS-PROT and ENZYME database. The accuracy of AFK-NN on the new large-scale dataset of oxidoreductases family is 83.3%, and the mean accuracy of the six families is 92.1%. PMID:17140725

  6. COMDYN: Software to study the dynamics of animal communities using a capture-recapture approach

    USGS Publications Warehouse

    Hines, J.E.; Boulinier, T.; Nichols, J.D.; Sauer, J.R.; Pollock, K.H.

    1999-01-01

    COMDYN is a set of programs developed for estimation of parameters associated with community dynamics using count data from two locations or time periods. It is Internet-based, allowing remote users either to input their own data, or to use data from the North American Breeding Bird Survey for analysis. COMDYN allows probability of detection to vary among species and among locations and time periods. The basic estimator for species richness underlying all estimators is the jackknife estimator proposed by Burnham and Overton. Estimators are presented for quantities associated with temporal change in species richness, including rate of change in species richness over time, local extinction probability, local species turnover and number of local colonizing species. Estimators are also presented for quantities associated with spatial variation in species richness, including relative richness at two locations and proportion of species present in one location that are also present at a second location. Application of the estimators to species richness estimation has been previously described and justified. The potential applications of these programs are discussed.

  7. Variables influencing the presence of subyearling fall Chinook salmon in shoreline habitats of the Hanford Reach, Columbia River

    USGS Publications Warehouse

    Tiffan, K.F.; Clark, L.O.; Garland, R.D.; Rondorf, D.W.

    2006-01-01

    Little information currently exists on habitat use by subyearling fall Chinook salmon Oncorhynchus tshawytscha rearing in large, main-stem habitats. We collected habitat use information on subyearlings in the Hanford Reach of the Columbia River during May 1994 and April-May 1995 using point abundance electrofishing. We analyzed measures of physical habitat using logistic regression to predict fish presence and absence in shoreline habitats. The difference between water temperature at the point of sampling and in the main river channel was the most important variable for predicting the presence and absence of subyearlings. Mean water velocities of 45 cm/s or less and habitats with low lateral bank slopes were also associated with a greater likelihood of subyearling presence. Intermediate-sized gravel and cobble substrates were significant predictors of fish presence, but small (256-mm) substrates were not. Our rearing model was accurate at predicting fish presence and absence using jackknifing (80% correct) and classification of observations from an independent data set (76% correct). The habitat requirements of fall Chinook salmon in the Hanford Reach are similar to those reported for juvenile Chinook salmon in smaller systems but are met in functionally different ways in a large river.

  8. Automated Prediction of CMEs Using Machine Learning of CME - Flare Associations

    NASA Astrophysics Data System (ADS)

    Qahwaji, R.; Colak, T.; Al-Omari, M.; Ipson, S.

    2008-04-01

    Machine-learning algorithms are applied to explore the relation between significant flares and their associated CMEs. The NGDC flares catalogue and the SOHO/LASCO CME catalogue are processed to associate X and M-class flares with CMEs based on timing information. Automated systems are created to process and associate years of flare and CME data, which are later arranged in numerical-training vectors and fed to machine-learning algorithms to extract the embedded knowledge and provide learning rules that can be used for the automated prediction of CMEs. Properties representing the intensity, flare duration, and duration of decline and duration of growth are extracted from all the associated (A) and not-associated (NA) flares and converted to a numerical format that is suitable for machine-learning use. The machine-learning algorithms Cascade Correlation Neural Networks (CCNN) and Support Vector Machines (SVM) are used and compared in our work. The machine-learning systems predict, from the input of a flare’s properties, if the flare is likely to initiate a CME. Intensive experiments using Jack-knife techniques are carried out and the relationships between flare properties and CMEs are investigated using the results. The predictive performance of SVM and CCNN is analysed and recommendations for enhancing the performance are provided.

  9. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

    PubMed Central

    McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

    2012-01-01

    Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408?315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/. PMID:22134646

  10. The fate of an immigrant: Ensis directus in the eastern German Bight

    NASA Astrophysics Data System (ADS)

    Dannheim, Jennifer; Rumohr, Heye

    2012-09-01

    We studied Ensis directus in the subtidal (7-16 m depth) of the eastern German Bight. The jack-knife clam that invaded in the German Bight in 1978 has all characteristics of a successful immigrant: Ensis directus has a high reproductive capacity (juveniles, July 2001: Amrumbank 1,914 m-2, Eiderstedt/Vogelsand: 11,638 m-2), short generation times and growths rapidly: maximum growth rates were higher than in former studies (mean: 3 mm month-1, 2nd year: up to 14 mm month-1). Ensis directus uses natural mechanisms for rapid dispersal, occurs gregariously and exhibits a wide environmental tolerance. However, optimal growth and population-structure annual gaps might be influenced by reduced salinity: at Vogelsand (transition area of Elbe river), maximum growth was lower (164 mm) than at the Eiderstedt site (outer range of Elbe river, L ? = 174 mm). Mass mortalities of the clams are probably caused by washout (video inspections), low winter temperature and strong storms. Ensis directus immigrated into the community finding its own habitat on mobile sands with strong tidal currents. Recent studies on E. directus found that the species neither suppresses native species nor takes over the position of an established one which backs up our study findings over rather short time scales. On the contrary, E. directus seems to favour the settlement of some deposit feeders. Dense clam mats might stabilise the sediment and function as a sediment-trap for organic matter. Ensis directus has neither become a nuisance to other species nor developed according to the `boom-and-bust' theory. The fate of the immigrant E. directus rather is a story of a successful trans-ocean invasion which still holds on 23 years after the first findings in the outer elbe estuary off Vogelsand.

  11. 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

  12. Validation of the ALARO-0 model within the EURO-CORDEX framework

    NASA Astrophysics Data System (ADS)

    Giot, O.; Termonia, P.; Degrauwe, D.; De Troch, R.; Caluwaerts, S.; Smet, G.; Berckmans, J.; Deckmyn, A.; De Cruz, L.; De Meutter, P.; Duerinckx, A.; Gerard, L.; Hamdi, R.; Van den Bergh, J.; Van Ginderachter, M.; Van Schaeybroeck, B.

    2015-10-01

    Using the regional climate model ALARO-0 the Royal Meteorological Institute of Belgium has performed two simulations of the past observed climate within the framework of the Coordinated Regional Climate Downscaling Experiment (CORDEX). The ERA-Interim reanalysis was used to drive the model for the period 1979-2010 on the EURO-CORDEX domain with two horizontal resolutions, 0.11 and 0.44 °. ALARO-0 is characterised by the new microphysics scheme 3MT, which allows for a better representation of convective precipitation. In Kotlarski et al. (2014) several metrics assessing the performance in representing seasonal mean near-surface air temperature and precipitation are defined and the corresponding scores are calculated for an ensemble of models for different regions and seasons for the period 1989-2008. Of special interest within this ensemble is the ARPEGE model by the Centre National de Recherches Météorologiques (CNRM), which shares a large amount of core code with ALARO-0. Results show that ALARO-0 is capable of representing the European climate in an acceptable way as most of the ALARO-0 scores lie within the existing ensemble. However, for near-surface air temperature some large biases, which are often also found in the ARPEGE results, persist. For precipitation, on the other hand, the ALARO-0 model produces some of the best scores within the ensemble and no clear resemblance to ARPEGE is found, which is attributed to the inclusion of 3MT. Additionally, a jackknife procedure is applied to the ALARO-0 results in order to test whether the scores are robust, by which we mean independent of the period used to calculate them. Periods of 20 years are sampled from the 32 year simulation and used to construct the 95 % confidence interval for each score. For most scores these intervals are very small compared to the total ensemble spread, implying that model differences in the scores are significant.

  13. 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.

  14. Three-Dimensional Spectral-Domain Optical Coherence Tomography Data Analysis for Glaucoma Detection

    PubMed Central

    Wollstein, Gadi; Bilonick, Richard A.; Folio, Lindsey S.; Nadler, Zach; Kagemann, Larry; Schuman, Joel S.

    2013-01-01

    Purpose To develop a new three-dimensional (3D) spectral-domain optical coherence tomography (SD-OCT) data analysis method using a machine learning technique based on variable-size super pixel segmentation that efficiently utilizes full 3D dataset to improve the discrimination between early glaucomatous and healthy eyes. Methods 192 eyes of 96 subjects (44 healthy, 59 glaucoma suspect and 89 glaucomatous eyes) were scanned with SD-OCT. Each SD-OCT cube dataset was first converted into 2D feature map based on retinal nerve fiber layer (RNFL) segmentation and then divided into various number of super pixels. Unlike the conventional super pixel having a fixed number of points, this newly developed variable-size super pixel is defined as a cluster of homogeneous adjacent pixels with variable size, shape and number. Features of super pixel map were extracted and used as inputs to machine classifier (LogitBoost adaptive boosting) to automatically identify diseased eyes. For discriminating performance assessment, area under the curve (AUC) of the receiver operating characteristics of the machine classifier outputs were compared with the conventional circumpapillary RNFL (cpRNFL) thickness measurements. Results The super pixel analysis showed statistically significantly higher AUC than the cpRNFL (0.855 vs. 0.707, respectively, p?=?0.031, Jackknife test) when glaucoma suspects were discriminated from healthy, while no significant difference was found when confirmed glaucoma eyes were discriminated from healthy eyes. Conclusions A novel 3D OCT analysis technique performed at least as well as the cpRNFL in glaucoma discrimination and even better at glaucoma suspect discrimination. This new method has the potential to improve early detection of glaucomatous damage. PMID:23408988

  15. Ngram time series model to predict activity type and energy cost from wrist, hip and ankle accelerometers: implications of age.

    PubMed

    Strath, Scott J; Kate, Rohit J; Keenan, Kevin G; Welch, Whitney A; Swartz, Ann M

    2015-11-01

    To develop and test time series single site and multi-site placement models, we used wrist, hip and ankle processed accelerometer data to estimate energy cost and type of physical activity in adults. Ninety-nine subjects in three age groups (18-39, 40-64, 65??+??years) performed 11 activities while wearing three triaxial accelereometers: one each on the non-dominant wrist, hip, and ankle. During each activity net oxygen cost (METs) was assessed. The time series of accelerometer signals were represented in terms of uniformly discretized values called bins. Support Vector Machine was used for activity classification with bins and every pair of bins used as features. Bagged decision tree regression was used for net metabolic cost prediction. To evaluate model performance we employed the jackknife leave-one-out cross validation method. Single accelerometer and multi-accelerometer site model estimates across and within age group revealed similar accuracy, with a bias range of??-0.03 to 0.01 METs, bias percent of??-0.8 to 0.3%, and a rMSE range of 0.81-1.04 METs. Multi-site accelerometer location models improved activity type classification over single site location models from a low of 69.3% to a maximum of 92.8% accuracy. For each accelerometer site location model, or combined site location model, percent accuracy classification decreased as a function of age group, or when young age groups models were generalized to older age groups. Specific age group models on average performed better than when all age groups were combined. A time series computation show promising results for predicting energy cost and activity type. Differences in prediction across age group, a lack of generalizability across age groups, and that age group specific models perform better than when all ages are combined needs to be considered as analytic calibration procedures to detect energy cost and type are further developed. PMID:26449155

  16. Historical shoreline mapping (II): application of the Digital Shoreline Mapping and Analysis Systems (DSMS/DSAS) to shoreline change mapping in Puerto Rico

    USGS Publications Warehouse

    Thieler, E. Robert; Danforth, William W.

    1994-01-01

    A new, state-of-the-art method for mapping historical shorelines from maps and aerial photographs, the Digital Shoreline Mapping System (DSMS), has been developed. The DSMS is a freely available, public domain software package that meets the cartographic and photogrammetric requirements of precise coastal mapping, and provides a means to quantify and analyze different sources of error in the mapping process. The DSMS is also capable of resolving imperfections in aerial photography that commonly are assumed to be nonexistent. The DSMS utilizes commonly available computer hardware and software, and permits the entire shoreline mapping process to be executed rapidly by a single person in a small lab. The DSMS generates output shoreline position data that are compatible with a variety of Geographic Information Systems (GIS). A second suite of programs, the Digital Shoreline Analysis System (DSAS) has been developed to calculate shoreline rates-of-change from a series of shoreline data residing in a GIS. Four rate-of-change statistics are calculated simultaneously (end-point rate, average of rates, linear regression and jackknife) at a user-specified interval along the shoreline using a measurement baseline approach. An example of DSMS and DSAS application using historical maps and air photos of Punta Uvero, Puerto Rico provides a basis for assessing the errors associated with the source materials as well as the accuracy of computed shoreline positions and erosion rates. The maps and photos used here represent a common situation in shoreline mapping: marginal-quality source materials. The maps and photos are near the usable upper limit of scale and accuracy, yet the shoreline positions are still accurate ±9.25 m when all sources of error are considered. This level of accuracy yields a resolution of ±0.51 m/yr for shoreline rates-of-change in this example, and is sufficient to identify the short-term trend (36 years) of shoreline change in the study area.

  17. Aboveground biomass and leaf area index (LAI) mapping for Niassa Reserve, northern Mozambique

    NASA Astrophysics Data System (ADS)

    Ribeiro, Natasha S.; Saatchi, Sassan S.; Shugart, Herman H.; Washington-Allen, Robert A.

    2008-09-01

    Estimations of biomass are critical in miombo woodlands because they represent the primary source of goods and services for over 80% of the population in southern Africa. This study was carried out in Niassa Reserve, northern Mozambique. The main objectives were first to estimate woody biomass and Leaf Area Index (LAI) using remotely sensed data [RADARSAT (C-band, ? = 5.7-cm)] and Landsat ETM+ derived Normalized Difference Vegetation Index (NDVI) and Simple Ratio (SR) calibrated by field measurements and, second to determine, at both landscape and plot scales, the environmental controls (precipitation, woody cover density, fire and elephants) of biomass and LAI. A land-cover map (72% overall accuracy) was derived from the June 2004 ETM+ mosaic. Field biomass and LAI were correlated with RADARSAT backscatter (rbiomass = 0.65, rLAI = 0.57, p < 0.0001) from July 2004, NDVI (rbiomass = 0.30, rLAI = 0.35; p < 0.0001) and SR (rbiomass = 0.36, rLAI = 0.40, p < 0.0001). A jackknife stepwise regression technique was used to develop the best predictive models for biomass (biomass = -5.19 + 0.074 * radarsat + 1.56 * SR, r2 = 0.55) and LAI (LAI = -0.66 + 0.01 * radarsat + 0.22 * SR, r2 = 0.45). Biomass and LAI maps were produced with an estimated peak of 18 kg m-2 and 2.80 m2 m-2, respectively. On the landscape-scale, both biomass and LAI were strongly determined by mean annual precipitation (F = 13.91, p = 0.0002). On the plot spatial scale, woody biomass was significantly determined by fire frequency, and LAI by vegetation type.

