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Sample records for jackknifing

  1. When Jackknifing Fails (Or Does It?)

    ERIC Educational Resources Information Center

    Wainer, Howard; Thissen, David

    1975-01-01

    In this study of robust regression techniques, it was found that the Jackknife does particularly poor in estimating a correlation when there are sharp deviations from normality. A simple example is provided. (RC)

  2. Testing variance components by two jackknife methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The jacknife method, a resampling technique, has been widely used for statistical tests for years. The pseudo value based jacknife method (defined as pseudo jackknife method) is commonly used to reduce the bias for an estimate; however, sometimes it could result in large variaion for an estmimate a...

  3. The Infinitesimal Jackknife with Exploratory Factor Analysis

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  4. 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

  5. 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.

  6. 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

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

    ERIC Educational Resources Information Center

    Jennrich, Robert I.

    2008-01-01

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

  8. The Infinitesimal Jackknife and Moment Structure Analysis Using Higher Order Moments.

    PubMed

    Jennrich, Robert; Satorra, Albert

    2016-03-01

    Mean corrected higher order sample moments are asymptotically normally distributed. It is shown that both in the literature and popular software the estimates of their asymptotic covariance matrices are incorrect. An introduction to the infinitesimal jackknife is given and it is shown how to use it to correctly estimate the asymptotic covariance matrices of higher order sample moments. Another advantage in using the infinitesimal jackknife is the ease with which it may be used when stacking or sub-setting estimators. The estimates given are used to test the goodness of fit of a non-linear factor analysis model. A computationally accelerated form for infinitesimal jackknife estimates is given. PMID:25361618

  9. 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

  10. Using the jackknife for estimation in log link Bernoulli regression models.

    PubMed

    Lipsitz, Stuart R; Fitzmaurice, Garrett M; Arriaga, Alex; Sinha, Debajyoti; Gawande, Atul A

    2015-02-10

    Bernoulli (or binomial) regression using a generalized linear model with a log link function, where the exponentiated regression parameters have interpretation as relative risks, is often more appropriate than logistic regression for prospective studies with common outcomes. In particular, many researchers regard relative risks to be more intuitively interpretable than odds ratios. However, for the log link, when the outcome is very prevalent, the likelihood may not have a unique maximum. To circumvent this problem, a 'COPY method' has been proposed, which is equivalent to creating for each subject an additional observation with the same covariates except the response variable has the outcome values interchanged (1's changed to 0's and 0's changed to 1's). The original response is given weight close to 1, while the new observation is given a positive weight close to 0; this approach always leads to convergence of the maximum likelihood algorithm, except for problems with convergence due to multicollinearity among covariates. Even though this method produces a unique maximum, when the outcome is very prevalent, and/or the sample size is relatively small, the COPY method can yield biased estimates. Here, we propose using the jackknife as a bias-reduction approach for the COPY method. The proposed method is motivated by a study of patients undergoing colorectal cancer surgery. PMID:25388125

  11. Jackknife-corrected parametric bootstrap estimates of growth rates in bivalve mollusks using nearest living relatives.

    PubMed

    Dexter, Troy A; Kowalewski, Micha?

    2013-12-01

    Quantitative estimates of growth rates can augment ecological and paleontological applications of body-size data. However, in contrast to body-size estimates, assessing growth rates is often time-consuming, expensive, or unattainable. Here we use an indirect approach, a jackknife-corrected parametric bootstrap, for efficient approximation of growth rates using nearest living relatives with known age-size relationships. The estimate is developed by (1) collecting a sample of published growth rates of closely related species, (2) calculating the average growth curve using those published age-size relationships, (3) resampling iteratively these empirically known growth curves to estimate the standard errors and confidence bands around the average growth curve, and (4) applying the resulting estimate of uncertainty to bracket age-size relationships of the species of interest. This approach was applied to three monophyletic families (Donacidae, Mactridae, and Semelidae) of mollusk bivalves, a group characterized by indeterministic shell growth, but widely used in ecological, paleontological, and geochemical research. The resulting indirect estimates were tested against two previously published geochemical studies and, in both cases, yielded highly congruent age estimates. In addition, a case study in applied fisheries was used to illustrate the potential of the proposed approach for augmenting aquaculture management practices. The resulting estimates of growth rates place body size data in a constrained temporal context and confidence intervals associated with resampling estimates allow for assessing the statistical uncertainty around derived temporal ranges. The indirect approach should allow for improved evaluation of diverse research questions, from sustainability of industrial shellfish harvesting to climatic interpretations of stable isotope proxies extracted from fossil skeletons. PMID:24071629

  12. Is It Useful and Safe to Maintain the Sitting Position During Only One Minute before Position Change to the Jack-knife Position?

    PubMed Central

    Park, Soo Young; Park, Jong Cook

    2010-01-01

    Background Conventional spinal saddle block is performed with the patient in a sitting position, keeping the patient sitting for between 3 to 10 min after injection of a drug. This amount of time, however, is long enough to cause prolonged postoperative urinary retention. The trend in this block is to lower the dose of local anesthetics, providing a selective segmental block; however, an optimal dose and method are needed for adequate anesthesia in variable situations. Therefore, in this study, we evaluated the question of whether only 1 min of sitting after drug injection would be sufficient and safe for minor anorectal surgery. Methods Two hundred and sixteen patients undergoing minor anorectal surgery under spinal anesthesia remained sitting for 1 min after completion of subarachnoid administration of 1 ml of a 0.5% hyperbaric bupivacaine solution (5 mg). They were then placed in the jack-knife position. After surgery, analgesia levels were assessed using loss of cold sensation in the supine position. The next day, urination and 11-point numeric rating scale (NRS) for postoperative pain were assessed. Results None of the patients required additional analgesics during surgical manipulation. Postoperative sensory levels were T10 [T8-T12] in patients, and no significant differences were observed between sex (P = 0.857), height (P = 0.065), obesity (P = 0.873), or age (P = 0.138). Urinary retention developed in only 7 patients (3.2%). In this group, NRS was 5.0 2.4 (P = 0.014). Conclusions The one-minute sitting position for spinal saddle block before the jack-knife position is a safe method for use with minor anorectal surgery and can reduce development of postoperative urinary retention. PMID:20830265

  13. Pre-collapse identification of sinkholes in unconsolidated media at Dead Sea area by `nanoseismic monitoring' (graphical jackknife location of weak sources by few, low-SNR records)

    NASA Astrophysics Data System (ADS)

    Wust-Bloch, Gilles Hillel; Joswig, Manfred

    2006-12-01

    The sudden failure of near-surface cavities and the resulting sinkholes have constituted a recent hazard affecting the populations, lifelines and the economy of the Dead Sea region. This paper describes how seismic monitoring techniques could detect the extremely low-energy signals produced by cavitation in unconsolidated, layered media. Dozens of such events were recorded within a radius of 200 m during several night-time experiments carried out along the western Dead Sea shores. The absence of prior knowledge about cavitation-induced events in unconsolidated media required an initial signal characterization, for which a series of source processes were simulated in the field under controlled conditions. The waveform analysis by sonograms recognizes two main groups of seismic events: impacts on dry material and impacts in liquid. Our analysis demonstrates that the discrimination between both types of source functions is robust despite the extreme nature of the scatter media. In addition to their association with specific source processes, these events can be precisely located by a graphical, error-resistant jackknifing approach. Using an extended ML scale, their source energy can be quantified, and related to standard seismic activity. In summary, it is now possible to monitor subsurface material failures before sinkhole collapse since the discrimination of impact signals on the basis of their frequency content is indicative of the maturity of the cavitation process.

  14. The Examining of Generalization Quantitative Scientific Findings by Using the Jackknife Method: An Application

    ERIC Educational Resources Information Center

    Kyari, Murat; Buyukozturk, Sener

    2009-01-01

    The outcomes which cannot be generalized are specific for a sample but are unable to be reflected to the rest of the population. The parameters that are reached at the end of the statistics that are scarce in sample arise doubts in the aspect of generalization. In these cases, parameter estimation may not be very stable and outlier values can

  15. 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

  16. 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

  17. 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

  18. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 6 2013-10-01 2013-10-01 false Marking and packing. 160.043-6 Section 160.043-6... Marking and packing. (a) General. Jackknives specified by this subpart shall be stamped or otherwise... opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed...

  19. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 6 2011-10-01 2011-10-01 false Marking and packing. 160.043-6 Section 160.043-6... Marking and packing. (a) General. Jackknives specified by this subpart shall be stamped or otherwise... opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed...

  20. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Marking and packing. 160.043-6 Section 160.043-6... Marking and packing. (a) General. Jackknives specified by this subpart shall be stamped or otherwise... opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed...

  1. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 6 2010-10-01 2010-10-01 false Marking and packing. 160.043-6 Section 160.043-6... Marking and packing. (a) General. Jackknives specified by this subpart shall be stamped or otherwise... opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed...

  2. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Marking and packing. 160.043-6 Section 160.043-6... Marking and packing. (a) General. Jackknives specified by this subpart shall be stamped or otherwise... opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed...

  3. [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

  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. 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…

  6. The use and misuse of statistics in space physics

    NASA Technical Reports Server (NTRS)

    Reiff, Patricia H.

    1990-01-01

    This paper presents several statistical techniques most commonly used in space physics, including Fourier analysis, linear correlation, auto- and cross-correlation, power spectral density and superimposed epoch analysis, and presents tests to assess the significance of the results. New techniques such as bootstrapping and jackknifing are presented. When no test of significance is in common usage, a plausible test is suggested.

  7. Use of Empirical Estimates of Shrinkage in Multiple Regression: A Caution.

    ERIC Educational Resources Information Center

    Kromrey, Jeffrey D.; Hines, Constance V.

    1995-01-01

    The accuracy of four empirical techniques to estimate shrinkage in multiple regression was studied through Monte Carlo simulation. None of the techniques provided unbiased estimates of the population squared multiple correlation coefficient, but the normalized jackknife and bootstrap techniques demonstrated marginally acceptable performance with

  8. 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

  9. 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.

  10. 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

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

    USGS Publications Warehouse

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

    1998-01-01

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

  12. 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 (Hbner) (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

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

    PubMed

    Flores, Luis A

    2011-03-01

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

  14. 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 (Hbner) (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

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

    USGS Publications Warehouse

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

    1978-01-01

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

  16. Prediction of resource volumes at untested locations using simple local prediction models

    USGS Publications Warehouse

    Attanasi, E.D.; Coburn, T.C.; Freeman, P.A.

    2006-01-01

    This paper shows how local spatial nonparametric prediction models can be applied to estimate volumes of recoverable gas resources at individual undrilled sites, at multiple sites on a regional scale, and to compute confidence bounds for regional volumes based on the distribution of those estimates. An approach that combines cross-validation, the jackknife, and bootstrap procedures is used to accomplish this task. Simulation experiments show that cross-validation can be applied beneficially to select an appropriate prediction model. The cross-validation procedure worked well for a wide range of different states of nature and levels of information. Jackknife procedures are used to compute individual prediction estimation errors at undrilled locations. The jackknife replicates also are used with a bootstrap resampling procedure to compute confidence bounds for the total volume. The method was applied to data (partitioned into a training set and target set) from the Devonian Antrim Shale continuous-type gas play in the Michigan Basin in Otsego County, Michigan. The analysis showed that the model estimate of total recoverable volumes at prediction sites is within 4 percent of the total observed volume. The model predictions also provide frequency distributions of the cell volumes at the production unit scale. Such distributions are the basis for subsequent economic analyses. ?? Springer Science+Business Media, LLC 2007.

  17. 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.

  18. Evaluating species richness: Biased ecological inference results from spatial heterogeneity in detection probabilities.

    PubMed

    McNew, Lance B; Handel, Colleen M

    2015-09-01

    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 multispecies 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 data set of bird observations in northwestern Alaska, USA, 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. PMID:26552273

  19. Repeated-measures bioassay with correlated errors and heterogeneous variances: a Monte Carlo study.

    PubMed

    Elashoff, J D

    1981-09-01

    The relative potency of two drugs may be estimated from a small experiment in which all K doses of each drug are given in order of increasing dose level to each of n aminals at one testing session. Fiducial limits are often estimated from Fieller's theorem, with the (2K - 1)(n - 1)-degree-of-freedom error term obtained from a two-way analysis of variance. Monte Carlo results indicate that this method can yield limits which are far too narrow when there is serial correlation between successive doses. The jackknife confidence limits are found to behave well for the models investigated. PMID:7317557

  20. Small-sample estimation of species richness applied to forest communities.

    PubMed

    Hwang, Wen-Han; Shen, Tsung-Jen

    2010-12-01

    Many well-known methods are available for estimating the number of species in a forest community. However, most existing methods result in considerable negative bias in applications, where field surveys typically represent only a small fraction of sampled communities. This article develops a new method based on sampling with replacement to estimate species richness via the generalized jackknife procedure. The proposed estimator yields small bias and reasonably accurate interval estimation even with small samples. The performance of the proposed estimator is compared with several typical estimators via simulation study using two complete census datasets from Panama and Malaysia. PMID:20002401

  1. 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.

  2. The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi, Fungi.

    PubMed

    Tehler, Anders; Little, Damon P; Farris, James S

    2003-08-01

    A data set with 1551 fungal sequences of the small subunit ribosomal RNA has been analysed phylogenetically. Four animal sequences were used to root the tree. The parsimony ratchet algorithm in combination with tree fusion was used to find most parsimonious trees and the parsimony jackknifing method was used to establish support frequencies. The full-length consensus tree, of the most parsimonious trees, is published and jackknife frequencies above 50% are plotted on the consensus tree at supported nodes. Until recently attempts to find the most parsimonious trees for large data sets were impractical, given current computational limitations. The parsimony ratchet in combination with tree fusion was found to be a very efficient method of rapid parsimony analysis of this large data set. Parsimony jackknifing is a very fast and efficient method for establishing group support. The results show that the Glomeromycota are the sister group to a monophyletic Dikaryomycota. The majority of the species in the Glomeromycota/Dikaryomycota group have a symbiotic lifestyle--a possible synapomorphy for a group 'Symbiomycota'. This would suggest that symbiosis between fungi and green plants evolved prior to the colonization of land by plants and not as a result of the colonization process. The Basidiomycotina and the Ascomycotina are both supported as monophyletic. The Urediniomycetes is the sister group to the rest of the Basidiomycotina successively followed in a grade by Ustilaginomycetes, Tremellomycetes, Dacrymycetales, Ceratobasidiales and Homobasidiomycetes each supported as monophyletic except the Homobasidiomycetes which are left unsupported. The ascomycete node begins with a polytomy consisting of the Pneumocystidomycetes, Schizosaccharomycetes, unsupported group with the Taphrinomycetes and Neolectales, and finally an unnamed, monophyletic and supported group including the Saccharomycetes and Euascomycetes. Within the Euascomycetes the inoperculate euascomycetes (Inoperculata) are supported as monophyletic excluding the Orbiliomycetes which are included in an unsupported operculate, pezizalean sister group together with Helvellaceae, Morchellaceae, Tuberaceae and others. Geoglossum is the sister group to the rest of the inoperculate euascomycetes. The Sordariomycetes, Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes are each highly supported as monophyletic. The Leotiomycetes and the Lecanoromycetes both appear in the consensus of the most parsimonious trees but neither taxon receives any jackknife support. PMID:14531615

  3. 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

  4. Performance of internal covariance estimators for cosmic shear correlation functions

    NASA Astrophysics Data System (ADS)

    Friedrich, O.; Seitz, S.; Eifler, T. F.; Gruen, D.

    2016-03-01

    Data re-sampling methods such as delete-one jackknife, bootstrap or the sub-sample covariance are common tools for estimating the covariance of large-scale structure probes. We investigate different implementations of these methods in the context of cosmic shear two-point statistics. Using lognormal simulations of the convergence field and the corresponding shear field we generate mock catalogues of a known and realistic covariance. For a survey of {˜ } 5000 ° ^2 we find that jackknife, if implemented by deleting sub-volumes of galaxies, provides the most reliable covariance estimates. Bootstrap, in the common implementation of drawing sub-volumes of galaxies, strongly overestimates the statistical uncertainties. In a forecast for the complete 5-yr Dark Energy Survey, we show that internally estimated covariance matrices can provide a large fraction of the true uncertainties on cosmological parameters in a 2D cosmic shear analysis. The volume inside contours of constant likelihood in the Ωm-σ8 plane as measured with internally estimated covariance matrices is on average ≳85 per cent of the volume derived from the true covariance matrix. The uncertainty on the parameter combination Σ _8 ˜ σ _8 Ω _m^{0.5} derived from internally estimated covariances is ˜90 per cent of the true uncertainty.

  5. Fast Fourier transform-based support vector machine for subcellular localization prediction using different substitution models.

    PubMed

    Wang, Zhimeng; Jiang, Lin; Li, Menglong; Sun, Lina; Lin, Rongying

    2007-09-01

    There are approximately 10(9) proteins in a cell. A hotspot in bioinformatics is how to identify a protein subcellular localization, if its sequence is known. In this paper, a method using fast Fourier transform-based support vector machine is developed to predict the subcellular localization of proteins from their physicochemical properties and structural parameters. The prediction accuracies reached 83% in prokaryotic organisms and 84% in eukaryotic organisms with the substitution model of the c-p-v matrix (c, composition; p, polarity; and v, molecular volume). The overall prediction accuracy was also evaluated using the "leave-one-out" jackknife procedure. The influence of the substitution model on prediction accuracy has also been discussed in the work. The source code of the new program is available on request from the authors. PMID:17805467

  6. A phylogenetic perspective on larval spine morphology in Leucorrhinia (Odonata: Libellulidae) based on ITS1, 5.8S, and ITS2 rDNA sequences.

    PubMed

    Hovmöller, Rasmus; Johansson, Frank

    2004-03-01

    Leucorrhinia (Odonata, Anisoptera, Libellulidae) consists of 14-15 species with a holarctic distribution. We have combined the morphological characters of a previous study with sequence data from the ITS1, 5.8S rDNA, and ITS2 regions of the nuclear ribosomal repeat. Cloning was used to investigate the intra-individual variation and such variation was found in all investigated species. Parsimony jackknifing was used to identify supported groups. The effect of sequence alignment and gap coding was explored by a modified sensitivity analysis. Loss of spines in Leucorrhinia larvae has occurred twice: once in Europe and once in North America. The role of spines as a defence against predation is discussed in a phylogenetic context. PMID:15012945

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

    PubMed

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

  8. 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

  9. Prediction of Pork Quality by Fuzzy Support Vector Machine Classifier

    NASA Astrophysics Data System (ADS)

    Zhang, Jianxi; Yu, Huaizhi; Wang, Jiamin

    Existing objective methods to evaluate pork quality in general do not yield satisfactory results and their applications in meat industry are limited. In this study, fuzzy support vector machine (FSVM) method was developed to evaluate and predict pork quality rapidly and nondestructively. Firstly, the discrete wavelet transform (DWT) was used to eliminate the noise component in original spectrum and the new spectrum was reconstructed. Then, considering the characteristic variables still exist correlation and contain some redundant information, principal component analysis (PCA) was carried out. Lastly, FSVM was developed to differentiate and classify pork samples into different quality grades using the features from PCA. Jackknife tests on the working datasets indicated that the prediction accuracies were higher than other methods.

  10. 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.

  11. 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.

  12. Latency as a region contrast: Measuring ERP latency differences with Dynamic Time Warping.

    PubMed

    Zoumpoulaki, A; Alsufyani, A; Filetti, M; Brammer, M; Bowman, H

    2015-12-01

    Methods for measuring onset latency contrasts are evaluated against a new method utilizing the dynamic time warping (DTW) algorithm. This new method allows latency to be measured across a region instead of single point. We use computer simulations to compare the methods' power and Type I error rates under different scenarios. We perform per-participant analysis for different signal-to-noise ratios and two sizes of window (broad vs. narrow). In addition, the methods are tested in combination with single-participant and jackknife average waveforms for different effect sizes, at the group level. DTW performs better than the other methods, being less sensitive to noise as well as to placement and width of the window selected. PMID:26372033

  13. A method for WD40 repeat detection and secondary structure prediction.

    PubMed

    Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

    2013-01-01

    WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

  14. 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

  15. 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.

  16. Temporal genetic variability and host sources of Escherichia coli associated with fecal pollution from domesticated animals in the shellfish culture environment of Xiangshan Bay, East China Sea.

    PubMed

    Fu, Ling-Lin; Shuai, Jiang-Bing; Wang, Yanbo; Ma, Hong-Jia; Li, Jian-Rong

    2011-10-01

    This study was conducted to analyze the genetic variability of Escherichia coli from domesticated animal wastes for microbial source tracking (MST) application in fecal contaminated shellfish growing waters of Xiangshan Bay, East China Sea. (GTG)(5) primer was used to generate 1363 fingerprints from E. coli isolated from feces of known 9 domesticated animal sources around this shellfish culture area. Jackknife analysis of the complete (GTG)(5)-PCR DNA fingerprint library indicated that isolates were assigned to the correct source groups with an 84.28% average rate of correct classification. Based on one-year source tracking data, the dominant sources of E. coli were swine, chickens, ducks and cows in this water area. Moreover, annual and spatial changes of E. coli concentrations and host sources may affect the level and distribution of zoonotic pathogen species in waters. Our findings will further contribute to preventing fecal pollution in aquatic environments and quality control of shellfish. PMID:21645948

  17. Linear regression in astronomy. II

    NASA Technical Reports Server (NTRS)

    Feigelson, Eric D.; Babu, Gutti J.

    1992-01-01

    A wide variety of least-squares linear regression procedures used in observational astronomy, particularly investigations of the cosmic distance scale, are presented and discussed. The classes of linear models considered are (1) unweighted regression lines, with bootstrap and jackknife resampling; (2) regression solutions when measurement error, in one or both variables, dominates the scatter; (3) methods to apply a calibration line to new data; (4) truncated regression models, which apply to flux-limited data sets; and (5) censored regression models, which apply when nondetections are present. For the calibration problem we develop two new procedures: a formula for the intercept offset between two parallel data sets, which propagates slope errors from one regression to the other; and a generalization of the Working-Hotelling confidence bands to nonstandard least-squares lines. They can provide improved error analysis for Faber-Jackson, Tully-Fisher, and similar cosmic distance scale relations.

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

    PubMed

    da Silva, Vitor H; Gonalves, 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

  19. Structural class tendency of polypeptide: A new conception in predicting protein structural class

    NASA Astrophysics Data System (ADS)

    Yu, Tao; Sun, Zhi-Bo; Sang, Jian-Ping; Huang, Sheng-You; Zou, Xian-Wu

    2007-12-01

    Prediction of protein domain structural classes is an important topic in protein science. In this paper, we proposed a new conception: structural class tendency of polypeptides (SCTP), which is based on the fact that a given amino acid fragment tends to be presented in certain type of proteins. The SCTP is obtained from an available training data set PDB40-B. When using the SCTP to predict protein structural classes by Intimate Sorting predictive method, we got the predictive accuracy (jackknife test) with 93.7%, 96.5%, and 78.6% for the testing data set PDB40-j, Chou&Maggiora and CHOU. These results indicate that the SCTP approach is quite encouraging and promising. This new conception provides an effective tool to extract valuable information from protein sequences.

  20. 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

  1. Measures of clinical agreement for nominal and categorical data: the kappa coefficient.

    PubMed

    Cyr, L; Francis, K

    1992-07-01

    The desire to determine the extent inter-rater measurements obtained in a clinical setting are free from measurement error and reflect true scores has spurned a renewed interest in assessment of reliability. The kappa coefficient is considered the statistic of choice to analyze the reliability of nominal and categorical types of data recorded on the same patient by more than one clinician. This paper presents a simple computer program written in PASCAL that can be used in a clinical environment to quickly determine the reliability of nominal or categorical data. This computer program calculates both weighted and non-weighted kappa coefficients with their corresponding standard errors as well as bias-correcting jackknife estimates of kappa for use with small sample sizes. PMID:1643847

  2. 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.

  3. Analysis of correlated ROC areas in diagnostic testing.

    PubMed

    Song, H H

    1997-03-01

    This paper focuses on methods of analysis of areas under receiver operating characteristic (ROC) curves. Analysis of ROC areas should incorporate the correlation structure of repeated measurements taken on the same set of cases and the paucity of measurements per treatment resulting from an effective summarization of cases into a few area measures of diagnostic accuracy. The repeated nature of ROC data has been taken into consideration in the analysis methods previously suggested by Swets and Pickett (1982, Evaluation of Diagnostic Systems: Methods from Signal Detection Theory), Hanley and McNeil (1983, Radiology 148, 839-843), and DeLong, DeLong, and Clarke-Pearson (1988, Biometrics 44, 837-845). DeLong et al.'s procedure is extended to a Wald test for general situations of diagnostic testing. The method of analyzing jackknife pseudovalues by treating them as data is extremely useful when the number of area measures to be tested is quite small. The Wald test based on covariances of multivariate multisample U-statistics is compared with two approaches of analyzing pseudovalues, the univariate mixed-model analysis of variance (ANOVA) for repeated measurements and the three-way factorial ANOVA. Monte Carlo simulations demonstrate that the three tests give good approximation to the nominal size at the 5% levels for large sample sizes, but the paired t-test using ROC areas as data lacks the power of the other three tests and Hanley and McNeil's method is inappropriate for testing diagnostic accuracies. The Wald statistic performs better than the ANOVAs of pseudovalues. Jackknifing schemes of multiple deletion where different structures of normal and diseased distributions are accounted for appear to perform slightly better than simple multiple-deletion schemes but no appreciable power difference is apparent, and deletion of too many cases at a time may sacrifice power. These methods have important applications in diagnostic testing in ROC studies of radiology and of medicine in general. PMID:9147602

  4. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.

    PubMed

    Moncalvo, J M; Lutzoni, F M; Rehner, S A; Johnson, J; Vilgalys, R

    2000-06-01

    Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets. PMID:12118409

  5. 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.

  6. Uncertainty Quantification of Kinematic Source Parameters using a Bayesian Approach

    NASA Astrophysics Data System (ADS)

    Razafindrakoto, H.; Mai, M.