  18. Lower-extremity strength profiles and gender-based classification of basketball players ages 9-22 years.

    PubMed

    Buchanan, Patricia A; Vardaxis, Vassilios G

    2009-03-01

    Despite an increase in women sports participants and recognition of gender differences in injury patterns (e.g., knee), few normative strength data exist beyond hamstrings and quadriceps measures. This study had 2 purposes: to assess the lower-extremity strength of women (W) and men (M) basketball players who were 9-22 years old, and to determine which strength measures most correctly classify the gender of 12- to 22-year-old athletes. Fifty basketball players (26 W, 24 M) without ligamentous or meniscal injury performed concentric isokinetic testing of bilateral hip, knee, and ankle musculature. We identified maximal peak torques for the hip (flexors, extensors, abductors, adductors), knee (flexors and extensors), and ankle (plantar flexors and dorsiflexors), and we formed periarticular (hip, knee, and ankle), antigravity, and total leg strength composite measures. We calculated mean and 95% confidence intervals. With body mass-height normalization, most age and gender differences were small. Mean values were typically higher for older vs. younger players and for men vs. women players. Mean values were often lower for girls 12-13 years vs. those 9-10 years. In the age group of 16-22 years, men had stronger knee flexors, hip flexors, plantar flexors, and total leg strength than women. Men who were 16-22 years old had stronger knee flexors and hip flexors than did younger men and women players. Based on discriminant function, knee strength measures did not adequately classify gender. Instead, total leg strength measures had correct gender classifications of 74 and 69% (jackknifed) with significant multivariate tests (p = 0.025). For researchers and practitioners, these results support strength assessment and training of the whole lower extremity, not just knee musculature. Limited strength differences between girls 9-10 years old and those 12-13 years old suggest that the peripubertal period is an important time to target strength development. PMID:19209081

  19. High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis

    PubMed Central

    Szafranski, Szymon P.; Wos-Oxley, Melissa L.; Vilchez-Vargas, Ramiro; Jáuregui, Ruy; Plumeier, Iris; Klawonn, Frank; Tomasch, Jürgen; Meisinger, Christa; Kühnisch, Jan; Sztajer, Helena; Pieper, Dietmar H.

    2014-01-01

    The oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens like Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia could be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health- and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis. PMID:25452281

  20. Modelling temperature, photoperiod and vernalization responses of Brunonia australis (Goodeniaceae) and Calandrinia sp. (Portulacaceae) to predict flowering time

    PubMed Central

    Cave, Robyn L.; Hammer, Graeme L.; McLean, Greg; Birch, Colin J.; Erwin, John E.; Johnston, Margaret E.

    2013-01-01

    Background and Aims Crop models for herbaceous ornamental species typically include functions for temperature and photoperiod responses, but very few incorporate vernalization, which is a requirement of many traditional crops. This study investigated the development of floriculture crop models, which describe temperature responses, plus photoperiod or vernalization requirements, using Australian native ephemerals Brunonia australis and Calandrinia sp. Methods A novel approach involved the use of a field crop modelling tool, DEVEL2. This optimization program estimates the parameters of selected functions within the development rate models using an iterative process that minimizes sum of squares residual between estimated and observed days for the phenological event. Parameter profiling and jack-knifing are included in DEVEL2 to remove bias from parameter estimates and introduce rigour into the parameter selection process. Key Results Development rate of B. australis from planting to first visible floral bud (VFB) was predicted using a multiplicative approach with a curvilinear function to describe temperature responses and a broken linear function to explain photoperiod responses. A similar model was used to describe the development rate of Calandrinia sp., except the photoperiod function was replaced with an exponential vernalization function, which explained a facultative cold requirement and included a coefficient for determining the vernalization ceiling temperature. Temperature was the main environmental factor influencing development rate for VFB to anthesis of both species and was predicted using a linear model. Conclusions The phenology models for B. australis and Calandrinia sp. described development rate from planting to VFB and from VFB to anthesis in response to temperature and photoperiod or vernalization and may assist modelling efforts of other herbaceous ornamental plants. In addition to crop management, the vernalization function could be used to identify plant communities most at risk from predicted increases in temperature due to global warming. PMID:23404991

  1. Morphometric analysis of pelvic sexual dimorphism in a contemporary Western Australian population.

    PubMed

    Franklin, Daniel; Cardini, Andrea; Flavel, Ambika; Marks, Murray K

    2014-09-01

    Requisite to routine casework involving unidentified skeletal remains is the formulation of an accurate biological profile, including sex estimation. Choice of method(s) is invariably related to preservation and by association, available bones. It is vital that the method applied affords statistical quantification of accuracy rates and predictive confidence so that evidentiary requirements for legal submission are satisfied. Achieving the latter necessitates the application of contemporary population-specific standards. This study examines skeletal pelvic dimorphism in contemporary Western Australian individuals to quantify the accuracy of using pelvic measurements to estimate sex and to formulate a series of morphometric standards. The sample comprises pelvic multi-slice computer tomography (MSCT) scans from 200 male and 200 female adults. Following 3D rendering, the 3D coordinates of 24 landmarks are acquired using OsiriX® (v.4.1.1) with 12 inter-landmark linear measurements and two angles acquired using MorphDb. Measurements are analysed using basic descriptive statistics and discriminant functions analyses employing jackknife validation of classification results. All except two linear measurements are dimorphic with sex differences explaining up to 65 % of sample variance. Transverse pelvic outlet and subpubic angle contribute most significantly to sex discrimination with accuracy rates between 100 % (complete pelvis-10 variables) and 81.2 % (ischial length). This study represents the initial forensic research into pelvic sexual dimorphism in a Western Australian population. Given these methods, we conclude that this highly dimorphic bone can be used to classify sex with a high degree of expected accuracy. PMID:24789357

  2. Estimation of sex from the anthropometric ear measurements of a Sudanese population.

    PubMed

    Ahmed, Altayeb Abdalla; Omer, Nosyba

    2015-09-01

    The external ear and its prints have multifaceted roles in medico-legal practice, e.g., identification and facial reconstruction. Furthermore, its norms are essential in the diagnosis of congenital anomalies and the design of hearing aids. Body part dimensions vary in different ethnic groups, so the most accurate statistical estimations of biological attributes are developed using population-specific standards. Sudan lacks comprehensive data about ear norms; moreover, there is a universal rarity in assessing the possibility of sex estimation from ear dimensions using robust statistical techniques. Therefore, this study attempts to establish data for normal adult Sudanese Arabs, assessing the existence of asymmetry and developing a population-specific equation for sex estimation. The study sample comprised 200 healthy Sudanese Arab volunteers (100 males and 100 females) in the age range of 18-30years. The physiognomic ear length and width, lobule length and width, and conchal length and width measurements were obtained by direct anthropometry, using a digital sliding caliper. Moreover, indices and asymmetry were assessed. Data were analyzed using basic descriptive statistics and discriminant function analyses employing jackknife validations of classification results. All linear dimensions used were sexually dimorphic except lobular lengths. Some of the variables and indices show asymmetry. Ear dimensions showed cross-validated sex classification accuracy ranging between 60.5% and 72%. Hence, the ear measurements cannot be used as an effective tool in the estimation of sex. However, in the absence of other more reliable means, it still can be considered a supportive trait in sex estimation. Further, asymmetry should be considered in identification from the ear measurements. PMID:25813757

  3. 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

  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. Demographic history and rare allele sharing among human populations

    PubMed Central

    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.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.

    2011-01-01

    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

  6. Comparison of subcellular responses for the evaluation and prediction of the chemotherapeutic response to cisplatin in lung adenocarcinoma using Raman spectroscopy.

    PubMed

    Nawaz, Haq; Bonnier, Franck; Meade, Aidan D; Lyng, Fiona M; Byrne, Hugh J

    2011-06-21

    Confocal Raman Micro-spectroscopy (CRM) is employed to examine the chemical and physiological effects of anticancer agents, using cisplatin and A549 adenocarcinoma cells as a model compound and test system respectively. Spectral responses of the membrane and cytoplasm of the cell are analysed independently and the results are compared to previously reported spectroscopic studies of the nucleus. Moreover, Raman spectra from the proteins extracted from the control and exposed samples are acquired and analysed to confirm the origin of the molecular changes of the cell membrane and cytoplasm of the A549 cells. Multivariate data analysis techniques including Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR) along with PLS-Jackknifing are used to analyse the data measured from the cell membrane and cytoplasm of the A549 cells and results are correlated with parallel measurements from the cytotoxicity assay MTT. A PLSR model is used to differentiate between the chemical effect of the chemotherapeutic agent and the physiological response of the A549 cells and to identify regions of the spectrum that are associated with these processes respectively. The PLSR model is also employed to predict, on the basis of the Raman spectra, the effective dose as well as the level of physiological response, using spectra data from the cytoplasmic and cell membrane regions. The effectiveness of the models based on spectral datasets from the cell membrane and cytoplasm is compared to similar models constructed using spectral data from the nuclear region as well as one combining spectral data from all regions. In all cases, higher prediction accuracy is found for regression against the cisplatin dose, and for both regression against the dose and the physiological response, nuclear data yield higher precision. PMID:21519610

  7. Do adolescent Ecstasy users have different attitudes towards drugs when compared to Marijuana users?

    PubMed Central

    Martins, Silvia S.; Storr, Carla L.; Alexandre, Pierre K.; Chilcoat, Howard D.

    2008-01-01

    Background Perceived risk and attitudes about the consequences of drug use, perceptions of others expectations and self-efficacy influence the intent to try drugs and continue drug use once use has started. We examine associations between adolescents’ attitudes and beliefs towards ecstasy use; because most ecstasy users have a history of marijuana use, we estimate the association for three groups of adolescents: non-marijuana/ecstasy users, marijuana users (used marijuana at least once but never used ecstasy) and ecstasy users (used ecstasy at least once). Methods Data from 5,049 adolescents aged 12–18 years old who had complete weighted data information in Round 2 of the Restricted Use Files (RUF) of the National Survey of Parents and Youth (NSPY). Data were analyzed using jackknife weighted multinomial logistic regression models. Results Adolescent marijuana and ecstasy users were more likely to approve of marijuana and ecstasy use as compared to non-drug using youth. Adolescent marijuana and ecstasy users were more likely to have close friends who approved of ecstasy as compared to non-drug using youth. The magnitudes of these two associations were stronger for ecstasy use than for marijuana use in the final adjusted model. Our final adjusted model shows that approval of marijuana and ecstasy use was more strongly associated with marijuana and ecstasy use in adolescence than perceived risk in using both drugs. Conclusion Information about the risks and consequences of ecstasy use need to be presented to adolescents in order to attempt to reduce adolescents’ approval of ecstasy use as well as ecstasy experimentation. PMID:18068314

  8. Essential protein identification based on essential protein-protein interaction prediction by Integrated Edge Weights.

    PubMed

    Jiang, Yuexu; Wang, Yan; Pang, Wei; Chen, Liang; Sun, Huiyan; Liang, Yanchun; Blanzieri, Enrico

    2015-07-15

    Essential proteins play a crucial role in cellular survival and development process. Experimentally, essential proteins are identified by gene knockouts or RNA interference, which are expensive and often fatal to the target organisms. Regarding this, an alternative yet important approach to essential protein identification is through computational prediction. Existing computational methods predict essential proteins based on their relative densities in a protein-protein interaction (PPI) network. Degree, betweenness, and other appropriate criteria are often used to measure the relative density. However, no matter what criterion is used, a protein is actually ordered by the attributes of this protein per se. In this research, we presented a novel computational method, Integrated Edge Weights (IEW), to first rank protein-protein interactions by integrating their edge weights, and then identified sub PPI networks consisting of those highly-ranked edges, and finally regarded the nodes in these sub networks as essential proteins. We evaluated IEW on three model organisms: Saccharomyces cerevisiae (S. cerevisiae), Escherichia coli (E. coli), and Caenorhabditis elegans (C. elegans). The experimental results showed that IEW achieved better performance than the state-of-the-art methods in terms of precision-recall and Jackknife measures. We had also demonstrated that IEW is a robust and effective method, which can retrieve biologically significant modules by its highly-ranked protein-protein interactions for S. cerevisiae, E. coli, and C. elegans. We believe that, with sufficient data provided, IEW can be used to any other organisms' essential protein identification. A website about IEW can be accessed from http://digbio.missouri.edu/IEW/index.html. PMID:25892709

  9. Late Results of Endorectal Flap in Management of High Type Perianal Fistula

    PubMed Central

    Ghahramani, Ladan; Bananzadeh, Ali Mohammad; Izadpanah, Ahmad; Hosseini, Seyed Vahid

    2012-01-01

    BACKGROUND Fistula-in-ano is a problematic perianal disease for physicians and patients because of its occasional difficulty in management. Due to the different types of fistulas seen in patients, careful approach is necessary to correctly choose from among the various surgical techniques. One surgical method for complex fistula is the endorectal advancement flap which has been frequently performed because of its low complication rate. METHODS This study enrolled 40 (33 males, 7 females) patients who suffered from high type fistula (greater than 30%-50% involvement of the external sphincter) as noted on digital rectal examination and endoanalsonography. Patients were seen at Shahid Faghihi Hospital, affiliated with Shiraz University of Medical Sciences, between 2007 and 2011. All enrolled patients received similar preoperational preparation. We used the jackknife operative position and determined the internal orifice of the fistula by inserting a probe, with injection of methylene blue or oxygen peroxide. Endorectal advancement flap included the mucosa, submucosa and thin portion of the muscle that completely covered the sutured internal orifice area. The external orifice was opened to adjust the external border of the external sphincter to allow for effective drainage. RESULTS All enrolled patients were followed for 36 months, which was noticeable statistically when compared with other study findings of high type fistula. The location of the external orifice, age, sex and bowel habits were not related to recurrence rate. CONCLUSION Endorectal advancement flap in selected patients who suffer from high type fistula seems to have beneficial effects with a low recurrence rate. Therefore, management of complex high type fistulas remains a challenging topic. PMID:24829651

  10. 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

  11. Detecting taxonomic signal in an under-utilised character system: geometric morphometrics of the forcipular coxae of Scutigeromorpha (Chilopoda)

    PubMed Central

    Gutierrez, Beatriz Lopez; MacLeod, Norman; Edgecombe, Gregory D.

    2011-01-01

    Abstract To date, the forcipules have played almost no role in determining the systematics of scutigeromorph centipedes though in his 1974 review of taxonomic characters Markus Würmli suggested some potentially informative variation might be found in these structures. Geometric morphometric analyses were used to evaluate Würmli’s suggestion, specifically to determine whether the shape of the forcipular coxa contains information useful for diagnosing species. The geometry of the coxae of eight species from the genera Sphendononema, Scutigera, Dendrothereua, Thereuonema, Thereuopoda, Thereuopodina, Allothereua and Parascutigera was characterised using a combination of landmark- and semi-landmark-based sampling methods to summarize group-specific morphological variation. Canonical variates analysis of shape data characterizing the forcipular coxae indicates that these structures differ significantly between taxa at various systematic levels. Models calculated for the canonical variates space facilitate identification of the main shape differences between genera, including overall length/width, curvature of the external coxal margin, and the extent to which the coxofemoral condyle projects laterally. Jackknifed discriminant function analysis demonstrates that forcipular coxal training-set specimens were assigned to correct species in 61% of cases on average, the most accurate assignments being those of Parascutigera (Parascutigera guttata) and Thereuonema (Thereuonema microstoma). The geographically widespread species Thereuopoda longicornis, Sphendononema guildingii, Scutigera coleoptrata, and Dendrothereua linceci exhibit the least diagnostic coxae in our dataset. Thereuopoda longicornis populations sampled from different parts of East and Southeast Asia were significantly discriminated from each other, suggesting that, in this case, extensive synonymy may be obscuring diagnosable inter-species coxal shape differences. PMID:22303095

  12. Comparative assessment of GIS-based methods and metrics for estimating long-term exposures to air pollution

    NASA Astrophysics Data System (ADS)

    Gulliver, John; de Hoogh, Kees; Fecht, Daniela; Vienneau, Danielle; Briggs, David

    2011-12-01

    The development of geographical information system techniques has opened up a wide array of methods for air pollution exposure assessment. The extent to which these provide reliable estimates of air pollution concentrations is nevertheless not clearly established. Nor is it clear which methods or metrics should be preferred in epidemiological studies. This paper compares the performance of ten different methods and metrics in terms of their ability to predict mean annual PM 10 concentrations across 52 monitoring sites in London, UK. Metrics analysed include indicators (distance to nearest road, traffic volume on nearest road, heavy duty vehicle (HDV) volume on nearest road, road density within 150 m, traffic volume within 150 m and HDV volume within 150 m) and four modelling approaches: based on the nearest monitoring site, kriging, dispersion modelling and land use regression (LUR). Measures were computed in a GIS, and resulting metrics calibrated and validated against monitoring data using a form of grouped jack-knife analysis. The results show that PM 10 concentrations across London show little spatial variation. As a consequence, most methods can predict the average without serious bias. Few of the approaches, however, show good correlations with monitored PM 10 concentrations, and most predict no better than a simple classification based on site type. Only land use regression reaches acceptable levels of correlation ( R2 = 0.47), though this can be improved by also including information on site type. This might therefore be taken as a recommended approach in many studies, though care is needed in developing meaningful land use regression models, and like any method they need to be validated against local data before their application as part of epidemiological studies.

  13. THREE-POINT CORRELATION FUNCTIONS OF SDSS GALAXIES: CONSTRAINING GALAXY-MASS BIAS

    SciTech Connect

    McBride, Cameron K.; Connolly, Andrew J.; Gardner, Jeffrey P.; Scranton, Ryan; Scoccimarro, Roman; Berlind, Andreas A.; MarIn, Felipe; Schneider, Donald P.

    2011-10-01

    We constrain the linear and quadratic bias parameters from the configuration dependence of the three-point correlation function (3PCF) in both redshift and projected space, utilizing measurements of spectroscopic galaxies in the Sloan Digital Sky Survey Main Galaxy Sample. We show that bright galaxies (M{sub r} < -21.5) are biased tracers of mass, measured at a significance of 4.5{sigma} in redshift space and 2.5{sigma} in projected space by using a thorough error analysis in the quasi-linear regime (9-27 h{sup -1} Mpc). Measurements on a fainter galaxy sample are consistent with an unbiased model. We demonstrate that a linear bias model appears sufficient to explain the galaxy-mass bias of our samples, although a model using both linear and quadratic terms results in a better fit. In contrast, the bias values obtained from the linear model appear in better agreement with the data by inspection of the relative bias and yield implied values of {sigma}{sub 8} that are more consistent with current constraints. We investigate the covariance of the 3PCF, which itself is a measurement of galaxy clustering. We assess the accuracy of our error estimates by comparing results from mock galaxy catalogs to jackknife re-sampling methods. We identify significant differences in the structure of the covariance. However, the impact of these discrepancies appears to be mitigated by an eigenmode analysis that can account for the noisy, unresolved modes. Our joint analysis of both redshift space and projected measurements allows us to identify systematic effects affecting constraints from the 3PCF.

  14. 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

  15. 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.

  16. 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.

  17. Modeling the Distribution of Cutaneous Leishmaniasis Vectors (Psychodidae: Phlebotominae) in Iran: A Potential Transmission in Disease Prone Areas.

    PubMed

    Hanafi-Bojd, Ahmad Ali; Yaghoobi-Ershadi, Mohammad Reza; Haghdoost, Ali Akbar; Akhavan, Amir Ahmad; Rassi, Yavar; Karimi, Ameneh; Charrahy, Zabihollah

    2015-07-01

    Cutaneous leishmaniasis (CL) is now the main vector-borne disease in Iran. Two forms of the disease exist in the country, transmitted by Phlebotomus papatasi and Phlebotomus sergenti s.l. Modeling distribution of the vector species is beneficial for preparedness and planning to interrupt the transmission cycle. Data on sand fly distribution during 1990-2013 were used to predict the niche suitability. MaxEnt algorithm model was used for prediction using bioclimatic and environmental variables (precipitation, temperature, altitude, slope, and aspect). Regularized training, area under the curve, and unregularized training gains were 0.916, 0.915, and 1.503, respectively, for Ph. papatasi. These values were calculated as 0.987, 0.923, and 1.588 for Ph. sergenti s.l. The jackknife test showed that the environmental variable with the highest gain when used in isolation has the mean temperature of the wettest quarter for both species, while slope decreases the gain the most when it is omitted from the model. Classification of probability of presence for two studied species was performed on five classes using equal intervals in ArcGIS. More than 60% probability of presence was considered as areas with high potential of CL transmission. These areas include arid and semiarid climates, mainly located in central part of the country. Mean of altitude, annual precipitation, and temperature in these areas were calculated 990 and 1,235?m, 273 and 226?mm, and 17.5 and 16.4°C for Ph. papatasi and Ph. sergenti s.l., respectively. These findings can be used in the prediction of CL transmission potential, as well as for planning the disease control interventions. PMID:26335462

  18. Prediction of protein S-nitrosylation sites based on adapted normal distribution bi-profile Bayes and Chou's pseudo amino acid composition.

    PubMed

    Jia, Cangzhi; Lin, Xin; Wang, Zhiping

    2014-01-01

    Protein S-nitrosylation is a reversible post-translational modification by covalent modification on the thiol group of cysteine residues by nitric oxide. Growing evidence shows that protein S-nitrosylation plays an important role in normal cellular function as well as in various pathophysiologic conditions. Because of the inherent chemical instability of the S-NO bond and the low abundance of endogenous S-nitrosylated proteins, the unambiguous identification of S-nitrosylation sites by commonly used proteomic approaches remains challenging. Therefore, computational prediction of S-nitrosylation sites has been considered as a powerful auxiliary tool. In this work, we mainly adopted an adapted normal distribution bi-profile Bayes (ANBPB) feature extraction model to characterize the distinction of position-specific amino acids in 784 S-nitrosylated and 1568 non-S-nitrosylated peptide sequences. We developed a support vector machine prediction model, iSNO-ANBPB, by incorporating ANBPB with the Chou's pseudo amino acid composition. In jackknife cross-validation experiments, iSNO-ANBPB yielded an accuracy of 65.39% and a Matthew's correlation coefficient (MCC) of 0.3014. When tested on an independent dataset, iSNO-ANBPB achieved an accuracy of 63.41% and a MCC of 0.2984, which are much higher than the values achieved by the existing predictors SNOSite, iSNO-PseAAC, the Li et al. algorithm, and iSNO-AAPair. On another training dataset, iSNO-ANBPB also outperformed GPS-SNO and iSNO-PseAAC in the 10-fold crossvalidation test. PMID:24918295

  19. Food selection among Atlantic Coast seaducks in relation to historic food habits

    USGS Publications Warehouse

    Perry, M.C.; Osenton, P.C.; Wells-Berlin, A. M.; Kidwell, D.M.

    2005-01-01

    Food selection among Atlantic Coast seaducks during 1999-2005 was determined from hunter-killed ducks and compared to data from historic food habits file (1885-1985) for major migrational and wintering areas in the Atlantic Flyway. Food selection was determined by analyses of the gullet (esophagus and proventriculus) and gizzard of 860 ducks and summarized by aggregate percent for each species. When sample size was adequate comparisons were made among age and sex groupings and also among local sites in major habitat areas. Common eiders in Maine and the Canadian Maritimes fed predominantly (53%) on the blue mussel (Mytilus edulis). Scoters in Massachusetts, Maine, and the Canadian Maritimes fed predominantly on the blue mussel (46%), Atlantic jackknife clam (Ensis directus; 19%), and Atlantic surf clam (Spisula solidissima; 15%), whereas scoters in the Chesapeake Bay fed predominantly on hooked mussel (Ischadium recurvum; 42%), the stout razor clam (Tagelus plebeius; 22%), and dwarf surf clam (Mulinia lateralis; 15%). The amethyst gem clam (Gemma gemma) was the predominant food (45%) of long-tailed ducks in Chesapeake Bay. Buffleheads and common goldeneyes fed on a mixed diet of mollusks and soft bodied invertebrates (amphipods, isopods and polychaetes). No major differences were noticed between the sexes in regard to food selection in any of the wintering areas. Comparisons to historic food habits in all areas failed to detect major differences. However, several invertebrate species recorded in historic samples were not found in current samples and two invasive species (Atlantic Rangia, Rangia cuneata and green crab, Carcinas maenas) were recorded in modem samples, but not in historic samples. Benthic sampling in areas where seaducks were collected showed a close correlation between consumption and availability. Each seaduck species appears to fill a unique niche in regard to feeding ecology, although there is much overlap of prey species selected. Understanding the trophic relationships of seaducks in coastal wintering areas will give managers a better understanding of habitat changes in regard to future environmental perturbations.

  20. Multiscale finite-frequency Rayleigh wave tomography of the Kaapvaal craton

    NASA Astrophysics Data System (ADS)

    Chevrot, S.; Zhao, L.

    2007-04-01

    We have measured phase delays of fundamental-mode Rayleigh waves for 12 events recorded by the Southern Africa Seismic Experiment at frequencies between 0.005 and 0.035 Hz. A novel multiscale finite-frequency tomographic method based on wavelet decomposition of 3-D sensitivity kernels for the phase of Rayleigh waves is used to map the shear velocities in the upper mantle beneath southern Africa. The kernels are computed by summing coupled normal modes over a very fine grid surrounding the seismic array. To estimate and minimize the biases in the model resulting from structures outside the tomographic grid, a jackknife inversion method is implemented. The contribution of heterogeneities outside the target volume is significant, but produces artefacts in the tomographic model that are easily identified and discarded before interpretation. With structures on length scales as short as 100 km retrieved beneath the array, the deep structure of the Kaapvaal craton is revealed with unprecedented detail. Outside the array, the corresponding resolution is 200 km. High velocity cratonic roots are confined to the Archean craton, and extend to depths of at least 250 km. Confirming earlier surface structural studies, we recognize two distinct units in the Kaapvaal craton. The eastern Witwatersrand block and the western Kimberley block are separated by a major near-vertical translithospheric boundary which coincides with the Colesberg Lineament. Lower than average velocities south and east of the Kaapvaal craton reveal extensive metasomatism and heating of the lithosphere, probably related to the Karoo magmatic event and to the opening of the South Atlantic Ocean.

  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. DNA hybridization evidence for the principal lineages of hummingbirds (Aves:Trochilidae).

    PubMed

    Bleiweiss, R; Kirsch, J A; Matheus, J C

    1997-03-01

    The spectacular evolutionary radiation of hummingbirds (Trochilidae) has served as a model system for many biological studies. To begin to provide a historical context for these investigations, we generated a complete matrix of DNA hybridization distances among 26 hummingbirds and an outgroup swift (Chaetura pelagica) to determine the principal hummingbird lineages. FITCH topologies estimated from symmetrized delta TmH-C values and subjected to various validation methods (bootstrapping, weighted jackknifing, branch length significance) indicated a fundamental split between hermit (Eutoxeres aquila, Threnetes ruckeri; Phaethornithinae) and nonhermit (Trochilinae) hummingbirds, and provided strong support for six principal nonhermit clades with the following branching order: (1) a predominantly lowland group comprising caribs (Eulampis holosericeus) and relatives (Androdon aequatorialis and Heliothryx barroti) with violet-ears (Colibri coruscans) and relatives (Doryfera ludovicae); (2) an Andean-associated clade of highly polytypic taxa (Eriocnemis, Heliodoxa, and Coeligena); (3) a second endemic Andean clade (Oreotrochilus chimborazo, Aglaiocercus coelestis, and Lesbia victoriae) paired with thorntails (Popelairia conversii); (4) emeralds and relatives (Chlorostilbon mellisugus, Amazilia tzacatl, Thalurania colombica, Orthorhyncus cristatus and Campylopterus villaviscensio); (5) mountain-gems (Lampornis clemenciae and Eugenes fulgens); and (6) tiny bee-like forms (Archilochus colubris, Myrtis fanny, Acestrura mulsant, and Philodice mitchellii). Corresponding analyses on a matrix of unsymmetrized delta values gave similar support for these relationships except that the branching order of the two Andean clades (2, 3 above) was unresolved. In general, subsidiary relationships were consistent and well supported by both matrices, sometimes revealing surprising associations between forms that differ dramatically in plumage and bill morphology. Our results also reveal some basic aspects of hummingbird ecologic and morphologic evolution. For example, most of the diverse endemic Andean assemblage apparently comprises two genetically divergent clades, whereas the majority of North American hummingbirds belong a single third clade. Genetic distances separating some morphologically distinct genera (Oreotrochilus, Aglaiocercus, Lesbia; Myrtis, Acestrura, Philodice) were no greater than among congeneric (Coeligena) species, indicating that, in hummingbirds, morphological divergence does not necessarily reflect level of genetic divergence. PMID:9066799

  3. 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.

  4. Evaluation of lossy data compression in primary interpretation for full-field digital mammography.

    PubMed

    Kovacs, Mark D; Reicher, Joshua J; Grotts, Jonathan F; Reicher, Murray A; Trambert, Michael A

    2015-03-01

    OBJECTIVE. For full-field digital mammography (FFDM), federal regulations prohibit lossy data compression for primary reading and archiving, unlike all other medical images, where reading physicians can apply their professional judgment in implementing lossy compression. Faster image transfer, lower costs, and greater access to expert mammographers would result from development of a safe standard for primary interpretation and archive of lossy-compressed FFDM images. This investigation explores whether JPEG 2000 80:1 lossy data compression affects clinical accuracy in digital mammography. MATERIALS AND METHODS. Randomized FFDM cases (n = 194) were interpreted by six experienced mammographers with and without JPEG 2000 80:1 lossy compression applied. A cancer-enriched population was used, with just less than half of the cases (42%) containing subtle (< 1 cm) biopsy-proven cancerous lesions, and the remaining cases were negative as proven by 2-year follow-up. Data were analyzed using the jackknife alternative free-response ROC (JAFROC) method. RESULTS. The differences in reader performance between lossy-compressed and non-lossy-compressed images using lesion localization (0.660 vs 0.671), true-positive fraction (0.879 vs 0.879), and false-positive fraction (0.283 vs 0.271) were not statistically significant. There was no difference in the JAFROC figure of merit between lossy-compressed and non-lossy-compressed images, with a mean difference of -0.01 (95% CI, -0.03 to 0.01; F1,5 = 2.30; p = 0.189). CONCLUSION. These results suggest that primary interpretation of JPEG 2000 80:1 lossy-compressed FFDM images may be viable without degradation of clinical quality. Benefits would include lower storage costs, faster telemammography, and enhanced access to expert mammographers. PMID:25714287

  5. 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

  6. Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy.