    2012-04-01

    Ground-motion simulations for seismic hazard analysis and dynamic rupture modeling suffer not only from the non-uniqueness of kinematic source models but also from the unknown robustness of source-inversion solutions. Therefore, adequate uncertainty analysis of kinematic source model parameters is critical to better understand the main factors that lead to rupture model variability, and to explore the robustness of kinematic source model parameters. Thanks to large improvements in computational tools, Bayesian techniques have become feasible to estimate comprehensive model uncertainties by producing the probability density functions (PDF) of model parameters. In this study, we use a Bayesian technique to infer the ensemble of all possible source models that are consistent with seismological data and the available prior information. Two different procedures are followed. In the first one, we use a two-step procedure that initially explores the parameter space in search for the best fitting model (using a non-linear optimization algorithm) and then applies a Markov Chain Monte Carlo (MCMC) method for Bayesian inference on the kinematic rupture parameters. The second procedure is a one-step procedure that immediately applies MCMC by assuming Gaussian uncertainty for the seismological data. This second technique is computationally cheaper and explores the full parameter space, but does not provide a best-fitting "reference solution". Our study presents synthetic tests based on the "Source Inversion Validation" (SIV) exercise. We analyze the performance of those two approaches in terms of efficiency, and their ability to image the known kinematic rupture details. For the two-step procedure, we additionally perform jackknife tests to examine the robust and sensitive features of the best-fitting model. Our results indicate that the well-resolved part of the fault is conserved through all the delete-one jackknife tests, and that the posterior PDF follows a Gaussian like distribution only within the well-resolved regions of the fault.

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

    PubMed Central

    Jůnek, Tomáš; Jůnková Vymyslická, Pavla; Hozdecká, Kateřina; 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

  8. [Comparative analysis of three length based methods for estimating growth of the tilapia Oreochromis aureus (Perciformes: Cichlidae) in a tropical lake of Mexico].

    PubMed

    Arellano-Torres, Andrés; Hernández Montaño, Daniel; Meléndez Galicia, Carlos

    2013-09-01

    A comparative analysis of three length based methods for estimating growth of the tilapia Oreochromis aureus (Perciformes: Cichlidae) in a tropical lake of Mexico. Several methods are now available to estimate fish individual growth based upon the distribution of body lengths in a population. Comparative analyses of length-based methods have been undertaken mainly for marine species; nevertheless, limited information is available for inland species. Tilapia is one of the most important freshwater fisheries and its growth parameters have been estimated by several authors, usually using one length-based method. Thus, the main objectives of this study were: a) to estimate growth parameters of O. aureus from Chapala lake, Mexico, using three length-based methods ELEFAN, PROJMAT and SLCA; b) to quantify the effect of input data variations in growth parameters estimates by the jackknife technique; and c) to compare the new estimates with those previously reported, through the standard growth index phi. We collected and analyzed a total of 1,973 specimens from commercial landings from January to December 2010. The three length-base methods used in the present study resulted in parameter estimates within the range of those reported in other studies. Results derived from jackknife analysis revealed lowest values in the error percentage and coefficient of variation for L infinity when applying ELEFAN, while PROJMAT showed lowest values in the precision estimators for K, which was very similar to ELEFAN. Estimates of the comparative growth index phi were also very similar to those reported for the same species when studied in different reservoirs. Considering our results, we suggest the use of ELEFAN rather than SLCA due to its accuracy to estimate growth parameters for O. aureus. PMID:24044136

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

    NASA Astrophysics Data System (ADS)

    Lpez-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.

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

    PubMed

    J?nek, Tom; J?nkov Vymyslick, Pavla; Hozdeck, Kate?ina; Hejcmanov, 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

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

    NASA Astrophysics Data System (ADS)

    Borges, Paulo A. V.; Hortal, Joaqun; Gabriel, Rosalina; Homem, Ndia

    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.

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

    USGS Publications Warehouse

    Kery, M.; Royle, J. Andrew

    2008-01-01

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

  13. Aftershock Relocation and Shear Wave Splitting in the Yuha Desert Following the 4 April 2010 M7.2 El Mayor-Cucapah Earthquake Kayla A. Kroll (UCR), Elizabeth S. Cochran (USGS), Keith Richards-Dinger (UCR)

    NASA Astrophysics Data System (ADS)

    Kroll, K.; Cochran, E. S.; Richards-Dinger, K. B.

    2011-12-01

    Following the 4 April 2010 El Mayor-Cucapah earthquake, 8 temporary seismometers were installed in the Yuha Desert region north of the Mexican border. During the deployment period, between 6 April and 14 June 2010, over 4,000 aftershocks, within a 20km by 14km study area in the Yuha Desert, are reported in the SCEDC catalog. We relocate the aftershocks and also determine shallow crustal anisotropy to illuminate the complex fault structure in this region. We compute the double difference hypocenter relocations using hypoDD with both manually picked P and S phase arrivals and waveform cross-correlations. We test three velocity models based on the Imperial Valley profile from the SCEC Community Velocity Model, Version 4 (CVM-S4), including the original profile and the profile with a 10% and 20% velocity reduction in Vp/Vs. We use a jackknife test in which the relocations are recomputed with one of the 13 stations removed in each test to estimate horizontal and vertical relative errors. By comparison with the LSQR errors of hypoDD, we find that scaling the LSQR errors by the jackknife/ LSQR error ratio provides a better error estimate. We find that the Imperial Valley profile with a 10% velocity reduction results in the lowest location errors. The absolute and relative relocation errors were reduced by at least an order of magnitude when compared to the original SCEDC catalog locations. We then use statistical uncertainties in the data to identify simple structures in the cloud of earthquake relocations. This modified collapsing method employs principal component analysis to identify three types of structures that a set of closely located events is most likely associated with: point, line or plane. With this method, collapsed locations provide insight to the poorly understood geologic structures in the Yuha Desert. Additionally, we measure the shallow crustal anisotropy using shear wave splitting techniques. Preliminary visual inspection of the data suggests clear split shear waves with relatively large delays. For more quantitative analysis of the data we use an automated shear wave splitting code to estimate the fast orientation and delay times for the roughly 2,900 relocated aftershocks. We will then examine the results for spatial and/or temporal variations in splitting parameters. Quantifying crack orientation and delay time parameters will allow us to infer whether the anisotropy is due to the local stress field and/or due to structure-induced anisotropy.

  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. 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

  16. HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease.

    PubMed

    Li, Shuyan; Lu, Jun; Li, Jiazhong; Chen, Ximing; Yao, Xiaojun; Xi, Lili

    2016-01-26

    The disruption of protein hydroxylation is highly associated with several serious diseases and consequently the identification of protein hydroxylation sites has attracted significant attention recently. Here, we report the development of an improved method, called HydPred, to identify protein hydroxylation sites (hydroxyproline and hydroxylysine) based on the synthetic minority over-sampling technique (SMOTE), the random forest (RF) algorithm and four blocks of newly composed features that are derived from the protein primary sequence. The HydPred method achieved the best prediction performance reported until now with Matthew's correlation coefficient values of 0.770 and 0.857 for hydroxyproline and hydroxylysine, respectively, according to jack-knife cross-validation. This represents an improvement of 8% for hydroxyproline and 19% for hydroxylysine compared to the best results of available predictors. The prediction performance of HydPred for the external validation of hydroxyproline and hydroxylysine was also improved compared with other published methods. We subsequently applied HydPred to study the association of disruption of hydroxylation sites with human inherited disease. The analyses suggested that the loss of hydroxylation sites is more likely to cause disease instead of the gain of hydroxylation sites and 52 different human inherited diseases were found to be highly associated with the loss of hydroxylation sites. Therefore, HydPred represents a new strategy to discover the molecular basis of pathogenesis associated with abnormal hydroxylation. HydPred is now available online as a user-friendly web server at . PMID:26661679

  17. iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

    PubMed Central

    Qiu, Wang-Ren; Lin, Wei-Zhong; Chou, Kuo-Chen

    2014-01-01

    Before becoming the native proteins during the biosynthesis, their polypeptide chains created by ribosome's translating mRNA will undergo a series of “product-forming” steps, such as cutting, folding, and posttranslational modification (PTM). Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases and epigenetic inheritance. One of the most important PTMs is the Arg- or Lys-methylation that occurs on arginine or lysine, respectively. Given a protein, which site of its Arg (or Lys) can be methylated, and which site cannot? This is the first important problem for understanding the methylation mechanism and drug development in depth. With the avalanche of protein sequences generated in the postgenomic age, its urgency has become self-evident. To address this problem, we proposed a new predictor, called iMethyl-PseAAC. In the prediction system, a peptide sample was formulated by a 346-dimensional vector, formed by incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general form of pseudo amino acid composition. It was observed by the rigorous jackknife test and independent dataset test that iMethyl-PseAAC was superior to any of the existing predictors in this area. PMID:24977164

  18. 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

  19. LabCaS: Labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields

    PubMed Central

    Fan, Yong-Xian; Zhang, Yang; Shen, Hong-Bin

    2014-01-01

    The calpain family of Ca2+-dependent cysteine proteases plays a vital role in many important biological processes which is closely related with a variety of pathological states. Activated calpains selectively cleave relevant substrates at specific cleavage sites, yielding multiple fragments that can have different functions from the intact substrate protein. Until now, our knowledge about the calpain functions and their substrate cleavage mechanisms are limited because the experimental determination and validation on calpain binding are usually laborious and expensive. In this work, we aim to develop a new computational approach (LabCaS) for accurate prediction of the calpain substrate cleavage sites from amino acid sequences. To overcome the imbalance of negative and positive samples in the machine-learning training which have been suffered by most of the former approaches when splitting sequences into short peptides, we designed a conditional random field algorithm that can label the potential cleavage sites directly from the entire sequences. By integrating the multiple amino acid features and those derived from sequences, LabCaS achieves an accurate recognition of the cleave sites for most calpain proteins. In a jackknife test on a set of 129 benchmark proteins, LabCaS generates an AUC score 0.862. The LabCaS program is freely available at: http://www.csbio.sjtu.edu.cn/bioinf/LabCaS. PMID:23180633

  20. Impact of climate change on communities: revealing species' contribution.

    PubMed

    Davey, Catherine M; Devictor, Vincent; Jonzn, Niclas; Lindstrm, Ake; Smith, Henrik G

    2013-05-01

    1. Although climate is known to play an important role in structuring biological communities, high-resolution analyses of recent climatic impacts on multiple components of diversity are still sparse. Additionally, there is a lack of knowledge about which species drive community response to environmental change. 2. We used a long-term breeding bird data set that encompasses a large latitudinal and altitudinal range to model the effect of temperature on spatial and temporal patterns in alpha and beta diversity. We also established a novel framework for identifying species-specific contributions to these macroecological patterns, hence combining two different approaches for identifying climatic impacts. 3. Alpha diversity increased over time, whilst beta diversity declined; both diversity metrics showed a significant relationship with recent temperature anomalies. By partitioning beta diversity, we showed that the decline was predominately driven by changes in species turnover rather than nestedness suggesting a process of replacement by more common species. 4. Using jackknife analyses we identified how individual species influenced the modelled relationships of diversity with temperature and time. Influential species tended to be habitat generalists with moderate to large distributions. 5. We demonstrate that different facets of avian diversity can respond rapidly to temperature anomalies and as a result have undergone significant changes in the last decade. In general, it appears that warming temperatures are driving compositional homogenization of temperate bird communities via range expansion of common generalist species. PMID:23398634

  1. Estimation of Purkait's triangle method and alternative models for sex assessment from the proximal femur in the Spanish population.

    PubMed

    Djorojevic, Mirjana; Roldán, Concepción; Botella, Miguel; Alemán, Inmaculada

    2016-01-01

    The current study was undertaken to test the validity and reproducibility of the Purkait triangle method and some alternative proposals for sex prediction from the proximal femur in the adult population of Spain. To that end, sexual dimorphism of the maximum femoral head diameter and the minimum femoral neck diameter were also evaluated. The study was conducted on 186 femora (109 males and 77 females) taken from the San José collection of identified individuals (Southern Spain). Discriminant function analyses (DFA) employing the jackknife procedure for cross-validations were considered. Overall, more than 94 % of individuals of both sexes were correctly classified. The most dimorphic single variable from the triangle method was the intertrochanteric apex distance (BC) that reached 85.5 % accuracy, falling below those obtained for the femoral head and femoral neck diameter, respectively, (89.8 and 91.9 %). Combining BC with the neck diameter, the predictive ability increased to 92.5 %; when femoral head diameter was added to the latter two, the classification success rate improved further up to 94.6 % (94.1 % after cross-validation). We conclude that the classification success rates of the Purkait's method remained considerably below any of those obtained with the models proposed in the present study which proved to be a much better and more reliable choice both as single predictors and in combination with other variables. PMID:25951948

  2. Assessing long-term pH change in an Australian river catchment using monitoring and palaeolimnological data.

    PubMed

    Tibby, John; Reid, Michael A; Fluin, Jennie; Hart, Barry T; Kershaw, A Peter

    2003-08-01

    Reviews of stream monitoring data suggest that there has been significant acidification (>1.0 pH unit at some sites) of Victorian streamwaters over the past 3 decades. To assess whether these declines are within the range of natural variability, we developed a diatom model for inferring past pH and applied it to a ca. 3500-yr diatom record from a flood plain lake, Callemondah 1 Billabong, on the Goulburn River, which has among the most substantial observed pH declines. The model has a jackkniffed r2 between diatom inferred and measured pH of 0.77 and a root mean square error of prediction of 0.35 pH units. In the pre-European period, pH was stable (range 6.5-6.7) for approximately 3000 yr. Since European settlement around 160 yr ago, diatom-inferred billabong pH has increased significantly by >0.5 units. We hypothesize that this increase in pH is related to processes associated with land clearance (e.g., increased base cation load and decreased organic acid load). There is no evidence of the recent monitored declines in the Callemondah record, which may indicate that that flood plain lakes and the main stream are experiencing divergent pH trends or that the temporal resolution in the billabong sediment record is insufficient to register recent declines. PMID:12966966

  3. Cell fingerprinting: an approach to classifying cells according to mass profiles of digests of protein extracts.

    PubMed

    Zhou, X; Gonnet, G; Hallett, M; Mnchbach, M; Folkers, G; James, P

    2001-05-01

    We present a statistical framework for classifying cells according to the set of peptide masses obtained by mass spectrometric analysis of digestions of whole cell protein extracts. The digest is separated by high performance liquid chromatography (HPLC) coupled directly to a mass spectrometer either by an electrospray interface or by collection to a matrix-assisted laser desorption/ionization target plate. Here, the mass to charge ratio, intensity, and HPLC retention time of the peptides are measured. We have used defined bacterial strains to test this approach. For each bacterium, this process is repeated for extracts obtained at different points in the growth curve in order to try and define an invariant set of signals that uniquely identify the bacterium. This paper presents algorithms for the creation of this cell fingerprint database and develops a Bayesian classification scheme for deciding whether or not an unknown bacterium has a match in the database. Our initial testing based on a limited data set of three bacteria indicates that our approach is feasible. Via a jack-knife test, our Bayesian classification scheme correctly identified the bacterium in 67.8% of the cases. PMID:11678037

  4. 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

  5. Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique.

    PubMed

    Tang, Hua; Chen, Wei; Lin, Hao

    2016-04-22

    Immunoglobulins, also called antibodies, are a group of cell surface proteins which are produced by the immune system in response to the presence of a foreign substance (called antigen). They play key roles in many medical, diagnostic and biotechnological applications. Correct identification of immunoglobulins is crucial to the comprehension of humoral immune function. With the avalanche of protein sequences identified in postgenomic age, it is highly desirable to develop computational methods to timely identify immunoglobulins. In view of this, we designed a predictor called "IGPred" by formulating protein sequences with the pseudo amino acid composition into which nine physiochemical properties of amino acids were incorporated. Jackknife cross-validated results showed that 96.3% of immunoglobulins and 97.5% of non-immunoglobulins can be correctly predicted, indicating that IGPred holds very high potential to become a useful tool for antibody analysis. For the convenience of most experimental scientists, a web-server for IGPred was established at http://lin.uestc.edu.cn/server/IGPred. We believe that the web-server will become a powerful tool to study immunoglobulins and to guide related experimental validations. PMID:26883492

  6. 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.

  7. 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

  8. Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

    PubMed Central

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2015-01-01

    Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences. PMID:26788119

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

    PubMed Central

    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

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

    PubMed Central

    Luebben, Jens; Gruene, Tim

    2015-01-01

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

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

    PubMed

    Luebben, Jens; Gruene, Tim

    2015-07-21

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

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

    PubMed

    Wang, Xiaofeng; Zhou, Yuan; Yan, Renxiang

    2015-07-01

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

  13. 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

  14. 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.

  15. 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

  16. 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 9.7σ. Cosmological constraints from the measurements in this work are presented in a companion paper (DES et al. 2015).

  17. Instability-based mechanism for body undulations in centipede locomotion

    NASA Astrophysics Data System (ADS)

    Aoi, Shinya; Egi, Yoshimasa; Tsuchiya, Kazuo

    2013-01-01

    Centipedes have many body segments and legs and they generate body undulations during terrestrial locomotion. Centipede locomotion has the characteristic that body undulations are absent at low speeds but appear at faster speeds; furthermore, their amplitude and wavelength increase with increasing speed. There are conflicting reports regarding whether the muscles along the body axis resist or support these body undulations and the underlying mechanisms responsible for the body undulations remain largely unclear. In the present study, we investigated centipede locomotion dynamics using computer simulation with a body-mechanical model and experiment with a centipede-like robot and then conducted dynamic analysis with a simple model to clarify the mechanism. The results reveal that body undulations in these models occur due to an instability caused by a supercritical Hopf bifurcation. We subsequently compared these results with data obtained using actual centipedes. The model and actual centipedes exhibit similar dynamic properties, despite centipedes being complex, nonlinear dynamic systems. Based on our findings, we propose a possible passive mechanism for body undulations in centipedes, similar to a follower force or jackknife instability. We also discuss the roles of the muscles along the body axis in generating body undulations in terms of our physical model.

  18. Instability-based mechanism for body undulations in centipede locomotion.

    PubMed

    Aoi, Shinya; Egi, Yoshimasa; Tsuchiya, Kazuo

    2013-01-01

    Centipedes have many body segments and legs and they generate body undulations during terrestrial locomotion. Centipede locomotion has the characteristic that body undulations are absent at low speeds but appear at faster speeds; furthermore, their amplitude and wavelength increase with increasing speed. There are conflicting reports regarding whether the muscles along the body axis resist or support these body undulations and the underlying mechanisms responsible for the body undulations remain largely unclear. In the present study, we investigated centipede locomotion dynamics using computer simulation with a body-mechanical model and experiment with a centipede-like robot and then conducted dynamic analysis with a simple model to clarify the mechanism. The results reveal that body undulations in these models occur due to an instability caused by a supercritical Hopf bifurcation. We subsequently compared these results with data obtained using actual centipedes. The model and actual centipedes exhibit similar dynamic properties, despite centipedes being complex, nonlinear dynamic systems. Based on our findings, we propose a possible passive mechanism for body undulations in centipedes, similar to a follower force or jackknife instability. We also discuss the roles of the muscles along the body axis in generating body undulations in terms of our physical model. PMID:23410369

  19. 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

  20. 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-ΛCDM expectation of >5σ in the range 30 < ℓ < 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 μK arcmin) over an effective area of 400 deg2 for an equivalent survey weight of 250,000 μK-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 >6σ.

  1. 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

  2. Hinged Plakin Domains Provide Specialized Degrees of Articulation in Envoplakin, Periplakin and Desmoplakin

    PubMed Central

    Al-Jassar, Caezar; Bernad?, Pau; Chidgey, Martyn; Overduin, Michael

    2013-01-01

    Envoplakin, periplakin and desmoplakin are cytoskeletal proteins that provide structural integrity within the skin and heart by resisting shear forces. Here we reveal the nature of unique hinges within their plakin domains that provides divergent degrees of flexibility between rigid long and short arms composed of spectrin repeats. The range of mobility of the two arms about the hinge is revealed by applying the ensemble optimization method to small-angle X-ray scattering data. Envoplakin and periplakin adopt L shaped conformations exhibiting a helicopter propeller-like mobility about the hinge. By contrast desmoplakin exhibits essentially unrestricted mobility by jack-knifing about the hinge. Thus the diversity of molecular jointing that can occur about plakin hinges includes L shaped bends, U turns and fully extended I orientations between rigid blocks of spectrin repeats. This establishes specialised hinges in plakin domains as a key source of flexibility that may allow sweeping of cellular spaces during assembly of cellular structures and could impart adaptability, so preventing irreversible damage to desmosomes and the cell cytoskeleton upon exposure to mechanical stress. PMID:23922795

  3. 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.

  4. 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.

  5. Differentiating prenatal exposure to methamphetamine and alcohol versus alcohol and not methamphetamine using tensor based brain morphometry and discriminant analysis

    PubMed Central

    Sowell, Elizabeth R.; Leow, Alex D.; Bookheimer, Susan Y.; Smith, Lynne M.; OConnor, Mary J.; Kan, Eric; Rosso, Carly; Houston, Suzanne; Dinov, Ivo D.; Thompson, Paul M.

    2010-01-01

    Here we investigate the effects of prenatal exposure to methamphetamine (MA) on local brain volume using magnetic resonance imaging. Because many who use MA during pregnancy also use alcohol, a known teratogen, we examined whether local brain volumes differed among 61 children (ages 5 to 15), 21 with prenatal MA exposure, 18 with concomitant prenatal alcohol exposure (the MAA group), 13 with heavy prenatal alcohol but not MA exposure (ALC group), and 27 unexposed controls (CON group). Volume reductions were observed in both exposure groups relative to controls in striatal and thalamic regions bilaterally, and right prefrontal and left occipitoparietal cortices. Striatal volume reductions were more severe in the MAA group than in the ALC group, and within the MAA group, a negative correlation between full-scale IQ (FSIQ) scores and caudate volume was observed. Limbic structures including the anterior and posterior cingulate, the inferior frontal gyrus (IFG) and ventral and lateral temporal lobes bilaterally were increased in volume in both exposure groups. Further, cingulate and right IFG volume increases were more pronounced in the MAA than ALC group. Discriminant function analyses using local volume measurements and FSIQ were used to predict group membership, yielding factor scores that correctly classified 72% of participants in jackknife analyses. These findings suggest that striatal and limbic structures, known to be sites of neurotoxicity in adult MA abusers, may be more vulnerable to prenatal MA exposure than alcohol exposure, and that more severe striatal damage is associated with more severe cognitive deficit. PMID:20237258

  6. Effects of Taxon Sampling in Reconstructions of Intron Evolution

    PubMed Central

    Nikitin, Mikhail A.; Aleoshin, Vladimir V.

    2013-01-01

    Introns comprise a considerable portion of eukaryotic genomes; however, their evolution is understudied. Numerous works of the last years largely disagree on many aspects of intron evolution. Interpretation of these differences is hindered because different algorithms and taxon sampling strategies were used. Here, we present the first attempt of a systematic evaluation of the effects of taxon sampling on popular intron evolution estimation algorithms. Using the taxon jackknife method, we compared the effect of taxon sampling on the behavior of intron evolution inferring algorithms. We show that taxon sampling can dramatically affect the inferences and identify conditions where algorithms are prone to systematic errors. Presence or absence of some key species is often more important than the taxon sampling size alone. Criteria of representativeness of the taxonomic sampling for reliable reconstructions are outlined. Presence of the deep-branching species with relatively high intron density is more important than sheer number of species. According to these criteria, currently available genomic databases are representative enough to provide reliable inferences of the intron evolution in animals, land plants, and fungi, but they underrepresent many groups of unicellular eukaryotes, including the well-studied Alveolata. PMID:23671844

  7. Prediction of carbamylated lysine sites based on the one-class k-nearest neighbor method.

    PubMed

    Huang, Guohua; Zhou, You; Zhang, Yuchao; Li, Bi-Qing; Zhang, Ning; Cai, Yu-Dong

    2013-11-01

    Protein carbamylation is one of the important post-translational modifications, which plays a pivotal role in a number of biological conditions, such as diseases, chronic renal failure and atherosclerosis. Therefore, recognition and identification of protein carbamylated sites are essential for disease treatment and prevention. Yet the mechanism of action of carbamylated lysine sites is still not realized. Thus it remains a largely unsolved challenge to uncover it, whether experimentally or theoretically. To address this problem, we have presented a computational framework for theoretically predicting and analyzing carbamylated lysine sites based on both the one-class k-nearest neighbor method and two-stage feature selection. The one-class k-nearest neighbor method requires no negative samples in training. Experimental results showed that by using 280 optimal features the presented method achieved promising performances of SN=82.50% for the jackknife test on the training set, and SN=66.67%, SP=100.00% and MCC=0.8097 for the independent test on the testing set, respectively. Further analysis of the optimal features provided insights into the mechanism of action of carbamylated lysine sites. It is anticipated that our method could be a potentially useful and essential tool for biologists to theoretically investigate carbamylated lysine sites. PMID:24056952

  8. Identification of core T cell network based on immunome interactome

    PubMed Central

    2014-01-01

    Background Data-driven studies on the dynamics of reconstructed protein-protein interaction (PPI) networks facilitate investigation and identification of proteins important for particular processes or diseases and reduces time and costs of experimental verification. Modeling the dynamics of very large PPI networks is computationally costly. Results To circumvent this problem, we created a link-weighted human immunome interactome and performed filtering. We reconstructed the immunome interactome and weighed the links using jackknife gene expression correlation of integrated, time course gene expression data. Statistical significance of the links was computed using the Global Statistical Significance (GloSS) filtering algorithm. P-values from GloSS were computed for the integrated, time course gene expression data. We filtered the immunome interactome to identify core components of the T cell PPI network (TPPIN). The interconnectedness of the major pathways for T cell survival and response, including the T cell receptor, MAPK and JAK-STAT pathways, are maintained in the TPPIN network. The obtained TPPIN network is supported both by Gene Ontology term enrichment analysis along with study of essential genes enrichment. Conclusions By integrating gene expression data to the immunome interactome and using a weighted network filtering method, we identified the T cell PPI immune response network. This network reveals the most central and crucial network in T cells. The approach is general and applicable to any dataset that contains sufficient information. PMID:24528953

  9. Flowering timing prediction in Australian native understorey species ( Acrotriche R.Br Ericaceae) using meteorological data

    NASA Astrophysics Data System (ADS)

    Schneemilch, Melanie; Kokkinn, Michael; Williams, Craig R.

    2012-01-01

    The aim of this study was to determine the climatic influences on floral development for five members of the Australian native plant genus Acrotriche R. Br (Ericaceae). An observed period of summer floral dormancy suggests temperature is involved in flowering regulation in these species. Models were developed to determine temperature requirements associated with the likelihood of flowering occurring on any one day. To this end, the timing of flowering and meteorological data were collated for several sites, and multivariate logistic regressions performed to identify variables with a significant influence on flowering timing. The resultant models described a large amount of variation in flowering presence/absence, with r 2 values ranging from 0.72 to 0.79. Temperature was identified as influential on both floral development and flowering timing in each of the study species. The positive influence of short photoperiods on flowering in three of the winter flowering species was not surprising. However, the reporting here of a significant association between interdiurnal temperature and flowering in one species is novel. The predictive power of the models was validated through a jackknife sequential recalculation approach, revealing strong positive and negative predictive ability for flowering for four of the five species. Applications of the models include assisting in determination of the suitability of areas for vegetation restoration and identifying the possible effects of climate change on flowering in the study species.

  10. Spider diversity (Arachnida: Araneae) in Atlantic Forest areas at Pedra Branca State Park, Rio de Janeiro, Brazil

    PubMed Central

    Pérez-González, Abel; Baptista, Renner L. C.

    2016-01-01

    Abstract Background There has never been any published work about the diversity of spiders in the city of Rio de Janeiro using analytical tools to measure diversity. The only available records for spider communities in nearby areas indicate 308 species in the National Park of Tijuca and 159 species in Marapendi Municipal Park. These numbers are based on a rapid survey and on an one-year survey respectively. New information This study provides a more thorough understanding of how the spider species are distributed at Pedra Branca State Park. We report a total of 14,626 spider specimens recorded from this park, representing 49 families and 373 species or morphospecies, including at least 73 undescribed species. Also, the distribution range of 45 species was expanded, and species accumulation curves estimate that there is a minimum of 388 (Bootstrap) and a maximum of 468 species (Jackknife2) for the sampled areas. These estimates indicates that the spider diversity may be higher than observed. PMID:26929710

  11. The shape of the buttocks. A useful guide for selection of anesthesia and patient position in anorectal surgery.

    PubMed

    Nivatvongs, S; Fang, D T; Kennedy, H L

    1983-02-01

    Recognition of the different shapes of the buttocks will help surgeons to appropriately select patients for anorectal surgery. Basically, there are three types of buttocks. In Type A, the mounds of the buttock make a low and gentle slope with the anal verge. In Type B, the mounds of the buttock are high and rise almost straight up from the anal verge. In Type C, the anus is located more anteriorly than normally. Patients with Type A buttocks are ideal candidates to use local anesthesia for hemorrhoidectomy and lateral internal sphincterotomy because it is easy to infiltrate the anesthetic agent into the anal canal. With Type C, this is somewhat more difficult, but no significant problem exists. For Type B buttocks, general or spinal anesthesia is recommended. For Types A and C buttocks, a lithotomy position will give an excellent exposure of the anorectal lumen for stripping the mucosa and submucosa. For Type B buttocks, a prone jack-knife position gives the best exposure. PMID:6822174

  12. DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites

    PubMed Central

    Wang, Xiaofeng; Yan, Renxiang; Song, Jiangning

    2016-01-01

    Protein dephosphorylation, which is an inverse process of phosphorylation, plays a crucial role in a myriad of cellular processes, including mitotic cycle, proliferation, differentiation, and cell growth. Compared with tyrosine kinase substrate and phosphorylation site prediction, there is a paucity of studies focusing on computational methods of predicting protein tyrosine phosphatase substrates and dephosphorylation sites. In this work, we developed two elegant models for predicting the substrate dephosphorylation sites of three specific phosphatases, namely, PTP1B, SHP-1, and SHP-2. The first predictor is called MGPS-DEPHOS, which is modified from the GPS (Group-based Prediction System) algorithm with an interpretable capability. The second predictor is called CKSAAP-DEPHOS, which is built through the combination of support vector machine (SVM) and the composition of k-spaced amino acid pairs (CKSAAP) encoding scheme. Benchmarking experiments using jackknife cross validation and 30 repeats of 5-fold cross validation tests show that MGPS-DEPHOS and CKSAAP-DEPHOS achieved AUC values of 0.921, 0.914 and 0.912, for predicting dephosphorylation sites of the three phosphatases PTP1B, SHP-1, and SHP-2, respectively. Both methods outperformed the previously developed kNN-DEPHOS algorithm. In addition, a web server implementing our algorithms is publicly available at http://genomics.fzu.edu.cn/dephossite/ for the research community. PMID:27002216

  13. EGS hydraulic stimulation monitoring by surface arrays - location accuracy and completeness magnitude: the Basel Deep Heat Mining Project case study

    NASA Astrophysics Data System (ADS)

    Häge, Martin; Blascheck, Patrick; Joswig, Manfred

    2013-01-01

    The potential and limits of monitoring induced seismicity by surface-based mini arrays was evaluated for the hydraulic stimulation of the Basel Deep Heat Mining Project. This project aimed at the exploitation of geothermal heat from a depth of about 4,630 m. As reference for our results, a network of borehole stations by Geothermal Explorers Ltd. provided ground truth information. We utilized array processing, sonogram event detection and outlier-resistant, graphical jackknife location procedures to compensate for the decrease in signal-to-noise ratio at the surface. We could correctly resolve the NNW-SSE striking fault plane by relative master event locations. Statistical analysis of our catalog data resulted in M L 0.36 as completeness magnitude, but with significant day-to-night dependency. To compare to the performance of borehole data with M W 0.9 as completeness magnitude, we applied two methods for converting M L to M W which raised our M C to M W in the range of 0.99-1.13. Further, the b value for the duration of our measurement was calculated to 1.14 (related to M L), respectively 1.66 (related to M W), but changes over time could not be resolved from the error bars.

  14. Synergism between constituents of multicomponent catalysts designed for ethanol steam reforming using partial least squares regression and artificial neural networks.

    PubMed

    Szijjrto, Gbor P; Tompos, Andrs; Hberger, Kroly; Margitfalvi, Jzsef L

    2012-02-01

    Effects of different catalyst components on the catalytic performance in steam reforming of ethanol have been investigated by means of Artificial Neural Networks (ANNs) and Partial Least Square regression (PLSR). The data base consisted of ca. 400 items (catalysts with varied composition), which were obtained from a former catalyst optimization procedure. Marten's uncertainty (jackknife) test showed that simultaneous addition of Ni and Co has crucial effect on the hydrogen production. The catalyst containing both Ni and Co provided remarkable hydrogen production at 450C. The addition of Ceas modifier to the bimetallic NiCo catalyst has high importance at lower temperatures: the hydrogen concentration is doubled at 350C. Addition of Pt had only little effect on the product distribution. The outliers in the data set have been investigated by means of Hotelling T2 control chart. Compositions containing high amount of Cu or Ce have been identified as outliers, which points to the nonlinear effect of Cu and Ce on the catalytic performance. ANNs were used for analysis of the non-linear effects: an optimum was found with increasing amount of Cu and Ce in the catalyst composition. Hydrogen production can be improved by Ce only in the absence of Zn. Additionally, negative cross-effect was evidenced between Ni and Cu. The above relationships have been visualized in Holographic Maps, too. Although predictive ability of PLSR is somewhat worse than that of ANN, PLSR provided indirect evidence that ANNs were trained adequately. PMID:21902647

  15. Analysis of metabolic pathway using hybrid properties.

    PubMed

    Chen, Lei; Cai, Yu-Dong; Shi, Xiao-He; Huang, Tao

    2012-01-01

    Given a compounds-forming system, i.e., a system consisting of some compounds and their relationship, can it form a biologically meaningful pathway? It is a fundamental problem in systems biology. Nowadays, a lot of information on different organisms, at both genetic and metabolic levels, has been collected and stored in some specific databases. Based on these data, it is feasible to address such an essential problem. Metabolic pathway is one kind of compounds-forming systems and we analyzed them in yeast by extracting different (biological and graphic) features from each of the 13,736 compounds-forming systems, of which 136 are positive pathways, i.e., known metabolic pathway from KEGG; while 13,600 were negative. Each of these compounds-forming systems was represented by 144 features, of which 88 are graph features and 56 biological features. "Minimum Redundancy Maximum Relevance" and "Incremental Feature Selection" were utilized to analyze these features and 16 optimal features were selected as being able to predict a query compounds- forming system most successfully. It was found through Jackknife cross-validation that the overall success rate of identifying the positive pathways was 74.26%. It is anticipated that this novel approach and encouraging result may give meaningful illumination to investigate this important topic. PMID:21919854

  16. Nucleosome positioning based on the sequence word composition.

    PubMed

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

    2012-01-01

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

  17. 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

  18. Fusing face-verification algorithms and humans.

    PubMed

    O'Toole, Alice J; Abdi, Herv; 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

  19. 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. (χ(2) = 6.02, P = 0.01), while individuals harboring Chilomastix sp. were less likely to have Capillaria sp. present (χ(2) = 4.03, P = 0.04). PMID:25686475

  20. Molecular evolution of rbcL in the mycoheterotrophic coralroot orchids (Corallorhiza Gagnebin, Orchidaceae).

    PubMed

    Barrett, Craig F; Freudenstein, John V

    2008-05-01

    The RuBisCO large subunit gene (rbcL) has been the focus of numerous plant phylogenetic studies and studies on molecular evolution in parasitic plants. However, there has been a lack of investigation of photosynthesis gene molecular evolution in fully mycoheterotrophic plants. These plants invade pre-existing mutualistic associations between ectomycorrhizal trees and fungi, from which they obtain fixed carbon and nutrients. The mycoheterotrophic orchid Corallorhiza contains both green (photosynthetic) and non-green (putatively nonphotosynthetic) species. We sequenced rbcL from 31 accessions of eight species of Corallorhiza and hypothesized that some lineages would have pseudogenes resulting from relaxation of purifying selection on RuBisCO's carboxylase function. Phylogenetic analysis of rbcL+ITS gave high jackknife support for relationships among species. We found evidence of pseudogene formation in all lineages of the Corallorhiza striata complex and in some lineages of the C. maculata complex. Evidence includes: stop codons, frameshifts, decreased d(S)/d(N) ratios, replacements not observed in photosynthetic species, rate heterogeneity, and high likelihood of neutral evolution. The evolution of rbcL in Corallorhiza may serve as an exemplary system in which to study the effects of relaxed evolutionary constraints on photosynthesis genes for >400 documented fully mycoheterotrophic plant species. PMID:18374606

  1. The impact of mammographic density and lesion location on detection

    NASA Astrophysics Data System (ADS)

    Al Mousa, Dana; Ryan, Elaine; Lee, Warwick; Nickson, Carolyn; Pietrzyk, Mariusz; Reed, Warren; Poulos, Ann; Li, Yanpeng; Brennan, Patrick

    2013-03-01

    The aim of this study is to examine the impact of breast density and lesion location on detection. A set of 55 mammographic images (23 abnormal images with 26 lesions and 32 normal images) were examined by 22 expert radiologists. The images were classified by an expert radiologist according to the Synoptic Breast Imaging Report of the National Breast Cancer Centre (NBCC) as having low mammographic density (D1<25% glandular and D2> 25-50% glandular) or high density (D3 51-75% glandular and D4> 75-glandular). The observers freely examined the images and located any malignancy using a 5-point confidence. Performance was defined using the following metrics: sensitivity, location sensitivity, specificity, receiver operating characteristic (ROC Az) curves and jackknife free-response receiver operator characteristics (JAFROC) figures of merit. Significant increases in sensitivity (p= 0.0174) and ROC (p=0.0001) values were noted for the higher density compared with lower density images according to NBCC classification. No differences were seen in radiologists' performance between lesions within or outside the fibroglandular region. In conclusion, analysis of our data suggests that radiologists scored higher using traditional metrics in higher mammographic density images without any improvement in lesion localisation. Lesion location whether within or outside the fibroglandular region appeared to have no impact on detection abilities suggesting that if a masking effect is present the impact is minimal. Eye-tracking analyses are ongoing.

  2. Non-coding RNA identification based on topology secondary structure and reading frame in organelle genome level.

    PubMed

    Wu, Cheng-Yan; Li, Qian-Zhong; Feng, Zhen-Xing

    2016-01-01

    Non-coding RNA (ncRNA) genes make transcripts as same as the encoding genes, and ncRNAs directly function as RNAs rather than serve as blueprints for proteins. As the function of ncRNA is closely related to organelle genomes, it is desirable to explore ncRNA function by confirming its provenance. In this paper, the topology secondary structure, motif and the triplets under three reading frames are considered as parameters of ncRNAs. A method of SVM combining the increment of diversity (ID) algorithm is applied to construct the classifier. When the method is applied to the ncRNA dataset less than 80% sequence identity, the overall accuracies reach 95.57%, 96.40% in the five-fold cross-validation and the jackknife test, respectively. Further, for the independent testing dataset, the average prediction success rate of our method achieved 93.24%. The higher predictive success rates indicate that our method is very helpful for distinguishing ncRNAs from various organelle genomes. PMID:26697761

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

    SciTech Connect

    Chiang, H. C.; Barkats, D.; Bock, J. J.; Hristov, V. V.; Jones, W. C.; Kovac, J. M.; Lange, A. E.; Mason, P. V.; Matsumura, T.; Ade, P. A. R.; Battle, J. O.; Dowell, C. D.; Nguyen, H. T.; Bierman, E. M.; Keating, B. G.; Duband, L.; Hivon, E. F.; Holzapfel, W. L.; Kuo, C. L.; Leitch, E. M.

    2010-03-10

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

  4. Tributaries under Mediterranean climate: their role in macrobenthos diversity maintenance.

    PubMed

    Maasri, Alain; Dumont, Bernard; Claret, Cécile; Archambaud-Suard, Gaït; Gandouin, Emmanuel; Franquet, Evelyne

    2008-07-01

    The taxonomic richness erosion and the role of tributaries in the maintenance of the taxonomic richness were considered in a Mediterranean catchment in southeastern France. Nine stations were chosen along the Arc stream (three stations downstream from an organic effluent and one station upstream from the pollution source) and on two groups of tributaries (three intermittent and two perennial). High biodiversity erosion was noticed in the main stem, revealing diffuse sources of pollution added to the expected effect of the localized organic pollution. Jackknife richness estimator and beta diversity indicated that the intermittent tributaries had the highest richness values and harboured 70% of the taxa recorded at the catchment scale. The intermittent flow tributaries seem to play a major role in maintaining the taxonomic richness in such catchments, highly impacted by anthropogenic activities. The detailed examination and the preservation of these ecosystems should be an important step in catchment management, and support the need for catchment-scale conservation of freshwater invertebrates. PMID:18558378

  5. Predicting bacteriophage proteins located in host cell with feature selection technique.

    PubMed

    Ding, Hui; Liang, Zhi-Yong; Guo, Feng-Biao; Huang, Jian; Chen, Wei; Lin, Hao

    2016-04-01

    A bacteriophage is a virus that can infect a bacterium. The fate of an infected bacterium is determined by the bacteriophage proteins located in the host cell. Thus, reliably identifying bacteriophage proteins located in the host cell is extremely important to understand their functions and discover potential anti-bacterial drugs. Thus, in this paper, a computational method was developed to recognize bacteriophage proteins located in host cells based only on their amino acid sequences. The analysis of variance (ANOVA) combined with incremental feature selection (IFS) was proposed to optimize the feature set. Using a jackknife cross-validation, our method can discriminate between bacteriophage proteins located in a host cell and the bacteriophage proteins not located in a host cell with a maximum overall accuracy of 84.2%, and can further classify bacteriophage proteins located in host cell cytoplasm and in host cell membranes with a maximum overall accuracy of 92.4%. To enhance the value of the practical applications of the method, we built a web server called PHPred (〈http://lin.uestc.edu.cn/server/PHPred〉). We believe that the PHPred will become a powerful tool to study bacteriophage proteins located in host cells and to guide related drug discovery. PMID:26945463

  6. 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

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

    PubMed

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

    2014-12-01

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

  8. Identifying the subfamilies of voltage-gated potassium channels using feature selection technique.

    PubMed

    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

  9. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets. PMID:26460680

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

    PubMed

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

    2007-01-01

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

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

    PubMed

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

    2014-10-30

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

  12. DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites.

    PubMed

    Wang, Xiaofeng; Yan, Renxiang; Song, Jiangning

    2016-01-01

    Protein dephosphorylation, which is an inverse process of phosphorylation, plays a crucial role in a myriad of cellular processes, including mitotic cycle, proliferation, differentiation, and cell growth. Compared with tyrosine kinase substrate and phosphorylation site prediction, there is a paucity of studies focusing on computational methods of predicting protein tyrosine phosphatase substrates and dephosphorylation sites. In this work, we developed two elegant models for predicting the substrate dephosphorylation sites of three specific phosphatases, namely, PTP1B, SHP-1, and SHP-2. The first predictor is called MGPS-DEPHOS, which is modified from the GPS (Group-based Prediction System) algorithm with an interpretable capability. The second predictor is called CKSAAP-DEPHOS, which is built through the combination of support vector machine (SVM) and the composition of k-spaced amino acid pairs (CKSAAP) encoding scheme. Benchmarking experiments using jackknife cross validation and 30 repeats of 5-fold cross validation tests show that MGPS-DEPHOS and CKSAAP-DEPHOS achieved AUC values of 0.921, 0.914 and 0.912, for predicting dephosphorylation sites of the three phosphatases PTP1B, SHP-1, and SHP-2, respectively. Both methods outperformed the previously developed kNN-DEPHOS algorithm. In addition, a web server implementing our algorithms is publicly available at http://genomics.fzu.edu.cn/dephossite/ for the research community. PMID:27002216

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

    PubMed Central

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

    2014-01-01

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

  14. 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.

  15. Effect of host plants on developmental time and life table parameters of Carposina sasakii (Lepidoptera: Carposinidae) under laboratory conditions.

    PubMed

    Lei, Xihong; Li, Dingxu; Li, Zheng; Zalom, Frank G; Gao, Lingwang; Shen, Zuorui

    2012-04-01

    Studies were designed to examine the effects of host plants (apricot, Prunus armeniaca L.; plum, Prunus salicina L.; peach, Prunus persica L.; jujube, Zizyphus jujuba Will.; apple, Malus domestica Mill.; and pear, Pyrus sorotina Will) on the development and life table parameters of the peach fruit moth, Carposina sasakii Matsumura (Lepidoptera: Carposinidae) under laboratory conditions. Peach fruit moth developed faster (12.48 d) and had the highest preimaginal survival rate (50.54%) on plum compared with the other host plants. Adult longevity was significantly longer on jujube for both female and male moths. Adult females from larvae reared on jujube and peach laid significantly greater numbers of eggs (214.50 and 197.94 eggs per female, respectively) compared with those reared on the other four host plants. Life-table parameters were calculated for each host plant and compared by jackknife procedures. The intrinsic rate of natural increase (r(m)) was significantly greatest on plum (0.1294 eggs per female per d), followed by jujube and apricot (0.1201 and 0.1128 eggs per female per d), respectively. Implications of the various measures of population performance are discussed. PMID:22507008

  16. Multiple Subject Barycentric Discriminant Analysis (MUSUBADA): How to Assign Scans to Categories without Using Spatial Normalization

    PubMed Central

    Abdi, Hervé; Williams, Lynne J.; Connolly, Andrew C.; Gobbini, M. Ida; Dunlop, Joseph P.; Haxby, James V.

    2012-01-01

    We present a new discriminant analysis (DA) method called Multiple Subject Barycentric Discriminant Analysis (MUSUBADA) suited for analyzing fMRI data because it handles datasets with multiple participants that each provides different number of variables (i.e., voxels) that are themselves grouped into regions of interest (ROIs). Like DA, MUSUBADA (1) assigns observations to predefined categories, (2) gives factorial maps displaying observations and categories, and (3) optimally assigns observations to categories. MUSUBADA handles cases with more variables than observations and can project portions of the data table (e.g., subtables, which can represent participants or ROIs) on the factorial maps. Therefore MUSUBADA can analyze datasets with different voxel numbers per participant and, so does not require spatial normalization. MUSUBADA statistical inferences are implemented with cross-validation techniques (e.g., jackknife and bootstrap), its performance is evaluated with confusion matrices (for fixed and random models) and represented with prediction, tolerance, and confidence intervals. We present an example where we predict the image categories (houses, shoes, chairs, and human, monkey, dog, faces,) of images watched by participants whose brains were scanned. This example corresponds to a DA question in which the data table is made of subtables (one per subject) and with more variables than observations. PMID:22548125

  17. Stability of gene contributions and identification of outliers in multivariate analysis of microarray data

    PubMed Central

    Baty, Florent; Jaeger, Daniel; Preiswerk, Frank; Schumacher, Martin M; Brutsche, Martin H

    2008-01-01

    Background Multivariate ordination methods are powerful tools for the exploration of complex data structures present in microarray data. These methods have several advantages compared to common gene-by-gene approaches. However, due to their exploratory nature, multivariate ordination methods do not allow direct statistical testing of the stability of genes. Results In this study, we developed a computationally efficient algorithm for: i) the assessment of the significance of gene contributions and ii) the identification of sample outliers in multivariate analysis of microarray data. The approach is based on the use of resampling methods including bootstrapping and jackknifing. A statistical package of R functions was developed. This package includes tools for both inferring the statistical significance of gene contributions and identifying outliers among samples. Conclusion The methodology was successfully applied to three published data sets with varying levels of signal intensities. Its relevance was compared with alternative methods. Overall, it proved to be particularly effective for the evaluation of the stability of microarray data. PMID:18570644

  18. Evaluation of marked-recapture for estimating striped skunk abundance

    USGS Publications Warehouse

    Greenwood, R.J.; Sargeant, A.B.; Johnson, D.H.

    1985-01-01

    The mark-recapture method for estimating striped skunk (Mephitis mephitis) abundance was evaluated by systematically livetrapping a radio-equipped population on a 31.4-km2 study area in North Dakota during late April of 1977 and 1978. The study population was 10 females and 13 males in 1977 and 20 females and 8 males in 1978. Skunks were almost exclusively nocturnal. Males traveled greater nightly distances than females (3.3 vs. 2.6 km, P < 0.05) and had larger home ranges (308 vs. 242 ha) although not significantly so. Increased windchill reduced night-time activity. The population was demographically but not geographically closed. Frequency of capture was positively correlated with time skunks spent on the study area. Little variation in capture probabilities was found among trap-nights. Skunks exhibited neither trap-proneness nor shyness. Capture rates in 1977 were higher for males than for females; the reverse occurred in 1978. Variation in individual capture rates was indicated among males in 1977 and among females in 1978. Ten estimators produced generally similar results, but all underestimated true population size. Underestimation was a function of the number of untrapped skunks, primarily those that spent limited time on the study area. The jackknife method produced the best estimates of skunk abundance.

  19. Stagewise pseudo-value regression for time-varying effects on the cumulative incidence.

    PubMed

    Zöller, Daniela; Schmidtmann, Irene; Weinmann, Arndt; Gerds, Thomas A; Binder, Harald

    2016-03-30

    In a competing risks setting, the cumulative incidence of an event of interest describes the absolute risk for this event as a function of time. For regression analysis, one can either choose to model all competing events by separate cause-specific hazard models or directly model the association between covariates and the cumulative incidence of one of the events. With a suitable link function, direct regression models allow for a straightforward interpretation of covariate effects on the cumulative incidence. In practice, where data can be right-censored, these regression models are implemented using a pseudo-value approach. For a grid of time points, the possibly unobserved binary event status is replaced by a jackknife pseudo-value based on the Aalen-Johansen method. We combine a stagewise regression technique with the pseudo-value approach to provide variable selection while allowing for time-varying effects. This is implemented by coupling variable selection between the grid times, but determining estimates separately. The effect estimates are regularized to also allow for model fitting with a low to moderate number of observations. This technique is illustrated in an application using clinical cancer registry data from hepatocellular carcinoma patients. The results are contrasted with traditional hazard-based modeling. In addition to a more straightforward interpretation, when using the proposed technique, the identification of time-varying effect patterns on the cumulative incidence is seen to be feasible with a moderate number of observations. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26510388

  20. 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

  1. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness.

    PubMed

    Kovacs, Amir; Yacoby, Keren; Gophna, Uri

    2010-04-01

    ARISA (automated ribosomal intergenic spacer analysis) is a commonly used method for microbial community analysis that provides estimates of microbial richness and diversity. Here we investigated the potential biases of ARISA in richness estimation by performing computer simulations using 722 complete genomes. Our simulations based on in silico PCR demonstrated that over 8% of bacterial strains represented by complete genomes will never yield a PCR fragment using ARISA primers, usually because their ribosomal RNA genes are not organized in an operon. Despite the tendency of ARISA to overestimate species richness, a strong linear correlation exists between the observed number of fragments, even after binning, and the actual number of species in the sample. This linearity is fairly robust to the taxon sampling in the database as it is also observed on subsets of the 722 genome database using a jackknife approach. However, this linearity disappears when the species richness is high and binned fragment lengths gradually become saturated. We suggest that for ARISA-based richness estimates, where the number of binned lengths observed ranges between 10 and 116, a correction should be used in order to obtain more accurate "species richness" results comparable to 16S rRNA clone-library data. PMID:20138144

  2. Visual search for tropical web spiders: the influence of plot length, sampling effort, and phase of the day on species richness.

    PubMed

    Pinto-Leite, C M; Rocha, P L B

    2012-12-01

    Empirical studies using visual search methods to investigate spider communities were conducted with different sampling protocols, including a variety of plot sizes, sampling efforts, and diurnal periods for sampling. We sampled 11 plots ranging in size from 5 by 10 m to 5 by 60 m. In each plot, we computed the total number of species detected every 10 min during 1 hr during the daytime and during the nighttime (0630 hours to 1100 hours, both a.m. and p.m.). We measured the influence of time effort on the measurement of species richness by comparing the curves produced by sample-based rarefaction and species richness estimation (first-order jackknife). We used a general linear model with repeated measures to assess whether the phase of the day during which sampling occurred and the differences in the plot lengths influenced the number of species observed and the number of species estimated. To measure the differences in species composition between the phases of the day, we used a multiresponse permutation procedure and a graphical representation based on nonmetric multidimensional scaling. After 50 min of sampling, we noted a decreased rate of species accumulation and a tendency of the estimated richness curves to reach an asymptote. We did not detect an effect of plot size on the number of species sampled. However, differences in observed species richness and species composition were found between phases of the day. Based on these results, we propose guidelines for visual search for tropical web spiders. PMID:23321102

  3. Ectomycorrhizal communities in a productive Tuber aestivum Vittad. orchard: composition, host influence and species replacement.

    PubMed

    Benucci, Gian Maria Niccolò; Raggi, Lorenzo; Albertini, Emidio; Grebenc, Tine; Bencivenga, Mattia; Falcinelli, Mario; Di Massimo, Gabriella

    2011-04-01

    Truffles (Tuber spp.) and other ectomycorrhizal species form species-rich assemblages in the wild as well as in cultivated ecosystems. We aimed to investigate the ectomycorrhizal communities of hazels and hornbeams that are growing in a 24-year-old Tuber aestivum orchard. We demonstrated that the ectomycorrhizal communities included numerous species and were phylogenetically diverse. Twenty-nine ectomycorrhizal taxa were identified. Tuber aestivum ectomycorrhizae were abundant (9.3%), only those of Tricholoma scalpturatum were more so (21.4%), and were detected in both plant symbionts with a variation in distribution and abundance between the two different hosts. The Thelephoraceae family was the most diverse, being represented by 12 taxa. The overall observed diversity represented 85% of the potential one as determined by a jackknife estimation of richness and was significantly higher in hazel than in hornbeam. The ectomycorrhizal communities of hornbeam trees were closely related phylogenetically, whereas no clear distribution pattern was observed for the communities in hazel. Uniform site characteristics indicated that ectomycorrhizal relationships were host mediated, but not host specific. Despite the fact that different plant species hosted diverse ectomycorrhizal communities and that the abundance of T. aestivum differed among sites, no difference was detected in the production of fruiting bodies. PMID:21223332

  4. 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

  5. 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 flares 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.