    PubMed

    Liu, Bin; Fang, Longyun; Wang, Shanyi; Wang, Xiaolong; Li, Hongtao; Chou, Kuo-Chen

    2015-11-21

    The microRNA (miRNA), a small non-coding RNA molecule, plays an important role in transcriptional and post-transcriptional regulation of gene expression. Its abnormal expression, however, has been observed in many cancers and other disease states, implying that the miRNA molecules are also deeply involved in these diseases, particularly in carcinogenesis. Therefore, it is important for both basic research and miRNA-based therapy to discriminate the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops). Most existing methods in this regard were based on the strategy in which RNA samples were formulated by a vector formed by their Kmer components. But the length of Kmers must be very short; otherwise, the vector's dimension would be extremely large, leading to the "high-dimension disaster" or overfitting problem. Inspired by the concept of "degenerate energy levels" in quantum mechanics, we introduced the "degenerate Kmer" (deKmer) to represent RNA samples. By doing so, not only we can accommodate long-range coupling effects but also we can avoid the high-dimension problem. Rigorous jackknife tests and cross-species experiments indicated that our approach is very promising. It has not escaped our notice that the deKmer approach can also be applied to many other areas of computational biology. A user-friendly web-server for the new predictor has been established at http://bioinformatics.hitsz.edu.cn/miRNA-deKmer/, by which users can easily get their desired results. PMID:26362104

  7. 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.

  8. [Forest lighting fire forecasting for Daxing'anling Mountains based on MAXENT model].

    PubMed

    Sun, Yu; Shi, Ming-Chang; Peng, Huan; Zhu, Pei-Lin; Liu, Si-Lin; Wu, Shi-Lei; He, Cheng; Chen, Feng

    2014-04-01

    Daxing'anling Mountains is one of the areas with the highest occurrence of forest lighting fire in Heilongjiang Province, and developing a lightning fire forecast model to accurately predict the forest fires in this area is of importance. Based on the data of forest lightning fires and environment variables, the MAXENT model was used to predict the lightning fire in Daxing' anling region. Firstly, we studied the collinear diagnostic of each environment variable, evaluated the importance of the environmental variables using training gain and the Jackknife method, and then evaluated the prediction accuracy of the MAXENT model using the max Kappa value and the AUC value. The results showed that the variance inflation factor (VIF) values of lightning energy and neutralized charge were 5.012 and 6.230, respectively. They were collinear with the other variables, so the model could not be used for training. Daily rainfall, the number of cloud-to-ground lightning, and current intensity of cloud-to-ground lightning were the three most important factors affecting the lightning fires in the forest, while the daily average wind speed and the slope was of less importance. With the increase of the proportion of test data, the max Kappa and AUC values were increased. The max Kappa values were above 0.75 and the average value was 0.772, while all of the AUC values were above 0.5 and the average value was 0. 859. With a moderate level of prediction accuracy being achieved, the MAXENT model could be used to predict forest lightning fire in Daxing'anling Mountains. PMID:25011305

  9. 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.

  10. Physico-chemical properties of PCDD/PCDFs and phthalate esters.

    PubMed

    Saçan, M T; Ozkul, M; Erdem, S S

    2005-10-01

    QSPR models for water solubility (S), n-octanol/water partition coefficient (K(OW)), and Henry's law constant (H) for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzo-p-furans (PCDFs) and phthalates have been established based on two different sets of parameters. Those parameters were topology based characteristic root index (CRI) and three semi-empirical molecular descriptors, namely--energies of the highest occupied and the lowest unoccupied molecular orbital (E(HOMO) and E(LUMO)), and dipole moment (mu). The best fit equation found by "forward multiple linear regression" showed that the topology based CRI was the most important parameter for the modelling of solubility and n-octanol/water partition coefficient. For n-octanol/water partition coefficient a two-parameter equation including the CRI and E(HOMO) with a correlation coefficient of r = 0.992 was obtained whereas a three-parameter equation for solubility and Henry's law constant including the CRI, E(LUMO) and mu with a correlation coefficient of r = 0.986 and r = 0.933 was obtained, respectively. E(HOMO) and mu didn't appear in the same model because of the collinearity. The results of modified jackknife tests indicated that the three models were statistically robust. Mean deviation of calculated values from experimental data amounted to 0.27, 0.17, and 0.28 log units for the three properties mentioned. The developed models have been used to predict the S, K(OW) and H of compounds not included in the training sets. PMID:16272043

  11. 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

  12. The projack: a resampling approach to correct for ranking bias in high-throughput studies

    PubMed Central

    Zhou, Yi-Hui; Wright, Fred A.

    2016-01-01

    The problem of ranked inference arises in a number of settings, for which the investigator wishes to perform parameter inference after ordering a set of \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$m$\\end{document} statistics. In contrast to inference for a single hypothesis, the ranking procedure introduces considerable bias, a problem known as the “winner's curse” in genetic association. We introduce the projack (for Prediction by Re- Ordered Jackknife and Cross-Validation, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$K$\\end{document}-fold). The projack is a resampling-based procedure that provides low-bias estimates of the expected ranked effect size parameter for a set of possibly correlated \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$z$\\end{document} statistics. The approach is flexible, and has wide applicability to high-dimensional datasets, including those arising from genomics platforms. Initially, motivated for the setting where original data are available for resampling, the projack can be extended to the situation where only the vector of \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$z$\\end{document} values is available. We illustrate the projack for correction of the winner's curse in genetic association, although it can be used much more generally. PMID:26040912

  13. An Ancient Origin for the Enigmatic Flat-Headed Frogs (Bombinatoridae: Barbourula) from the Islands of Southeast Asia

    PubMed Central

    Blackburn, David C.; Bickford, David P.; Diesmos, Arvin C.; Iskandar, Djoko T.; Brown, Rafe M.

    2010-01-01

    Background The complex history of Southeast Asian islands has long been of interest to biogeographers. Dispersal and vicariance events in the Pleistocene have received the most attention, though recent studies suggest a potentially more ancient history to components of the terrestrial fauna. Among this fauna is the enigmatic archaeobatrachian frog genus Barbourula, which only occurs on the islands of Borneo and Palawan. We utilize this lineage to gain unique insight into the temporal history of lineage diversification in Southeast Asian islands. Methodology/Principal Findings Using mitochondrial and nuclear genetic data, multiple fossil calibration points, and likelihood and Bayesian methods, we estimate phylogenetic relationships and divergence times for Barbourula. We determine the sensitivity of focal divergence times to specific calibration points by jackknife approach in which each calibration point is excluded from analysis. We find that relevant divergence time estimates are robust to the exclusion of specific calibration points. Barbourula is recovered as a monophyletic lineage nested within a monophyletic Costata. Barbourula diverged from its sister taxon Bombina in the Paleogene and the two species of Barbourula diverged in the Late Miocene. Conclusions/Significance The divergences within Barbourula and between it and Bombina are surprisingly old and represent the oldest estimates for a cladogenetic event resulting in living taxa endemic to Southeast Asian islands. Moreover, these divergence time estimates are consistent with a new biogeographic scenario: the Palawan Ark Hypothesis. We suggest that components of Palawan's terrestrial fauna might have “rafted” on emergent portions of the North Palawan Block during its migration from the Asian mainland to its present-day position near Borneo. Further, dispersal from Palawan to Borneo (rather than Borneo to Palawan) may explain the current day disjunct distribution of this ancient lineage. PMID:20711504

  14. [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

  15. Simulating cosmic reionization: how large a volume is large enough?

    NASA Astrophysics Data System (ADS)

    Iliev, Ilian T.; Mellema, Garrelt; Ahn, Kyungjin; Shapiro, Paul R.; Mao, Yi; Pen, Ue-Li

    2014-03-01

    We present the largest-volume (425 Mpc h-1 = 607 Mpc on a side) full radiative transfer simulation of cosmic reionization to date. We show that there is significant additional power in density fluctuations at very large scales. We systematically investigate the effects this additional power has on the progress, duration and features of reionization and on selected reionization observables. We find that comoving volume of ˜100 Mpc h-1 per side is sufficient for deriving a convergent mean reionization history, but that the reionization patchiness is significantly underestimated. We use jackknife splitting to quantify the convergence of reionization properties with simulation volume. We find that sub-volumes of ˜100 Mpc h-1 per side or larger yield convergent reionization histories, except for the earliest times, but smaller volumes of ˜50 Mpc h-1 or less are not well converged at any redshift. Reionization history milestones show significant scatter between the sub-volumes, as high as ?z ˜ 1 for ˜50 Mpc h-1 volumes. If we only consider mean-density sub-regions the scatter decreases, but remains at ?z ˜ 0.1-0.2 for the different size sub-volumes. Consequently, many potential reionization observables like 21-cm rms, 21-cm PDF skewness and kurtosis all show good convergence for volumes of ˜200 Mpc h-1, but retain considerable scatter for smaller volumes. In contrast, the three-dimensional 21-cm power spectra at large scales (k < 0.25 h Mpc-1) do not fully converge for any sub-volume size. These additional large-scale fluctuations significantly enhance the 21-cm fluctuations, which should improve the prospects of detection considerably, given the lower foregrounds and greater interferometer sensitivity at higher frequencies.

  16. 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

  17. PRIMUS: Galaxy clustering as a function of luminosity and color at 0.2 < z < 1

    SciTech Connect

    Skibba, Ramin A.; Smith, M. Stephen M.; Coil, Alison L.; Mendez, Alexander J.; Moustakas, John; Aird, James; Blanton, Michael R.; Bray, Aaron D.; Eisenstein, Daniel J.; Cool, Richard J.; Wong, Kenneth C.; Zhu, Guangtun

    2014-04-01

    We present measurements of the luminosity and color-dependence of galaxy clustering at 0.2 < z < 1.0 in the Prism Multi-object Survey. We quantify the clustering with the redshift-space and projected two-point correlation functions, ?(r{sub p} , ?) and w{sub p} (r{sub p} ), using volume-limited samples constructed from a parent sample of over ?130, 000 galaxies with robust redshifts in seven independent fields covering 9 deg{sup 2} of sky. We quantify how the scale-dependent clustering amplitude increases with increasing luminosity and redder color, with relatively small errors over large volumes. We find that red galaxies have stronger small-scale (0.1 Mpc h {sup –1} < r{sub p} < 1 Mpc h {sup –1}) clustering and steeper correlation functions compared to blue galaxies, as well as a strong color dependent clustering within the red sequence alone. We interpret our measured clustering trends in terms of galaxy bias and obtain values of b {sub gal} ? 0.9-2.5, quantifying how galaxies are biased tracers of dark matter depending on their luminosity and color. We also interpret the color dependence with mock catalogs, and find that the clustering of blue galaxies is nearly constant with color, while redder galaxies have stronger clustering in the one-halo term due to a higher satellite galaxy fraction. In addition, we measure the evolution of the clustering strength and bias, and we do not detect statistically significant departures from passive evolution. We argue that the luminosity- and color-environment (or halo mass) relations of galaxies have not significantly evolved since z ? 1. Finally, using jackknife subsampling methods, we find that sampling fluctuations are important and that the COSMOS field is generally an outlier, due to having more overdense structures than other fields; we find that 'cosmic variance' can be a significant source of uncertainty for high-redshift clustering measurements.

  18. Population pharmacokinetics and Bayesian estimation of tacrolimus exposure in paediatric liver transplant recipients

    PubMed Central

    Kassir, Nastya; Labbé, Line; Delaloye, Jean-Romain; Mouksassi, Mohamad-Samer; Lapeyraque, Anne-Laure; Alvarez, Fernando; Lallier, Michel; Beaunoyer, Mona; Théorêt, Yves; Litalien, Catherine

    2014-01-01

    Aims The objectives of this study were to develop a population pharmacokinetic (PopPK) model for tacrolimus in paediatric liver transplant patients and determine optimal sampling strategies to estimate tacrolimus exposure accurately. Methods Twelve hour intensive pharmacokinetic profiles from 30 patients (age 0.4–18.4 years) receiving tacrolimus orally were analysed. The PopPK model explored the following covariates: weight, age, sex, type of transplant, age of liver donor, liver function tests, albumin, haematocrit, drug interactions, drug formulation and time post-transplantation. Optimal sampling strategies were developed and validated with jackknife. Results A two-compartment model with first-order absorption and elimination and lag time described the data. Weight was included on all pharmacokinetic parameters. Typical apparent clearance and central volume of distribution were 12.1 l h?1 and 31.3 l, respectively. The PopPK approach led to the development of optimal sampling strategies, which allowed estimation of tacrolimus pharmacokinetics and area under the concentration–time curve (AUC) on the basis of practical sampling schedules (three or four sampling times within 4 h) with clinically acceptable prediction error limit. The mean bias and precision of the Bayesian vs. reference (trapezoidal) AUCs ranged from ?2.8 to ?1.9% and from 7.4 to 12.5%, respectively. Conclusions The PopPK of tacrolimus and empirical Bayesian estimates represent an accurate and convenient method to predict tacrolimus AUC(0–12) in paediatric liver transplant recipients, despite high between-subject variability in pharmacokinetics and patient demographics. The developed optimal sampling strategies will allow the undertaking of prospective trials to define the tacrolimus AUC-based therapeutic window and dosing guidelines in this population. PMID:24977292

  19. 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.

  20. Classification of Birds and Bats Using Flight Tracks

    SciTech Connect

    Cullinan, Valerie I.; Matzner, Shari; Duberstein, Corey A.

    2015-05-01

    Classification of birds and bats that use areas targeted for offshore wind farm development and the inference of their behavior is essential to evaluating the potential effects of development. The current approach to assessing the number and distribution of birds at sea involves transect surveys using trained individuals in boats or airplanes or using high-resolution imagery. These approaches are costly and have safety concerns. Based on a limited annotated library extracted from a single-camera thermal video, we provide a framework for building models that classify birds and bats and their associated behaviors. As an example, we developed a discriminant model for theoretical flight paths and applied it to data (N = 64 tracks) extracted from 5-min video clips. The agreement between model- and observer-classified path types was initially only 41%, but it increased to 73% when small-scale jitter was censored and path types were combined. Classification of 46 tracks of bats, swallows, gulls, and terns on average was 82% accurate, based on a jackknife cross-validation. Model classification of bats and terns (N = 4 and 2, respectively) was 94% and 91% correct, respectively; however, the variance associated with the tracks from these targets is poorly estimated. Model classification of gulls and swallows (N ? 18) was on average 73% and 85% correct, respectively. The models developed here should be considered preliminary because they are based on a small data set both in terms of the numbers of species and the identified flight tracks. Future classification models would be greatly improved by including a measure of distance between the camera and the target.

  1. Rapid field identification of subjects involved in firearm-related crimes based on electroanalysis coupled with advanced chemometric data treatment.