  6. Phylogenetic analysis identifies the invertebrate pathogen Helicosporidium sp. as a green alga (Chlorophyta).

    PubMed

    Tartar, Aurlien; Boucias, Drion G; Adams, Byron J; Becnel, James J

    2002-01-01

    Historically, the invertebrate pathogens of the genus Helicosporidium were considered to be either protozoa or fungi, but the taxonomic position of this group has not been considered since 1931. Recently, a Helicosporidium sp., isolated from the blackfly Simulium jonesi Stone & Snoddy (Diptera: Simuliidae), has been amplified in the heterologous host Helicoverpa zea. Genomic DNA has been extracted from gradient-purified cysts. The 185, 28S and 5.8S regions of the Helicosporidium rDNA, as well as partial sequences of the actin and beta-tubulin genes, were amplified by PCR and sequenced. Comparative analysis of these nucleotide sequences was performed using neighbour-joining and maximum-parsimony methods. All inferred phylogenetic trees placed Helicosporidium sp. among the green algae (Chlorophyta), and this association was supported by bootstrap and parsimony jackknife values. Phylogenetic analysis focused on the green algae depicted Helicosporidium sp. as a close relative of Prototheca wickerhamii and Prototheca zopfii (Chlorophyta, Trebouxiophyceae), two achlorophylous, pathogenic green algae. On the basis of this phylogenetic analysis, Helicosporidium sp. is clearly neither a protist nor a fungus, but appears to be the first described algal invertebrate pathogen. These conclusions lead us to propose the transfer of the genus Helicosporidium to Chlorophyta, Trebouxiophyceae. PMID:11837312

  7. 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.

  8. Multimodal Voxel-Based Meta-Analysis of White Matter Abnormalities in Alzheimer's Disease.

    PubMed

    Yin, Rui-Hua; Tan, Lan; Liu, Yong; Wang, Wen-Ying; Wang, Hui-Fu; Jiang, Teng; Zhang, Yu; Gao, Junling; Canu, Elisa; Migliaccio, Raffaella; Filippi, Massimo; Gorno-Tempini, Maria Luisa; Yu, Jin-Tai

    2015-01-01

    An increasing number of MRI investigations suggest that patients with Alzheimer's disease (AD) show not only gray matter decreases but also white matter (WM) abnormalities, including WM volume (WMV) deficits and integrity disruption of WM pathways. In this study, we applied multimodal voxel-wise meta-analytical methods to study WMV and fractional anisotropy in AD. Fourteen studies including 723 participants (340 with AD and 383 controls) were involved. The meta-analysis was performed using effect size signed differential mapping. Significant WMV reductions were observed in bilateral inferior temporal gyrus, splenium of corpus callosum, right parahippocampal gyrus, and hippocampus. Decreased fractional anisotropy was identified mainly in left posterior limb of internal capsule, left anterior corona radiata, left thalamus, and left caudate nucleus. Significant decreases of both WMV and fractional anisotropy were found in left caudate nucleus, left superior corona radiata, and right inferior temporal gyrus. Most findings showed to be highly replicable in the jackknife sensitivity analyses. In conclusion, AD patients show widespread WM abnormalities mainly in bilateral structures related to advanced mental and nervous activities. PMID:26401571

  9. Optimizing the feature set for a Bayesian network for breast cancer diagnosis using genetic algorithm techniques

    NASA Astrophysics Data System (ADS)

    Wang, Xiao Hui; Zheng, Bin; Chang, Yuan-Hsiang; Good, Walter F.

    1999-05-01

    This study investigates the degree to which the performance of Bayesian belief networks (BBNs), for computer-assisted diagnosis of breast cancer, can be improved by optimizing their input feature sets using a genetic algorithm (GA). 421 cases (all women) were used in this study, of which 92 were positive for breast cancer. Each case contained both non-image information and image information derived from mammograms by radiologists. A GA was used to select an optimal subset of features, from a total of 21, to use as the basis for a BBN classifier. The figure-of-merit used in the GA's evaluation of feature subsets was Az, the area under the ROC curve produced by the corresponding BBN classifier. For each feature subset evaluated by the GA, a BBN was developed to classify positive and negative cases. Overall performance of the BBNs was evaluated using a jackknife testing method to calculate Az, for their respective ROC curves. The Az value of the BBN incorporating all 21 features was 0.851 plus or minus 0.012. After a 93 generation search, the GA found an optimal feature set with four non-image and four mammographic features, which achieved an Az value of 0.927 plus or minus 0.009. This study suggests that GAs are a viable means to optimize feature sets, and optimizing feature sets can result in significant performance improvements.

  10. 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

  11. 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

  12. 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

  13. 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

  14. Prevention of facial pressure ulcers using the Mayfield clamp for sacral tumor resection.

    PubMed

    Goodwin, C Rory; Recinos, Pablo F; Omeis, Ibrahim; Momin, Eric N; Witham, Timothy F; Bydon, Ali; Gokaslan, Ziya L; Wolinsky, Jean-Paul

    2011-01-01

    Sacral neoplasm resection is managed via partial or total sacrectomy that is performed via the Kraske approach. The combination of the patients positioning and the relatively long operative time required for this procedure increase the risk of pressure ulcers. Facial pressure ulcers can cause tissue necrosis and/or ulceration in a highly visible area, leading to a cosmetically disfiguring lesion. Here, the authors report the use of a Mayfield clamp in the positioning of patients undergoing sacral tumor resection to prevent facial pressure ulceration. After the patient is placed prone in the Kraske or Jackknife position, the hips and knees are flexed with arms to the side. Then while in the prone position, the patient is physically placed in pins, and the Mayfield clamp is fixated at the center of the metal arch via the Mayfield sitting adapter to the Andrews frame, suspending the head (and face) over the table. The authors find that this technique prevents the development of facial pressure ulcers, and it has the potential to be used in patients positioned in the Kraske position for other surgical procedures. PMID:21142454

  15. Coupling SWAT and ANN models for enhanced daily streamflow prediction

    NASA Astrophysics Data System (ADS)

    Noori, Navideh; Kalin, Latif

    2016-02-01

    To improve daily flow prediction in unmonitored watersheds a hybrid model was developed by combining a quasi-distributed watershed model and artificial neural network (ANN). Daily streamflow data from 29 nearby watersheds in and around the city of Atlanta, Southeastern United States, with leave-one-site-out jackknifing technique were used to build the flow predictive models during warm and cool seasons. Daily streamflow was first simulated with the Soil and Water Assessment Tool (SWAT) and then the SWAT simulated baseflow and stormflow were used as inputs to ANN. Out of the total 29 test watersheds, 62% and 83% of them had Nash-Sutcliffe values above 0.50 during the cool and warm seasons, respectively (considered good or better). As the percent forest cover or the size of test watershed increased, the performances of the models gradually decreased during both warm and cool seasons. This indicates that the developed models work better in urbanized watersheds. In addition, SWAT and SWAT Calibration Uncertainty Procedure (SWAT-CUP) program were run separately for each station to compare the flow prediction accuracy of the hybrid approach to SWAT. Only 31% of the sites during the calibration and 34% of validation runs had ENASH values ⩾0.50. This study showed that coupling ANN with semi-distributed models can lead to improved daily streamflow predictions in ungauged watersheds.

  16. Geometry preserving projections algorithm for predicting membrane protein types.

    PubMed

    Wang, Tong; Xia, Tian; Hu, Xiao-ming

    2010-01-21

    Given a new uncharacterized protein sequence, a biologist may want to know whether it is a membrane protein or not? If it is, which membrane protein type it belongs to? Knowing the type of an uncharacterized membrane protein often provides useful clues for finding the biological function of the query protein, developing the computational methods to address these questions can be really helpful. In this study, a sequence encoding scheme based on combing pseudo position-specific score matrix (PsePSSM) and dipeptide composition (DC) is introduced to represent protein samples. However, this sequence encoding scheme would correspond to a very high dimensional feature vector. A dimensionality reduction algorithm, the so-called geometry preserving projections (GPP) is introduced to extract the key features from the high-dimensional space and reduce the original high-dimensional vector to a lower-dimensional one. Finally, the K-nearest neighbor (K-NN) and support vector machine (SVM) classifiers are employed to identify the types of membrane proteins based on their reduced low-dimensional features. Our jackknife and independent dataset test results thus obtained are quite encouraging, which indicate that the above methods are used effectively to deal with this complicated problem of predicting the membrane protein type. PMID:19800352

  17. 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

  18. iMethyl-PseAAC: identification of protein methylation sites via a pseudo amino acid composition approach.

    PubMed

    Qiu, Wang-Ren; Xiao, Xuan; Lin, Wei-Zhong; Chou, Kuo-Chen

    2014-01-01

    Before becoming the native proteins during the biosynthesis, their polypeptide chains created by ribosome's translating mRNA will undergo a series of "product-forming" steps, such as cutting, folding, and posttranslational modification (PTM). Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases and epigenetic inheritance. One of the most important PTMs is the Arg- or Lys-methylation that occurs on arginine or lysine, respectively. Given a protein, which site of its Arg (or Lys) can be methylated, and which site cannot? This is the first important problem for understanding the methylation mechanism and drug development in depth. With the avalanche of protein sequences generated in the postgenomic age, its urgency has become self-evident. To address this problem, we proposed a new predictor, called iMethyl-PseAAC. In the prediction system, a peptide sample was formulated by a 346-dimensional vector, formed by incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general form of pseudo amino acid composition. It was observed by the rigorous jackknife test and independent dataset test that iMethyl-PseAAC was superior to any of the existing predictors in this area. PMID:24977164

  19. 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

  20. A causal proportional hazards estimator for the effect of treatment actually received in a randomized trial with all-or-nothing compliance.

    PubMed

    Loeys, T; Goetghebeur, E

    2003-03-01

    Survival data from randomized trials are most often analyzed in a proportional hazards (PH) framework that follows the intention-to-treat (ITT) principle. When not all the patients on the experimental arm actually receive the assigned treatment, the ITT-estimator mixes its effect on treatment compliers with its absence of effect on noncompliers. The structural accelerated failure time (SAFT) models of Robins and Tsiatis are designed to consistently estimate causal effects on the treated, without direct assumptions about the compliance selection mechanism. The traditional PH-model, however, has not yet led to such causal interpretation. In this article, we examine a PH-model of treatment effect on the treated subgroup. While potential treatment compliance is unobserved in the control arm, we derive an estimating equation for the Compliers PROPortional Hazards Effect of Treatment (C-PROPHET). The jackknife is used for bias correction and variance estimation. The method is applied to data from a recently finished clinical trial in cancer patients with liver metastases. PMID:12762446

  1. 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

  2. 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

  3. 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.

  4. A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

    PubMed

    Chen, Jing; Xu, Huimin; He, Ping-An; Dai, Qi; Yao, Yuhua

    2016-01-01

    Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based. The original and consensus sequences were combined with physicochemical properties. And elements information of different rows and columns in position-specific scoring matrix were taken into consideration simultaneously for more core and essence information. Computational methods based on gene ontology (GO) have been demonstrated to be superior to methods based on other features. Then principal component analysis (PCA) is applied for feature selection and reduced vectors are input to a support vector machine (SVM) to predict protein subcellular localization. The proposed method can achieve a prediction accuracy of 98.28% and 97.87% on a stringent Gram-positive (Gpos) and Gram-negative (Gneg) dataset with Jackknife test, respectively. At last, we calculate "absolute true overall accuracy (ATOA)", which is stricter than overall accuracy. The ATOA obtained from the proposed method is also up to 97.32% and 93.06% for Gpos and Gneg. From both the rationality of testing procedure and the success rates of test results, the current method can improve the prediction quality of protein subcellular localization. PMID:26724384

  5. AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes.

    PubMed

    Lin, Hao; Chen, Wei; Ding, Hui

    2013-01-01

    The structure and activity of enzymes are influenced by pH value of their surroundings. Although many enzymes work well in the pH range from 6 to 8, some specific enzymes have good efficiencies only in acidic (pH<5) or alkaline (pH>9) solution. Studies have demonstrated that the activities of enzymes correlate with their primary sequences. It is crucial to judge enzyme adaptation to acidic or alkaline environment from its amino acid sequence in molecular mechanism clarification and the design of high efficient enzymes. In this study, we developed a sequence-based method to discriminate acidic enzymes from alkaline enzymes. The analysis of variance was used to choose the optimized discriminating features derived from g-gap dipeptide compositions. And support vector machine was utilized to establish the prediction model. In the rigorous jackknife cross-validation, the overall accuracy of 96.7% was achieved. The method can correctly predict 96.3% acidic and 97.1% alkaline enzymes. Through the comparison between the proposed method and previous methods, it is demonstrated that the proposed method is more accurate. On the basis of this proposed method, we have built an online web-server called AcalPred which can be freely accessed from the website (http://lin.uestc.edu.cn/server/AcalPred). We believe that the AcalPred will become a powerful tool to study enzyme adaptation to acidic or alkaline environment. PMID:24130738

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

    PubMed Central

    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

  7. Prospective Clinical Study of 551 Cases of Liposuction and Abdominoplasty Performed Individually and in Combination

    PubMed Central

    2013-01-01

    Background: Despite the popularity of these procedures, there are limited published prospective studies evaluating liposuction and abdominoplasty. Lipoabdominoplasty is a subject of recent attention. Several investigators have recommended alternative techniques that preserve the Scarpa fascia in an effort to reduce complications, particularly the risk of seromas. Methods: Over a 5-year period, 551 consecutive patients were treated with ultrasonic liposuction alone (n = 384), liposuction/abdominoplasty (n = 150), or abdominoplasty alone (n = 17). In lipoabdominoplasties, the abdomen and flanks were first treated with liposuction. A traditional flap dissection was used for all abdominoplasties. Scalpel dissection was used rather than electrodissection. A supine jackknife position was used in surgery to provide maximum hip flexion, allowing a secure deep fascial repair. Results: The complication rate after liposuction was 4.2% vs 50% for patients treated with an abdominoplasty. Approximately half of the abdominoplasty complications were minor scar deformities, including widened umbilical scars (17.3%) that were revised. The seroma rate after abdominoplasties was 5.4%; there were no seromas after liposuction alone. Conclusions: Lipoabdominoplasty may be performed safely, so that patients may benefit from both modalities. The seroma rate is reduced by avoiding electrodissection, making Scarpa fascia preservation a moot point. A deep fascial repair keeps the abdominoplasty scar within the bikini line. Deep venous thrombosis and other complications may be minimized with precautions that do not include anticoagulation. PMID:25289226

  8. Exploring FROC paradigm: initial experience with clinical applications

    NASA Astrophysics Data System (ADS)

    Volokh, Lana; Liu, Chi; Tsui, Benjamin M. W.

    2006-03-01

    Design of receiver-operating characteristic (ROC)-based paradigm and data analysis methods that capture and adequately address the complexity of clinical decision-making will facilitate the development and evaluation of new image acquisition, reconstruction and processing techniques. We compare the JAFROC (Jackknife free-response ROC) to traditional ROC paradigm and analysis in two image evaluation studies. The first study is designed to address advantages of "free response" features of JAFROC paradigm in a breast lesion detection task. We developed tools allowing the acquisition of FROC-type rating data and use them on a set of simulated scintimammography images. Four observers participated in a small preliminary study. Rating data are then analyzed using traditional ROC and JAFROC techniques. The second study is aimed at comparing the diagnostic quality of myocardial perfusion SPECT (MPS) images obtained with different quantitative image reconstruction and compensation methods in an ongoing clinical trial. The observer assesses status of each of the three main vascular territories for each patient. This experimental set-up uses standardized locations of vascular territories on myocardial polar plot images, and a fixed number of three rating scores per patient. We compare results from the newly available JAFROC versus the traditional ROC analysis technique previously applied in similar studies, using a set of data from an on-going clinical trial. Comparison of two analysis methodologies reveals generally consistent behavior, corresponding to theoretical predictions.

  9. 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.

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

    PubMed

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

    2010-06-01

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

  11. Evaluation of Residual Cellularity and Proliferation on Preoperatively Treated Breast Cancer: A Comparison between Image Analysis and Light Microscopy Analysis

    PubMed Central

    Corletto, Valentina; Verderio, Paolo; Giardini, Roberto; Cipriani, Sonia; Di Palma, Silvana; Rilke, Franco

    1998-01-01

    Histopathology has been suggested as a reliable method for tumour reduction evaluation of preoperatively treated breast cancer. Immunocytochemistry can be used to enhance the visibility of residual tumour cellularity and in the evaluation of its proliferative activity. We compared Image Analysis (IA) with Light Microscopy Analysis (LMA) on sections of breast carcinomas treated with preoperative chemo? or chemo/radiotherapy in the evaluation of the Neoplastic Cell Density (NCD) (69 cases) and the Proliferation Index (PI) (35 cases). NCD was expressed as the immunoreactive area to cytokeratin over the total original neoplastic area and PI was expressed as the number of immunostained tumoural nuclei with MIB1 MoAb over the total of tumoural nuclei. The intraobserver agreement and that between IA and LMA for both indices were estimated by the common (Kw) and the jackknife weighted kappa statistic (K~w). The extent of agreement of each considered category was also assessed by means of the category?specific kappa statistics (Kcs). The intraobserver agreement within LMA for NCD and PI and that between IA and LMA for PI were both satisfactory. Upon evaluation of the NCD, the agreement between IA and LMA showed unsatisfactory results, especially when the ratio between the residual tumour cells and the background was critical. PMID:9692682

  12. Allocation and discrimination based on human odontometric data.

    PubMed

    Kieser, J A; Groeneveld, H T

    1989-07-01

    This study contrasts the confidence with which individuals may be grouped and then re-allocated on the basis of odontometric data. These data are derived from the mesiodistal and buccolingual diameters of 202 Lengua Indians of Paraguay (100 males, 102 females), 125 Caucasoid schoolchildren (59 male, 66 female), and 206 Negroes (106 male, 100 female). Multivariate intergroup discrimination is effected by means of canonical and stepwise discriminant analysis, whilst allocation is evaluated by means of posterior and typicality probabilities. Bias is reduced by means of a jackknifing procedure. High levels of discriminatory confidence (each Wilk's Lambda, P less than 0.01) are matched by high percentage correct classification (Caucasoid, 67.4-75.0%; Negro, 71.0-77.3%; Amerindian, 65.2-78.1%). However, these results are not matched by allocatory procedures: only 21.7% of caucasoids, 21.4% of Negroes, and 28.8% of Amerindians could be re-allocated with probabilities in excess of 80%. It is concluded that while multivariate discriminant techniques may be usefully employed in the separation of different populations, individuals may not be assigned with the same degree of confidence, even with an a priori knowledge of their group membership. PMID:2764085

  13. Age-stage, two-sex life table of Brontispa longissima (Gestro) (Coleoptera: Hispidae) feeding on four palm plant varieties.

    PubMed

    Jin, Tao; Lin, Yu-Ying; Jin, Qi-An; Wen, Hai-Bo; Peng, Zheng-Qiang

    2012-10-01

    The life history of Brontispa longissima (Gestro) (Coleoptera: Hispidae), reared under laboratory conditions on leaves of coconut (Cocos nucifera L.), royal palm [Roystonea regia (Kunth) O.F.Cook], bottle palm [Hyophorbe lagenicaulis (L. Bailey) H.E.Moore], and fishtail palm (Caryota ochlandra Hance) was analyzed using age-stage, two-sex life table. Means and standard errors of population growth parameters were calculated using the jackknife method. Moreover, survival rate and fecundity data were applied to project the population for revealing the different stage structure. The mean intrinsic rates of population growth when reared on each respective leaf type were 0.032, 0.031, 0.019, and 0.044. Individuals reared on C. nucifera achieved the highest net reproduction rate at 114.5 offspring per female. The mean generation times of B. longissima ranged from 93.2 d (reared on C. ochlandrai) to 161.5 d (reared on H. lagenicaulis). Projections from survival rate and fecundity data indicated that B. longissima populations can row considerably faster on C. ochlandra than on the other three host plants. The results validate the two-stage life history approach taken, providing an essential tool for developing and testing future control strategies. PMID:23068179

  14. 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.

  15. Use of Repetitive DNA Sequences and the PCR To Differentiate Escherichia coli Isolates from Human and Animal Sources

    PubMed Central

    Dombek, Priscilla E.; Johnson, LeeAnn K.; Zimmerley, Sara T.; Sadowsky, Michael J.

    2000-01-01

    The rep-PCR DNA fingerprint technique, which uses repetitive intergenic DNA sequences, was investigated as a way to differentiate between human and animal sources of fecal pollution. BOX and REP primers were used to generate DNA fingerprints from Escherichia coli strains isolated from human and animal sources (geese, ducks, cows, pigs, chickens, and sheep). Our initial studies revealed that the DNA fingerprints obtained with the BOX primer were more effective for grouping E. coli strains than the DNA fingerprints obtained with REP primers. The BOX primer DNA fingerprints of 154 E. coli isolates were analyzed by using the Jaccard band-matching algorithm. Jackknife analysis of the resulting similarity coefficients revealed that 100% of the chicken and cow isolates and between 78 and 90% of the human, goose, duck, pig, and sheep isolates were assigned to the correct source groups. A dendrogram constructed by using Jaccard similarity coefficients almost completely separated the human isolates from the nonhuman isolates. Multivariate analysis of variance, a form of discriminant analysis, successfully differentiated the isolates and placed them in the appropriate source groups. Taken together, our results indicate that rep-PCR performed with the BOX A1R primer may be a useful and effective tool for rapidly determining sources of fecal pollution. PMID:10831440

  16. 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).

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

    PubMed Central

    Stein, H S; Jones, I S

    1988-01-01

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

  18. Evaluation of Mesopuff II to study SO{sub x} deposition in the Great Lakes region

    SciTech Connect

    Ahuja, S.; Kumar, A.

    1997-12-31

    The MESOPUFF II modeling package for long range transport (LRT) is evaluated in a region wide analysis in the five Great Lake states of Illinois, Michigan, Indiana, Ohio and Pennsylvania. The emission inventories for these states were reduced to eighteen sources according to the concept of mixing rules of multi-component systems. Six receptor locations coinciding with monitoring stations were selected for the purpose of comparing predicted and monitored twelve-hourly ground level concentrations. Time periods were selected during which the receptors were not likely to be influenced by wind patterns from regions not included in this study i.e., Canada. The evaluation study included six statistical measures of performance in four different methods of comparison. The confidence limits on these parameters were determined using the bootstrap, jackknife, seductive and robust resampling techniques. The model was found to be adequately accurate in its predictions based on criteria set in previous studies as well as some set in particular for this study. Subsequently the model was also used to predict pollutant removal by using the wet and dry deposition algorithms used by the MESOPUFF modeling package. The results of the deposition analysis was compared with results obtained in past studies. The relative effect of local sources ({approximately}100 km) was determined by running the model for sources in Ohio only in order to determine the impact of long range transport.

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

    PubMed

    Morales, Jess; Mandow, Anthony; Martnez, Jorge L; Reina, Antonio J; Garca-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

  20. 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).

  1. Predicting cancerlectins by the optimal g-gap dipeptides

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

  2. 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; Jrgensen, 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

  3. Predicting the Types of J-Proteins Using Clustered Amino Acids

    PubMed Central

    Feng, Pengmian; Zuo, Yongchun

    2014-01-01

    J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer properties and cell death. Thus, reliably annotating the types of J-proteins is essential to better understand their molecular functions. In the present work, a support vector machine based method was developed to identify the types of J-proteins using the tripeptide composition of reduced amino acid alphabet. In the jackknife cross-validation, the maximum overall accuracy of 94% was achieved on a stringent benchmark dataset. We also analyzed the amino acid compositions by using analysis of variance and found the distinct distributions of amino acids in each family of the J-proteins. To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed. PMID:24804260

  4. 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.

  5. Identification of pathogenic fungi with an optoelectronic nose

    PubMed Central

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

    2014-01-01

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

  6. 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.

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

    SciTech Connect

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom

    2010-09-13

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

  8. 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.

  9. A Novel Feature Extraction Method with Feature Selection to Identify Golgi-Resident Protein Types from Imbalanced Data

    PubMed Central

    Yang, Runtao; Zhang, Chengjin; Gao, Rui; Zhang, Lina

    2016-01-01

    The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew’s Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions. PMID:26861308

  10. Caries-preventive Effect of Supervised Toothbrushing and Sealants.

    PubMed

    Hilgert, L A; Leal, S C; Mulder, J; Creugers, N H J; Frencken, J E

    2015-09-01

    To investigate the effectiveness of 3 caries-preventive measures on high- and low-caries risk occlusal surfaces of first permanent molars over 3 y. This cluster-randomized controlled clinical trial covered 242 schoolchildren, 6 to 7 y old, from low socioeconomic areas. At baseline, caries risk was assessed at the tooth surface level, through a combination of ICDAS II (International Caries Detection and Assessment System) and fissure depth codes. High-caries risk occlusal surfaces were treated according to daily supervised toothbrushing (STB) at school and 2 sealants: composite resin (CR) and atraumatic restorative treatment-high-viscosity glass-ionomer cement (ART-GIC). Low-caries risk occlusal surfaces received STB or no intervention. Evaluations were performed after 0.5, 1, 2, and 3 y. A cavitated dentine carious lesion was considered a failure. Data were analyzed according to the proportional hazard rate regression model with frailty correction, Wald test, analysis of variance, and t test, according to the jackknife procedure for calculating standard errors. The cumulative survival rates of cavitated dentine carious lesion-free, high-caries risk occlusal surfaces were 95.6%, 91.4%, and 90.2% for STB, CR, and ART-GIC, respectively, over 3 y, which were not statistically significantly different. For low-caries risk occlusal surfaces, no statistically significant difference was observed between the cumulative survival rate of the STB group (94.8%) and the no-intervention group (92.1%) over 3 y. There was neither a difference among STB, CR, and ART-GIC on school premises in preventing cavitated dentine carious lesions in high-caries risk occlusal surfaces of first permanent molars nor a difference between STB and no intervention for low-caries risk occlusal surfaces of first permanent molars over 3 y. PMID:26116491

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

    PubMed Central

    2009-01-01

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

  12. 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.

  13. 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.

  14. A New Estimate of the Earth's Land Surface Temperature History

    NASA Astrophysics Data System (ADS)

    Muller, R. A.; Curry, J. A.; Groom, D.; Jacobsen, B.; Perlmutter, S.; Rohde, R. A.; Rosenfeld, A.; Wickham, C.; Wurtele, J.

    2011-12-01

    The Berkeley Earth Surface Temperature team has re-evaluated the world's atmospheric land surface temperature record using a linear least-squares method that allow the use of all the digitized records back to 1800, including short records that had been excluded by prior groups. We use the Kriging method to estimate an optimal weighting of stations to give a world average based on uniform weighting of the land surface. We have assembled a record of the available data by merging 1.6 billion temperature reports from 16 pre-existing data archives; this data base will be made available for public use. The former Global Historic Climatology Network (GHCN) monthly data base shows a sudden drop in the number of stations reporting monthly records from 1980 to the present; we avoid this drop by calculating monthly averages from the daily records. By using all the data, we reduce the effects of potential data selection bias. We make an independent estimate of the urban heat island effect by calculating the world land temperature trends based on stations chosen to be far from urban sites. We calculate the effect of poor station quality, as documented in the US by the team led by Anthony Watts by estimating the temperature trends based solely on the stations ranked good (1,2 or 1,2,3 in the NOAA ranking scheme). We avoid issues of homogenization bias by using raw data; at times when the records are discontinuous (e.g. due to station moves) we break the record into smaller segments and analyze those, rather than attempt to correct the discontinuity. We estimate the uncertainties in the final results using the jackknife procedure developed by J. Tukey. We calculate spatial uncertainties by measuring the effects of geographical exclusion on recent data that have good world coverage. The results we obtain are compared to those published by the groups at NOAA, NASA-GISS, and Hadley-CRU in the UK.

  15. Microbial diversity of biofilms in dental unit water systems.

    PubMed

    Singh, Ruby; Stine, O Colin; Smith, David L; Spitznagel, John K; Labib, Mohamed E; Williams, Henry N

    2003-06-01

    We investigated the microbial diversity of biofilms found in dental unit water systems (DUWS) by three methods. The first was microscopic examination by scanning electron microscopy (SEM), acridine orange staining, and fluorescent in situ hybridization (FISH). Most bacteria present in the biofilm were viable. FISH detected the beta and gamma, but not the alpha, subclasses of Proteobacteria: In the second method, 55 cultivated biofilm isolates were identified with the Biolog system, fatty acid analysis, and 16S ribosomal DNA (rDNA) sequencing. Only 16S identified all 55 isolates, which represented 13 genera. The most common organisms, as shown by analyses of 16S rDNA, belonged to the genera Afipia (28%) and Sphingomonas (16%). The third method was a culture-independent direct amplification and sequencing of 165 subclones from community biofilm 16S rDNA. This method revealed 40 genera: the most common ones included Leptospira (20%), Sphingomonas (14%), Bacillus (7%), Escherichia (6%), Geobacter (5%), and Pseudomonas (5%). Some of these organisms may be opportunistic pathogens. Our results have demonstrated that a biofilm in a health care setting may harbor a vast diversity of organisms. The results also reflect the limitations of culture-based techniques to detect and identify bacteria. Although this is the greatest diversity reported in DUWS biofilms, other genera may have been missed. Using a technique based on jackknife subsampling, we projected that a 25-fold increase in the number of subclones sequenced would approximately double the number of genera observed, reflecting the richness and high diversity of microbial communities in these biofilms. PMID:12788744

  16. 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

  17. Technical efficiency of district hospitals: Evidence from Namibia using Data Envelopment Analysis

    PubMed Central

    Zere, Eyob; Mbeeli, Thomas; Shangula, Kalumbi; Mandlhate, Custodia; Mutirua, Kautoo; Tjivambi, Ben; Kapenambili, William

    2006-01-01

    Background In most countries of the sub-Saharan Africa, health care needs have been increasing due to emerging and re-emerging health problems. However, the supply of health care resources to address the problems has been continuously declining, thus jeopardizing the progress towards achieving the health-related Millennium Development Goals. Namibia is no exception to this. It is therefore necessary to quantify the level of technical inefficiency in the countries so as to alert policy makers of the potential resource gains to the health system if the hospitals that absorb a lion's share of the available resources are technically efficient. Method All public sector hospitals (N = 30) were included in the study. Hospital capacity utilization ratios and the data envelopment analysis (DEA) technique were used to assess technical efficiency. The DEA model used three inputs and two outputs. Data for four financial years (1997/98 to 2000/2001) was used for the analysis. To test for the robustness of the DEA technical efficiency scores the Jackknife analysis was used. Results The findings suggest the presence of substantial degree of pure technical and scale inefficiency. The average technical efficiency level during the given period was less than 75%. Less than half of the hospitals included in the study were located on the technically efficient frontier. Increasing returns to scale is observed to be the predominant form of scale inefficiency. Conclusion It is concluded that the existing level of pure technical and scale inefficiency of the district hospitals is considerably high and may negatively affect the government's initiatives to improve access to quality health care and scaling up of interventions that are necessary to achieve the health-related Millennium Development Goals. It is recommended that the inefficient hospitals learn from their efficient peers identified by the DEA model so as to improve the overall performance of the health system. PMID:16566818

  18. 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.

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

    SciTech Connect

    Ruschin, Mark; Timberg, Pontus; Ba ring th, Magnus; Hemdal, Bengt; Svahn, Tony; Saunders, Rob S.; Samei, Ehsan; Andersson, Ingvar; Mattsson, Soeren; Chakraborty, Dev P.; Tingberg, Anders

    2007-02-15

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

  20. 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.

  1. Nestedness in centipede (Chilopoda) assemblages on continental islands (Aegean, Greece)

    NASA Astrophysics Data System (ADS)

    Simaiakis, Stylianos Michail; Martínez-Morales, Miguel Angel

    2010-05-01

    In natural ecosystems, species assemblages among isolated ecological communities such as continental islands often show a nested pattern in which biotas of sites with low species richness are non-random subsets of biotas of richer sites. The distribution of centipede (Chilopoda) species in the central and south Aegean archipelago was tested for nestedness. To achieve this aim we used distribution data for 53 species collected on 24 continental Aegean islands (Kyklades and Dodekanisa). Based on the first-order jackknife estimator, most of islands were comprehensively surveyed. In order to quantify nestedness, we used the nestedness temperature calculator (NTC) as well as the nestedness metric based on overlap and decreasing Fill (NODF). NTC indicated that data exhibited a high degree of nestedness in the central and south Aegean island complexes. As far as the Kyklades and Dodekanisa are concerned, NTC showed less nested centipede structures than the 24 islands. Likewise, NODF revealed a significant degree of nestedness in central and south Aegean islands. It also showed that biotas matrices without singletons were more nested than the complete ones (Aegean, Kyklades and Dodekanisa). The two commonest centipede taxa (lithobiomorphs and geophilomorphs) contributed differently to centipede assemblages. In the Kyklades and Dodekanisa, geophilomorphs did not show a reliable nested arrangement unlike lithobiomorphs. In relation to the entire data set, nestedness was positively associated with the degree of isolation. In the Kyklades altitudinal range best explained nestedness patterns, while in Dodekanisa habitat heterogeneity proved to be more important for the centipede communities. Island area does not seem to be a significant explanatory variable. Some of our results from the Kyklades were critically compared with those for terrestrial isopod and land snail nested assemblages from the same geographical area. The complex geological and palaeogeographical history of the Aegean archipelago partly accounted for the pattern of centipede assemblages.

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

    PubMed

    Rocha, Ednaldo Cndido; Silva, Elias; Martins, Sebastio Venncio; Barreto, Francisco Cndido Cardoso

    2006-09-01

    We evaluated seasonal species presence and richness, and abundance of medium and large sized mammalian terrestrial fauna in the "Mrio 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

  3. pRNAm-PC: Predicting N(6)-methyladenosine sites in RNA sequences via physical-chemical properties.

    PubMed

    Liu, Zi; Xiao, Xuan; Yu, Dong-Jun; Jia, Jianhua; Qiu, Wang-Ren; Chou, Kuo-Chen

    2016-03-15

    Just like PTM or PTLM (post-translational modification) in proteins, PTCM (post-transcriptional modification) in RNA plays very important roles in biological processes. Occurring at adenine (A) with the genetic code motif (GAC), N(6)-methyldenosine (m(6)A) is one of the most common and abundant PTCMs in RNA found in viruses and most eukaryotes. Given an uncharacterized RNA sequence containing many GAC motifs, which of them can be methylated, and which cannot? It is important for both basic research and drug development to address this problem. Particularly with the avalanche of RNA sequences generated in the postgenomic age, it is highly demanded to develop computational methods for timely identifying the N(6)-methyldenosine sites in RNA. Here we propose a new predictor called pRNAm-PC, in which RNA sequence samples are expressed by a novel mode of pseudo dinucleotide composition (PseDNC) whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross covariance transformations. It was observed via a rigorous jackknife test that, in comparison with the existing predictor for the same purpose, pRNAm-PC achieved remarkably higher success rates in both overall accuracy and stability, indicating that the new predictor will become a useful high-throughput tool for identifying methylation sites in RNA, and that the novel approach can also be used to study many other RNA-related problems and conduct genome analysis. A user-friendly Web server for pRNAm-PC has been established at http://www.jci-bioinfo.cn/pRNAm-PC, by which users can easily get their desired results without needing to go through the mathematical details. PMID:26748145

  4. Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

    PubMed Central

    Kaushik, Swati; Mutt, Eshita; Chellappan, Ajithavalli; Sankaran, Sandhya; Srinivasan, Narayanaswamy; Sowdhamini, Ramanathan

    2013-01-01

    Background Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectively. In this study, examination of serine proteases of prolyl oligopeptidase, rhomboid and subtilisin protein families were carried out using plant serine proteases as queries from two genomes including A. thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST. Methodology/Principal Findings We have proposed to start with multiple queries of classical serine protease members to identify remote homologues in families, using a rigorous approach like Cascade PSI-BLAST. We found that classical sequence based approaches, like PSI-BLAST, showed very low sequence coverage in identifying plant serine proteases. The algorithm was applied on enriched sequence database of homologous domains and we obtained overall average coverage of 88% at family, 77% at superfamily or fold level along with specificity of ?100% and Mathews correlation coefficient of 0.91. Similar approach was also implemented on 13 other protein families representing every structural class in SCOP database. Further investigation with statistical tests, like jackknifing, helped us to better understand the influence of neighbouring protein families. Conclusions/Significance Our study suggests that employment of multiple queries of a family for the Cascade PSI-BLAST searches is useful for predicting distant relationships effectively even at superfamily level. We have proposed a generalized strategy to cover all the distant members of a particular family using multiple query sequences. Our findings reveal that prior selection of sequences as query and the presence of neighbouring families can be important for covering the search space effectively in minimal computational time. This study also provides an understanding of the bridging role of related families. PMID:23437136

  5. Personal and Network Dynamics in Performance of Knowledge Workers: A Study of Australian Breast Radiologists

    PubMed Central

    Tavakoli Taba, Seyedamir; Hossain, Liaquat; Heard, Robert; Brennan, Patrick; Lee, Warwick; Lewis, Sarah

    2016-01-01

    Materials and Methods In this paper, we propose a theoretical model based upon previous studies about personal and social network dynamics of job performance. We provide empirical support for this model using real-world data within the context of the Australian radiology profession. An examination of radiologists’ professional network topology through structural-positional and relational dimensions and radiologists’ personal characteristics in terms of knowledge, experience and self-esteem is provided. Thirty one breast imaging radiologists completed a purpose designed questionnaire regarding their network characteristics and personal attributes. These radiologists also independently read a test set of 60 mammographic cases: 20 cases with cancer and 40 normal cases. A Jackknife free response operating characteristic (JAFROC) method was used to measure the performance of the radiologists’ in detecting breast cancers. Results Correlational analyses showed that reader performance was positively correlated with the social network variables of degree centrality and effective size, but negatively correlated with constraint and hierarchy. For personal characteristics, the number of mammograms read per year and self-esteem (self-evaluation) positively correlated with reader performance. Hierarchical multiple regression analysis indicated that the combination of number of mammograms read per year and network’s effective size, hierarchy and tie strength was the best fitting model, explaining 63.4% of the variance in reader performance. The results from this study indicate the positive relationship between reading high volumes of cases by radiologists and expertise development, but also strongly emphasise the association between effective social/professional interactions and informal knowledge sharing with high performance. PMID:26918644

  6. Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification.

    PubMed

    Mondal, Sukanta; Bhavna, Rajasekaran; Mohan Babu, Rajasekaran; Ramakumar, Suryanarayanarao

    2006-11-21

    Conotoxins are disulfide rich small peptides that target a broad spectrum of ion-channels and neuronal receptors. They offer promising avenues in the treatment of chronic pain, epilepsy and cardiovascular diseases. Assignment of newly sequenced mature conotoxins into appropriate superfamilies using a computational approach could provide valuable preliminary information on the biological and pharmacological functions of the toxins. However, creation of protein sequence patterns for the reliable identification and classification of new conotoxin sequences may not be effective due to the hypervariability of mature toxins. With the aim of formulating an in silico approach for the classification of conotoxins into superfamilies, we have incorporated the concept of pseudo-amino acid composition to represent a peptide in a mathematical framework that includes the sequence-order effect along with conventional amino acid composition. The polarity index attribute, which encodes information such as residue surface buriability, polarity, and hydropathy, was used to store the sequence-order effect. Several methods like BLAST, ISort (Intimate Sorting) predictor, least Hamming distance algorithm, least Euclidean distance algorithm and multi-class support vector machines (SVMs), were explored for superfamily identification. The SVMs outperform other methods providing an overall accuracy of 88.1% for all correct predictions with generalized squared correlation of 0.75 using jackknife cross-validation test for A, M, O and T superfamilies and a negative set consisting of short cysteine rich sequences from different eukaryotes having diverse functions. The computed sensitivity and specificity for the superfamilies were found to be in the range of 84.0-94.1% and 80.0-95.5%, respectively, attesting to the efficacy of multi-class SVMs for the successful in silico classification of the conotoxins into their superfamilies. PMID:16890961

  7. Region-specific transcriptional response to chronic nicotine in rat brain

    PubMed Central

    Konu, Özlen; Kane, Justin K.; Barrett, Tanya; Vawter, Marquis P.; Chang, Ruying; Ma, Jennie Z.; Donovan, David M.; Sharp, Burt; Becker, Kevin G.; Li, Ming D.

    2010-01-01

    Even though nicotine has been shown to modulate mRNA expression of a variety of genes, a comprehensive high-throughput study of the effects of nicotine on the tissue-specific gene expression profiles has been lacking in the literature. In this study, cDNA microarrays containing 1117 genes and ESTs were used to assess the transcriptional response to chronic nicotine treatment in rat, based on four brain regions, i.e. prefrontal cortex (PFC), nucleus accumbens (NAs), ventral tegmental area (VTA), and amygdala (AMYG). On the basis of a non-parametric resampling method, an index (called jackknifed reliability index, JRI) was proposed, and employed to determine the inherent measurement error across multiple arrays used in this study. Upon removal of the outliers, the mean correlation coefficient between duplicate measurements increased to 0.978±0.0035 from 0.941 ±0.045. Results from principal component analysis and pairwise correlations suggested that brain regions studied were highly similar in terms of their absolute expression levels, but exhibited divergent transcriptional responses to chronic nicotine administration. For example, PFC and NAs were significantly more similar to each other (r=0.7; P<10−14) than to either VTA or AMYG. Furthermore, we confirmed our microarray results for two representative genes, i.e. the weak inward rectifier K+ channel (TWIK-1), and phosphate and tensin homolog (PTEN) by using real-time quantitative RT-PCR technique. Finally, a number of genes, involved in MAPK, phosphatidylinositol, and EGFR signaling pathways, were identified and proposed as possible targets in response to nicotine administration. © 2001 Elsevier Science B.V. All rights reserved. PMID:11478936

  8. iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition.

    PubMed

    Liu, Bin; Xu, Jinghao; Lan, Xun; Xu, Ruifeng; Zhou, Jiyun; Wang, Xiaolong; Chou, Kuo-Chen

    2014-01-01

    Playing crucial roles in various cellular processes, such as recognition of specific nucleotide sequences, regulation of transcription, and regulation of gene expression, DNA-binding proteins are essential ingredients for both eukaryotic and prokaryotic proteomes. With the avalanche of protein sequences generated in the postgenomic age, it is a critical challenge to develop automated methods for accurate and rapidly identifying DNA-binding proteins based on their sequence information alone. Here, a novel predictor, called "iDNA-Prot|dis", was established by incorporating the amino acid distance-pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC) vector. The former can capture the characteristics of DNA-binding proteins so as to enhance its prediction quality, while the latter can reduce the dimension of PseAAC vector so as to speed up its prediction process. It was observed by the rigorous jackknife and independent dataset tests that the new predictor outperformed the existing predictors for the same purpose. As a user-friendly web-server, iDNA-Prot|dis is accessible to the public at http://bioinformatics.hitsz.edu.cn/iDNA-Prot_dis/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step protocol guide is provided on how to use the web-server to get their desired results without the need to follow the complicated mathematic equations that are presented in this paper just for the integrity of its developing process. It is anticipated that the iDNA-Prot|dis predictor may become a useful high throughput tool for large-scale analysis of DNA-binding proteins, or at the very least, play a complementary role to the existing predictors in this regard. PMID:25184541

  9. iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking.

    PubMed

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

    2013-01-01

    Involved in many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, G-protein-coupled receptors (GPCRs) are among the most frequent targets of therapeutic drugs. It is time-consuming and expensive to determine whether a drug and a GPCR are to interact with each other in a cellular network purely by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (dimensional) structure of protein, unfortunately their usage is quite limited because the 3D structures for most GPCRs are still unknown. To overcome the situation, a sequence-based classifier, called "iGPCR-drug", was developed to predict the interactions between GPCRs and drugs in cellular networking. In the predictor, the drug compound is formulated by a 2D (dimensional) fingerprint via a 256D vector, GPCR by the PseAAC (pseudo amino acid composition) generated with the grey model theory, and the prediction engine is operated by the fuzzy K-nearest neighbour algorithm. Moreover, a user-friendly web-server for iGPCR-drug was established at http://www.jci-bioinfo.cn/iGPCR-Drug/. 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 this paper just for its integrity. The overall success rate achieved by iGPCR-drug via the jackknife test was 85.5%, which is remarkably higher than the rate by the existing peer method developed in 2010 although no web server was ever established for it. It is anticipated that iGPCR-Drug may become a useful high throughput tool for both basic research and drug development, and that the approach presented here can also be extended to study other drug - target interaction networks. PMID:24015221

  10. Hyperspectral determination of feed quality constituents in temperate pastures: Effect of processing methods on predictive relationships from partial least squares regression

    NASA Astrophysics Data System (ADS)

    Thulin, Susanne; Hill, Michael J.; Held, Alex; Jones, Simon; Woodgate, Peter

    2012-10-01

    Development of predictive relationships between hyperspectral reflectance and the chemical constituents of grassland vegetation could support routine remote sensing assessment of feed quality in standing pastures. In this study, partial least squares regression (PLSR) and spectral transforms are used to derive predictive models for estimation of crude protein and digestibility (quality), and lignin and cellulose (non-digestible fractions) from field-based spectral libraries and chemical assays acquired from diverse pasture sites in Victoria, Australia between 2000 and 2002. The best predictive models for feed quality were obtained with continuum removal with spectral bands normalised to the depth of absorption features for digestibility (adjusted R2 = 0.82, root mean square error of prediction (RMSEP) = 3.94), and continuum removal with spectral bands normalised to the area of the absorption features for crude protein (adjusted R2 = 0.62, RMSEP = 3.18) and cellulose (adjusted R2 = 0.73, RMSEP = 2.37). The results for lignin were poorer with the best performing model based on the first derivative of log transformed reflectance (adjusted R2 = 0.44, RMSEP = 1.87). The best models were dominated by first derivative transforms, and by limiting the models to significant variables with "Jack-knifing". X-loading results identified wavelengths near or outside major absorption features as important predictors. This study showed that digestibility, as a broad measure of feed quality, could be effectively predicted from PLSR derived models of spectral reflectance derived from field spectroscopy. The models for cellulose and crude protein showed potential for qualitative assessment; however the results for lignin were poor. Implementation of spectral prediction models such as these, with hyperspectral sensors having a high signal to noise ratio, could deliver feed quality information to complement spatial biomass and growth data, and improve feed management for extensive grazing systems.

  11. The effect of compression on confidence during the detection of skull fractures in CT

    NASA Astrophysics Data System (ADS)

    Nikolovski, Ines; McEntee, Mark F.; Bourne, Roger; Pietrzyk, Mariusz W.; Evanoff, Michael G.; Brennan, Patrick C.; Tay, Kevin

    2012-02-01

    As part of a study to establish whether detection of cranial vault fractures is affected by JPEG 2000 30:1 and 60:1 lossy compression when compared to JPEG 2000 lossless compression we looked at the effects on confidence ratings 55 CT images, with three levels of JPEG 2000 compression (lossless, 30:1 & 60:1) were presented to 14 senior radiologists, 12 from the American Board of Radiology and 2 form Australia, 7 of whom were MSK specialists and 7 were neuroradiologists. 32 Images contained a single skull fracture while 23 were normal. Images were displayed on one calibrated, secondary LCD, in an ambient lighting of 32.2 lux. Observers were asked to identify the presence or absence of a fracture and where a fracture was present to locate and rate their confidence in its presence. A jack-knifed alternate free-response receiver operating characteristic (JAFROC) and a ROC methodology was employed and the DBM MRMC and ANOVA were used to explore differences between the lossless and lossy compressed images. A significant trend of increased confidence in true and false positive scores was seen with JPEG2000 Lossy 60:1 compression. An ANOVA on the mean confidence rating obtained for correct (TP) and incorrect (FP) localization skull fractions demonstrated that this was a significant difference between lossless and 60:1 [FP, p<0.001 TP, p<0.014] and 30:1 and 60:1 [FP, p<0.014 TP, p<0.037].

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

    PubMed

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

    2010-04-01

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

  13. 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

  14. 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

  15. 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.

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

    PubMed

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

    2014-04-01

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

  17. Flood flow estimation in ungauged basins, application to a nordic environment

    NASA Astrophysics Data System (ADS)

    Ouarda, T. B. M. J.; Crsteanu, A. A.; Bobe, B.

    2003-04-01

    Design flood estimates at ungauged sites or at gauged sites with short records can be obtained through regional estimation techniques. It is important to accurately estimate the values of these design floods to avoid over- and under-estimation of hydraulic structures. Various methods have been employed for the regional analysis of extreme hydrological events. These regionalization approaches make different assumptions and hypotheses concerning the hydrological phenomena being modeled, rely on various types of continuous and non-continuous data, and often fall under completely different theories. The dam safety law in the Province of Quebec, Canada, makes it compulsory to have accurate estimates of design and operational floods at all locations in the Province. A general tool, based on regional estimation, was developed to allow the estimation of flood characteristics on any river in any location in the Province of Quebec. First flood frequency analysis was carried out in all gauged sites in the territory of study and flood quantiles were estimated in each site based on the best fitting distribution. Regional estimation techniques are then used for the automatic estimation of flood characteristics in any ungauged location by transferring information from gauged sites to ungauged ones. Regional estimation is carried out based on previously estimated flood characteristics in gauged sites and based on physiographic and meteorological characteristics in the site of interest. Geostatistical methods are used within the developed tool, in a GIS framework, to estimate automatically the physiographic and meteorological characteristics for any basin in the Province based on digitized maps of the relevant information. A Jack-knife approach is used to demonstrate the usefulness of this tool, which is shown to be precise, unbiased and accurate.

  18. 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

  19. 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 Italys 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.

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

    PubMed

    Gutierrez, Beatriz Lopez; Macleod, Norman; Edgecombe, Gregory D

    2011-01-01

    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 Wrmli suggested some potentially informative variation might be found in these structures. Geometric morphometric analyses were used to evaluate Wrmli'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

  1. 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.

  2. iGPCR-Drug: A Web Server for Predicting Interaction between GPCRs and Drugs in Cellular Networking

    PubMed Central

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

    2013-01-01

    Involved in many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, G-protein-coupled receptors (GPCRs) are among the most frequent targets of therapeutic drugs. It is time-consuming and expensive to determine whether a drug and a GPCR are to interact with each other in a cellular network purely by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (dimensional) structure of protein, unfortunately their usage is quite limited because the 3D structures for most GPCRs are still unknown. To overcome the situation, a sequence-based classifier, called “iGPCR-drug”, was developed to predict the interactions between GPCRs and drugs in cellular networking. In the predictor, the drug compound is formulated by a 2D (dimensional) fingerprint via a 256D vector, GPCR by the PseAAC (pseudo amino acid composition) generated with the grey model theory, and the prediction engine is operated by the fuzzy K-nearest neighbour algorithm. Moreover, a user-friendly web-server for iGPCR-drug was established at http://www.jci-bioinfo.cn/iGPCR-Drug/. 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 this paper just for its integrity. The overall success rate achieved by iGPCR-drug via the jackknife test was 85.5%, which is remarkably higher than the rate by the existing peer method developed in 2010 although no web server was ever established for it. It is anticipated that iGPCR-Drug may become a useful high throughput tool for both basic research and drug development, and that the approach presented here can also be extended to study other drug – target interaction networks. PMID:24015221

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  4. The effect of image processing on the detection of cancers in digital mammography.

    PubMed

    Warren, Lucy M; Given-Wilson, Rosalind M; Wallis, Matthew G; Cooke, Julie; Halling-Brown, Mark D; Mackenzie, Alistair; Chakraborty, Dev P; Bosmans, Hilde; Dance, David R; Young, Kenneth C

    2014-08-01

    OBJECTIVE. The objective of our study was to investigate the effect of image processing on the detection of cancers in digital mammography images. MATERIALS AND METHODS. Two hundred seventy pairs of breast images (both breasts, one view) were collected from eight systems using Hologic amorphous selenium detectors: 80 image pairs showed breasts containing subtle malignant masses; 30 image pairs, biopsy-proven benign lesions; 80 image pairs, simulated calcification clusters; and 80 image pairs, no cancer (normal). The 270 image pairs were processed with three types of image processing: standard (full enhancement), low contrast (intermediate enhancement), and pseudo-film-screen (no enhancement). Seven experienced observers inspected the images, locating and rating regions they suspected to be cancer for likelihood of malignancy. The results were analyzed using a jackknife-alternative free-response receiver operating characteristic (JAFROC) analysis. RESULTS. The detection of calcification clusters was significantly affected by the type of image processing: The JAFROC figure of merit (FOM) decreased from 0.65 with standard image processing to 0.63 with low-contrast image processing (p = 0.04) and from 0.65 with standard image processing to 0.61 with film-screen image processing (p = 0.0005). The detection of noncalcification cancers was not significantly different among the image-processing types investigated (p > 0.40). CONCLUSION. These results suggest that image processing has a significant impact on the detection of calcification clusters in digital mammography. For the three image-processing versions and the system investigated, standard image processing was optimal for the detection of calcification clusters. The effect on cancer detection should be considered when selecting the type of image processing in the future. PMID:25055275

  5. 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 6.910.1 mGy). JAFROC FOM for ANLM and FBP were 0.84 (95% CI 0.750.92) and 0.84 (95% CI 0.750.92), and were statistically non-inferior to IR (FOM 0.84; 95% CI 0.760.93). 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

  6. 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.