    PubMed

    Cetó, Xavier; O'Mahony, Aoife M; Samek, Izabela A; Windmiller, Joshua R; del Valle, Manel; Wang, Joseph

    2012-12-01

    We demonstrate a novel system for the detection and discrimination of varying levels of exposure to gunshot residue from subjects in various control scenarios. Our aim is to address the key challenge of minimizing the false positive identification of individuals suspected of discharging a firearm. The chemometric treatment of voltammetric data from different controls using Canonical Variate Analysis (CVA) provides several distinct clusters for each scenario examined. Multiple samples were taken from subjects in controlled tests such as secondary contact with gunshot residue (GSR), loading a firearm, and postdischarge of a firearm. These controls were examined at both bare carbon and gold-modified screen-printed electrodes using different sampling methods: the 'swipe' method with integrated sampling and electroanalysis and a more traditional acid-assisted q-tip swabbing method. The electroanalytical fingerprint of each sample was examined using square-wave voltammetry; the resulting data were preprocessed with Fast Fourier Transform (FFT), followed by CVA treatment. High levels of discrimination were thus achieved in each case over 3 classes of samples (reflecting different levels of involvement), achieving maximum accuracy, sensitivity, and specificity values of 100% employing the leave-one-out validation method. Further validation with the 'jack-knife' technique was performed, and the resulting values were in good agreement with the former method. Additionally, samples from subjects in daily contact with relevant metallic constituents were analyzed to assess possible false positives. This system may serve as a potential method for a portable, field-deployable system aimed at rapidly identifying a subject who has loaded or discharged a firearm to verify involvement in a crime, hence providing law enforcement personnel with an invaluable forensic tool in the field. PMID:23121395

  2. Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

    PubMed Central

    Braun, Edward L.

    2014-01-01

    The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order. PMID:24795852

  3. Making Mosquito Taxonomy Useful: A Stable Classification of Tribe Aedini that Balances Utility with Current Knowledge of Evolutionary Relationships

    PubMed Central

    Wilkerson, Richard C.; Linton, Yvonne-Marie; Fonseca, Dina M.; Schultz, Ted R.; Price, Dana C.; Strickman, Daniel A.

    2015-01-01

    The tribe Aedini (Family Culicidae) contains approximately one-quarter of the known species of mosquitoes, including vectors of deadly or debilitating disease agents. This tribe contains the genus Aedes, which is one of the three most familiar genera of mosquitoes. During the past decade, Aedini has been the focus of a series of extensive morphology-based phylogenetic studies published by Reinert, Harbach, and Kitching (RH&K). Those authors created 74 new, elevated or resurrected genera from what had been the single genus Aedes, almost tripling the number of genera in the entire family Culicidae. The proposed classification is based on subjective assessments of the “number and nature of the characters that support the branches” subtending particular monophyletic groups in the results of cladistic analyses of a large set of morphological characters of representative species. To gauge the stability of RH&K’s generic groupings we reanalyzed their data with unweighted parsimony jackknife and maximum-parsimony analyses, with and without ordering 14 of the characters as in RH&K. We found that their phylogeny was largely weakly supported and their taxonomic rankings failed priority and other useful taxon-naming criteria. Consequently, we propose simplified aedine generic designations that 1) restore a classification system that is useful for the operational community; 2) enhance the ability of taxonomists to accurately place new species into genera; 3) maintain the progress toward a natural classification based on monophyletic groups of species; and 4) correct the current classification system that is subject to instability as new species are described and existing species more thoroughly defined. We do not challenge the phylogenetic hypotheses generated by the above-mentioned series of morphological studies. However, we reduce the ranks of the genera and subgenera of RH&K to subgenera or informal species groups, respectively, to preserve stability as new data become available. PMID:26226613

  4. Estimating individual glomerular volume in the human kidney: clinical perspectives

    PubMed Central

    Puelles, Victor G.; Zimanyi, Monika A.; Samuel, Terence; Hughson, Michael D.; Douglas-Denton, Rebecca N.; Bertram, John F.

    2012-01-01

    Background. Measurement of individual glomerular volumes (IGV) has allowed the identification of drivers of glomerular hypertrophy in subjects without overt renal pathology. This study aims to highlight the relevance of IGV measurements with possible clinical implications and determine how many profiles must be measured in order to achieve stable size distribution estimates. Methods. We re-analysed 2250 IGV estimates obtained using the disector/Cavalieri method in 41 African and 34 Caucasian Americans. Pooled IGV analysis of mean and variance was conducted. Monte-Carlo (Jackknife) simulations determined the effect of the number of sampled glomeruli on mean IGV. Lin’s concordance coefficient (RC), coefficient of variation (CV) and coefficient of error (CE) measured reliability. Results. IGV mean and variance increased with overweight and hypertensive status. Superficial glomeruli were significantly smaller than juxtamedullary glomeruli in all subjects (P < 0.01), by race (P < 0.05) and in obese individuals (P < 0.01). Subjects with multiple chronic kidney disease (CKD) comorbidities showed significant increases in IGV mean and variability. Overall, mean IGV was particularly reliable with nine or more sampled glomeruli (RC > 0.95, <5% difference in CV and CE). These observations were not affected by a reduced sample size and did not disrupt the inverse linear correlation between mean IGV and estimated total glomerular number. Conclusions. Multiple comorbidities for CKD are associated with increased IGV mean and variance within subjects, including overweight, obesity and hypertension. Zonal selection and the number of sampled glomeruli do not represent drawbacks for future longitudinal biopsy-based studies of glomerular size and distribution. PMID:21984554

  5. 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

  6. Lethal and Demographic Impact of Chlorpyrifos and Spinosad on the Ectoparasitoid Habrobracon hebetor (Say) (Hymenoptera: Braconidae).

    PubMed

    Mahdavi, V; Saber, M; Rafiee-Dastjerdi, H; Kamita, S G

    2015-12-01

    The appropriate use of biological agents and chemical compounds is necessary to establish successful integrated pest management (IPM) programs. Thus, the off-target effects of pesticides on biological control agents are essential considerations of IPM. In this study, the effects of lethal and sublethal concentrations of chlorpyrifos and spinosad on the demographic parameters of Habrobracon hebetor (Say) (Hymenoptera: Braconidae) were assessed. Bioassays were carried out on immature and adult stages by using dipping and contact exposure of dry pesticide residue on an inert material, respectively. The lethal concentration (LC)50 values of chlorpyrifos and spinosad were 3.69 and 151.37 ppm, respectively, on the larval stage and 1.75 and 117.37 ppm, respectively, on adults. Hazard quotient (HQ) values for chlorpyrifos and spinosad were 400 and 2.2, respectively, on the larval stage and 857.14 and 2.84, respectively, on adults. A low lethal concentration (LC30) was used to assess the sublethal effects of both pesticides on the surviving females. In each treatment, 25 survivors were randomly selected and transferred into 6-cm Petri dishes. Adults were provided daily with last instars of Anagasta kuehniella (Zeller) as a host until all of the females died. The number of eggs laid, percent of larvae hatched, longevity, and sex ratio were recorded. Stable population growth parameters were estimated by the Jackknife method. In control, chlorpyrifos, and spinosad treatments, the intrinsic rates of increase (r m) values were 0.23, 0.10, and 0.21, respectively. The results of this study suggest a relative compatibility between spinosad use and H. hebetor. Finally, further studies should be conducted under natural conditions to verify the compatibility of spinosad with H. hebetor in IPM programs. PMID:26280986

  7. Normal modes splitting estimations from recent large earthquakes

    NASA Astrophysics Data System (ADS)

    Gourdin-sangouard, C.; Nolet, G.; Laske, G.; Masters, G.

    2011-12-01

    The observation of the splitting of normal modes was a very active research field in the 1990's but has seen little improvement since then. Paradoxically, in the last ten years the number of high-quality, digital broadband stations has grown by almost an order of magnitude, and the last decade has seen no shortage of strong earthquakes. The time is therefore ripe to revisit the topic. Recent large earthquakes recorded by the global seismic network are studied to compute and determinate the splitting characteristics of normal mode multiplets. Our ultimate goal is to use these data together with multiple-frequency travel times to invert for structure of the Earth's mantle. In a first effort, we analyzed nearly 80 earthquakes in the period 2000-2010 using a mode stripping technique. This allowed us to do a rigorous quality control. We strip multiplets of different spectra computed from more 15000 recordings of 50 events. Since we desire to get informations about the lower mantle, the maximum angular order studied is 12 for a maximum frequency of 5 mHz. In the second step, we use the autoregressive estimation technique of Masters et al. (GJI, 2000), which allows for solving the splitting matrix system without knowledge of the earthquake source. We present results from the first step that show how we use the technique to strip multiplets of different spectra computed from three components of multiple events in the period of study to select suitable data for subsequent autoregressive estimation. New estimations of splitting are also computed for a variety of multiplets. We also present splitting estimates from the autoregressive technique and make a comparison with earlier data, as well as with recent efforts by other groups to re-determine mode splitting. We check the robustess of this estimates using a 'jackknifing' test in which we repeatedly remove a random fraction (10%) of the data and recompute the coefficients.

  8. 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.

  9. Using the Peters--Belson method to measure health care disparities from complex survey data.

    PubMed

    Graubard, B I; Sowmya Rao, R; Gastwirth, Joseph L

    2005-09-15

    The Peters-Belson (PB) method uses regression to assess wage discrimination and can also be used to analyse disparities for a variety of health care issues, e.g. cancer screening. The PB method estimates the proportion of an overall disparity that is not explained by the covariates in the regression, e.g. education, which may be due to discrimination. This method first fits a regression model with individual-level covariates to the majority/advantaged group and then uses the fitted model to estimate the expected values for minority-group members had they been members of the majority group. The data on disparities in health care available to biomedical researchers differ from data used in legal cases as it is often obtained from large-scale studies or surveys with complex sample designs involving stratified multi-stage cluster sampling. Sample surveys with a large representative sample of various racial/ethnic groups and the extensive collection of important social-demographic variables provide excellent sources of data for assessing disparity for a wide range of health behaviours. We extend the PB method for multiple logistic and linear regressions of simple random samples to weighted data from complex designed survey samples. Because of the weighting and complex sample designs, we show how to apply the Taylor linearization method and delete-one-group jackknife methods to obtain estimates of standard errors for the estimated disparity. Data from the 1998 National Health Interview Survey on racial differences in cancer screening among women is used to illustrate the PB method. PMID:16118808

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

    PubMed

    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

  11. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach.

    PubMed

    Zeng, Yu-hong; Guo, Yan-zhi; Xiao, Rong-quan; Yang, Li; Yu, Le-zheng; Li, Meng-long

    2009-07-21

    The submitochondria location of a mitochondrial protein is very important for further understanding the structure and function of this protein. Hence, it is of great practical significance to develop an automated and reliable method for timely identifying the submitochondria locations of novel mitochondrial proteins. In this study, a sequence-based algorithm combining the augmented Chou's pseudo amino acid composition (Chou's PseAA) based on auto covariance (AC) is developed to predict protein submitochondria locations and membrane protein types in mitochondria inner membrane. The model fully considers the sequence-order effects between residues a certain distance apart in the sequence by AC combined with eight representative descriptors for both common proteins and membrane proteins. As a result of jackknife cross-validation tests, the method for submitochondria location prediction yields the accuracies of 91.8%, 96.4% and 66.1% for inner membrane, matrix, and outer membrane, respectively. The total accuracy is 89.7%. When predicting membrane protein types in mitochondria inner membrane, the method achieves the prediction performance with the accuracies of 98.4%, 64.3% and 86.7% for multi-pass inner membrane, single-pass inner membrane, and matrix side inner membrane, where the total accuracy is 93.6%. The overall performance of our method is better than the achievements of the previous studies. So our method can be an effective supplementary tool for future proteomics studies. The prediction software and all data sets used in this article are freely available at http://chemlab.scu.edu.cn/Predict_subMITO/index.htm. PMID:19341746

  12. Monitoring hydrofrac-induced seismicity by surface arrays - the DHM-Project Basel case study

    NASA Astrophysics Data System (ADS)

    Blascheck, P.; Häge, M.; Joswig, M.

    2012-04-01

    The method "nanoseismic monitoring" was applied during the hydraulic stimulation at the Deep-Heat-Mining-Project (DHM-Project) Basel. Two small arrays in a distance of 2.1 km and 4.8 km to the borehole recorded continuously for two days. During this time more than 2500 seismic events were detected. The method of the surface monitoring of induced seismicity was compared to the reference which the hydrofrac monitoring presented. The latter was conducted by a network of borehole seismometers by Geothermal Explorers Limited. Array processing provides a outlier resistant, graphical jack-knifing localization method which resulted in a average deviation towards the reference of 850 m. Additionally, by applying the relative localization master-event method, the NNW-SSE strike direction of the reference was confirmed. It was shown that, in order to successfully estimate the magnitude of completeness as well as the b-value at the event rate and detection sensibility present, 3 h segments of data are sufficient. This is supported by two segment out of over 13 h of evaluated data. These segments were chosen so that they represent a time during the high seismic noise during normal working hours in daytime as well as the minimum anthropogenic noise at night. The low signal-to-noise ratio was compensated by the application of a sonogram event detection as well as a coincidence analysis within each array. Sonograms allow by autoadaptive, non-linear filtering to enhance signals whose amplitudes are just above noise level. For these events the magnitude was determined by the master-event method, allowing to compute the magnitude of completeness by the entire-magnitude-range method provided by the ZMAP toolbox. Additionally, the b-values were determined and compared to the reference values. An introduction to the method of "nanoseismic monitoring" will be given as well as the comparison to reference data in the Basel case study.

  13. Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes

    PubMed Central

    2015-01-01

    Background Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been developed for predicting the binding affinity of protein-protein complexes based on structure and functional information. This work aims to predict the binding affinity of heterodimeric protein complexes from sequences only. Results This work proposes a support vector machine (SVM) based binding affinity classifier, called SVM-BAC, to classify heterodimeric protein complexes based on the prediction of their binding affinity. SVM-BAC identified 14 of 580 sequence descriptors (physicochemical, energetic and conformational properties of the 20 amino acids) to classify 216 heterodimeric protein complexes into low and high binding affinity. SVM-BAC yielded the training accuracy, sensitivity, specificity, AUC and test accuracy of 85.80%, 0.89, 0.83, 0.86 and 83.33%, respectively, better than existing machine learning algorithms. The 14 features and support vector regression were further used to estimate the binding affinities (Pkd) of 200 heterodimeric protein complexes. Prediction performance of a Jackknife test was the correlation coefficient of 0.34 and mean absolute error of 1.4. We further analyze three informative physicochemical properties according to their contribution to prediction performance. Results reveal that the following properties are effective in predicting the binding affinity of heterodimeric protein complexes: apparent partition energy based on buried molar fractions, relations between chemical structure and biological activity in principal component analysis IV, and normalized frequency of beta turn. Conclusions The proposed sequence-based prediction method SVM-BAC uses an optimal feature selection method to identify 14 informative features to classify and predict binding affinity of heterodimeric protein complexes. The characterization analysis revealed that the average numbers of beta turns and hydrogen bonds at protein-protein interfaces in high binding affinity complexes are more than those in low binding affinity complexes. PMID:26681483

  14. Spatial downscaling and mapping of daily precipitation and air temperature using daily station data and monthly mean maps

    NASA Astrophysics Data System (ADS)

    Flint, A. L.; Flint, L. E.; Stern, M. A.