  7. 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

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

    PubMed Central

    2013-01-01

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

  9. 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

  10. Predicting Transcriptional Activity of Multiple Site p53 Mutants Based on Hybrid Properties

    PubMed Central

    Xu, Zhongping; Huang, Yun; Kong, Xiangyin; Cai, Yu-Dong; Chou, Kuo-Chen

    2011-01-01

    As an important tumor suppressor protein, reactivate mutated p53 was found in many kinds of human cancers and that restoring active p53 would lead to tumor regression. In this work, we developed a new computational method to predict the transcriptional activity for one-, two-, three- and four-site p53 mutants, respectively. With the approach from the general form of pseudo amino acid composition, we used eight types of features to represent the mutation and then selected the optimal prediction features based on the maximum relevance, minimum redundancy, and incremental feature selection methods. The Mathew's correlation coefficients (MCC) obtained by using nearest neighbor algorithm and jackknife cross validation for one-, two-, three- and four-site p53 mutants were 0.678, 0.314, 0.705, and 0.907, respectively. It was revealed by the further optimal feature set analysis that the 2D (two-dimensional) structure features composed the largest part of the optimal feature set and maybe played the most important roles in all four types of p53 mutant active status prediction. It was also demonstrated by the optimal feature sets, especially those at the top level, that the 3D structure features, conservation, physicochemical and biochemical properties of amino acid near the mutation site, also played quite important roles for p53 mutant active status prediction. Our study has provided a new and promising approach for finding functionally important sites and the relevant features for in-depth study of p53 protein and its action mechanism. PMID:21857971

  11. 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 16.4C 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

  12. Neuroanatomic localization of priming effects for famous faces with latency-corrected event-related potentials.

    PubMed

    Kashyap, Rajan; Ouyang, Guang; Sommer, Werner; Zhou, Changsong

    2016-02-01

    The late components of event-related brain potentials (ERPs) pose a difficult problem in source localization. One of the reasons is the smearing of these components in conventional averaging because of trial-to-trial latency-variability. The smearing problem may be addressed by reconstructing the ERPs after latency synchronization with the Residue Iteration Decomposition (RIDE) method. Here we assessed whether the benefits of RIDE at the surface level also improve source localization of RIDE-reconstructed ERPs (RERPs) measured in a face priming paradigm. Separate source models for conventionally averaged ERPs and RERPs were derived and sources were localized for both early and late components. Jackknife averaging on the data was used to reduce the residual variance during source localization compared to conventional source model fitting on individual subject data. Distances between corresponding sources of both ERP and RERP models were measured to check consistency in both source models. Sources for activity around P100, N170, early repetition effect (ERE/N250r) and late repetition effect (LRE/N400) were reported and priming effects in these sources were evaluated for six time windows. Significant improvement in priming effect of the late sources was found from the RERP source model, especially in the Medio-Temporal Lobe, Prefrontal Cortex, and Anterior Temporal Lobe. Consistent with previous studies, we found early priming effects in the right hemisphere and late priming effects in the left hemisphere. Also, the priming effects in right hemisphere outnumbered the left hemisphere, signifying dominance of right hemisphere in face recognition. In conclusion, RIDE reconstructed ERPs promise a comprehensive understanding of the time-resolved dynamics the late sources play during face recognition. PMID:26683085

  13. Historical extension of operational NDVI products for livestock insurance in Kenya

    NASA Astrophysics Data System (ADS)

    Vrieling, Anton; Meroni, Michele; Shee, Apurba; Mude, Andrew G.; Woodard, Joshua; de Bie, C. A. J. M. (Kees); Rembold, Felix

    2014-05-01

    Droughts induce livestock losses that severely affect Kenyan pastoralists. Recent index insurance schemes have the potential of being a viable tool for insuring pastoralists against drought-related risk. Such schemes require as input a forage scarcity (or drought) index that can be reliably updated in near real-time, and that strongly relates to livestock mortality. Generally, a long record (>25 years) of the index is needed to correctly estimate mortality risk and calculate the related insurance premium. Data from current operational satellites used for large-scale vegetation monitoring span over a maximum of 15 years, a time period that is considered insufficient for accurate premium computation. This study examines how operational NDVI datasets compare to, and could be combined with the non-operational recently constructed 30-year GIMMS AVHRR record (1981-2011) to provide a near-real time drought index with a long term archive for the arid lands of Kenya. We compared six freely available, near-real time NDVI products: five from MODIS and one from SPOT-VEGETATION. Prior to comparison, all datasets were averaged in time for the two vegetative seasons in Kenya, and aggregated spatially at the administrative division level at which the insurance is offered. The feasibility of extending the resulting aggregated drought indices back in time was assessed using jackknifed R2 statistics (leave-one-year-out) for the overlapping period 2002-2011. We found that division-specific models were more effective than a global model for linking the division-level temporal variability of the index between NDVI products. Based on our results, good scope exists for historically extending the aggregated drought index, thus providing a longer operational record for insurance purposes. We showed that this extension may have large effects on the calculated insurance premium. Finally, we discuss several possible improvements to the drought index.

  14. Benthic macrofauna habitat associations in Willapa Bay, Washington, USA

    NASA Astrophysics Data System (ADS)

    Ferraro, Steven P.; Cole, Faith A.

    2007-02-01

    Estuary-wide benthic macrofauna-habitat associations in Willapa Bay, Washington, United States, were determined for 4 habitats (eelgrass [ Zostera marina], Atlantic cordgrass [ Spartina alterniflora], mud shrimp [ Upogebia pugettensis], ghost shrimp [ Neotrypaea californiensis]) in 1996 and 7 habitats (eelgrass, Atlantic cordgrass, mud shrimp, ghost shrimp, oyster [ Crassostrea gigas], bare mud/sand, subtidal) in 1998. Most benthic macrofaunal species inhabited multiple habitats; however, 2 dominants, a fanworm, Manayunkia aestuarina, in Spartina, and a sand dollar, Dendraster excentricus, in subtidal, were rare or absent in all other habitats. Benthic macrofaunal Bray-Curtis similarity varied among all habitats except eelgrass and oyster. There were significant differences among habitats within- and between-years on several of the following ecological indicators: mean number of species ( S), abundance ( A), biomass ( B), abundance of deposit (AD), suspension (AS), and facultative (AF) feeders, Swartz's index (SI), Brillouin's index ( H), and jackknife estimates of habitat species richness (HSR). In the 4 habitats sampled in both years, A was about 2.5× greater in 1996 (a La Niña year) than 1998 (a strong El Niño year) yet relative values of S, A, B, AD, AS, SI, and H among the habitats were not significantly different, indicating strong benthic macrofauna-habitat associations despite considerable climatic and environmental variability. In general, the rank order of habitats on indicators associated with high diversity and productivity (high S, A, B, SI, H, HSR) was eelgrass = oyster ≥ Atlantic cordgrass ≥ mud shrimp ≥ bare mud/sand ≥ ghost shrimp = subtidal. Vegetation, burrowing shrimp, and oyster density and sediment %silt + clay and %total organic carbon were generally poor, temporally inconsistent predictors of ecological indicator variability within habitats. The benthic macrofauna-habitat associations in this study can be used to help identify critical habitats, prioritize habitats for environmental protection, index habitat suitability, assess habitat equivalency, and as habitat value criteria in ecological risk assessments in Willapa Bay.

  15. 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.

  16. High-resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis.

    PubMed

    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; Wagner-Döbler, Irene

    2015-02-01

    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

  17. 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

  18. iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

    PubMed Central

    Liu, Bin; Xu, Jinghao; Lan, Xun; Xu, Ruifeng; Zhou, Jiyun; Wang, Xiaolong; Chou, Kuo-Chen

    2014-01-01

    Playing crucial roles in various cellular processes, such as recognition of specific nucleotide sequences, regulation of transcription, and regulation of gene expression, DNA-binding proteins are essential ingredients for both eukaryotic and prokaryotic proteomes. With the avalanche of protein sequences generated in the postgenomic age, it is a critical challenge to develop automated methods for accurate and rapidly identifying DNA-binding proteins based on their sequence information alone. Here, a novel predictor, called “iDNA-Prot|dis”, was established by incorporating the amino acid distance-pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC) vector. The former can capture the characteristics of DNA-binding proteins so as to enhance its prediction quality, while the latter can reduce the dimension of PseAAC vector so as to speed up its prediction process. It was observed by the rigorous jackknife and independent dataset tests that the new predictor outperformed the existing predictors for the same purpose. As a user-friendly web-server, iDNA-Prot|dis is accessible to the public at http://bioinformatics.hitsz.edu.cn/iDNA-Prot_dis/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step protocol guide is provided on how to use the web-server to get their desired results without the need to follow the complicated mathematic equations that are presented in this paper just for the integrity of its developing process. It is anticipated that the iDNA-Prot|dis predictor may become a useful high throughput tool for large-scale analysis of DNA-binding proteins, or at the very least, play a complementary role to the existing predictors in this regard. PMID:25184541

  19. [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

  20. Combined triaxial accelerometry and heart rate telemetry for the physiological characterization of Latin dance in non-professional adults.

    PubMed

    Domene, Pablo A; Easton, Chris

    2014-03-01

    The purpose of this study was to value calibrate, cross-validate, and determine the reliability of a combined triaxial accelerometry and heart rate telemetry technique for characterizing the physiological and physical activity parameters of Latin dance. Twenty-two non-professional adult Latin dancers attended two laboratory-based dance trials each. After familiarization and a standardized warm-up, a multi-stage (3 x 5-minute) incremental (based on song tempo) Afro-Cuban salsa choreography was performed while following a video displayed on a projection screen. Data were collected with a portable indirect calorimeter, a heart rate telemeter, and wrist-, hip-, and ankle-mounted ActiGraph GT3X+ accelerometers. Prediction equations for energy expenditure and step count were value calibrated using forced entry multiple regression and cross-validated using a delete-one jackknife approach with additional Bland-Altman analysis. The average dance intensity reached 6.09 0.96 kcal/kg/h and demanded 45.9 11.3% of the heart rate reserve. Predictive ability of the derived models was satisfactory, where R(2) = 0.80; SEE = 0.44 kcal/kg/h and R(2) = 0.74; SEE = 3 step/min for energy expenditure and step count, respectively. Dependent t-tests indicated no differences between predicted and measured values for both energy expenditure (t65 = -0.25, p = 0.80) and step count (t65 = -0.89, p = 0.38). The 95% limits of agreement for energy expenditure and step count were -0.98 to 0.95 kcal/kg/h and -7 to 7 step/min, respectively. Latin dance to salsa music elicits physiological responses representative of moderate to vigorous physical activity, and a wrist-worn accelerometer with simultaneous heart rate measurement constitutes a valid and reliable technique for the prediction of energy expenditure and step count during Latin dance. PMID:24568801

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. Flexible Meta-Regression to Assess the Shape of the BenzeneLeukemia ExposureResponse Curve

    PubMed Central

    Vlaanderen, Jelle; Portengen, Ltzen; Rothman, Nathaniel; Lan, Qing; Kromhout, Hans; Vermeulen, Roel

    2010-01-01

    Background Previous evaluations of the shape of the benzeneleukemia exposureresponse curve (ERC) were based on a single set or on small sets of human occupational studies. Integrating evidence from all available studies that are of sufficient quality combined with flexible meta-regression models is likely to provide better insight into the functional relation between benzene exposure and risk of leukemia. Objectives We used natural splines in a flexible meta-regression method to assess the shape of the benzeneleukemia ERC. Methods We fitted meta-regression models to 30 aggregated risk estimates extracted from nine human observational studies and performed sensitivity analyses to assess the impact of a priori assessed study characteristics on the predicted ERC. Results The natural spline showed a supralinear shape at cumulative exposures less than 100 ppm-years, although this model fitted the data only marginally better than a linear model (p = 0.06). Stratification based on study design and jackknifing indicated that the cohort studies had a considerable impact on the shape of the ERC at high exposure levels (> 100 ppm-years) but that predicted risks for the low exposure range (< 50 ppm-years) were robust. Conclusions Although limited by the small number of studies and the large heterogeneity between studies, the inclusion of all studies of sufficient quality combined with a flexible meta-regression method provides the most comprehensive evaluation of the benzeneleukemia ERC to date. The natural spline based on all data indicates a significantly increased risk of leukemia [relative risk (RR) = 1.14; 95% confidence interval (CI), 1.041.26] at an exposure level as low as 10 ppm-years. PMID:20064779

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

    PubMed

    Cet, 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

  10. 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

  11. 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

  12. Effect of host plants on developmental time and life table parameters of Amphitetranychus viennensis (Acari: Tetranychidae).

    PubMed

    Kafil, Maryam; Allahyari, Hossein; Saboori, Alireza

    2007-01-01

    The effect of host plant species including black cherry (Prunus serotina cv. Irani), cherry (Prunus avium cv. siahe Mashhad) and apple (Malus domestica cv. shafi Abadi) was studied on biological parameters of Amphitetranychus viennensis (Zacher) in the laboratory at 25 +/- 1 degrees C, 70 +/- 10% RH and 16L: 8D photoperiod. Duration of each life stage, longevity, reproduction rate, the intrinsic rate of natural increase (rm), net reproductive rate (R0), mean generation time (T), doubling time (DT), and finite rate of increase (lambda) of the hawthorn spider mite on the three host plants were calculated. Differences in fertility life table parameters of the spider mite among host plants were analyzed using pseudo-values, which were produced by jackknife re-sampling. The results indicated that black cherry might be the most suitable plant for hawthorn spider mite due to the shorter developmental period (10.6 days), longer adult longevity (25.5 days), higher reproduction (65.6 eggs), and intrinsic rate of natural increase (0.194 females/female/day). Cherry was the least suitable host plant. To determine the effect of host shifts, the mite was transferred from black cherry onto cherry and apple. In the first generation after shifting to apple, the developmental period, reproduction and life table parameters were negatively influenced. However, population growth parameters in the first generation on cherry were actually better than after three generations on this new host. This underscores the relevance of the mites' recent breeding history for life table studies. PMID:17710558

  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. Comparative analysis of different retrieval methods for mapping grassland leaf area index using airborne imaging spectroscopy

    NASA Astrophysics Data System (ADS)

    Atzberger, Clement; Darvishzadeh, Roshanak; Immitzer, Markus; Schlerf, Martin; Skidmore, Andrew; le Maire, Guerric

    2015-12-01

    Fine scale maps of vegetation biophysical variables are useful status indicators for monitoring and managing national parks and endangered habitats. Here, we assess in a comparative way four different retrieval methods for estimating leaf area index (LAI) in grassland: two radiative transfer model (RTM) inversion methods (one based on look-up-tables (LUT) and one based on predictive equations) and two statistical modelling methods (one partly, the other entirely based on in situ data). For prediction, spectral data were used that had been acquired over Majella National Park in Italy by the airborne hyperspectral HyMap instrument. To assess the performance of the four investigated models, the normalized root mean squared error (nRMSE) and coefficient of determination (R2) between estimates and in situ LAI measurements are reported (n = 41). Using a jackknife approach, we also quantified the accuracy and robustness of empirical models as a function of the size of the available calibration data set. The results of the study demonstrate that the LUT-based RTM inversion yields higher accuracies for LAI estimation (R2 = 0.91, nRMSE = 0.18) as compared to RTM inversions based on predictive equations (R2 = 0.79, nRMSE = 0.38). The two statistical methods yield accuracies similar to the LUT method. However, as expected, the accuracy and robustness of the statistical models decrease when the size of the calibration database is reduced to fewer samples. The results of this study are of interest for the remote sensing community developing improved inversion schemes for spaceborne hyperspectral sensors applicable to different vegetation types. The examples provided in this paper may also serve as illustrations for the drawbacks and advantages of physical and empirical models.

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

    PubMed

    Saan, 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

  16. 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. Lins 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

  17. 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.

  18. 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.

  19. 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.

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

    PubMed

    Shen, Hong-Bin; Chou, Kuo-Chen

    2007-02-15

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

  1. Effect of herbicide combinations on Bt-maize rhizobacterial diversity.

    PubMed

    Valverde, José R; Marín, Silvia; Mellado, Rafael P

    2014-11-28

    Reports of herbicide resistance events are proliferating worldwide, leading to new cultivation strategies using combinations of pre-emergence and post-emergence herbicides. We analyzed the impact during a one-year cultivation cycle of several herbicide combinations on the rhizobacterial community of glyphosate-tolerant Bt-maize and compared them to those of the untreated or glyphosate-treated soils. Samples were analyzed using pyrosequencing of the V6 hypervariable region of the 16S rRNA gene. The sequences obtained were subjected to taxonomic, taxonomy-independent, and phylogeny-based diversity studies, followed by a statistical analysis using principal components analysis and hierarchical clustering with jackknife statistical validation. The resilience of the microbial communities was analyzed by comparing their relative composition at the end of the cultivation cycle. The bacterial communites from soil subjected to a combined treatment with mesotrione plus s-metolachlor followed by glyphosate were not statistically different from those treated with glyphosate or the untreated ones. The use of acetochlor plus terbuthylazine followed by glyphosate, and the use of aclonifen plus isoxaflutole followed by mesotrione clearly affected the resilience of their corresponding bacterial communities. The treatment with pethoxamid followed by glyphosate resulted in an intermediate effect. The use of glyphosate alone seems to be the less aggressive one for bacterial communities. Should a combined treatment be needed, the combination of mesotrione and s-metolachlor shows the next best final resilience. Our results show the relevance of comparative rhizobacterial community studies when novel combined herbicide treatments are deemed necessary to control weed growth.. PMID:25394507

  2. Robust Estimation of Precipitation Extremes from Short-Period Regional Climate Downscales

    NASA Astrophysics Data System (ADS)

    Apling, D.; Darmenova, K.; Higgins, G. J.

    2011-12-01

    The US Southwest is likely to experience significant changes in precipitation patterns in coming decades as a result of regional climate change. One serious issue is to better understand extreme precipitation events, which affect infrastructure planning, and human life and safety management. Extreme precipitation events are characterized by the maximum expectation of accumulated precipitation over a short time period, which has a long-period return over some number of years; e.g., the 100-year return of daily precipitation. These measures are statistics drawn from Extreme Value Theory, and can be challenging to accurately and reliably estimate for short data sets. Regional Climate Models (RCM) are often run for shorter decadal periods, both to economize on computational expense, and to characterize specific decadal time bands. In each case, one needs robust statistical estimation algorithms to accurately and reliably retrieve the precipitation recurrence statistics. To produce these important decision-aiding products, we added several processes to an otherwise conventional Peaks Over Threshold technique operating on the combined grid-scale and cumuliform precipitation outputs from our 12 kilometer Weather Research and Forecasting (WRF) downscale of the National Centers for Environmental Prediction (NCEP) reanalysis fields for the ten year period of 2000-2009 over the Southwest US. These processes included interleaved sub-year intermediate aggregations, correlated sample corrections, distributional tail feature extraction, and trimmed set tail fitting with jackknife error estimation. The process resulted in estimated 100-year return 24-hour accumulated precipitation expectations with accompanying error bounds, which compare well to established historical precipitation statistics.

  3. Differentiation of fecal Escherichia coli from human, livestock, and poultry sources by rep-PCR DNA fingerprinting on the shellfish culture area of East China Sea.

    PubMed

    Ma, Hong-Jia; Fu, Ling-Lin; Li, Jian-Rong

    2011-05-01

    The rep-PCR DNA fingerprinting performed with REP, BOX A1R, and (GTG)(5) primers was investigated as a way to differentiate between human, livestock, and poultry sources of fecal pollution on the area of Xiangshan Bay, East China Sea. Of the three methods, the BOX-PCR DNA fingerprints analyzed by jack-knife algorithm were revealed high rate of correct classification (RCC) with 91.30, 80.39, 89.39, 86.14, 93.24, 87.72, and 89.28% of human, cattle, swine, chicken, duck, sheep, and goose E. coli isolates classified into the correct host source, respectively. The average rate of correct classification (ARCC) of REP-, BOX-, and (GTG)(5)-PCR patterns was 79.88, 88.21, and 86.39%, respectively. Although the highest amount of bands in (GTG)(5)-PCR fingerprints could be observed, the discriminatory efficacy of BOX-PCR was superior to both REP- and (GTG)(5)-PCR. Moreover, the similarity of 459 isolates originated from shellfish and growing water was compared with fecal-obtained strains. The results showed that 92.4 and 96.2% E. coli strains isolated from midstream and downstream shellfish samples, respectively, had a ? 80% similarity with corresponding strains isolated from fecal samples. It was indicated that E. coli in feces could spread from human sewage or domestic farms to the surrounding shellfish culture water, and potentially affect the quality of shellfish. This work suggests that rep-PCR fingerprinting can be a promising genotypic tool applied in the shellfish growing water management on East China Sea for source identification of fecal pollution. PMID:21279641

  4. External Quality Assessment (EQA) program for the preanalytical and analytical immunohistochemical determination of HER2 in breast cancer: an experience on a regional scale

    PubMed Central

    2013-01-01

    Background An External Quality Assessment (EQA) program was developed to investigate the state of the art of HER2 immunohistochemical determination in breast cancer (BC) in 16 Pathology Departments in the Lazio Region (Italy). This program was implemented through two specific steps to evaluate HER2 staining (step 1) and interpretation (step 2) reproducibility among participants. Methods The management activities of this EQA program were assigned to the Coordinating Center (CC), the Revising Centers (RCs) and the Participating Centers (PCs). In step 1, 4 BC sections, selected by RCs, were stained by each PC using their own procedures. In step 2, each PC interpreted HER2 score in 10 BC sections stained by the CC. The concordance pattern was evaluated by using the kappa category-specific statistic and/or the weighted kappa statistic with the corresponding 95% Jackknife confidence interval. Results In step 1, a substantial/almost perfect agreement was reached between the PCs for scores 0 and 3+ whereas a moderate and fair agreement was observed for scores 1+ and 2+, respectively. In step 2, a fully satisfactory agreement was observed for 6 out of the 16 PCs and a quite satisfactory agreement was obtained for the remaining 10 PCs. Conclusions Our findings highlight that in the whole HER2 evaluation process the two intermediate categories, scores 1+ and 2+, are less reproducible than scores 0 and 3+. These findings are relevant in clinical practice where the choice of treatment is based on HER2 positivity, suggesting the need to share evaluation procedures within laboratories and implement educational programs. PMID:23965490

  5. 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

  6. 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 -47.7-0.0C, and ART of 26.1-45.0C. 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

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

    PubMed Central

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

    2016-01-01

    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

  8. 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

  9. 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

  10. A Novel Feature Extraction Method with Feature Selection to Identify Golgi-Resident Protein Types from Imbalanced Data.

    PubMed

    Yang, Runtao; Zhang, Chengjin; Gao, Rui; Zhang, Lina

    2016-01-01

    The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew's Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions. PMID:26861308

  11. Testate Amoebae as Paleohydrological Proxies in the Florida Everglades

    NASA Astrophysics Data System (ADS)

    Andrews, T.; Booth, R.; Bernhardt, C. E.; Willard, D. A.

    2011-12-01

    The largest wetland restoration effort ever attempted, the Comprehensive Everglades Restoration Plan (CERP), is currently underway in the Florida Everglades, and a critical goal of CERP is reestablishment of the pre-drainage (pre-AD 1880) hydrology. Paleoecological research in the greater Everglades ecosystem is underway to reconstruct past water levels and variability throughout the system, providing a basis for restoration targets. Testate amoebae, a group of unicellular organisms that form decay-resistant tests, have been successfully used in northern-latitude bogs to reconstruct past wetland hydrology; however, their application in other peatland types, particularly at lower latitudes, has not been well studied. We assessed the potential use of testate amoebae as tools to reconstruct the past hydrology of the Everglades. Modern surface samples were collected from the Everglades National Park and Water Conservation Areas, across a water table gradient that included four vegetation types (tree island interior, tree island edge, sawgrass transition, slough). Community composition was quantified and compared to environmental conditions (water table, pH, vegetation) using ordination and gradient-analysis approaches. Results of nonmetric multidimensional scaling revealed that the most important pattern of community change, representing about 30% of the variance in the dataset, was related to water-table depth (r2=0.32). Jackknifed cross-validation of a transfer function for water table depth, based on a simple weighted average model, indicated the potential for testate amoebae in studies of past Everglades hydrology (RMSEP = 9 cm, r2=0.47). Although the performance of the transfer function was not as good as those from northern-latitude bogs, our results suggest that testate amoebae could be could be a valuable tool in paleohydrological studies of the Everglades, particularly when used with other hydrological proxies (e.g., pollen, plant macrofossils, diatoms).

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  14. 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

  15. 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.

  16. Sodium and potassium intakes among US adults: NHANES 200320081234

    PubMed Central

    Zhang, Zefeng; Carriquiry, Alicia L; Gunn, Janelle P; Kuklina, Elena V; Saydah, Sharon H; Yang, Quanhe; Moshfegh, Alanna J

    2012-01-01

    Background: The American Heart Association (AHA), Institute of Medicine (IOM), and US Departments of Health and Human Services and Agriculture (USDA) Dietary Guidelines for Americans all recommend that Americans limit sodium intake and choose foods that contain potassium to decrease the risk of hypertension and other adverse health outcomes. Objective: We estimated the distributions of usual daily sodium and potassium intakes by sociodemographic and health characteristics relative to current recommendations. Design: We used 24-h dietary recalls and other data from 12,581 adults aged ?20 y who participated in NHANES in 20032008. Estimates of sodium and potassium intakes were adjusted for within-individual day-to-day variation by using measurement error models. SEs and 95% CIs were assessed by using jackknife replicate weights. Results: Overall, 99.4% (95% CI: 99.3%, 99.5%) of US adults consumed more sodium daily than recommended by the AHA (<1500 mg), and 90.7% (89.6%, 91.8%) consumed more than the IOM Tolerable Upper Intake Level (2300 mg). In US adults who are recommended by the Dietary Guidelines to further reduce sodium intake to 1500 mg/d (ie, African Americans aged ?51 y or persons with hypertension, diabetes, or chronic kidney disease), 98.8% (98.4%, 99.2%) overall consumed >1500 mg/d, and 60.4% consumed >3000 mg/dmore than double the recommendation. Overall, <2% of US adults and ?5% of US men consumed ?4700 mg K/d (ie, met recommendations for potassium). Conclusion: Regardless of recommendations or sociodemographic or health characteristics, the vast majority of US adults consume too much sodium and too little potassium. PMID:22854410

  17. 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

  18. 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.