    2013-12-01

    Accurate maps of daily weather variables are an essential component of hydrologic and ecologic modeling. Here we present a four-step method that uses daily station data and transient monthly maps of precipitation and air temperature. This method uses the monthly maps to help interpolate between stations for more accurate production of daily maps at any spatial resolution. The first step analyzes the quality of the each station's data using a discrepancy analysis that compares statistics derived from a statistical jack-knifing approach with a time-series evaluation of discrepancies generated for each station. Although several methods could be used for the second step of producing initial maps, such as kriging, splines, etc., we used a gradient plus inverse distance squared method that was developed to produce accurate climate maps for sparse data regions with widely separated and few climate stations, far fewer than would be needed for techniques such as kriging. The gradient plus inverse distance squared method uses local gradients in the climate parameters, easting, northing, and elevation, to adjust the inverse distance squared estimates for local gradients such as lapse rates, inversions, or rain shadows at scales of 10's of meters to kilometers. The third step is to downscale World Wide Web (web) based transient monthly data, such as Precipitation-Elevation Regression on Independent Slope Method (PRISM) for the US (4 km or 800 m maps) or Climate Research Unit (CRU 3.1) data sets (40 km for global applications) to the scale of the daily data's digital elevation model. In the final step the downscaled transient monthly maps are used to adjust the daily time-series mapped data (~30 maps/month) for each month. These adjustments are used to scale daily maps so that summing them for precipitation or averaging them for temperature would more accurately reproduce the variability in selected monthly maps. This method allows for individual days to have maxima or minima values away from the station locations based on the underlying geographic structure of the monthly maps. We compare our results with the web based 12 km Variable Infiltration Capacity model (VIC) daily data and the 1 km DayMet daily data as well as make comparisons of the month summation or average of daily data sets with the PRISM and CRU data sets. There were mixed results in the comparisons with some good agreement and some bad agreement, even between VIC and DayMet. These daily maps are intended to be used as input to daily hydrological models. The results will provide more insight into the significance of the differences, at least from a hydrology perspective.

  15. Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program

    PubMed Central

    Gragert, Loren; Maiers, Martin; Chatterjee, Ansu; Albrecht, Mark

    2015-01-01

    Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions. These measures are of particular interest in the field of hematopoietic stem cell transplant (HSCT). Donor/Recipient suitability for HSCT is determined by Human Leukocyte Antigen (HLA) similarity. Match predictions rely upon a precise description of HLA diversity, yet classical estimates are inaccurate given the heavy-tailed nature of the distribution. This directly affects HSCT matching and diversity measures in broader fields such as species richness. We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions. Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual. Indeed, our discovery rate of all U.S. European American haplotypes is estimated at 23.45% based upon sampling 3.97% of the population, leaving a large number of unobserved haplotypes. Population coverage, however, is much higher at 99.4% given that 90% of European Americans carry one of the 4.5% most frequent haplotypes. Alleles were found to be less diverse suggesting the current registry represents most alleles in the population. Thus, for HSCT registries, haplotype discovery will remain high with continued recruitment to a very deep level of sampling, but population coverage will not. Finally, we compared the convergence of our power-law versus classical diversity estimators such as Capture recapture, Chao, ACE and Jackknife methods. When fit to the haplotype data, our estimator displayed favorable properties in terms of convergence (with respect to sampling depth) and accuracy (with respect to diversity estimates). This suggests that power-law based estimators offer a valid alternative to classical diversity estimators and may have broad applicability in the field of population genetics. PMID:25901749

  16. Source mechanisms of the 2000 earthquake swarm in the West Bohemia/Vogtland region (Central Europe)

    NASA Astrophysics Data System (ADS)

    Horálek, Josef; Šílený, Jan

    2013-08-01

    An earthquake swarm of magnitudes up to ML = 3.2 occurred in the region of West Bohemia/Vogtland (border area between Czech Republic and Germany) in autumn 2000. This swarm consisted of nine episodic phases and lasted 4 months. We retrieved source mechanisms of 102 earthquakes with magnitudes between ML = 1.6 and 3.2 applying inversion of the peak amplitudes of direct P and SH waves, which were determined from ground motion seismograms. The investigated events cover the whole swarm activity in both time and space. We use data from permanent stations of seismic network WEBNET and from temporal stations, which were deployed in the epicentral area during the swarm; the number of stations varied from 7 to 18. The unconstrained moment tensor (MT) expression of the mechanism, which describes a general system of dipoles, that is both double-couple (DC) and non-DC sources, was applied. MTs of each earthquake were estimated by inversion of three different sets of data: P-wave amplitudes only, P- and SH-wave amplitudes and P-wave amplitudes along with the SH-wave amplitudes from a priori selected four `base' WEBNET stations, the respective MT solutions are nearly identical for each event investigated. The resultant mechanisms of all events are dominantly DCs with only insignificant non-DC components mostly not exceeding 10 per cent. We checked reliability of the MTs in jackknife trials eliminating some data; we simulated the mislocation of hypocentre or contaminated the P- and SH-wave amplitudes by accidental errors. These tests proved stable and well constrained MT solutions. The massive dominance of the DC in all investigated events implies that the 2000 swarm consisted of a large number of pure shears along a fault plane. The focal mechanisms indicate both oblique-normal and oblique-thrust faulting, however, the oblique-normal faulting prevails. The predominant strikes and dips of the oblique-normal events fit well the geometry of the main fault plane Nový Kostel (NK) and also match the strike, dip and rake of the largest ML = 4.6 earthquake of a strong swarm in 1985/86. On the contrary, the 2000 source mechanisms differ substantially from those of the 1997-swarm (which took place in two fault segments at the edge of the main NK fault plane) in both the faulting and the content of non-DC components. Further, we found that the scalar seismic moment M0 is related to the local magnitude ML used by WEBNET as M0 ? 101.12ML, which differs from the scaling law using moment magnitude Mw, that is M0 ? 101.5Mw.

  17. Detection of B-Mode Polarization at Degree Angular Scales by BICEP2

    NASA Astrophysics Data System (ADS)

    BICEP2 Collaboration; 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.

    2014-06-01

    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 ?KCMB?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 305?. 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.

  18. Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide.

    PubMed

    Kissling, Wilm Daniel; Dalby, Lars; Fløjgaard, Camilla; Lenoir, Jonathan; Sandel, Brody; Sandom, Christopher; Trøjelsgaard, Kristian; Svenning, Jens-Christian

    2014-07-01

    Ecological trait data are essential for understanding the broad-scale distribution of biodiversity and its response to global change. For animals, diet represents a fundamental aspect of species' evolutionary adaptations, ecological and functional roles, and trophic interactions. However, the importance of diet for macroevolutionary and macroecological dynamics remains little explored, partly because of the lack of comprehensive trait datasets. We compiled and evaluated a comprehensive global dataset of diet preferences of mammals ("MammalDIET"). Diet information was digitized from two global and cladewide data sources and errors of data entry by multiple data recorders were assessed. We then developed a hierarchical extrapolation procedure to fill-in diet information for species with missing information. Missing data were extrapolated with information from other taxonomic levels (genus, other species within the same genus, or family) and this extrapolation was subsequently validated both internally (with a jack-knife approach applied to the compiled species-level diet data) and externally (using independent species-level diet information from a comprehensive continentwide data source). Finally, we grouped mammal species into trophic levels and dietary guilds, and their species richness as well as their proportion of total richness were mapped at a global scale for those diet categories with good validation results. The success rate of correctly digitizing data was 94%, indicating that the consistency in data entry among multiple recorders was high. Data sources provided species-level diet information for a total of 2033 species (38% of all 5364 terrestrial mammal species, based on the IUCN taxonomy). For the remaining 3331 species, diet information was mostly extrapolated from genus-level diet information (48% of all terrestrial mammal species), and only rarely from other species within the same genus (6%) or from family level (8%). Internal and external validation showed that: (1) extrapolations were most reliable for primary food items; (2) several diet categories ("Animal", "Mammal", "Invertebrate", "Plant", "Seed", "Fruit", and "Leaf") had high proportions of correctly predicted diet ranks; and (3) the potential of correctly extrapolating specific diet categories varied both within and among clades. Global maps of species richness and proportion showed congruence among trophic levels, but also substantial discrepancies between dietary guilds. MammalDIET provides a comprehensive, unique and freely available dataset on diet preferences for all terrestrial mammals worldwide. It enables broad-scale analyses for specific trophic levels and dietary guilds, and a first assessment of trait conservatism in mammalian diet preferences at a global scale. The digitalization, extrapolation and validation procedures could be transferable to other trait data and taxa. PMID:25165528

  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. 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

  1. iLM-2L: A two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou?s general PseAAC.

    PubMed

    Ju, Zhe; Cao, Jun-Zhe; Gu, Hong

    2015-11-21

    As one of the most critical post-translational modifications, lysine methylation plays a key role in regulating various protein functions. In order to understand the molecular mechanism of lysine methylation, it is important to identify lysine methylation sites and their methylation degrees accurately. As the traditional experimental methods are time-consuming and labor-intensive, several computational methods have been developed for the identification of methylation sites. However, the prediction accuracy of existing computational methods is still unsatisfactory. Moreover, they are only focused on predicting whether a query lysine residue is a methylation site, without considering its methylation degrees. In this paper, a novel two-level predictor named iLM-2L is proposed to predict lysine methylation sites and their methylation degrees using composition of k-spaced amino acid pairs feature coding scheme and support vector machine algorithm. The 1st level is to identify whether a query lysine residue is a methylation site, and the 2nd level is to identify which methylation degree(s) the query lysine residue belongs to if it has been predicted as a methyllysine site in the 1st level identification. The iLM-2L achieves a promising performance with a Sensitivity of 76.46%, a Specificity of 91.90%, an Accuracy of 85.31% and a Matthew?s correlation coefficient of 69.94% for the 1st level as well as a Precision of 84.81%, an accuracy of 79.35%, a recall of 80.83%, an Absolute_Ture of 73.89% and a Hamming_loss of 15.63% for the 2nd level in jackknife test. As illustrated by independent test, the performance of iLM-2L outperforms other existing lysine methylation site predictors significantly. A matlab software package for iLM-2L can be freely downloaded from https://github.com/juzhe1120/Matlab_Software/blob/master/iLM-2L_Matlab_Software.rar. PMID:26254214

  2. 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.

  3. Observer Performance in the Detection and Classification of Malignant Hepatic Nodules and Masses with CT Image-Space Denoising and Iterative Reconstruction1

    PubMed Central

    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.

    2015-01-01

    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 jack-knife 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. PMID:26020436

  4. Revised and annotated checklist of aquatic and semi-aquatic Heteroptera of Hungary with comments on biodiversity patterns.

    PubMed

    Boda, Pál; Bozóki, Tamás; Vásárhelyi, Tamás; Bakonyi, Gábor; Várbíró, Gábor

    2015-01-01

    A basic knowledge of regional faunas is necessary to follow the changes in macroinvertebrate communities caused by environmental influences and climatic trends in the future. We collected all the available data on water bugs in Hungary using an inventory method, a UTM grid based database was built, and Jackknife richness estimates and species accumulation curves were calculated. Fauna compositions were compared among Central-European states. As a result, an updated and annotated checklist for Hungary is provided, containing 58 species in 21 genera and 12 families. A total 66.8% of the total UTM 10 × 10 km squares in Hungary possess faunistic data for water bugs. The species number in grid cells numbered from 0 to 42, and their diversity patterns showed heterogeneity. The estimated species number of 58 is equal to the actual number of species known from the country. The asymptotic shape of the accumulative species curve predicts that additional sampling efforts will not increase the number of species currently known from Hungary. These results suggest that the number of species in the country was estimated correctly and that the species accumulation curve levels off at an asymptotic value. Thus a considerable increase in species richness is not expected in the future. Even with the species composition changing the chance of species turn-over does exist. Overall, 36.7% of the European water bug species were found in Hungary. The differences in faunal composition between Hungary and its surrounding countries were caused by the rare or unique species, whereas 33 species are common in the faunas of the eight countries. Species richness does show a correlation with latitude, and similar species compositions were observed in the countries along the same latitude. The species list and the UTM-based database are now up-to-date for Hungary, and it will provide a basis for future studies of distributional and biodiversity patterns, biogeography, relative abundance and frequency of occurrences important in community ecology, or the determination of conservation status. PMID:25987880

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

    SciTech Connect

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

    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.

  6. Spatial Distribution of Sand Fly Vectors and Eco-Epidemiology of Cutaneous Leishmaniasis Transmission in Colombia

    PubMed Central

    Ferro, Cristina; López, Marla; Fuya, Patricia; Lugo, Ligia; Cordovez, Juan Manuel; González, Camila

    2015-01-01

    Background Leishmania is transmitted by Phlebotominae insects that maintain the enzootic cycle by circulating between sylvatic and domestic mammals; humans enter the cycles as accidental hosts due to the vector’s search for blood source. In Colombia, leishmaniasis is an endemic disease and 95% of all cases are cutaneous (CL), these cases have been reported in several regions of the country where the intervention of sylvatic areas by the introduction of agriculture seem to have an impact on the rearrangement of new transmission cycles. Our study aimed to update vector species distribution in the country and to analyze the relationship between vectors’ distribution, climate, land use and CL prevalence. Methods A database with geographic information was assembled, and ecological niche modeling was performed to explore the potential distribution of each of the 21 species of medical importance in Colombia, using thirteen bioclimatic variables, three topographic and three principal components derived from NDVI. Binary models for each species were obtained and related to both land use coverage, and a CL prevalence map with available epidemiological data. Finally, maps of species potential distribution were summed to define potential species richness in the country. Results In total, 673 single records were obtained with Lutzomyia gomezi, Lutzomyia longipalpis, Psychodopygus panamensis, Psathyromyia shannoni and Pintomyia evansi the species with the highest number of records. Eighteen species had significant models, considering the area under the curve and the jackknife results: L. gomezi and P. panamensis had the widest potential distribution. All sand fly species except for Nyssomyia antunesi are mainly distributed in regions with rates of prevalence between 0.33 to 101.35 cases per 100,000 inhabitants and 76% of collection data points fall into transformed ecosystems. Discussion Distribution ranges of sand flies with medical importance in Colombia correspond predominantly to disturbed areas, where the original land coverage is missing therefore increasing the domiciliation potential. We highlight the importance of the use of distribution maps as a tool for the development of strategies for prevention and control of diseases. PMID:26431546

  7. Revised and annotated checklist of aquatic and semi-aquatic Heteroptera of Hungary with comments on biodiversity patterns

    PubMed Central

    Boda, Pál; Bozóki, Tamás; Vásárhelyi, Tamás; Bakonyi, Gábor; Várbíró, Gábor

    2015-01-01

    Abstract A basic knowledge of regional faunas is necessary to follow the changes in macroinvertebrate communities caused by environmental influences and climatic trends in the future. We collected all the available data on water bugs in Hungary using an inventory method, a UTM grid based database was built, and Jackknife richness estimates and species accumulation curves were calculated. Fauna compositions were compared among Central-European states. As a result, an updated and annotated checklist for Hungary is provided, containing 58 species in 21 genera and 12 families. A total 66.8% of the total UTM 10 × 10 km squares in Hungary possess faunistic data for water bugs. The species number in grid cells numbered from 0 to 42, and their diversity patterns showed heterogeneity. The estimated species number of 58 is equal to the actual number of species known from the country. The asymptotic shape of the accumulative species curve predicts that additional sampling efforts will not increase the number of species currently known from Hungary. These results suggest that the number of species in the country was estimated correctly and that the species accumulation curve levels off at an asymptotic value. Thus a considerable increase in species richness is not expected in the future. Even with the species composition changing the chance of species turn-over does exist. Overall, 36.7% of the European water bug species were found in Hungary. The differences in faunal composition between Hungary and its surrounding countries were caused by the rare or unique species, whereas 33 species are common in the faunas of the eight countries. Species richness does show a correlation with latitude, and similar species compositions were observed in the countries along the same latitude. The species list and the UTM-based database are now up-to-date for Hungary, and it will provide a basis for future studies of distributional and biodiversity patterns, biogeography, relative abundance and frequency of occurrences important in community ecology, or the determination of conservation status. PMID:25987880

  8. Intertidal benthic macrofauna of rare rocky fragments in the Amazon region.

    PubMed

    Morais, Gisele Cavalcante; Lee, James Tony

    2014-03-01

    Rock fragment fields are important habitat for biodiversity maintenance in coastal regions, particularly when located in protected areas dominated by soft sediments. Researches in this habitat have received surprisingly little attention on the Amazon Coast, despite rock fragments provide refuges, nursery grounds and food sources for a variety of benthic species. The present survey describes the mobile macroinvertebrate species composition and richness of the intertidal rocky fragments in Areuá Island within the "Mãe Grande de Curuçá" Marine Extractive Reserve (RESEX) on the Brazilian Amazon Coast. Samples were collected during the dry (August and November 2009) and rainy seasons (March and May 2010) on the upper and lower intertidal zone, using a 625cm2 quadrat. At each season and intertidal zone, macroinvertebrate samples were collected along four transects (20m each) parallel to the waterline, and within each transect two quadrats were randomly sampled. Macroinvertebrates were identified, density determined, and biomass values obtained to characterize benthic diversity from the rocky fragments. The Jackknife procedure was used to estimate species richness from different intertidal zones during the dry and rainy seasons. Macrofaunal community comprised 85 taxa, with 17 "unique" taxa, 40 taxa were common to both intertidal zones and seasons, and 23 taxa have been recorded for the first time on the Brazilian Amazon Coast. Species richness was estimated at 106 +/- 9.7 taxa and results suggest that sampling effort was representative. Polychaeta was the most dominant in species number, followed by Malacostraca and Gastropoda. Regarding frequency of occurrence, Crustacean species Dynamenella tropica, Parhyale sp. and Petrolisthes armatus were the most frequent representing >75% of frequency of occurrence and 39 taxa were least frequent representing <5% of frequency of occurrence. Occurrence of crustaceans and polychaetes were particularly noteworthy in all intertidal zones and seasons, represented by 15 and 13 taxa, respectively. The most representative class in abundance and biomass was Malacostraca that represented more than half of all individuals sampled, and was dominated by Petrolisthes armatus. The latter was one of the most frequent, numerous and higher biomass species in the samples. In general, results indicated greater richness and biomass in the lower zone. Additionally, richness and density increase during the rainy season. Rock fragment fields in Areuá Island are rich in microhabitats and include a diverse array of species in a limited area. Our results underline the importance of rock fragment fields in Areuá Island for the maintenance of biodiversity in the Amazon Coast. PMID:24912344

  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. Adaptive Statistical Iterative Reconstruction-Applied Ultra-Low-Dose CT with Radiography-Comparable Radiation Dose: Usefulness for Lung Nodule Detection

    PubMed Central

    Yoon, Hyun Jung; Hwang, Hye Sun; Moon, Jung Won; Lee, Kyung Soo

    2015-01-01

    Objective To assess the performance of adaptive statistical iterative reconstruction (ASIR)-applied ultra-low-dose CT (ULDCT) in detecting small lung nodules. Materials and Methods Thirty patients underwent both ULDCT and standard dose CT (SCT). After determining the reference standard nodules, five observers, blinded to the reference standard reading results, independently evaluated SCT and both subsets of ASIR- and filtered back projection (FBP)-driven ULDCT images. Data assessed by observers were compared statistically. Results Converted effective doses in SCT and ULDCT were 2.81 ± 0.92 and 0.17 ± 0.02 mSv, respectively. A total of 114 lung nodules were detected on SCT as a standard reference. There was no statistically significant difference in sensitivity between ASIR-driven ULDCT and SCT for three out of the five observers (p = 0.678, 0.735, < 0.01, 0.038, and < 0.868 for observers 1, 2, 3, 4, and 5, respectively). The sensitivity of FBP-driven ULDCT was significantly lower than that of ASIR-driven ULDCT in three out of the five observers (p < 0.01 for three observers, and p = 0.064 and 0.146 for two observers). In jackknife alternative free-response receiver operating characteristic analysis, the mean values of figure-of-merit (FOM) for FBP, ASIR-driven ULDCT, and SCT were 0.682, 0.772, and 0.821, respectively, and there were no significant differences in FOM values between ASIR-driven ULDCT and SCT (p = 0.11), but the FOM value of FBP-driven ULDCT was significantly lower than that of ASIR-driven ULDCT and SCT (p = 0.01 and 0.00). Conclusion Adaptive statistical iterative reconstruction-driven ULDCT delivering a radiation dose of only 0.17 mSv offers acceptable sensitivity in nodule detection compared with SCT and has better performance than FBP-driven ULDCT. PMID:26357505

  11. 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

  12. Predicting Neuroinflammation in Morphine Tolerance for Tolerance Therapy from Immunostaining Images of Rat Spinal Cord

    PubMed Central

    Lin, Shinn-Long; Chang, Fang-Lin; Ho, Shinn-Ying; Charoenkwan, Phasit; Wang, Kuan-Wei; Huang, Hui-Ling

    2015-01-01

    Long-term morphine treatment leads to tolerance which attenuates analgesic effect and hampers clinical utilization. Recent studies have sought to reveal the mechanism of opioid receptors and neuroinflammation by observing morphological changes of cells in the rat spinal cord. This work proposes a high-content screening (HCS) based computational method, HCS-Morph, for predicting neuroinflammation in morphine tolerance to facilitate the development of tolerance therapy using immunostaining images for astrocytes, microglia, and neurons in the spinal cord. HCS-Morph first extracts numerous HCS-based features of cellular phenotypes. Next, an inheritable bi-objective genetic algorithm is used to identify a minimal set of features by maximizing the prediction accuracy of neuroinflammation. Finally, a mathematic model using a support vector machine with the identified features is established to predict drug-treated images to assess the effects of tolerance therapy. The dataset consists of 15 saline controls (1 ?l/h), 15 morphine-tolerant rats (15 ?g/h), and 10 rats receiving a co-infusion of morphine (15 ?g/h) and gabapentin (15 ?g/h, Sigma). The three individual models of astrocytes, microglia, and neurons for predicting neuroinflammation yielded respective Jackknife test accuracies of 96.67%, 90.00%, and 86.67% on the 30 rats, and respective independent test accuracies of 100%, 90%, and 60% on the 10 co-infused rats. The experimental results suggest that neuroinflammation activity expresses more predominantly in astrocytes and microglia than in neuron cells. The set of features for predicting neuroinflammation from images of astrocytes comprises mean cell intensity, total cell area, and second-order geometric moment (relating to cell distribution), relevant to cell communication, cell extension, and cell migration, respectively. The present investigation provides the first evidence for the role of gabapentin in the attenuation of morphine tolerance from phenotypic changes of astrocytes and microglia. Based on neuroinflammation prediction, the proposed computer-aided image diagnosis system can greatly facilitate the development of tolerance therapy with anti-inflammatory drugs. PMID:26437460

  13. 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

  14. Computer-aided detection of breast masses: Four-view strategy for screening mammography

    SciTech Connect

    Wei Jun; Chan Heangping; Zhou Chuan; Wu Yita; Sahiner, Berkman; Hadjiiski, Lubomir M.; Roubidoux, Marilyn A.; Helvie, Mark A.

    2011-04-15

    Purpose: To improve the performance of a computer-aided detection (CAD) system for mass detection by using four-view information in screening mammography. Methods: The authors developed a four-view CAD system that emulates radiologists' reading by using the craniocaudal and mediolateral oblique views of the ipsilateral breast to reduce false positives (FPs) and the corresponding views of the contralateral breast to detect asymmetry. The CAD system consists of four major components: (1) Initial detection of breast masses on individual views, (2) information fusion of the ipsilateral views of the breast (referred to as two-view analysis), (3) information fusion of the corresponding views of the contralateral breast (referred to as bilateral analysis), and (4) fusion of the four-view information with a decision tree. The authors collected two data sets for training and testing of the CAD system: A mass set containing 389 patients with 389 biopsy-proven masses and a normal set containing 200 normal subjects. All cases had four-view mammograms. The true locations of the masses on the mammograms were identified by an experienced MQSA radiologist. The authors randomly divided the mass set into two independent sets for cross validation training and testing. The overall test performance was assessed by averaging the free response receiver operating characteristic (FROC) curves of the two test subsets. The FP rates during the FROC analysis were estimated by using the normal set only. The jackknife free-response ROC (JAFROC) method was used to estimate the statistical significance of the difference between the test FROC curves obtained with the single-view and the four-view CAD systems. Results: Using the single-view CAD system, the breast-based test sensitivities were 58% and 77% at the FP rates of 0.5 and 1.0 per image, respectively. With the four-view CAD system, the breast-based test sensitivities were improved to 76% and 87% at the corresponding FP rates, respectively. The improvement was found to be statistically significant (p<0.0001) by JAFROC analysis. Conclusions: The four-view information fusion approach that emulates radiologists' reading strategy significantly improves the performance of breast mass detection of the CAD system in comparison with the single-view approach.

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

    SciTech Connect

    Masotti, Matteo; Lanconelli, Nico; Campanini, Renato

    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.

  16. 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.

  17. Stock assessment of fishery target species in Lake Koka, Ethiopia.

    PubMed

    Tesfaye, Gashaw; Wolff, Matthias

    2015-09-01

    Effective management is essential for small-scale fisheries to continue providing food and livelihoods for households, particularly in developing countries where other options are often limited. Studies on the population dynamics and stock assessment on fishery target species are thus imperative to sustain their fisheries and the benefits for the society. In Lake Koka (Ethiopia), very little is known about the vital population parameters and exploitation status of the fishery target species: tilapia Oreochromis niloticus, common carp Cyprinus carpio and catfish Clarias gariepinus. Our study, therefore, aimed at determining the vital population parameters and assessing the status of these target species in Lake Koka using length frequency data collected quarterly from commercial catches from 2007-2012. A total of 20,097 fish specimens (distributed as 7,933 tilapia, 6,025 catfish and 6,139 common carp) were measured for the analysis. Von Bertalarffy growth parameters and their confidence intervals were determined from modal progression analysis using ELEFAN I and applying the jackknife technique. Mortality parameters were determined from length-converted catch curves and empirical models. The exploitation status of these target species were then assessed by computing exploitation rates (E) from mortality parameters as well as from size indicators i.e., assessing the size distribution of fish catches relative to the size at maturity (Lm), the size that provides maximum cohort biomass (Lopt) and the abundance of mega-spawners. The mean value of growth parameters L?, K and the growth performance index ø' were 44.5 cm, 0.41/year and 2.90 for O. niloticus, 74.1 cm, 0.28/year and 3.19 for C. carpio and 121.9 cm, 0.16/year and 3.36 for C. gariepinus, respectively. The 95 % confidence intervals of the estimates were also computed. Total mortality (Z) estimates were 1.47, 0.83 and 0.72/year for O. niloticus, C. carpio and C. gariepinus, respectively. Our study suggest that O. niloticus is in a healthy state, while C. gariepinus show signs of growth overfishing (when both exploitation rate (E) and size indicators were considered). In case of C. carpio, the low exploitation rate encountered would point to underfishing, while the size indicators of the catches would suggest that too small fish are harvested leading to growth overfishing. We concluded that fisheries production in Lake Koka could be enhanced by increasing E toward optimum level of exploitation (Eopt) for the underexploited C. carpio and by increasing the size at first capture (Lc) toward the Lopt, range for all target species. PMID:26666131

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

    SciTech Connect

    Spekkens, Kristine; Mason, Brian S.; Aguirre, James E.; Nhan, Bang

    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.

  19. Are the orbital poles of binary stars in the solar neighbourhood anisotropically distributed?

    NASA Astrophysics Data System (ADS)

    Agati, J.-L.; Bonneau, D.; Jorissen, A.; Soulié, E.; Udry, S.; Verhas, P.; Dommanget, J.

    2015-02-01

    We test whether or not the orbital poles of the systems in the solar neighbourhood are isotropically distributed on the celestial sphere. The problem is plagued by the ambiguity on the position of the ascending node. Of the 95 systems closer than 18 pc from the Sun with an orbit in the 6th Catalogue of Orbits of Visual Binaries, the pole ambiguity could be resolved for 51 systems using radial velocity collected in the literature and CORAVEL database or acquired with the HERMES/Mercator spectrograph. For several systems, we can correct the erroneous nodes in the 6th Catalogue of Orbits and obtain new combined spectroscopic/astrometric orbits for seven systems [WDS 01083+5455Aa,Ab; 01418+4237AB; 02278+0426AB (SB2); 09006+4147AB (SB2); 16413+3136AB; 17121+4540AB; 18070+3034AB]. We used of spherical statistics to test for possible anisotropy. After ordering the binary systems by increasing distance from the Sun, we computed the false-alarm probability for subsamples of increasing sizes, from N = 1 up to the full sample of 51 systems. Rayleigh-Watson and Beran tests deliver a false-alarm probability of 0.5% for the 20 systems closer than 8.1 pc. To evaluate the robustness of this conclusion, we used a jackknife approach, for which we repeated this procedure after removing one system at a time from the full sample. The false-alarm probability was then found to vary between 1.5% and 0.1%, depending on which system is removed. The reality of the deviation from isotropy can thus not be assessed with certainty at this stage, because only so few systems are available, despite our efforts to increase the sample. However, when considering the full sample of 51 systems, the concentration of poles toward the Galactic position l = 46.0°, b = 37°, as observed in the 8.1 pc sphere, totally vanishes (the Rayleigh-Watson false-alarm probability then rises to 18%). Tables 1-3 and Appendices are available in electronic form at http://www.aanda.org† Deceased October 1, 2014.

  20. Two-Phase Analysis in Consensus Genetic Mapping

    PubMed Central

    Ronin, Y.; Mester, D.; Minkov, D.; Belotserkovski, R.; Jackson, B. N.; Schnable, P. S.; Aluru, S.; Korol, A.