  19. Analysis of the successional patterns of insects on carrion in southwest Virginia.

    PubMed

    Tabor, Kimberly L; Brewster, Carlyle C; Fell, Richard D

    2004-07-01

    Studies of carrion-insect succession on domestic pig, Sus scrofa L., were conducted in the spring and summer of 2001 and 2002 in Blacksburg, VA, to identify and analyze the successional patterns of the taxa of forensic importance in southwest Virginia. Forty-seven insect taxa were collected in the spring. These were represented by 11 families (Diptera: Calliphoridae, Sarcophagidae, Muscidae, Sepsidae, Piophilidae; Coleoptera: Staphylinidae, Silphidae, Cleridae, Trogidae, Dermestidae, Histeridae). In the summer, 33 taxa were collected that were represented by all of the families collected in the spring, except Trogidae. The most common flies collected were the calliphorids: Phormia regina (Meigen) and Phaenicia coeruleiviridis (Macquart). The most common beetles were Creophilus maxillosus L. (Staphylinidae), Oiceoptoma noveboracense Forster, Necrophila americana L., Necrodes surinamensis (F.) (Silphidae), Euspilotus assimilis (Paykull), and Hister abbreviatus F. (Histeridae). Occurrence matrices were constructed for the successional patterns of insect taxa during 21 sampling intervals in the spring and 8 intervals in the summer studies. Jackknife estimates (mean+/-95% confidence limits) of overall Jaccard similarity in insect taxa among sampling intervals in the occurrence matrices were 0.213+/-0.081 (spring 2001), 0.194+/-0.043 (summer 2001), 0.257+/-0.068 (spring 2002), and 0.274+/-0.172 (summer 2002). Permutation analyses of the occurrence matrices showed that the patterns of succession of insect taxa were similar between spring 2001 and 2002 (P = 0.001) and between summer 2001 and 2002 (P = 0.007). The successional patterns seem to be typical for the seasonal periods and provide data on baseline fauna for estimating postmortem interval in cases of human death. This study is the first of its kind for southwest Virginia. PMID:15311476

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

    PubMed Central

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

    2001-01-01

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

  2. 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.

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

    PubMed Central

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

    2010-01-01

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

  4. Predicting physical activity energy expenditure using accelerometry in adults from sub-Sahara Africa.

    PubMed

    Assah, Felix K; Ekelund, Ulf; Brage, Soren; Corder, Kirsten; Wright, Antony; Mbanya, Jean C; Wareham, Nicholas J

    2009-08-01

    Lack of physical activity may be an important etiological factor in the current epidemiological transition characterized by increasing prevalence of obesity and chronic diseases in sub-Sahara Africa. However, there is a dearth of data on objectively measured physical activity energy expenditure (PAEE) in this region. We sought to develop regression equations using body composition and accelerometer counts to predict PAEE. We conducted a cross-sectional study of 33 adult volunteers from an urban (n = 16) and a rural (n = 17) residential site in Cameroon. Energy expenditure was measured by doubly labeled water (DLW) over a period of seven consecutive days. Simultaneously, a hip-mounted Actigraph accelerometer recorded body movement. PAEE prediction equations were derived using accelerometer counts, age, sex, and body composition variables, and cross-validated by the jack-knife method. The Bland and Altman limits of agreement (LOAs) approach was used to assess agreement. Our results show that PAEE (kJ/kg/day) was significantly and positively correlated with activity counts from the accelerometer (r = 0.37, P = 0.03). The derived equations explained 14-40% of the variance in PAEE. Age, sex, and accelerometer counts together explained 34% of the variance in PAEE, with accelerometer counts alone explaining 14%. The LOAs between DLW and the derived equations were wide, with predicted PAEE being up to 60 kJ/kg/day below or above the measured value. In summary, the derived equations performed better than existing published equations in predicting PAEE from accelerometer counts in this population. Accelerometry could be used to predict PAEE in this population and, therefore, has important applications for monitoring population levels of total physical activity patterns. PMID:19247268

  5. Predicting physical activity energy expenditure using accelerometry in adults from sub-Sahara Africa

    PubMed Central

    Assah, Felix K.; Ekelund, Ulf; Brage, Soren; Corder, Kirsten; Wright, Antony; Mbanya, Jean Claude; Wareham, Nicholas J.

    2009-01-01

    Lack of physical activity may be an important etiological factor in the current epidemiological transition characterised by increasing prevalence of obesity and chronic diseases in sub-Sahara Africa. However, there is a dearth of data on objectively measured physical activity energy expenditure (PAEE) in this region. We sought to develop regression equations using body composition and accelerometer counts to predict PAEE. We conducted a cross-sectional study of 33 adult volunteers from an urban (n=16) and a rural (n=17) residential site in Cameroon. Energy expenditure was measured by doubly labelled water over a period of 7 consecutive days. Simultaneously, a hip-mounted Actigraph accelerometer recorded body movement. PAEE prediction equations were derived using accelerometer counts, age, sex and body composition variables, and cross-validated by the jack-knife method. The Bland and Altman limits of agreement (LOA) approach was used to assess agreement. Our results show that PAEE (kJkg?1day?1) was significantly and positively correlated with activity counts from the accelerometer (r=0.37, p=0.03). The derived equations explained 14 to 40% of the variance in PAEE. Age, sex and accelerometer counts together explained 34% of the variance in PAEE, with accelerometer counts alone explaining 14%. The LOA between DLW and the derived equations were wide, with predicted PAEE being up to 60 kJkg?1day?1 below or above the measured value. In summary, the derived equations performed better than existing published equations in predicting PAEE from accelerometer counts in this population. Accelerometry could be used to predict PAEE in this population and therefore has important applications for monitoring population levels of total physical activity patterns. PMID:19247268

  6. 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

  7. 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

  8. 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.

  9. European multicentre study to define disease activity criteria for systemic sclerosis.* II. Identification of disease activity variables and development of preliminary activity indexes

    PubMed Central

    Valentini, G; Della, R; Bombardieri, S; Bencivelli, W; Silman, A; D'Angelo, S; Cerinic, M; Belch, J; Black, C; Bruhlmann, P; Czirjak, L; De Luca, A; Drosos, A; Ferri, C; Gabrielli, A; Giacomelli, R; Hayem, G; Inanc, M; McHugh, N; Nielsen, H; Rosada, M; Scorza, R; Stork, J; Sysa, A; van den Hoogen, F H J; Vlachoyiannopoulo..., P

    2001-01-01

    OBJECTIVETo develop criteria for disease activity in systemic sclerosis (SSc) that are valid, reliable, and easy to use.?METHODSInvestigators from 19European centres completed a standardised clinical chart for a consecutive number of patients with SSc. Three protocol management members blindly evaluated each chart and assigned a disease activity score on a semiquantitative scale of 0-10. Two of them, in addition, gave a blinded, qualitative evaluation of disease activity ("inactive to moderately active" or "active to very active" disease). Both these evaluations were found to be reliable. A final disease activity score and qualitative evaluation of disease activity were arrived at by consensus for each patient; the former represented the gold standard for subsequent analyses. The correlations between individual items in the chart and this gold standard were then analysed.?RESULTSA total of 290patients with SSc (117with diffuse SSc (dSSc) and 173with limited SSc (lSSc)) were enrolled in the study. The items (including ?-factorsthat is, worsening according to the patient report) that were found to correlate with the gold standard on multiple regression were used to construct three separate 10-point indices of disease activity: (a) ?-cardiopulmonary (4.0), ?-skin (3.0), ?-vascular (2.0), and ?-articular/muscular (1.0) for patients with dSSc; (b) ?-skin (2.5), erythrocyte sedimentation rate (ESR) >30 mm/1st h (2.5), ?-cardiopulmonary (1.5), ?-vascular (1.0), arthritis (1.0), hypocomplementaemia (1.0), and scleredema (0.5) for lSSc; (c) ?-cardiopulmonary (2.0), ?-skin (2.0), ESR >30 mm/1st h (1.5), total skin score >20 (1.0), hypocomplementaemia (1.0), scleredema (0.5), digital necrosis (0.5), ?-vascular (0.5), arthritis (0.5), TLCO <80% (0.5) for all patients with SSc. The three indexes were validated by the jackknife technique. Finally, receiver operating characteristic curves were constructed in order to define the value of the index with the best discriminant capacity for "active to very active" patients.?CONCLUSIONSThree feasible, reliable, and valid preliminary indices to define disease activity in SSc were constructed.?? PMID:11350848

  10. Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction.

    PubMed

    Shen, H-B; Yang, J; Chou, K-C

    2007-07-01

    With the avalanche of newly-found protein sequences emerging in the post genomic era, it is highly desirable to develop an automated method for fast and reliably identifying their subcellular locations because knowledge thus obtained can provide key clues for revealing their functions and understanding how they interact with each other in cellular networking. However, predicting subcellular location of eukaryotic proteins is a challenging problem, particularly when unknown query proteins do not have significant homology to proteins of known subcellular locations and when more locations need to be covered. To cope with the challenge, protein samples are formulated by hybridizing the information derived from the gene ontology database and amphiphilic pseudo amino acid composition. Based on such a representation, a novel ensemble hybridization classifier was developed by fusing many basic individual classifiers through a voting system. Each of these basic classifiers was engineered by the KNN (K-Nearest Neighbor) principle. As a demonstration, a new benchmark dataset was constructed that covers the following 18 localizations: (1) cell wall, (2) centriole, (3) chloroplast, (4) cyanelle, (5) cytoplasm, (6) cytoskeleton, (7) endoplasmic reticulum, (8) extracell, (9) Golgi apparatus, (10) hydrogenosome, (11) lysosome, (12) mitochondria, (13) nucleus, (14) peroxisome, (15) plasma membrane, (16) plastid, (17) spindle pole body, and (18) vacuole. To avoid the homology bias, none of the proteins included has > or =25% sequence identity to any other in a same subcellular location. The overall success rates thus obtained via the 5-fold and jackknife cross-validation tests were 81.6 and 80.3%, respectively, which were 40-50% higher than those performed by the other existing methods on the same strict dataset. The powerful predictor, named "Euk-PLoc", is available as a web-server at http://202.120.37.186/bioinf/euk . Furthermore, to support the need of people working in the relevant areas, a downloadable file will be provided at the same website to list the results predicted by Euk-PLoc for all eukaryotic protein entries (excluding fragments) in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The large-scale results will be updated twice a year to include the new entries of eukaryotic proteins and reflect the continuous development of Euk-PLoc. PMID:17235453

  11. Development of waveform inversion techniques for using body-wave waveforms to infer localized three-dimensional seismic structure and an application to D"

    NASA Astrophysics Data System (ADS)

    Kawai, K.; Konishi, K.; Geller, R. J.; Fuji, N.

    2013-12-01

    In order to further extract information on localized three-dimensional seismic structure from observed seismic data, we have developed and applied methods for seismic waveform inversion. Deriving algorithms for the calculation of synthetic seismograms and their partial derivatives, development of efficient software for their computation and for data handling, correction for near-source and near-receiver structure, and choosing appropriate parameterization of the model space are the key steps in such an inversion. We formulate the inverse problem of waveform inversion for localized structure, computing partial derivatives of waveforms with respect to the 3-D elastic moduli at arbitrary points in space for anisotropic and anelastic media. Our method does not use any great circle approximations in computing the synthetics and their partial derivatives. In order to efficiently solve the inverse problem we use the conjugate gradient (CG) method. We apply our methods to inversion for the three-dimensional shear wave structure in the lowermost mantle beneath Central America and the Western Pacific using waveforms in the period band from 12.5 to 200~s. Checkerboard tests show that waveform inversion of S, ScS, and the other phases which arrive between them can resolve laterally heterogenous shear-wave structure in the lowermost mantle using waves propagating only in a relatively limited range of azimuths. Checkerboard tests show that white noise has little impact on the results of waveform inversion. Various tests such as a jackknife test show that our model is robust. We verify the near-orthogonality of partial derivatives with respect to structure inside and outside the target region; we find that although datasets with only a small number of waveforms (e.g., waveforms recorded by stations for only a single event) cannot resolve structure inside and outside the target region, a dataset with a large number of waveforms can almost completely remove the effects of near-source and near-receiver structure. Waveform inversion with a large dataset is thus confirmed to be a promising approach to infer 3-D seismic fine structure in the Earth's deep interior.

  12. 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

  13. 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

  14. Frequency analysis of hydrological extremes in Tuscany (Italy)

    NASA Astrophysics Data System (ADS)

    Caporali, E.; Petrucci, A.

    2009-09-01

    Extreme values analyses are usually applied in environmental studies to identify protection systems against the effects of extreme events of environmental processes. A common problem is to assess the return period of rare geophysical occurrences, such as floods or precipitation events, for a site or a group of sites, as they play a relevant role for many water management issues. Due to the variability inherent in a random sample of hydrologic data, many hydrologic frequency studies of extreme values are carried out on a regional basis. Over a territory of about 23000 km2, in Tuscany region, located in central Italy, the time series of annual rainfall maxima of different durations and time series of annual discharge maxima, in the period from 1923 to 2008, are investigated. Particularly, the analysis is carried out on the time series of daily rainfall maxima and annual rainfall maxima of five different durations (1, 3, 6, 12, and 24 hours), of about 600 rain gauges. In the same period, also the discharge data, recorded in several rivers in Tuscany, are investigated. More than 300 gauge stations compose the whole hydrometric dataset, but only 75 have discharge data useful for the analysis. A review of previous works, where subdivisions into zones and sub zones of the Tuscany Region were defined, and the first and second level of a regional hierarchical procedure based on the Two Component Extreme Value (TCEV) distribution were developed, is briefly discussed here. While the third level of the regional hierarchical procedure of the different annual hydrological maxima above is revisited and procedures of uncertainty measurements are proposed. In order to analyse the spatial variability of the investigated variables, a multivariate analysis is also proposed, with the aim to model the relationship among the spatial variability of the variables and the territory characteristics. The territory characteristics and some hydrological samples characteristics are used in the developed models. The used variables are extended to ungauged sites using spatial interpolations such as Kriging and IDW methods. The goodness of the developed models, applied to each defined zones, and different hydrological estremes, is verified with a Jackknife procedure to quantitatively asses the sensitivity of its coefficients. Because of the complex nature of the procedure (identifying subregions, finding a subregional distribution function, scaling by index rainfall), a bootstrap procedure is also developed to assess the uncertainty measure. The obtained results are quite satisfying but the need of uncertainty measurements connected to point estimates deserves a deeper analysis. The estimation procedure could be improved considering the penalized spline regression approach. The possibility to apply a non parametric small area estimation is therefore explored.

  15. 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

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

    PubMed

    Gmez-Daz, Elena; Gonzlez-Solis, Jacob

    2007-07-01

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

  17. Long-term changes and spatio-temporal variability of the growing season temperature in Europe during the last Millennium

    NASA Astrophysics Data System (ADS)

    Guiot, Joel; Corona, Christophe

    2010-05-01

    A gridded reconstruction of April to September temperature was produced for Europe based on tree-rings, documentaries, pollen and ice cores. The majority of the proxy series have an annual resolution. For a better inference of long-term climate variations, they were completed by number of low resolution data (decadal or more), mostly on pollen and ice-core data. An original spectral analogue method was devised to deal with this heterogeneous dataset, and especially to preserve the long-term variations and the variability of the temperature series. It is the condition is to make pertinent the comparison of the recent climate changes to a broader context of 1400 years. The reconstruction of the April-September temperature was validated with a Jack-knife technique, and it was also compared with other spatially gridded temperature reconstructions, literature data, and glacier advance and retreat curves. We also attempted to relate the spatial distribution of European temperature anomalies to known solar and volcanic forcings. We found that (1) our results are sound back to A.D. 750; (2) conditions during the last decade have exceeded all those known during the last millennium; (3) before the 20th century, cold periods can partly be explained by low solar activity and/or high volcanic activity and that Medieval Warm Period (MWP) is consistent with a high solar activity; (4) during the 20th century, however only anthropogenic forcing can explain the exceptionally high temperature rise; (5) based on an analysis of the distribution of extreme temperatures, the maximum event of the Medieval Period (1.1C higher than the 1960-1990 reference period) had a return period of more than 1000 years, but this recently fell to less than 26 years; (6) all decades before AD 1350 were warm on average but relatively heterogeneous, while the last decade was homogeneously warmer. These results support the fact that we are facing an unprecedented changing climate in Europe unlike any known in the last 1000 years, as pointed out previously. The new result is that this anthropogenic change is characterised by spatial homogeneity and changes as well in average temperatures than in distribution of extreme events, while natural climate forcings induce warm periods with heterogeneous spatial patterns and less frequent extreme events. This study demonstrates that recent changes in temperature differ substantially from temperature changes reconstructed in the past and are well in excess of normal variations experienced in previous centuries and caused by natural forcings.

  18. BLAST: CORRELATIONS IN THE COSMIC FAR-INFRARED BACKGROUND AT 250, 350, AND 500 mum REVEAL CLUSTERING OF STAR-FORMING GALAXIES

    SciTech Connect

    Viero, Marco P.; Martin, Peter G.; Netterfield, Calvin B.; Ade, Peter A. R.; Griffin, Matthew; Hargrave, Peter C.; Mauskopf, Philip; Moncelsi, Lorenzo; Pascale, Enzo; Bock, James J.; Chapin, Edward L.; Halpern, Mark; Marsden, Gaelen; Devlin, Mark J.; Klein, Jeff; Gundersen, Joshua O.; Hughes, David H.; MacTavish, Carrie J.; Negrello, Mattia; Olmi, Luca

    2009-12-20

    We detect correlations in the cosmic far-infrared background due to the clustering of star-forming galaxies in observations made with the Balloon-borne Large Aperture Submillimeter Telescope, at 250, 350, and 500 mum. We perform jackknife and other tests to confirm the reality of the signal. The measured correlations are well fitted by a power law over scales of 5'-25', with DELTAI/I = 15.1% +- 1.7%. We adopt a specific model for submillimeter sources in which the contribution to clustering comes from sources in the redshift ranges 1.3 <= z <= 2.2, 1.5 <= z <= 2.7, and 1.7 <= z <= 3.2, at 250, 350, and 500 mum, respectively. With these distributions, our measurement of the power spectrum, P(k{sub t}heta), corresponds to linear bias parameters, b = 3.8 +- 0.6, 3.9 +- 0.6, and 4.4 +- 0.7, respectively. We further interpret the results in terms of the halo model, and find that at the smaller scales, the simplest halo model fails to fit our results. One way to improve the fit is to increase the radius at which dark matter halos are artificially truncated in the model, which is equivalent to having some star-forming galaxies at z >= 1 located in the outskirts of groups and clusters. In the context of this model, we find a minimum halo mass required to host a galaxy is log(M{sub min}/M{sub sun}) = 11.5{sup +0.4}{sub -0.1}, and we derive effective biases b{sub eff} = 2.2 +- 0.2, 2.4 +- 0.2, and 2.6 +- 0.2, and effective masses log(M{sub eff}/M{sub odot})=12.9+-0.3, 12.8 +- 0.2, and 12.7 +- 0.2, at 250, 350 and 500 mum, corresponding to spatial correlation lengths of r{sub 0} = 4.9, 5.0, and 5.2+-0.7 h{sup -1}Mpc, respectively. Finally, we discuss implications for clustering measurement strategies with Herschel and Planck.

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

    NASA Technical Reports Server (NTRS)

    Spencer, Roy W.; Braswell, William D.

    2001-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  1. 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.

  2. 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 Areu Island within the "Me Grande de Curu" 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 Areu 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 Areu Island for the maintenance of biodiversity in the Amazon Coast. PMID:24912344

  3. A Deep Search for Extended Radio Continuum Emission from Dwarf Spheroidal Galaxies: Implications for Particle Dark Matter

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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 deg2 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 ?sub <~ 7 mJy beam-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 ~10' resolution of our observations, foregrounds contribute a standard deviation of 1.8 mJy beam-1 <= ?ast <= 5.7 mJy beam-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 ? = 100 GeV annihilating into b\\bar{b} final states and B = 1 ?G, upper limits on the annihilation cross-section for Ursa Major II and Willman I are log (lang?vrang?, cm3 s-1) <~ -25 for the preferred set of charged particle propagation parameters adopted by CPU07; this is comparable to that inferred at ?-ray energies from the two-year Fermi Large Area Telescope data. We discuss three avenues for improving the constraints on lang?vrang? presented here, and conclude that deep radio observations of dSphs are highly complementary to indirect WIMP searches at higher energies.

  4. 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

  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. 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.

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

    PubMed

    Boda, Pl; Bozki, Tams; Vsrhelyi, Tams; Bakonyi, Gbor; Vrbr, Gbor

    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

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

    PubMed Central

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

    2014-01-01

    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

  9. 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 2.15C. 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 30S 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.

  10. Growing Season Temperatures in Europe and Climate Forcings Over the Past 1400 Years

    PubMed Central

    Guiot, Joel; Corona, Christophe

    2010-01-01

    Background The lack of instrumental data before the mid-19th-century limits our understanding of present warming trends. In the absence of direct measurements, we used proxies that are natural or historical archives recording past climatic changes. A gridded reconstruction of spring-summer temperature was produced for Europe based on tree-rings, documentaries, pollen assemblages and ice cores. The majority of proxy series have an annual resolution. For a better inference of long-term climate variation, they were completed by low-resolution data (decadal or more), mostly on pollen and ice-core data. Methodology/Principal Findings An original spectral analog method was devised to deal with this heterogeneous dataset, and to preserve long-term variations and the variability of temperature series. So we can replace the recent climate changes in a broader context of the past 1400 years. This preservation is possible because the method is not based on a calibration (regression) but on similarities between assemblages of proxies. The reconstruction of the April-September temperatures was validated with a Jack-knife technique. It was also compared to other spatially gridded temperature reconstructions, literature data, and glacier advance and retreat curves. We also attempted to relate the spatial distribution of European temperature anomalies to known solar and volcanic forcings. Conclusions We found that our results were accurate back to 750. Cold periods prior to the 20th century can be explained partly by low solar activity and/or high volcanic activity. The Medieval Warm Period (MWP) could be correlated to higher solar activity. During the 20th century, however only anthropogenic forcing can explain the exceptionally high temperature rise. Warm periods of the Middle Age were spatially more heterogeneous than last decades, and then locally it could have been warmer. However, at the continental scale, the last decades were clearly warmer than any period of the last 1400 years. The heterogeneity of MWP versus the homogeneity of the last decades is likely an argument that different forcings could have operated. These results support the fact that we are living a climate change in Europe never seen in the past 1400 years. PMID:20376366

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

    NASA Astrophysics Data System (ADS)

    Rossi, Giuseppe; Caporali, Enrica

    2010-05-01

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

  12. Warfarin Anticoagulant Therapy: A Southern Italy Pharmacogenetics-Based Dosing Model

    PubMed Central

    Mazzaccara, Cristina; Conti, Valeria; Liguori, Rosario; Simeon, Vittorio; Toriello, Mario; Severini, Angelo; Perricone, Corrado; Meccariello, Alfonso; Meccariello, Pasquale; Vitale, Dino Franco; Filippelli, Amelia; Sacchetti, Lucia

    2013-01-01

    Background and Aim Warfarin is the most frequently prescribed anticoagulant worldwide. However, warfarin therapy is associated with a high risk of bleeding and thromboembolic events because of a large interindividual dose-response variability. We investigated the effect of genetic and non genetic factors on warfarin dosage in a South Italian population in the attempt to setup an algorithm easily applicable in the clinical practice. Materials and Methods A total of 266 patients from Southern Italy affected by cardiovascular diseases were enrolled and their clinical and anamnestic data recorded. All patients were genotyped for CYP2C9*2,*3, CYP4F2*3, VKORC1 -1639 G>A by the TaqMan assay and for variants VKORC1 1173 C>T and VKORC1 3730 G>A by denaturing high performance liquid chromatography and direct sequencing. The effect of genetic and not genetic factors on warfarin dose variability was tested by multiple linear regression analysis, and an algorithm based on our data was established and then validated by the Jackknife procedure. Results Warfarin dose variability was influenced, in decreasing order, by VKORC1-1639 G>A (29.7%), CYP2C9*3 (11.8%), age (8.5%), CYP2C9*2 (3.5%), gender (2.0%) and lastly CYP4F2*3 (1.7%); VKORC1 1173 C>T and VKORC1 3730 G>A exerted a slight effect (<1% each). Taken together, these factors accounted for 58.4% of the warfarin dose variability in our population. Data obtained with our algorithm significantly correlated with those predicted by the two online algorithms: Warfarin dosing and Pharmgkb (p<0.001; R2 = 0.805 and p<0.001; R2 = 0.773, respectively). Conclusions Our algorithm, which is based on six polymorphisms, age and gender, is user-friendly and its application in clinical practice could improve the personalized management of patients undergoing warfarin therapy. PMID:23990957

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

    PubMed Central

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

    2014-01-01

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

  14. 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

  15. Frequency-dependent Lg Q within the continental United States

    USGS Publications Warehouse

    Erickson, D.; McNamara, D.E.; Benz, H.M.

    2004-01-01

    Frequency-dependent crustal attenuation (1/Q) is determined for seven distinct physiographic/tectonic regions of the continental United States using high-quality Lg waveforms recorded on broadband stations in the frequency band 0.5 to 16 Hz. Lg attenuation is determined from time-domain amplitude measurements in one-octave frequency bands centered on the frequencies 0.75, 1.0, 3.0, 6.0, and 12.0 Hz. Modeling errors are determined using a delete-j jackknife resampling technique. The frequency-dependent quality factor is modeled in the form of Q = Q0f??. Regions were initially selected based on tectonic provinces but were eventually limited and adjusted to maximize ray path coverage in each area. Earthquake data was recorded on several different networks and constrained to events occurring within the crust (<40 km depth) and at least mb 3.5 in size. A singular value decomposition inversion technique was applied to the data to simultaneously solve for source and receiver terms along with Q for each region at specific frequencies. The lowest crustal Q was observed in northern and southern California where Q is described by the functions Q = 152(?? 37)f0.72(??0.16) and Q = 105(??26) f0.67(??0.16), respectively. The Basin and Range Province, Pacific Northwest, and Rocky Mountain states also display lower Q and a strong frequency dependence characterized by the functions Q = 200(??40)f0.68(??0.12), Q = 152(??49) f0.76(??0.18), and Q = 166(??37) f0.61(??0.14), respectively. In contrast, in the central and northeast United States Q functions are Q = 640(?? 225) f0.344(??0.22) and Q = 650(??143) f0.36(??0.14), respectively, show a high crustal Q and a weaker frequency dependence. These results improve upon previous Lg modeling by subdividing the United States into smaller, distinct tectonic regions and using significantly more data that provide improved constraints on frequency-dependent attenuation and errors. A detailed attenuation map of the continental United States can provide significant input into hazard map mitigation. Both scattering and intrinsic attenuation mechanisms are likely to play a comparable role in the frequency range considered in the study.

  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. 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.

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

    PubMed Central

    2014-01-01

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

  19. 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

  20. 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.

  1. 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 μl/h), 15 morphine-tolerant rats (15 μg/h), and 10 rats receiving a co-infusion of morphine (15 μg/h) and gabapentin (15 μg/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

  2. Evaluation of clinical image processing algorithms used in digital mammography.

    PubMed

    Zanca, Federica; Jacobs, Jurgen; Van Ongeval, Chantal; Claus, Filip; Celis, Valerie; Geniets, Catherine; Provost, Veerle; Pauwels, Herman; Marchal, Guy; Bosmans, Hilde

    2009-03-01

    Screening is the only proven approach to reduce the mortality of breast cancer, but significant numbers of breast cancers remain undetected even when all quality assurance guidelines are implemented. With the increasing adoption of digital mammography systems, image processing may be a key factor in the imaging chain. Although to our knowledge statistically significant effects of manufacturer-recommended image processings have not been previously demonstrated, the subjective experience of our radiologists, that the apparent image quality can vary considerably between different algorithms, motivated this study. This article addresses the impact of five such algorithms on the detection of clusters of microcalcifications. A database of unprocessed (raw) images of 200 normal digital mammograms, acquired with the Siemens Novation DR, was collected retrospectively. Realistic simulated microcalcification clusters were inserted in half of the unprocessed images. All unprocessed images were subsequently processed with five manufacturer-recommended image processing algorithms (Agfa Musica 1, IMS Raffaello Mammo 1.2, Sectra Mamea AB Sigmoid, Siemens OPVIEW v2, and Siemens OPVIEW v1). Four breast imaging radiologists were asked to locate and score the clusters in each image on a five point rating scale. The free-response data were analyzed by the jackknife free-response receiver operating characteristic (JAFROC) method and, for comparison, also with the receiver operating characteristic (ROC) method. JAFROC analysis revealed highly significant differences between the image processings (F = 8.51, p < 0.0001), suggesting that image processing strongly impacts the detectability of clusters. Siemens OPVIEW2 and Siemens OPVIEW1 yielded the highest and lowest performances, respectively. ROC analysis of the data also revealed significant differences between the processing but at lower significance (F = 3.47, p = 0.0305) than JAFROC. Both statistical analysis methods revealed that the same six pairs of modalities were significantly different, but the JAFROC confidence intervals were about 32% smaller than ROC confidence intervals. This study shows that image processing has a significant impact on the detection of microcalcifications in digital mammograms. Objective measurements, such as described here, should be used by the manufacturers to select the optimal image processing algorithm. PMID:19378737

  3. 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.

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

    PubMed Central

    2015-01-01

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

  5. 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

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

    PubMed

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

    2014-06-20

    We report results from the BICEP2 experiment, a cosmic microwave background (CMB) polarimeter specifically designed to search for the signal of inflationary gravitational waves in the B-mode power spectrum around ℓ∼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  μK(CMB)√s. BICEP2 observed from the South Pole for three seasons from 2010 to 2012. A low-foreground region of sky with an effective area of 380 square deg was observed to a depth of 87 nK deg in Stokes Q and U. In this paper we describe the observations, data reduction, maps, simulations, and results. We find an excess of B-mode power over the base lensed-ΛCDM expectation in the range 30 < ℓ < 150, inconsistent with the null hypothesis at a significance of >5σ. 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 3σ significance and its spectral index is found to be consistent with that of the CMB, disfavoring dust at 1.7σ. The observed B-mode power spectrum is well fit by a lensed-ΛCDM+tensor theoretical model with tensor-to-scalar ratio r = 0.20_(-0.05)(+0.07), with r = 0 disfavored at 7.0σ. Accounting for the contribution of foreground, dust will shift this value downward by an amount which will be better constrained with upcoming data sets. PMID:24996078

  7. 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.

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

    PubMed Central

    2013-01-01

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

  9. Detection of prostate cancer by integration of line-scan diffusion, T2-mapping and T2-weighted magnetic resonance imaging; a multichannel statistical classifier.

    PubMed

    Chan, Ian; Wells, William; Mulkern, Robert V; Haker, Steven; Zhang, Jianqing; Zou, Kelly H; Maier, Stephan E; Tempany, Clare M C

    2003-09-01

    A multichannel statistical classifier for detecting prostate cancer was developed and validated by combining information from three different magnetic resonance (MR) methodologies: T2-weighted, T2-mapping, and line scan diffusion imaging (LSDI). From these MR sequences, four different sets of image intensities were obtained: T2-weighted (T2W) from T2-weighted imaging, Apparent Diffusion Coefficient (ADC) from LSDI, and proton density (PD) and T2 (T2 Map) from T2-mapping imaging. Manually segmented tumor labels from a radiologist, which were validated by biopsy results, served as tumor "ground truth." Textural features were extracted from the images using co-occurrence matrix (CM) and discrete cosine transform (DCT). Anatomical location of voxels was described by a cylindrical coordinate system. A statistical jack-knife approach was used to evaluate our classifiers. Single-channel maximum likelihood (ML) classifiers were based on 1 of the 4 basic image intensities. Our multichannel classifiers: support vector machine (SVM) and Fisher linear discriminant (FLD), utilized five different sets of derived features. Each classifier generated a summary statistical map that indicated tumor likelihood in the peripheral zone (PZ) of the prostate gland. To assess classifier accuracy, the average areas under the receiver operator characteristic (ROC) curves over all subjects were compared. Our best FLD classifier achieved an average ROC area of 0.839(+/-0.064), and our best SVM classifier achieved an average ROC area of 0.761(+/-0.043). The T2W ML classifier, our best single-channel classifier, only achieved an average ROC area of 0.599(+/-0.146). Compared to the best single-channel ML classifier, our best multichannel FLD and SVM classifiers have statistically superior ROC performance (P=0.0003 and 0.0017, respectively) from pairwise two-sided t-test. By integrating the information from multiple images and capturing the textural and anatomical features in tumor areas, summary statistical maps can potentially aid in image-guided prostate biopsy and assist in guiding and controlling delivery of localized therapy under image guidance. PMID:14528961

  10. Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources.

    PubMed

    Seurinck, Sylvie; Verstraete, Willy; Siciliano, Steven D

    2003-08-01

    Despite efforts to minimize fecal input into waterways, this kind of pollution continues to be a problem due to an inability to reliably identify nonpoint sources. Our objective was to find candidate source-specific Escherichia coli fingerprints as potential genotypic markers for raw sewage, horses, dogs, gulls, and cows. We evaluated 16S-23S rRNA intergenic spacer region (ISR)-PCR and repetitive extragenic palindromic (rep)-PCR analyses of E. coli isolates as tools to identify nonpoint fecal sources. The BOXA1R primer was used for rep-PCR analysis. A total of 267 E. coli isolates from different fecal sources were typed with both techniques. E. coli was found to be highly diverse. Only two candidate source-specific E. coli fingerprints, one for cow and one for raw sewage, were identified out of 87 ISR fingerprints. Similarly, there was only one candidate source-specific E. coli fingerprint for horse out of 59 BOX fingerprints. Jackknife analysis resulted in an average rate of correct classification (ARCC) of 83% for BOX-PCR analysis and 67% for ISR-PCR analysis for the five source categories of this study. When nonhuman sources were pooled so that each isolate was classified as animal or human derived (raw sewage), ARCCs of 82% for BOX-PCR analysis and 72% for ISR-PCR analysis were obtained. Critical factors affecting the utility of these methods, namely sample size and fingerprint stability, were also assessed. Chao1 estimation showed that generally 32 isolates per fecal source individual were sufficient to characterize the richness of the E. coli population of that source. The results of a fingerprint stability experiment indicated that BOX and ISR fingerprints were stable in natural waters at 4, 12, and 28 degrees C for 150 days. In conclusion, 16S-23S rRNA ISR-PCR and rep-PCR analyses of E. coli isolates have the potential to identify nonpoint fecal sources. A fairly small number of isolates was needed to find candidate source-specific E. coli fingerprints that were stable under the simulated environmental conditions. PMID:12902290

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Garcia-Yeguas, Araceli; Ivan, Koulakov; Ibaez Jesus, M.; Valenti, Sallars.

    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 Caadas-Teide-Pico Viejo volcanic complex. Las Caadas 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 Montaa 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 Caadas 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 Caadas system.

  13. 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.

  14. 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.

  15. 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

  16. Solid-state molecular rotators of anilinium and adamantylammonium in [Ni(dmit)2](-) salts with diverse magnetic properties.

    PubMed

    Akutagawa, Tomoyuki; Sato, Daisuke; Koshinaka, Hiroyuki; Aonuma, Masaaki; Noro, Shin-ichiro; Takeda, Sadamu; Nakamura, Takayoshi

    2008-07-01

    Supramolecular rotators of hydrogen-bonding assemblies between anilinium (Ph-NH 3 (+)) or adamantylammonium (AD-NH 3 (+)) and dibenzo[18]crown-6 (DB[18]crown-6) or meso-dicyclohexano[18]crown-6 (DCH[18]crown-6) were introduced into [Ni(dmit) 2] salts (dmit (2-) is 2-thioxo-1,3-dithiole-4,5-dithiolate). The ammonium moieties of Ph-NH 3 (+) and AD-NH 3 (+) cations were interacted through N-H (+) approximately O hydrogen bonding with the six oxygen atoms of crown ethers, forming 1:1 supramolecular rotator-stator structures. X-ray crystal-structure analyses revealed a jackknife-shaped conformation of DB[18]crown-6, in which two benzene rings were twisted along the same direction, in (Ph-NH 3 (+))(DB[18]crown-6)[Ni(dmit) 2] (-) ( 1) and (AD-NH 3 (+))(DB[18]crown-6)[Ni(dmit) 2] (-) ( 3), whereas the conformational flexibility of two dicyclohexyl rings was observed in (Ph-NH 3 (+))(DCH[18]crown-6)[Ni(dmit) 2] (-) ( 2) and (AD-NH 3 (+))(DCH[18]crown-6)[Ni(dmit) 2] (-) ( 4). Sufficient space for the molecular rotation of the adamantyl group was achieved in the crystals of salts 3 and 4, whereas the rotation of the phenyl group in salts 1 and 2 was rather restricted by the nearest neighboring molecules. The rotation of the adamantyl group in salts 3 and 4 was evidenced from the temperature-dependent wide-line (1)H NMR spectra, dielectric properties, and X-ray crystal structure analysis. ab initio calculations showed that the potential energy barriers for the rotations of adamantyl groups in salts 3 (Delta E approximately 18 kJmol (-1)) and 4 (Delta E approximately 15 kJmol (-1)) were similar to those of ethane ( approximately 12 kJmol (-1)) and butane (17-25 kJmol (-1)) around the C-C single bond, which were 1 order of magnitude smaller than those of phenyl groups in salts 1 (Delta E approximately 180 kJmol (-1)) and 2 (Delta E approximately 340 kJmol (-1)). 1D or 2D [Ni(dmit) 2] (-) anion arrangements were observed in the crystals according to the shape of crown ether derivatives. The 2D weak intermolecular interactions between [Ni(dmit) 2] (-) anions in salts 1 and 3 led to Curie-Weiss behavior with weak antiferromagnetic interaction, whereas 1D interactions through lateral sulfur-sulfur atomic contacts between [Ni(dmit) 2] (-) anions were observed in salts 2 and 4, whose magnetic behaviors were dictated by ferromagnetic (salt 2) and singlet-triplet (salt 4) intermolecular magnetic interactions, respectively. PMID:18510285

  17. 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

  18. Fossil Chironomidae (Insecta: Diptera) as quantitative indicators of past salinity in African lakes

    NASA Astrophysics Data System (ADS)

    Eggermont, Hilde; Heiri, Oliver; Verschuren, Dirk

    2006-08-01

    We surveyed sub-fossil chironomid assemblages in surface sediments of 73 low- to mid-elevation lakes in tropical East Africa (Uganda, Kenya, Tanzania, Ethiopia) to develop inference models for quantitative paleosalinity reconstruction. Using a calibration data set of 67 lakes with surface-water conductivity between 34 and 68,800 ?S/cm, trial models based on partial least squares (PLS), weighted-averaging (WA), weighted-averaging partial least squares (WA-PLS), maximum likelihood (ML), and the weighted modern analogue technique (WMAT) produced jack-knifed coefficients of determination ( r2) between 0.83 and 0.87, and root-mean-squared errors of prediction (RMSEP) between 0.27 and 0.31 log 10 conductivity units, values indicating that fossil assemblages of African Chironomidae can be valuable indicators of past salinity change. The new inference models improve on previous models, which were calibrated with presence-absence data from live collections, by the much greater information content of the calibration data set, and greater probability of finding good modern analogues for fossil assemblages. However, inferences still suffered to a greater (WA, WMAT) or lesser (WA-PLS, PLS and ML) extent from weak correlation between chironomid species distribution and salinity in a broad range of fresh waters, and apparent threshold response of African chironomid communities to salinity change near 3000 ?S/cm. To improve model sensitivity in freshwater lakes we expanded the calibration data set with 11 dilute (6-61 ?S/cm) high-elevation lakes on Mt. Kenya (Kenya) and the Ruwenzori Mts. (Uganda). This did not appreciably improve models' error statistics, in part because it introduced a secondary environmental gradient to the faunal data, probably temperature. To evaluate whether a chironomid-based salinity inference model calibrated in East African lakes could be meaningfully used for environmental reconstruction elsewhere on the continent, we expanded the calibration data set with 8 fresh (15-168 ?S/cm) lakes in Cameroon, West Africa, and one hypersaline desert lake in Chad. This experiment yielded poorer error statistics, primarily because the need to amalgamate East and West African sister taxa reduced overall taxonomic resolution and increased the mean tolerance range of retained taxa. However, the merged data set constrained better the salinity optimum of several freshwater taxa, and further increased the probability of finding good modern analogues. We then used chironomid stratigraphic data and independent proxy reconstructions from two fluctuating lakes in Kenya to compare the performance of new and previous African salinity-inference models. This analysis revealed significant differences between the various numerical techniques in reconstructed salinity trends through time, due to their different sensitivity to the presence or relative abundance of certain key taxa, combined with the above-mentioned threshold faunal response to salinity change. Simple WA and WMAT produced ecologically sensible reconstructions because their step-like change in inferred conductivity near 3000 ?S/cm mirrors the relatively rapid transitions between fresh and saline lake phases associated with climate-driven lake-level change in shallow tropical closed-basin lakes. Statistical camouflaging of this threshold faunal response in WA-PLS and ML models resulted in less trustworthy reconstructions of past salinity in lakes crossing the freshwater-saline boundary. We conclude that selection of a particular inference model should not only be based on statistical performance measures, but consider chironomid community ecology in the study region, and the amplitude of reconstructed environmental change relative to the modern environmental gradient represented in the calibration data set.

  19. Validation Analysis of the Shoal Groundwater Flow and Transport Model

    SciTech Connect

    A. Hassan; J. Chapman

    2008-11-01

    Environmental restoration at the Shoal underground nuclear test is following a process prescribed by a Federal Facility Agreement and Consent Order (FFACO) between the U.S. Department of Energy, the U.S. Department of Defense, and the State of Nevada. Characterization of the site included two stages of well drilling and testing in 1996 and 1999, and development and revision of numerical models of groundwater flow and radionuclide transport. Agreement on a contaminant boundary for the site and a corrective action plan was reached in 2006. Later that same year, three wells were installed for the purposes of model validation and site monitoring. The FFACO prescribes a five-year proof-of-concept period for demonstrating that the site groundwater model is capable of producing meaningful results with an acceptable level of uncertainty. The corrective action plan specifies a rigorous seven step validation process. The accepted groundwater model is evaluated using that process in light of the newly acquired data. The conceptual model of ground water flow for the Project Shoal Area considers groundwater flow through the fractured granite aquifer comprising the Sand Springs Range. Water enters the system by the infiltration of precipitation directly on the surface of the mountain range. Groundwater leaves the granite aquifer by flowing into alluvial deposits in the adjacent basins of Fourmile Flat and Fairview Valley. A groundwater divide is interpreted as coinciding with the western portion of the Sand Springs Range, west of the underground nuclear test, preventing flow from the test into Fourmile Flat. A very low conductivity shear zone east of the nuclear test roughly parallels the divide. The presence of these lateral boundaries, coupled with a regional discharge area to the northeast, is interpreted in the model as causing groundwater from the site to flow in a northeastward direction into Fairview Valley. Steady-state flow conditions are assumed given the absence of groundwater withdrawal activities in the area. The conceptual and numerical models were developed based upon regional hydrogeologic investigations conducted in the 1960s, site characterization investigations (including ten wells and various geophysical and geologic studies) at Shoal itself prior to and immediately after the test, and two site characterization campaigns in the 1990s for environmental restoration purposes (including eight wells and a year-long tracer test). The new wells are denoted MV-1, MV-2, and MV-3, and are located to the northnortheast of the nuclear test. The groundwater model was generally lacking data in the north-northeastern area; only HC-1 and the abandoned PM-2 wells existed in this area. The wells provide data on fracture orientation and frequency, water levels, hydraulic conductivity, and water chemistry for comparison with the groundwater model. A total of 12 real-number validation targets were available for the validation analysis, including five values of hydraulic head, three hydraulic conductivity measurements, three hydraulic gradient values, and one angle value for the lateral gradient in radians. In addition, the fracture dip and orientation data provide comparisons to the distributions used in the model and radiochemistry is available for comparison to model output. Goodness-of-fit analysis indicates that some of the model realizations correspond well with the newly acquired conductivity, head, and gradient data, while others do not. Other tests indicated that additional model realizations may be needed to test if the model input distributions need refinement to improve model performance. This approach (generating additional realizations) was not followed because it was realized that there was a temporal component to the data disconnect: the new head measurements are on the high side of the model distributions, but the heads at the original calibration locations themselves have also increased over time. This indicates that the steady-state assumption of the groundwater model is in error. To test the robustness of the model despite the transient nature of the heads, the newly acquired MV hydraulic head values were trended back to their likely values in 1999, the date of the calibration measurements. Additional statistical tests are performed using both the backward-projected MV heads and the observed heads to identify acceptable model realizations. A jackknife approach identified two possible threshold values to consider. For the analysis using the backward-trended heads, either 458 or 818 realizations (out of 1,000) are found acceptable, depending on the threshold chosen. The analysis using the observed heads found either 284 or 709 realizations acceptable. The impact of the refined set of realizations on the contaminant boundary was explored using an assumed starting mass of a single radionuclide and the acceptable realizations from the backward-trended analysis.

  20. The Muenster Red Sky Survey: Large-scale structures in the universe

    NASA Astrophysics Data System (ADS)

    Ungruhe, R.; Seitter, W. C.; Duerbeck, H. W.

    2003-01-01

    We present a large-scale galaxy catalogue for the red spectral region which covers an area of 5 000 square degrees. It contains positions, red magnitudes, radii, ellipticities and position angles of about 5.5 million galaxies. Together with the APM catalogue (4,300 square degrees) in the blue spectral region, this catalogue forms at present the largest coherent data base for cosmological investigations in the southern hemisphere. 217 ESO Southern Sky Atlas R Schmidt plates with galactic latitudes -45 degrees were digitized with the two PDS microdensitometers of the Astronomisches Institut Münster, with a step width of 15 microns, corresponding to 1.01 arcseconds per pixel. All data were stored on different storage media and are available for further investigations. Suitable search parameters must be chosen in such a way that all objects are found on the plates, and that the percentage of artificial objects remains as low as possible. Based on two reference areas on different plates, a search threshold of 140 PDS density units and a minimum number of four pixels per object were chosen. The detected objects were stored, according to size, in frames of different size length. Each object was investigated in its frame, and 18 object parameters were determined. The classification of objects into stars, galaxies and perturbed objects was done with an automatic procedure which makes use of combinations of computed object parameters. In the first step, the perturbed objects are removed from the catalogue. Double objects and noise objects can be excluded on the basis of symmetry properties, while for satellite trails, a new classification criterium based on apparent magnitude, effective radius and apparent ellipticity, was developed. For the remaining objects, a star/galaxy separation was carried out. For bright objects, the relation between apparent magnitude and effective radius serves as the discriminating property, for fainter objects, the relation between effective radius and central intensity was used. In addition, a few regions of enhanced object density like dwarf galaxies and star clusters were removed from the catalogue. Because error estimates of the automatic classificationprocedure are very uncertain, an extensive visual check of the automatic classification was carried out. A large number of objects previously classified automatically - 1.3 million galaxies, 815,000 stars and 647,000 perturbed objects - was re-classified by eye. We found that galaxies suffer most from misclassification. Down to magnitude 13, the error is, independent of galactic latitude, at least 60%. Between13th and 17th magnitude, the percentage of misclassified galaxies for b < -45 degrees drops continuously to between 15% and 30%, and is clearly dependent on galactic latitude. The classification of galaxies at low galactic latitudes is most strongly affected; in these regions only half of the galaxies are correctly classified. Errors found in this work thus lie by a factor 2-3 above values quoted in the literature.Stars show classification errors of at most 10%, whose level increases towards fainter magnitudes. The classification accuracy is less dependent on galactic latitude than in the case of galaxies. As concerns artifacts, noticeable classification errors occur only for objects brighter than magnitude 15, which is mainly caused by saturation effects of the photographic emulsion. At magnitudes fainter than 15th,the error is below 5%. No dependence from galactic latitude is seen. These investigations show that the automatic classification yields satisfactory results only in certain magnitude intervals, which depend on galactic latitude. The object magnitudes are influenced by the desensitization of the emulsion during exposure and by the vignetting of the telescope. Objects at the plate margins appear systematically too faint. The magnitudes were corrected by means of measured number densities of galaxies and stars, which were determined in 63 fields around the galactic southpole. The difference of the magnitude zero-point between the center and the margin of a plate amounts to approximately 0.05 mag after correction of the margin desensitization. Because of their high central intensity, stars reach the saturation limit of the emulsion already at magnitude 17. Thus bright stars appear systematically too faint. The saturation effect can be corrected by means of a point-spread function, which is calculated from the unsaturated parts of the stellar intensity profiles. The magnitude corrections for the saturation are carried out for each plate separately. In order to establish a unique magnitude zero-point for the 217 single plates, a mutual adjustment of neighbouring fields by means of their overlap regions was done. The procedure was carried out separately for stars and galaxies. In total, 1,005 overlap regions for galaxies and 1,103 regions for stars were available. The zero-point error after adjustment amounts to 0.06 mag for galaxies and 0.07 mag for stars. The external calibration of the photographic rF magnitudes was carried out by means of CCD sequences obtained with three telescopes in Chile and South Africa. In total, photometric V, R data for 1,037 galaxies and 1,058 stars in 92 fields are available. The transformation between photographic and CCD magnitudes requires a relation between F and VR.It was carried out separately for stars and galaxies, because they show different colour transformations. After the transformation of the photographic rF magnitudes to the standard Johnson R system, the errors of the local magnitude zero-point amount to 0.11 mag. for galaxies and 0.15 mag for stars. Because of the large areal extent of the catalogue, the galaxy magnitudes must be corrected for interstellar extinction. Magnitude corrections are based on hydrogen column densitiesof interstellar dust. Extinction corrections amount to up to0.1 mag for 55% of galaxies, and 0.2 mag for another 35%. For the remaining 10%, the corrections are above 0.2 mag.The iteration procedure for the indirect adjustment of single platesmay cause a magnitude gradient in north-south or east-west direction. Investigations of the magnitude differences between photographic and CCD magnitudes versus right ascension and declination show no significant gradients.In order to generate a complete catalogue of galaxies and stars, all double or multiple objects that occur in overlap regions have to be excluded. After the merging of all single plates (including half of the overlap regions), both catalogues contain 5.5 million galaxies and 20.2 million stars. The completeness of the catalogues was investigated from the comparison of counts of stars and galaxies with simulations. The limit of completenessis at magnitude18.3 for galaxies, and at 18.8 for stars. In the case of galaxies, a clear deficit is seen for galaxies down to magitude 16 in comparison with the simulation. Neither by taking into account galaxy evolution, nor by changes in the cosmological parameters, an adjustment of the simulation to the catalogue counts was possible. These results and those of others support the assumption that we are dealing with a real galaxy deficit. The determined slope of 0.66 of the galaxy counts is, within the limits of accuracy, in agreement with the measured values of other authors. No comparable star counts are available. The N-point angular correlation function were determined from various sub-catalogues consisting of 9, 25, 63, 121 and 152 fields as well asfor limiting magnitudes from magnitudes 15.0 to 19.0. The computation of chance distributions was carried out for galaxy counts in cells with side borders from 25''to 28.4''. Averaged correlation functions and their coefficients were determined by means of factorial moments. The delete-d jackknife procedure was applied for the error estimate, with 200 replications per subcatalogue. The 2-point angular correlation function shows a linear trend in logarithmic plots for all sub-catalogues on scales from 0.02 to 2degrees.Within this range, it can be parametrized by a power law omega2 = A theta exp(1-gamma). Depending on sub-catalogue, the gamma values scatter between 1.63 and 1.73. They show a good agreement with the EDSGC, APM and MRSP catalogues. The parametrization of the amplitudeof the 2-point angular correlation versus apparent magnitude yields beta values between 0.267 and 0.322, which are in accordance with beta values from model calculations. The curve form of the 2-point angularcorrelation function shows a significantly flatter decline on scales exceeding 2 degrees which cannot be reproduced by the standard CDM-model. The correlation functions of higher order intersect at a point theta_S, whose position depends on the limiting magnitude. For scales theta theta_S,they decay very quickly. Since the higher orders only occur in galaxyclusters, the intersection can be taken as a measure for the cluster size.Correlations for the third to fifth order that still exist on large scalesindicate that, compared to the size of galaxy clusters, larger structuresexist, the superclusters. The correlation function coefficients with N larger or equal to 3 show characteristicplateaus for all limiting magnitudes, whose length depends on the order considered. Simulations have shown that the plateaus ofsmall scales point towards a strong non-linear cluster formation. The meaning of plateaus on large scales is not yet known. Comparisons with the APM- and MRSP-catalogues show a good agreement, both in the shape as well asin the amplitudes of the coefficients. Only the EDSGC shows significantly higher amplitudes on small scales, which are likely caused by wronglyclassified and/or doubly counted galaxies. This paper is an edited and translated version of a Ph.D. thesis, submitted by R. Ungruhe to Muenster University in 1998. It is released to make the results from this work available to a larger scientific community. Since the data of the galaxy catalogue will also be made available through the NED/IPAC database, its users can make themselves familiar with the methods of analysis and of the construction of the catalogue. Another paper, "Angular and three-dimensional correlation functions determined from the Muenster Red Sky Survey" by P. Boschan (the second referee of the Ph.D. thesis), published in Monthly Notices of the Royal Astronomical Society, Vol. 334, pp. 297-309, is to a very large part based on the contents of the thesis. It should be noted that it was written without the knowledge and without the permission of the author of the Ph.D. thesis.