    2012-01-01

    Numerous mapping projects conducted on different species have generated an abundance of mapping data. Consequently, many multilocus maps have been constructed using diverse mapping populations and marker sets for the same organism. The quality of maps varies broadly among populations, marker sets, and software used, necessitating efforts to integrate the mapping information and generate consensus maps. The problem of consensus genetic mapping (MCGM) is by far more challenging compared with genetic mapping based on a single dataset, which by itself is also cumbersome. The additional complications introduced by consensus analysis include inter-population differences in recombination rate and exchange distribution along chromosomes; variations in dominance of the employed markers; and use of different subsets of markers in different labs. Hence, it is necessary to handle arbitrary patterns of shared sets of markers and different level of mapping data quality. In this article, we introduce a two-phase approach for solving MCGM. In phase 1, for each dataset, multilocus ordering is performed combined with iterative jackknife resampling to evaluate the stability of marker orders. In this phase, the ordering problem is reduced to the well-known traveling salesperson problem (TSP). Namely, for each dataset, we look for order that gives minimum sum of recombination distances between adjacent markers. In phase 2, the optimal consensus order of shared markers is selected from the set of allowed orders and gives the minimal sum of total lengths of nonconflicting maps of the chromosome. This criterion may be used in different modifications to take into account the variation in quality of the original data (population size, marker quality, etc.). In the foregoing formulation, consensus mapping is considered as a specific version of TSP that can be referred to as “synchronized TSP.” The conflicts detected after phase 1 are resolved using either a heuristic algorithm over the entire chromosome or an exact/heuristic algorithm applied subsequently to the revealed small non-overlapping regions with conflicts separated by non-conflicting regions. The proposed approach was tested on a wide range of simulated data and real datasets from maize. PMID:22670224

  1. 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

  2. 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

  3. Computer-aided detection of breast masses: Four-view strategy for screening mammography

    PubMed Central

    Wei, Jun; Chan, Heang-Ping; Zhou, Chuan; Wu, Yi-Ta; Sahiner, Berkman; Hadjiiski, Lubomir M.; Roubidoux, Marilyn A.; Helvie, Mark A.

    2011-01-01

    Purpose: To improve the performance of a computer-aided detection (CAD) system for mass detection by using four-view information in screening mammography. Methods: The authors developed a four-view CAD system that emulates radiologists’ reading by using the craniocaudal and mediolateral oblique views of the ipsilateral breast to reduce false positives (FPs) and the corresponding views of the contralateral breast to detect asymmetry. The CAD system consists of four major components: (1) Initial detection of breast masses on individual views, (2) information fusion of the ipsilateral views of the breast (referred to as two-view analysis), (3) information fusion of the corresponding views of the contralateral breast (referred to as bilateral analysis), and (4) fusion of the four-view information with a decision tree. The authors collected two data sets for training and testing of the CAD system: A mass set containing 389 patients with 389 biopsy-proven masses and a normal set containing 200 normal subjects. All cases had four-view mammograms. The true locations of the masses on the mammograms were identified by an experienced MQSA radiologist. The authors randomly divided the mass set into two independent sets for cross validation training and testing. The overall test performance was assessed by averaging the free response receiver operating characteristic (FROC) curves of the two test subsets. The FP rates during the FROC analysis were estimated by using the normal set only. The jackknife free-response ROC (JAFROC) method was used to estimate the statistical significance of the difference between the test FROC curves obtained with the single-view and the four-view CAD systems. Results: Using the single-view CAD system, the breast-based test sensitivities were 58% and 77% at the FP rates of 0.5 and 1.0 per image, respectively. With the four-view CAD system, the breast-based test sensitivities were improved to 76% and 87% at the corresponding FP rates, respectively. The improvement was found to be statistically significant (p<0.0001) by JAFROC analysis. Conclusions: The four-view information fusion approach that emulates radiologists’ reading strategy significantly improves the performance of breast mass detection of the CAD system in comparison with the single-view approach. PMID:21626920

  4. First high resolution P wave velocity structure beneath Tenerife Island, (Canary Islands, Spain)

    NASA Astrophysics Data System (ADS)

    Garcia-Yeguas, Araceli; Ivan, Koulakov; Ibañez Jesus, M.; Valenti, Sallarès.

    2010-05-01

    3D velocity structure distribution has been imaged for first time using high resolution traveltime seismic tomography of the active volcano of Tenerife Island (Canary Islands, Spain). It is located in the Atlantic Ocean. In this island is situated the Teide stratovolcano (3718 m high) that is part of the Cañadas-Teide-Pico Viejo volcanic complex. Las Cañadas is a caldera system more than 20 kilometers wide where at least four distinct caldera processes have been identified. Evidence for many explosive eruptions in the volcanic complex has been found; the last noticeable explosive eruption (sub-plinean) occurred at Montaña Blanca around 2000 years ago. During the last 300 years, six effusive eruptions have been reported, the last of which took place at Chinyero Volcano on 18 November 1909. In January 2007, a seismic active experiment was carried out as part of the TOM-TEIDEVS project. About 6850 air gun shots were fired on the sea and recorded on a dense local seismic land network consisting of 150 independent (three component) seismic stations. The good quality of the recorded data allowed identifying P-wave arrivals up to offsets of 30-40 km obtaining more than 63000 traveltimes used in the tomographic inversion. The images have been obtained using ATOM-3D code (Koulakov, 2009). This code uses ray bending algorithms in the ray tracing for the forward modelling and in the inversion step it uses gradient methods. The velocity models show a very heterogeneous upper crust that is usual in similar volcanic environment. The tomographic images points out the no-existence of a magmatic chamber near to the surface and below Pico Teide. The ancient Las Cañadas caldera borders are clearly imaged featuring relatively high seismic velocity. Moreover, we have found a big low velocity anomaly in the northwest dorsal of the island. The last eruption took place in 1909 in this area. Furthermore, in the southeast another low velocity anomaly has been imaged. Several resolution and accuracy tests were carried out to quantify the reliability of the final velocity models. Checkerboard tests show that the well-resolved are located up to 6-8 km depth. Also we carried out synthetic tests in which we successfully reproduce single anomalies observed in the velocity models. Especially we have study carefully the low velocity anomalies found in the NW and SE, which have been recovered successfully. The jack-knife technique have been used and our results are stable if we remove the 50% of the data for different stations, but if we reject all the data for some stations, the velocity models can change. These tests assure the uniqueness of the first 3D velocity model that characterizes the internal structure of the Tenerife Island. As main conclusions of our work we can remark: a) This is the first 3-D velocity image of the area; b) we have observed low velocity anomalies near to surface that could be associated to the presence of magma, water reservoirs and volcanic landslides; c) high velocity anomalies could be related to ancient volcanic episodes or basement structures; d) our results could help to resolve many questions relate to the evolution of the volcanic system, as the presence or not of big landslides, calderic explosions or others; e) this image is a very important tool to improve the knowledge of the volcanic hazard, and therefore volcanic risk. We would like to highlight the importance of take into account the risk of eruption in other areas besides Pico Teide-Las Cañadas system.

  5. Dynamics of interfaces and detergency

    NASA Astrophysics Data System (ADS)

    Johnson, Edward George

    Laser light scattering (LLS) methods have been used to study the surface wave dispersion and surface viscoelasticity of aqueous solutions of the zwitterionic surfactant n-hexadecyl-n,n-dimethyl-3-ammonio-1- propanesulphonate (HDPS), which has CMC 0.027mM. These studies have probed a surface wavenumber range of 400jackknife approach. It is demonstrated that the contribution of the empirical term to the total error associated with the drop volume method is typically smaller than the systematic percentage error.

  6. 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

  7. A Perspective on Simulations of Environmental Systems and Prediction Uncertainty

    NASA Astrophysics Data System (ADS)

    Hill, M. C.; Tiedeman, C. R.

    2003-12-01

    Prediction uncertainty is the likely discrepancy between model predictions and the actual, unrealized system responses. Contributions to uncertainty include anything that causes inaccurate predictions. This can include numerical model solution error and capability limitation, data error and deficiency, and conceptual model error. For example, using conceptual models to build simulations forces ideas about system behavior that are often vague and(or) wrong to be tested against measurements. Closer correspondence between the simulation and measurements often indicates the model more accurately represents a system. However, when models are calibrated, predictive capability can be degraded by fitting measurements too closely. This can occur when the model is overparameterized and close model fit is achieved by fitting measurement and other errors. The connection between such errors and prediction accuracy is clear, and thorough evaluation of such errors and the possibility of overfitting are critical. This is especially true for stochastic and Bayesian methods applied to models with many parameters, for which overfitting is controlled using prior information and smoothness constraints that may not be well understood by the modeler. When a reasonably accurate simulation of a system has been achieved through careful model development, calibration, and error evaluation, the simulation itself becomes an invaluable tool for sensitivity analysis, data assessment, and uncertainty evaluation. Three categories of sensitivity and data assessment methods include techniques for identifying (1) the importance of observations important to parameter values (observations that dominate model calibration); (2) parameter values that dominate the predictions; and (3) observations that dominate the predictions. For instance, gradient-based methods such as composite scaled sensitivities, prediction scaled sensitivities and the value of improved information, and the observation-prediction statistic are used to address the three categories, respectively. These local-sensitivity methods assume model linearity, but have found to be useful for nonlinear ground-water models. More computationally intensive methods that do not assume model linearity include variance-based global sensitivity analysis methods for identifying parameters important to predictions, and jackknife and bootstrap methods for identifying observations that dominate predictions. Uncertainty evaluation methods can be categorized as gradient, selective sampling, and random sampling methods. Gradient methods include linear and nonlinear confidence intervals, and are limited to propagating uncertainties related to parameter values. Selective sampling often involves establishing a most probable and one or more worst-case scenarios. Random sampling includes Monte Carlo methods such as Latin-Hypercube sampling, and can produce results similar to nonlinear confidence intervals if only parameter values are sampled and if simulations with poor model fit are omitted. Model development and evaluation are obviously complex endeavors involving a number of steps. To make wise societal decisions based on environmental model predictions, it is important to establish solid methods for evaluating the importance of observations and parameters to predictions and for quantifying prediction uncertainty.

  8. SIFlore, a dataset of geographical distribution of vascular plants covering five centuries of knowledge in France: Results of a collaborative project coordinated by the Federation of the National Botanical Conservatories

    PubMed Central

    Just, Anaïs; Gourvil, Johan; Millet, Jérôme; Boullet, Vincent; Milon, Thomas; Mandon, Isabelle; Dutrève, Bruno

    2015-01-01

    Abstract More than 20 years ago, the French Muséum National d’Histoire Naturelle1 (MNHN, Secretariat of the Fauna and Flora) published the first part of an atlas of the flora of France at a 20km spatial resolution, accounting for 645 taxa (Dupont 1990). Since then, at the national level, there has not been any work on this scale relating to flora distribution, despite the obvious need for a better understanding. In 2011, in response to this need, the Federation des Conservatoires Botaniques Nationaux2 (FCBN, http://www.fcbn.fr) launched an ambitious collaborative project involving eleven national botanical conservatories of France. The project aims to establish a formal procedure and standardized system for data hosting, aggregation and publication for four areas: flora, fungi, vegetation and habitats. In 2014, the first phase of the project led to the development of the national flora dataset: SIFlore. As it includes about 21 million records of flora occurrences, this is currently the most comprehensive dataset on the distribution of vascular plants (Tracheophyta) in the French territory. SIFlore contains information for about 15'454 plant taxa occurrences (indigenous and alien taxa) in metropolitan France and Reunion Island, from 1545 until 2014. The data records were originally collated from inventories, checklists, literature and herbarium records. SIFlore was developed by assembling flora datasets from the regional to the national level. At the regional level, source records are managed by the national botanical conservatories that are responsible for flora data collection and validation. In order to present our results, a geoportal was developed by the Fédération des conservatoires botaniques nationaux that allows the SIFlore dataset to be publically viewed. This portal is available at: http://siflore.fcbn.fr. As the FCBN belongs to the Information System for Nature and Landscapes’ (SINP), a governmental program, the dataset is also accessible through the websites of the National Inventory of Natural Heritage (http://www.inpn.fr) and the Global Biodiversity Information Facility (http://www.gbif.fr). SIFlore is regularly updated with additional data records. It is also planned to expand the scope of the dataset to include information about taxon biology, phenology, ecology, chorology, frequency, conservation status and seed banks. A map showing an estimation of the dataset completeness (based on Jackknife 1 estimator) is presented and included as a numerical appendix. Purpose: SIFlore aims to make the data of the flora of France available at the national level for conservation, policy management and scientific research. Such a dataset will provide enough information to allow for macro-ecological reviews of species distribution patterns and, coupled with climatic or topographic datasets, the identification of determinants of these patterns. This dataset can be considered as the primary indicator of the current state of knowledge of flora distribution across France. At a policy level, and in the context of global warming, this should promote the adoption of new measures aiming to improve and intensify flora conservation and surveys. PMID:26491386

  9. Program package for multicanonical simulations of U(1) lattice gauge theory-Second version

    NASA Astrophysics Data System (ADS)

    Bazavov, Alexei; Berg, Bernd A.

    2013-03-01

    A new version STMCMUCA_V1_1 of our program package is available. It eliminates compatibility problems of our Fortran 77 code, originally developed for the g77 compiler, with Fortran 90 and 95 compilers. New version program summaryProgram title: STMC_U1MUCA_v1_1 Catalogue identifier: AEET_v1_1 Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language: Fortran 77 compatible with Fortran 90 and 95 Computers: Any capable of compiling and executing Fortran code Operating systems: Any capable of compiling and executing Fortran code RAM: 10 MB and up depending on lattice size used No. of lines in distributed program, including test data, etc.: 15059 No. of bytes in distributed program, including test data, etc.: 215733 Keywords: Markov chain Monte Carlo, multicanonical, Wang-Landau recursion, Fortran, lattice gauge theory, U(1) gauge group, phase transitions of continuous systems Classification: 11.5 Catalogue identifier of previous version: AEET_v1_0 Journal Reference of previous version: Computer Physics Communications 180 (2009) 2339-2347 Does the new version supersede the previous version?: Yes Nature of problem: Efficient Markov chain Monte Carlo simulation of U(1) lattice gauge theory (or other continuous systems) close to its phase transition. Measurements and analysis of the action per plaquette, the specific heat, Polyakov loops and their structure factors. Solution method: Multicanonical simulations with an initial Wang-Landau recursion to determine suitable weight factors. Reweighting to physical values using logarithmic coding and calculating jackknife error bars. Reasons for the new version: The previous version was developed for the g77 compiler Fortran 77 version. Compiler errors were encountered with Fortran 90 and Fortran 95 compilers (specified below). Summary of revisions: epsilon=one/10**10 is replaced by epsilon/10.0D10 in the parameter statements of the subroutines u1_bmha.f, u1_mucabmha.f, u1wl_backup.f, u1wlread_backup.f of the folder Libs/U1_par. For the tested compilers script files are added in the folder ExampleRuns and readme.txt files are now provided in all subfolders of ExampleRuns. The gnuplot driver files produced by the routine hist_gnu.f of Libs/Fortran are adapted to syntax required by gnuplot version 4.0 and higher. Restrictions: Due to the use of explicit real*8 initialization the conversion into real*4 will require extra changes besides replacing the implicit.sta file by its real*4 version. Unusual features: The programs have to be compiled the script files like those contained in the folder ExampleRuns as explained in the original paper. Running time: The prepared test runs took up to 74 minutes to execute on a 2 GHz PC.

  10. 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.